Diff for /imach/src/imach.c between versions 1.328 and 1.362

version 1.328, 2022/07/27 17:40:48 version 1.362, 2024/06/28 08:00:31
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.362  2024/06/28 08:00:31  brouard
     Summary: 0.99s6
   
     * imach.c (Module): s6 errors with age*age (harmless).
   
     Revision 1.361  2024/05/12 20:29:32  brouard
     Summary: Version 0.99s5
   
     * src/imach.c Version 0.99s5 In fact, the covariance of total life
     expectancy e.. with a partial life expectancy e.j is high,
     therefore the complete matrix of variance covariance has to be
     included in the formula of the standard error of the proportion of
     total life expectancy spent in a specific state:
     var(X/Y)=mu_x^2/mu_y^2*(sigma_x^2/mu_x^2 -2
     sigma_xy/mu_x/mu_y+sigma^2/mu_y^2).  Also an error with mle=-3
     made the program core dump. It is fixed in this version.
   
     Revision 1.360  2024/04/30 10:59:22  brouard
     Summary: Version 0.99s4 and estimation of std of e.j/e..
   
     Revision 1.359  2024/04/24 21:21:17  brouard
     Summary: First IMaCh version using Brent Praxis software based on Buckhardt and Gegenfürtner C codes
   
     Revision 1.6  2024/04/24 21:10:29  brouard
     Summary: First IMaCh version using Brent Praxis software based on Buckhardt and Gegenfürtner C codes
   
     Revision 1.5  2023/10/09 09:10:01  brouard
     Summary: trying to reconsider
   
     Revision 1.4  2023/06/22 12:50:51  brouard
     Summary: stil on going
   
     Revision 1.3  2023/06/22 11:28:07  brouard
     *** empty log message ***
   
     Revision 1.2  2023/06/22 11:22:40  brouard
     Summary: with svd but not working yet
   
     Revision 1.353  2023/05/08 18:48:22  brouard
     *** empty log message ***
   
     Revision 1.352  2023/04/29 10:46:21  brouard
     *** empty log message ***
   
     Revision 1.351  2023/04/29 10:43:47  brouard
     Summary: 099r45
   
     Revision 1.350  2023/04/24 11:38:06  brouard
     *** empty log message ***
   
     Revision 1.349  2023/01/31 09:19:37  brouard
     Summary: Improvements in models with age*Vn*Vm
   
     Revision 1.347  2022/09/18 14:36:44  brouard
     Summary: version 0.99r42
   
     Revision 1.346  2022/09/16 13:52:36  brouard
     * src/imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
   
     Revision 1.345  2022/09/16 13:40:11  brouard
     Summary: Version 0.99r41
   
     * imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
   
     Revision 1.344  2022/09/14 19:33:30  brouard
     Summary: version 0.99r40
   
     * imach.c (Module): Fixing names of variables in T_ (thanks to Feinuo)
   
     Revision 1.343  2022/09/14 14:22:16  brouard
     Summary: version 0.99r39
   
     * imach.c (Module): Version 0.99r39 with colored dummy covariates
     (fixed or time varying), using new last columns of
     ILK_parameter.txt file.
   
     Revision 1.342  2022/09/11 19:54:09  brouard
     Summary: 0.99r38
   
     * imach.c (Module): Adding timevarying products of any kinds,
     should work before shifting cotvar from ncovcol+nqv columns in
     order to have a correspondance between the column of cotvar and
     the id of column.
     (Module): Some cleaning and adding covariates in ILK.txt
   
     Revision 1.341  2022/09/11 07:58:42  brouard
     Summary: Version 0.99r38
   
     After adding change in cotvar.
   
     Revision 1.340  2022/09/11 07:53:11  brouard
     Summary: Version imach 0.99r37
   
     * imach.c (Module): Adding timevarying products of any kinds,
     should work before shifting cotvar from ncovcol+nqv columns in
     order to have a correspondance between the column of cotvar and
     the id of column.
   
     Revision 1.339  2022/09/09 17:55:22  brouard
     Summary: version 0.99r37
   
     * imach.c (Module): Many improvements for fixing products of fixed
     timevarying as well as fixed * fixed, and test with quantitative
     covariate.
   
     Revision 1.338  2022/09/04 17:40:33  brouard
     Summary: 0.99r36
   
     * imach.c (Module): Now the easy runs i.e. without result or
     model=1+age only did not work. The defautl combination should be 1
     and not 0 because everything hasn't been tranformed yet.
   
     Revision 1.337  2022/09/02 14:26:02  brouard
     Summary: version 0.99r35
   
     * src/imach.c: Version 0.99r35 because it outputs same results with
     1+age+V1+V1*age for females and 1+age for females only
     (education=1 noweight)
   
     Revision 1.336  2022/08/31 09:52:36  brouard
     *** empty log message ***
   
     Revision 1.335  2022/08/31 08:23:16  brouard
     Summary: improvements...
   
     Revision 1.334  2022/08/25 09:08:41  brouard
     Summary: In progress for quantitative
   
     Revision 1.333  2022/08/21 09:10:30  brouard
     * src/imach.c (Module): Version 0.99r33 A lot of changes in
     reassigning covariates: my first idea was that people will always
     use the first covariate V1 into the model but in fact they are
     producing data with many covariates and can use an equation model
     with some of the covariate; it means that in a model V2+V3 instead
     of codtabm(k,Tvaraff[j]) which calculates for combination k, for
     three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
     the equation model is restricted to two variables only (V2, V3)
     and the combination for V2 should be codtabm(k,1) instead of
     (codtabm(k,2), and the code should be
     codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
     made. All of these should be simplified once a day like we did in
     hpxij() for example by using precov[nres] which is computed in
     decoderesult for each nres of each resultline. Loop should be done
     on the equation model globally by distinguishing only product with
     age (which are changing with age) and no more on type of
     covariates, single dummies, single covariates.
   
     Revision 1.332  2022/08/21 09:06:25  brouard
     Summary: Version 0.99r33
   
     * src/imach.c (Module): Version 0.99r33 A lot of changes in
     reassigning covariates: my first idea was that people will always
     use the first covariate V1 into the model but in fact they are
     producing data with many covariates and can use an equation model
     with some of the covariate; it means that in a model V2+V3 instead
     of codtabm(k,Tvaraff[j]) which calculates for combination k, for
     three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
     the equation model is restricted to two variables only (V2, V3)
     and the combination for V2 should be codtabm(k,1) instead of
     (codtabm(k,2), and the code should be
     codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
     made. All of these should be simplified once a day like we did in
     hpxij() for example by using precov[nres] which is computed in
     decoderesult for each nres of each resultline. Loop should be done
     on the equation model globally by distinguishing only product with
     age (which are changing with age) and no more on type of
     covariates, single dummies, single covariates.
   
     Revision 1.331  2022/08/07 05:40:09  brouard
     *** empty log message ***
   
     Revision 1.330  2022/08/06 07:18:25  brouard
     Summary: last 0.99r31
   
     *  imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function
   
     Revision 1.329  2022/08/03 17:29:54  brouard
     *  imach.c (Module): Many errors in graphs fixed with Vn*age covariates.
   
   Revision 1.328  2022/07/27 17:40:48  brouard    Revision 1.328  2022/07/27 17:40:48  brouard
   Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage    Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage
   
Line 1137  Important routines Line 1316  Important routines
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
 /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */  /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
   /* #define POWELLORIGINCONJUGATE  /\* Don't use conjugate but biggest decrease if valuable *\/ */
   /* #define NOTMINFIT */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 1188  typedef struct { Line 1369  typedef struct {
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 16384 /* Was 256 and 1024 and 2048. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
   #define GNUPLOTVERSION 5.1
   double gnuplotversion=GNUPLOTVERSION;
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 132  #define FILENAMELENGTH 256
   
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 128 /**< Maximum number of parameters for the optimization */  #define MAXPARM 216 /**< Maximum number of parameters for the optimization was 128 */
 #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
Line 1231  typedef struct { Line 1414  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="July 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";  char copyright[]="April 2024,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2024";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */  int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   int debugILK=0; /* debugILK is set by a #d in a comment line */
 int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */  int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
 /* Number of covariates model=V2+V1+ V3*age+V2*V4 */  /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
 int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */  /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */  int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
 int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 */  int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
 int cptcovsnq=0; /**< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 */  int cptcovs=0; /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
   int cptcovsnq=0; /**< cptcovsnq number of SIMPLE covariates in the model but non quantitative V2+V1 =2 */
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
   int cptcovprodage=0; /**< Number of fixed covariates with age: V3*age or V2*V3*age 1 */
   int cptcovprodvage=0; /**< Number of varying covariates with age: V7*age or V7*V6*age */
   int cptcovdageprod=0; /**< Number of doubleproducts with age, since 0.99r44 only: age*Vn*Vm for gnuplot printing*/
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of single dummy covariates (fixed or time varying) to vary for printing results (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */
 int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */  int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
 int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */  int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
 int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */  int ncovvt=0; /* Total number of effective (wave) varying covariates (dummy or quantitative or products [without age]) in the model */
   int ncovvta=0; /*  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
   int ncovta=0; /*age*V3*V2 +age*V2+agev3+ageV4  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
   int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
   int ncovva=0; /* +age*V6 + age*V7+ge*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
 int nsd=0; /**< Total number of single dummy variables (output) */  int nsd=0; /**< Total number of single dummy variables (output) */
 int nsq=0; /**< Total number of single quantitative variables (output) */  int nsq=0; /**< Total number of single quantitative variables (output) */
 int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */  int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
Line 1255  int nqfveff=0; /**< nqfveff Number of Qu Line 1447  int nqfveff=0; /**< nqfveff Number of Qu
 int ntveff=0; /**< ntveff number of effective time varying variables */  int ntveff=0; /**< ntveff number of effective time varying variables */
 int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs+1 declared globally ;*/
 int nobs=10;  /* Number of observations in the data lastobs-firstobs */  int nobs=10;  /* Number of observations in the data lastobs-firstobs */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */  int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)*nlstate*ncovmodel; */
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
 int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  int ncovmodel=0, ncovcol=0;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 int  nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */   int nqv=0, ntv=0, nqtv=0;    /* Total number of quantitative variables, time variable (dummy), quantitative and time variable*/
   int ncovcolt=0; /* ncovcolt=ncovcol+nqv+ntv+nqtv; total of covariates in the data, not in the model equation*/ 
 int popbased=0;  int popbased=0;
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav=0; /* Maxim number of waves */  int maxwav=0; /* Maxim number of waves */
 int jmin=0, jmax=0; /* min, max spacing between 2 waves */  int jmin=0, jmax=0; /* min, max spacing between 2 waves */
 int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */   int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */ 
 int gipmx=0, gsw=0; /* Global variables on the number of contributions   int gipmx = 0;
   double gsw = 0; /* Global variables on the number of contributions
                    to the likelihood and the sum of weights (done by funcone)*/                     to the likelihood and the sum of weights (done by funcone)*/
 int mle=1, weightopt=0;  int mle=1, weightopt=0;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
Line 1332  extern time_t time(); Line 1527  extern time_t time();
   
 struct tm start_time, end_time, curr_time, last_time, forecast_time;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
 time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   time_t   rlast_btime; /* raw time */
 struct tm tm;  struct tm tm;
   
 char strcurr[80], strfor[80];  char strcurr[80], strfor[80];
Line 1340  char *endptr; Line 1536  char *endptr;
 long lval;  long lval;
 double dval;  double dval;
   
   /* This for praxis gegen */
     /* int prin=1; */
     double h0=0.25;
     double macheps;
     double ffmin;
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
Line 1394  int *ncodemaxwundef;  /* ncodemax[j]= Nu Line 1596  int *ncodemaxwundef;  /* ncodemax[j]= Nu
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs; /* Global pointer */  double **pmmij, ***probs; /* Global pointer */
 double ***mobaverage, ***mobaverages; /* New global variable */  double ***mobaverage, ***mobaverages; /* New global variable */
   double **precov; /* New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up)  */
 double *ageexmed,*agecens;  double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   double anprojd, mprojd, jprojd; /* For eventual projections */    double anprojd, mprojd, jprojd; /* For eventual projections */
Line 1409  double  **covar; /**< covar[j,i], value Line 1612  double  **covar; /**< covar[j,i], value
                   * covar=matrix(0,NCOVMAX,1,n);                     * covar=matrix(0,NCOVMAX,1,n); 
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
 double **coqvar; /* Fixed quantitative covariate nqv */  double **coqvar; /* Fixed quantitative covariate nqv */
 double ***cotvar; /* Time varying covariate ntv */  double ***cotvar; /* Time varying covariate start at ncovcol + nqv + (1 to ntv) */
 double ***cotqvar; /* Time varying quantitative covariate itqv */  double ***cotqvar; /* Time varying quantitative covariate itqv */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
Line 1418  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1621  int **nbcode, *Tvar; /**< model=V2 => Tv
        *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12          *  V1   V2   V3   V4  V5  V6  V7  V8  Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12 
        *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv         *  <          ncovcol=6   >   nqv=2 (V7 V8)                   dv dv  dv  qtv    dv dv  dvv qtv
        *                                                             ntv=3     nqtv=1         *                                                             ntv=3     nqtv=1
        *  cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11         *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
        * For time varying covariate, quanti or dummies         * For time varying covariate, quanti or dummies
        *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti         *       cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
        *       cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti         *       cotvar[wav][ncovcol+nqv+ iv(1 to nqtv)][i]= [(1 to nqtv)][i]=(V12) quanti
        *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1         *       cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
        *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1         *       cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
        *       covar[k,i], value of kth fixed covariate dummy or quanti :         *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 + V9 + V9*age + V10
        *   k=  1    2      3       4     5       6      7        8   9     10       11          *   k=  1    2      3       4     5       6      7        8   9     10       11 
Line 1434  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1637  int **nbcode, *Tvar; /**< model=V2 => Tv
   # States 1=Coresidence, 2 Living alone, 3 Institution    # States 1=Coresidence, 2 Living alone, 3 Institution
   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi    # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
 */  */
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  /*           V5+V4+ V3+V4*V3 +V5*age+V2 +V1*V2+V1*age+V1+V4*V3*age */
 /*    k        1  2   3   4     5    6    7     8    9 */  /*    kmodel  1  2   3    4     5     6    7     8     9    10 */
 /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/  /*Typevar[k]=  0  0   0   2     1    0    2     1     0    3 *//*0 for simple covariate (dummy, quantitative,*/
                                                          /* fixed or varying), 1 for age product, 2 for*/                                                                 /* fixed or varying), 1 for age product, 2 for*/
                                                          /* product */                                                                 /* product without age, 3 for age and double product   */
 /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */  /*Dummy[k]=    1  0   0   1     3    1    1     2     0     3  *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
                                                          /*(single or product without age), 2 dummy*/                                                                  /*(single or product without age), 2 dummy*/
                                                          /* with age product, 3 quant with age product*/                                                                 /* with age product, 3 quant with age product*/
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*Tvar[k]=     5  4   3   6     5    2    7     1     1     6 */
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  /*    nsd         1   2                               3 */ /* Counting single dummies covar fixed or tv */
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  /*TnsdVar[Tvar]   1   2                               3 */ 
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  /*Tvaraff[nsd]    4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
 /*    nsq      1                     2                 */ /* Counting single quantit tv */  /*TvarsD[nsd]     4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
 /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */  /*TvarsDind[nsd]  2   3                               9 */ /* position K of single dummy cova */
 /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */  /*    nsq      1                     2                  */ /* Counting single quantit tv */
 /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */  /* TvarsQ[k]   5                     2                  */ /* Number of single quantitative cova */
 /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */  /* TvarsQind   1                     6                  */ /* position K of single quantitative cova */
 /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */  /* Tprod[i]=k             1               2             */ /* Position in model of the ith prod without age */
 /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */  /* cptcovage                    1               2         3 */ /* Counting cov*age in the model equation */
   /* Tage[cptcovage]=k            5               8         10 */ /* Position in the model of ith cov*age */
   /* model="V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
   /*  p Tvard[1][1]@21 = {6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0}*/
   /*  p Tvard[2][1]@21 = {7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0 <repeats 11 times>} */
   /* p Tvardk[1][1]@24 = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0}*/
   /* p Tvardk[1][1]@22 = {0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0} */
   /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2               */ /* Position in model of the ith prod without age */
   /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
 /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */  /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
 /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */  /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
 /* Type                    */  /* Type                    */
Line 1461  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1672  int **nbcode, *Tvar; /**< model=V2 => Tv
 /*           D  Q  D  D  Q */  /*           D  Q  D  D  Q */
 /*                         */  /*                         */
 int *TvarsD;  int *TvarsD;
   int *TnsdVar;
 int *TvarsDind;  int *TvarsDind;
 int *TvarsQ;  int *TvarsQ;
 int *TvarsQind;  int *TvarsQind;
Line 1468  int *TvarsQind; Line 1680  int *TvarsQind;
 #define MAXRESULTLINESPONE 10+1  #define MAXRESULTLINESPONE 10+1
 int nresult=0;  int nresult=0;
 int parameterline=0; /* # of the parameter (type) line */  int parameterline=0; /* # of the parameter (type) line */
 int TKresult[MAXRESULTLINESPONE];  int TKresult[MAXRESULTLINESPONE]; /* TKresult[nres]=k for each resultline nres give the corresponding combination of dummies */
 int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */  int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
 int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */  int modelresult[MAXRESULTLINESPONE][NCOVMAX];/* modelresult[k3]=k1: k1th position in the model corresponds to the k3 position in the resultline */
 int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */  int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
 double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
   double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
   int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
   double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
 double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
 int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */  int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
   
 /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1  /* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
   # States 1=Coresidence, 2 Living alone, 3 Institution    # States 1=Coresidence, 2 Living alone, 3 Institution
Line 1495  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3 Line 1710  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3
 int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */  int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
 int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */  int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
 int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */  int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   int *TvarVV; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarVVind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarVVA; /* We count ncovvt time varying covariates (single or products with age) and put their name into TvarVVA */
   int *TvarVVAind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarAVVA; /* We count ALL ncovta time varying covariates (single or products with age) and put their name into TvarVVA */
   int *TvarAVVAind; /* We count ALL ncovta time varying covariates (single or products without age) and put their name into TvarVV */
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age */
         /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         /* TvarVV={3,1,3,1,3}, for V3 and then the product V1*V3 is decomposed into V1 and V3 */         
         /* TvarVVind={2,5,5,6,6}, for V3 and then the product V1*V3 is decomposed into V1 and V3 and V1*V3*age into 6,6 */               
 int *Tvarsel; /**< Selected covariates for output */  int *Tvarsel; /**< Selected covariates for output */
 double *Tvalsel; /**< Selected modality value of covariate for output */  double *Tvalsel; /**< Selected modality value of covariate for output */
 int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 age*Vn*Vm */
 int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
 int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
 int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */  int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
Line 1511  int *TmodelInvQind; /** Tmodelqind[1]=1 Line 1736  int *TmodelInvQind; /** Tmodelqind[1]=1
 int *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard;  int **Tvard;
   int **Tvardk;
 int *Tprod;/**< Gives the k position of the k1 product */  int *Tprod;/**< Gives the k position of the k1 product */
 /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */  /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
 int *Tposprod; /**< Gives the k1 product from the k position */  int *Tposprod; /**< Gives the k1 product from the k position */
Line 1634  char *trimbb(char *out, char *in) Line 1860  char *trimbb(char *out, char *in)
   return s;    return s;
 }  }
   
   char *trimbtab(char *out, char *in)
   { /* Trim  blanks or tabs in line but keeps first blanks if line starts with blanks */
     char *s;
     s=out;
     while (*in != '\0'){
       while( (*in == ' ' || *in == '\t')){ /* && *(in+1) != '\0'){*/
         in++;
       }
       *out++ = *in++;
     }
     *out='\0';
     return s;
   }
   
 /* char *substrchaine(char *out, char *in, char *chain) */  /* char *substrchaine(char *out, char *in, char *chain) */
 /* { */  /* { */
 /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
Line 1660  char *trimbb(char *out, char *in) Line 1900  char *trimbb(char *out, char *in)
 char *substrchaine(char *out, char *in, char *chain)  char *substrchaine(char *out, char *in, char *chain)
 {  {
   /* Substract chain 'chain' from 'in', return and output 'out' */    /* Substract chain 'chain' from 'in', return and output 'out' */
   /* in="V1+V1*age+age*age+V2", chain="age*age" */    /* in="V1+V1*age+age*age+V2", chain="+age*age" out="V1+V1*age+V2" */
   
   char *strloc;    char *strloc;
   
   strcpy (out, in);     strcpy (out, in);                   /* out="V1+V1*age+age*age+V2" */
   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */    strloc = strstr(out, chain); /* strloc points to out at "+age*age+V2"  */
   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); /* strloc=+age*age+V2 chain="+age*age", out="V1+V1*age+age*age+V2" */
   if(strloc != NULL){     if(strloc != NULL){ 
     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */      /* will affect out */ /* strloc+strlen(chain)=|+V2 = "V1+V1*age+age*age|+V2" */ /* Will also work in Unicodek */
     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); /* move number of bytes corresponding to the length of "+V2" which is 3, plus one is 4 (including the null)*/
     /* strcpy (strloc, strloc +strlen(chain));*/      /* equivalent to strcpy (strloc, strloc +strlen(chain)) if no overlap; Copies from "+V2" to V1+V1*age+ */
   }    }
   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);  /* strloc=+V2 chain="+age*age", in="V1+V1*age+age*age+V2", out="V1+V1*age+V2" */
   return out;    return out;
 }  }
   
Line 1680  char *substrchaine(char *out, char *in, Line 1920  char *substrchaine(char *out, char *in,
 char *cutl(char *blocc, char *alocc, char *in, char occ)  char *cutl(char *blocc, char *alocc, char *in, char occ)
 {  {
   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'     /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')       and alocc starts after first occurence of char 'occ' : ex cutl(blocc,alocc,"abcdef2ghi2j",'2')
      gives alocc="abcdef" and blocc="ghi2j".       gives alocc="abcdef" and blocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
Line 1746  int nbocc(char *s, char occ) Line 1986  int nbocc(char *s, char occ)
   return j;    return j;
 }  }
   
   int nboccstr(char *textin, char *chain)
   {
     /* Counts the number of occurence of "chain"  in string textin */
     /*  in="+V7*V4+age*V2+age*V3+age*V4"  chain="age" */
     char *strloc;
     
     int i,j=0;
   
     i=0;
   
     strloc=textin; /* strloc points to "^+V7*V4+age+..." in textin */
     for(;;) {
       strloc= strstr(strloc,chain); /* strloc points to first character of chain in textin if found. Example strloc points^ to "+V7*V4+^age" in textin  */
       if(strloc != NULL){
         strloc = strloc+strlen(chain); /* strloc points to "+V7*V4+age^" in textin */
         j++;
       }else
         break;
     }
     return j;
     
   }
 /* void cutv(char *u,char *v, char*t, char occ) */  /* void cutv(char *u,char *v, char*t, char occ) */
 /* { */  /* { */
 /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
Line 2394  void linmin(double p[], double xi[], int Line 2656  void linmin(double p[], double xi[], int
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
   
   /**** praxis gegen ****/
   
   /* This has been tested by Visual C from Microsoft and works */
   /* meaning tha valgrind could be wrong */
   /*********************************************************************/
   /*      f u n c t i o n     p r a x i s                              */
   /*                                                                   */
   /* praxis is a general purpose routine for the minimization of a     */
   /* function in several variables. the algorithm used is a modifi-    */
   /* cation of conjugate gradient search method by powell. the changes */
   /* are due to r.p. brent, who gives an algol-w program, which served */
   /* as a basis for this function.                                     */
   /*                                                                   */
   /* references:                                                       */
   /*     - powell, m.j.d., 1964. an efficient method for finding       */
   /*       the minimum of a function in several variables without      */
   /*       calculating derivatives, computer journal, 7, 155-162       */
   /*     - brent, r.p., 1973. algorithms for minimization without      */
   /*       derivatives, prentice hall, englewood cliffs.               */
   /*                                                                   */
   /*     problems, suggestions or improvements are always wellcome     */
   /*                       karl gegenfurtner   07/08/87                */
   /*                                           c - version             */
   /*********************************************************************/
   /*                                                                   */
   /* usage: min = praxis(tol, macheps, h, n, prin, x, func)      */
   /* macheps has been suppressed because it is replaced by DBL_EPSILON */
   /* and if it was an argument of praxis (as it is in original brent)  */
   /* it should be declared external */
   /* usage: min = praxis(tol, h, n, prin, x, func)      */
   /* was    min = praxis(fun, x, n);                                   */
   /*                                                                   */
   /*  fun        the function to be minimized. fun is called from      */
   /*             praxis with x and n as arguments                      */
   /*  x          a double array containing the initial guesses for     */
   /*             the minimum, which will contain the solution on       */
   /*             return                                                */
   /*  n          an integer specifying the number of unknown           */
   /*             parameters                                            */
   /*  min        praxis returns the least calculated value of fun      */
   /*                                                                   */
   /* some additional global variables control some more aspects of     */
   /* the inner workings of praxis. setting them is optional, they      */
   /* are all set to some reasonable default values given below.        */
   /*                                                                   */
   /*   prin      controls the printed output from the routine.         */
   /*             0 -> no output                                        */
   /*             1 -> print only starting and final values             */
   /*             2 -> detailed map of the minimization process         */
   /*             3 -> print also eigenvalues and vectors of the        */
   /*                  search directions                                */
   /*             the default value is 1                                */
   /*  tol        is the tolerance allowed for the precision of the     */
   /*             solution. praxis returns if the criterion             */
   /*             2 * ||x[k]-x[k-1]|| <= sqrt(macheps) * ||x[k]|| + tol */
   /*             is fulfilled more than ktm times.                     */
   /*             the default value depends on the machine precision    */
   /*  ktm        see just above. default is 1, and a value of 4 leads  */
   /*             to a very(!) cautious stopping criterion.             */
   /*  h0 or step       is a steplength parameter and should be set equal     */
   /*             to the expected distance from the solution.           */
   /*             exceptionally small or large values of step lead to   */
   /*             slower convergence on the first few iterations        */
   /*             the default value for step is 1.0                     */
   /*  scbd       is a scaling parameter. 1.0 is the default and        */
   /*             indicates no scaling. if the scales for the different */
   /*             parameters are very different, scbd should be set to  */
   /*             a value of about 10.0.                                */
   /*  illc       should be set to true (1) if the problem is known to  */
   /*             be ill-conditioned. the default is false (0). this    */
   /*             variable is automatically set, when praxis finds      */
   /*             the problem to be ill-conditioned during iterations.  */
   /*  maxfun     is the maximum number of calls to fun allowed. praxis */
   /*             will return after maxfun calls to fun even when the   */
   /*             minimum is not yet found. the default value of 0      */
   /*             indicates no limit on the number of calls.            */
   /*             this return condition is only checked every n         */
   /*             iterations.                                           */
   /*                                                                   */
   /*********************************************************************/
   
   #include <math.h>
   #include <stdio.h>
   #include <stdlib.h>
   #include <float.h> /* for DBL_EPSILON */
   /* #include "machine.h" */
   
   
   /* extern void minfit(int n, double eps, double tol, double **ab, double q[]); */
   /* extern void minfit(int n, double eps, double tol, double ab[N][N], double q[]); */
   /* control parameters */
   /* control parameters */
   #define SQREPSILON 1.0e-19
   /* #define EPSILON 1.0e-8 */ /* in main */
   
   double tol = SQREPSILON,
          scbd = 1.0,
          step = 1.0;
   int    ktm = 1,
          /* prin = 2, */
          maxfun = 0,
          illc = 0;
          
   /* some global variables */
   static int i, j, k, k2, nl, nf, kl, kt;
   /* static double s; */
   double sl, dn, dmin,
          fx, f1, lds, ldt, sf, df,
          qf1, qd0, qd1, qa, qb, qc,
          m2, m4, small_windows, vsmall, large, 
          vlarge, ldfac, t2;
   /* static double d[N], y[N], z[N], */
   /*        q0[N], q1[N], v[N][N]; */
   
   static double *d, *y, *z;
   static double  *q0, *q1, **v;
   double *tflin; /* used in flin: return (*fun)(tflin, n); */
   double *e; /* used in minfit, don't konw how to free memory and thus made global */
   /* static double s, sl, dn, dmin, */
   /*        fx, f1, lds, ldt, sf, df, */
   /*        qf1, qd0, qd1, qa, qb, qc, */
   /*        m2, m4, small, vsmall, large,  */
   /*        vlarge, ldfac, t2; */
   /* static double d[N], y[N], z[N], */
   /*        q0[N], q1[N], v[N][N]; */
   
   /* these will be set by praxis to point to it's arguments */
   static int prin; /* added */
   static int n;
   static double *x;
   static double (*fun)();
   /* static double (*fun)(double *x, int n); */
   
   /* these will be set by praxis to the global control parameters */
   /* static double h, macheps, t; */
   extern double macheps;
   static double h;
   static double t;
   
   static double 
   drandom()       /* return random no between 0 and 1 */
   {
      return (double)(rand()%(8192*2))/(double)(8192*2);
   }
   
   static void sort()              /* d and v in descending order */
   {
      int k, i, j;
      double s;
   
      for (i=1; i<=n-1; i++) {
          k = i; s = d[i];
          for (j=i+1; j<=n; j++) {
              if (d[j] > s) {
                 k = j;
                 s = d[j];
              }
          }
          if (k > i) {
             d[k] = d[i];
             d[i] = s;
             for (j=1; j<=n; j++) {
                 s = v[j][i];
                 v[j][i] = v[j][k];
                 v[j][k] = s;
             }
          }
      }
   }
   
   double randbrent ( int *naught )
   {
     double ran1, ran3[127], half;
     int ran2, q, r, i, j;
     int init=0; /* false */
     double rr;
     /* REAL*8 RAN1,RAN3(127),HALF */
   
     /*     INTEGER RAN2,Q,R */
     /*     LOGICAL INIT */
     /*     DATA INIT/.FALSE./ */
     /*     IF (INIT) GO TO 3 */
     if(!init){ 
   /*       R = MOD(NAUGHT,8190) + 1 *//* 1804289383 rand () */
       r = *naught % 8190 + 1;/* printf(" naught r %d %d",*naught,r); */
       ran2=127;
       for(i=ran2; i>0; i--){
   /*       RAN2 = 128 */
   /*       DO 2 I=1,127 */
         ran2 = ran2-1;
   /*          RAN2 = RAN2 - 1 */
         ran1 = -pow(2.0,55);
   /*          RAN1 = -2.D0**55 */
   /*          DO 1 J=1,7 */
         for(j=1; j<=7;j++){
   /*             R = MOD(1756*R,8191) */
           r = (1756*r) % 8191;/* printf(" i=%d (1756*r)%8191=%d",j,r); */
           q=r/32;
   /*             Q = R/32 */
   /* 1           RAN1 = (RAN1 + Q)*(1.0D0/256) */
           ran1 =(ran1+q)*(1.0/256);
         }
   /* 2        RAN3(RAN2) = RAN1 */
         ran3[ran2] = ran1; /* printf(" ran2=%d ran1=%.7g \n",ran2,ran1); */ 
       }
   /*       INIT = .TRUE. */
       init=1;
   /* 3     IF (RAN2.EQ.1) RAN2 = 128 */
     }
     if(ran2 == 0) ran2 = 126;
     else ran2 = ran2 -1;
     /* RAN2 = RAN2 - 1 */
     /* RAN1 = RAN1 + RAN3(RAN2) */
     ran1 = ran1 + ran3[ran2];/* printf("BIS ran2=%d ran1=%.7g \n",ran2,ran1);  */
     half= 0.5;
     /* HALF = .5D0 */
     /* IF (RAN1.GE.0.D0) HALF = -HALF */
     if(ran1 >= 0.) half =-half;
     ran1 = ran1 +half;
     ran3[ran2] = ran1;
     rr= ran1+0.5;
     /* RAN1 = RAN1 + HALF */
     /*   RAN3(RAN2) = RAN1 */
     /*   RANDOM = RAN1 + .5D0 */
   /*   r = ( ( double ) ( *seed ) ) * 4.656612875E-10; */
     return rr;
   }
   static void matprint(char *s, double **v, int m, int n)
   /* char *s; */
   /* double v[N][N]; */
   {
   #define INCX 8
     int i;
    
     int i2hi;
     int ihi;
     int ilo;
     int i2lo;
     int jlo=1;
     int j;
     int j2hi;
     int jhi;
     int j2lo;
     ilo=1;
     ihi=n;
     jlo=1;
     jhi=n;
     
     printf ("\n" );
     printf ("%s\n", s );
     for ( j2lo = jlo; j2lo <= jhi; j2lo = j2lo + INCX )
     {
       j2hi = j2lo + INCX - 1;
       if ( n < j2hi )
       {
         j2hi = n;
       }
       if ( jhi < j2hi )
       {
         j2hi = jhi;
       }
   
       /* fprintf ( ficlog, "\n" ); */
       printf ("\n" );
   /*
     For each column J in the current range...
   
     Write the header.
   */
       /* fprintf ( ficlog, "  Col:  "); */
       printf ("Col:");
       for ( j = j2lo; j <= j2hi; j++ )
       {
         /* fprintf ( ficlog, "  %7d     ", j - 1 ); */
         /* printf (" %9d      ", j - 1 ); */
         printf (" %9d      ", j );
       }
       /* fprintf ( ficlog, "\n" ); */
       /* fprintf ( ficlog, "  Row\n" ); */
       /* fprintf ( ficlog, "\n" ); */
       printf ("\n" );
       printf ("  Row\n" );
       printf ("\n" );
   /*
     Determine the range of the rows in this strip.
   */
       if ( 1 < ilo ){
         i2lo = ilo;
       }else{
         i2lo = 1;
       }
       if ( m < ihi ){
         i2hi = m;
       }else{
         i2hi = ihi;
       }
   
       for ( i = i2lo; i <= i2hi; i++ ){
   /*
     Print out (up to) 5 entries in row I, that lie in the current strip.
   */
         /* fprintf ( ficlog, "%5d:", i - 1 ); */
         /* printf ("%5d:", i - 1 ); */
         printf ("%5d:", i );
         for ( j = j2lo; j <= j2hi; j++ )
         {
           /* fprintf ( ficlog, "  %14g", a[i-1+(j-1)*m] ); */
           /* printf ("%14.7g  ", a[i-1+(j-1)*m] ); */
              /* printf("%14.7f  ", v[i-1][j-1]); */
              printf("%14.7f  ", v[i][j]);
           /* fprintf ( stdout, "  %14g", a[i-1+(j-1)*m] ); */
         }
         /* fprintf ( ficlog, "\n" ); */
         printf ("\n" );
       }
     }
    
      /* printf("%s\n", s); */
      /* for (k=0; k<n; k++) { */
      /*     for (i=0; i<n; i++) { */
      /*         /\* printf("%20.10e ", v[k][i]); *\/ */
      /*     } */
      /*     printf("\n"); */
      /* } */
   #undef INCX  
   }
   
   void vecprint(char *s, double *x, int n)
   /* char *s; */
   /* double x[N]; */
   {
      int i=0;
      
      printf(" %s", s);
      /* for (i=0; i<n; i++) */
      for (i=1; i<=n; i++)
        printf ("  %14.7g",  x[i] );
        /* printf("  %8d: %14g\n", i, x[i]); */
      printf ("\n" ); 
   }
   
   static void print()             /* print a line of traces */
   {
    
   
      printf("\n");
      /* printf("... chi square reduced to ... %20.10e\n", fx); */
      /* printf("... after %u function calls ...\n", nf); */
      /* printf("... including %u linear searches ...\n", nl); */
      printf("%10d    %10d%14.7g",nl, nf, fx);
      vecprint("... current values of x ...", x, n);
   }
   /* static void print2(int n, double *x, int prin, double fx, int nf, int nl) */ /* print a line of traces */
   static void print2() /* print a line of traces */
   {
     int i; double fmin=0.;
   
      /* printf("\n"); */
      /* printf("... chi square reduced to ... %20.10e\n", fx); */
      /* printf("... after %u function calls ...\n", nf); */
      /* printf("... including %u linear searches ...\n", nl); */
      /* printf("%10d    %10d%14.7g",nl, nf, fx); */
     printf ( "\n" );
     printf ( "  Linear searches      %d", nl );
     /* printf ( "  Linear searches      %d\n", nl ); */
     /* printf ( "  Function evaluations %d\n", nf ); */
     /* printf ( "  Function value FX = %g\n", fx ); */
     printf ( "  Function evaluations %d", nf );
     printf ( "  Function value FX = %.12lf\n", fx );
   #ifdef DEBUGPRAX
      printf("n=%d prin=%d\n",n,prin);
   #endif
      if(fx <= fmin) printf(" UNDEFINED "); else  printf("%14.7g",log(fx-fmin));
      if ( n <= 4 || 2 < prin )
      {
        /* for(i=1;i<=n;i++)printf("%14.7g",x[i-1]); */
        for(i=1;i<=n;i++)printf("%14.7g",x[i]);
        /* r8vec_print ( n, x, "  X:" ); */
      }
      printf("\n");
    }
   
   
   /* #ifdef MSDOS */
   /* static double tflin[N]; */
   /* #endif */
   
   static double flin(double l, int j)
   /* double l; */
   {
      int i;
      /* #ifndef MSDOS */
      /*    double tflin[N]; */
      /* #endif    */
      /* double *tflin; */ /* Be careful to put tflin on a vector n */
   
      /* j is used from 0 to n-1 and can be -1 for parabolic search */
   
      /* if (j != -1) {            /\* linear search *\/ */
      if (j > 0) {         /* linear search */
        /* for (i=0; i<n; i++){ */
        for (i=1; i<=n; i++){
             tflin[i] = x[i] + l *v[i][j];
   #ifdef DEBUGPRAX
             /* printf("     flin i=%14d t=%14.7f x=%14.7f l=%14.7f v[%d,%d]=%14.7f nf=%14d\n",i+1, tflin[i],x[i],l,i,j,v[i][j],nf); */
             printf("     flin i=%14d t=%14.7f x=%14.7f l=%14.7f v[%d,%d]=%14.7f nf=%14d\n",i, tflin[i],x[i],l,i,j,v[i][j],nf);
   #endif
        }
      }
      else {                       /* search along parabolic space curve */
         qa = l*(l-qd1)/(qd0*(qd0+qd1));
         qb = (l+qd0)*(qd1-l)/(qd0*qd1);
         qc = l*(l+qd0)/(qd1*(qd0+qd1));
   #ifdef DEBUGPRAX      
         printf("     search along a parabolic space curve. j=%14d nf=%14d l=%14.7f qd0=%14.7f qd1=%14.7f\n",j,nf,l,qd0,qd1);
   #endif
         /* for (i=0; i<n; i++){ */
         for (i=1; i<=n; i++){
             tflin[i] = qa*q0[i]+qb*x[i]+qc*q1[i];
   #ifdef DEBUGPRAX
             /* printf("      parabole i=%14d t(i)=%14.7f q0=%14.7f x=%14.7f q1=%14.7f\n",i+1,tflin[i],q0[i],x[i],q1[i]); */
             printf("      parabole i=%14d t(i)=%14.7e q0=%14.7e x=%14.7e q1=%14.7e\n",i,tflin[i],q0[i],x[i],q1[i]);
   #endif
         }
      }
      nf++;
   
   #ifdef NR_SHIFT
         return (*fun)((tflin-1), n);
   #else
        /* return (*fun)(tflin, n);*/
         return (*fun)(tflin);
   #endif
   }
   
   void minny(int j, int nits, double *d2, double *x1, double f1, int fk)
   /* double *d2, *x1, f1; */
   {
   /* here j is from 0 to n-1 and can be -1 for parabolic search  */
     /*      MINIMIZES F FROM X IN THE DIRECTION V(*,J) */
             /*      UNLESS J<1, WHEN A QUADRATIC SEARCH IS DONE */
             /*      IN THE PLANE DEFINED BY Q0, Q1 AND X. */
             /*      D2 AN APPROXIMATION TO HALF F'' (OR ZERO), */
             /*      X1 AN ESTIMATE OF DISTANCE TO MINIMUM, */
             /*      RETURNED AS THE DISTANCE FOUND. */
             /*       IF FK = TRUE THEN F1 IS FLIN(X1), OTHERWISE */
             /*       X1 AND F1 ARE IGNORED ON ENTRY UNLESS FINAL */
             /*       FX > F1. NITS CONTROLS THE NUMBER OF TIMES */
             /*       AN ATTEMPT IS MADE TO HALVE THE INTERVAL. */
             /* SIDE EFFECTS: USES AND ALTERS X, FX, NF, NL. */
             /*       IF J < 1 USES VARIABLES Q... . */
             /*       USES H, N, T, M2, M4, LDT, DMIN, MACHEPS; */
      int k, i, dz;
      double x2, xm, f0, f2, fm, d1, t2, sf1, sx1;
      double s;
      double macheps;
      macheps=pow(16.0,-13.0);
      sf1 = f1; sx1 = *x1;
      k = 0; xm = 0.0; fm = f0 = fx; dz = *d2 < macheps;
      /* h=1.0;*/ /* To be revised */
   #ifdef DEBUGPRAX
      /* printf("min macheps=%14g h=%14g step=%14g t=%14g fx=%14g\n",macheps,h, step,t, fx);  */
      /* Where is fx coming from */
      printf("   min macheps=%14g h=%14g  t=%14g fx=%.9lf dirj=%d\n",macheps, h, t, fx, j);
      matprint("  min vectors:",v,n,n);
   #endif
      /* find step size */
      s = 0.;
      /* for (i=0; i<n; i++) s += x[i]*x[i]; */
      for (i=1; i<=n; i++) s += x[i]*x[i];
      s = sqrt(s);
      if (dz)
         t2 = m4*sqrt(fabs(fx)/dmin + s*ldt) + m2*ldt;
      else
         t2 = m4*sqrt(fabs(fx)/(*d2) + s*ldt) + m2*ldt;
      s = s*m4 + t;
      if (dz && t2 > s) t2 = s;
      if (t2 < small_windows) t2 = small_windows;
      if (t2 > 0.01*h) t2 = 0.01 * h;
      if (fk && f1 <= fm) {
         xm = *x1;
         fm = f1;
      }
   #ifdef DEBUGPRAX
      printf("   additional flin X1=%14.7f t2=%14.7f *f1=%14.7f fm=%14.7f fk=%d\n",*x1,t2,f1,fm,fk);
   #endif   
      if (!fk || fabs(*x1) < t2) {
        *x1 = (*x1 >= 0 ? t2 : -t2); 
         /* *x1 = (*x1 > 0 ? t2 : -t2); */ /* kind of error */
   #ifdef DEBUGPRAX
        printf("    additional flin X1=%16.10e dirj=%d fk=%d\n",*x1, j, fk);
   #endif
         f1 = flin(*x1, j);
   #ifdef DEBUGPRAX
       printf("    after flin f1=%18.12e dirj=%d fk=%d\n",f1, j,fk);
   #endif
      }
      if (f1 <= fm) {
         xm = *x1;
         fm = f1;
      }
   L0: /*L0 loop or next */
   /*
     Evaluate FLIN at another point and estimate the second derivative.
   */
      if (dz) {
         x2 = (f0 < f1 ? -(*x1) : 2*(*x1));
   #ifdef DEBUGPRAX
         printf("     additional second flin x2=%14.8e x1=%14.8e f0=%14.8e f1=%18.12e dirj=%d\n",x2,*x1,f0,f1,j);
   #endif
         f2 = flin(x2, j);
   #ifdef DEBUGPRAX
         printf("     additional second flin x2=%16.10e x1=%16.10e f1=%18.12e f0=%18.10e f2=%18.10e fm=%18.10e\n",x2, *x1, f1,f0,f2,fm);
   #endif
         if (f2 <= fm) {
            xm = x2;
            fm = f2;
         }
         /* d2 is the curvature or double difference f1 doesn't seem to be accurately computed */
         *d2 = (x2*(f1-f0) - (*x1)*(f2-f0))/((*x1)*x2*((*x1)-x2));
   #ifdef DEBUGPRAX
         double d11,d12;
         d11=(f1-f0)/(*x1);d12=(f2-f0)/x2;
         printf(" d11=%18.12e d12=%18.12e d11-d12=%18.12e x1-x2=%18.12e (d11-d12)/(x2-(*x1))=%18.12e\n", d11 ,d12, d11-d12, x2-(*x1), (d11-d12)/(x2-(*x1)));
         printf(" original computing f1=%18.12e *d2=%16.10e f0=%18.12e f1-f0=%16.10e f2-f0=%16.10e\n",f1,*d2,f0,f1-f0, f2-f0);
         double ff1=7.783920622852e+04;
         double f1mf0=9.0344736236e-05;
         *d2 = (f1mf0)/ (*x1)/((*x1)-x2) - (f2-f0)/x2/((*x1)-x2);
         /* *d2 = (ff1-f0)/ (*x1)/((*x1)-x2) - (f2-f0)/x2/((*x1)-x2); */
         printf(" simpliff computing *d2=%16.10e f1mf0=%18.12e,f1=f0+f1mf0=%18.12e\n",*d2,f1mf0,f0+f1mf0);
         *d2 = ((f1-f0)/ (*x1) - (f2-f0)/x2)/((*x1)-x2);
         printf(" overlifi computing *d2=%16.10e\n",*d2);
   #endif
         *d2 = ((f1-f0)/ (*x1) - (f2-f0)/x2)/((*x1)-x2);      
      }
   #ifdef DEBUGPRAX
         printf("    additional second flin xm=%14.8e fm=%14.8e *d2=%14.8e\n",xm, fm,*d2);
   #endif
      /*
        Estimate the first derivative at 0.
      */
      d1 = (f1-f0)/(*x1) - *x1**d2; dz = 1;
      /*
         Predict the minimum.
       */
      if (*d2 <= small_windows) {
        x2 = (d1 < 0 ? h : -h);
      }
      else {
         x2 = - 0.5*d1/(*d2);
      }
   #ifdef DEBUGPRAX
       printf("   AT d1=%14.8e d2=%14.8e small=%14.8e dz=%d x1=%14.8e x2=%14.8e\n",d1,*d2,small_windows,dz,*x1,x2);
   #endif
       if (fabs(x2) > h)
         x2 = (x2 > 0 ? h : -h);
   L1:  /* L1 or try loop */
   #ifdef DEBUGPRAX
       printf("   AT predicted minimum flin x2=%14.8e x1=%14.8e K=%14d NITS=%14d dirj=%d\n",x2,*x1,k,nits,j);
   #endif
      f2 = flin(x2, j); /* x[i]+x2*v[i][j] */
   #ifdef DEBUGPRAX
      printf("   after flin f0=%14.8e f1=%14.8e f2=%14.8e fm=%14.8e\n",f0,f1,f2, fm);
   #endif
      if ((k < nits) && (f2 > f0)) {
   #ifdef DEBUGPRAX
        printf("  NO SUCCESS SO TRY AGAIN;\n");
   #endif
        k++;
        if ((f0 < f1) && (*x1*x2 > 0.0))
          goto L0; /* or next */
        x2 *= 0.5;
        goto L1;
      }
      nl++;
   #ifdef DEBUGPRAX
      printf(" bebeBE end of min x1=%14.8e x2=%14.8e f1=%14.8e f2=%14.8e f0=%14.8e fm=%14.8e d2=%14.8e\n",*x1, x2, f1, f2, f0, fm, *d2);
   #endif
      if (f2 > fm) x2 = xm; else fm = f2;
      if (fabs(x2*(x2-*x1)) > small_windows) {
         *d2 = (x2*(f1-f0) - *x1*(fm-f0))/(*x1*x2*(*x1-x2));
      }
      else {
         if (k > 0) *d2 = 0;
      }
   #ifdef DEBUGPRAX
      printf(" bebe end of min x1 might be very wrong x1=%14.8e fx=%14.8e d2=%14.8e\n",*x1, fx, *d2);
   #endif
      if (*d2 <= small_windows) *d2 = small_windows;
      *x1 = x2; fx = fm;
      if (sf1 < fx) {
         fx = sf1;
         *x1 = sx1;
      }
     /*
       Update X for linear search.
     */
   #ifdef DEBUGPRAX
      printf("  end of min x1=%14.8e fx=%14.8e d2=%14.8e\n",*x1, fx, *d2);
   #endif
      
      /* if (j != -1) */
      /*    for (i=0; i<n; i++) */
      /*        x[i] += (*x1)*v[i][j]; */
      if (j > 0)
         for (i=1; i<=n; i++)
             x[i] += (*x1)*v[i][j];
   }
   
   void quad()     /* look for a minimum along the curve q0, q1, q2        */
   {
      int i;
      double l, s;
   
      s = fx; fx = qf1; qf1 = s; qd1 = 0.0;
      /* for (i=0; i<n; i++) { */
      for (i=1; i<=n; i++) {
          s = x[i]; l = q1[i]; x[i] = l; q1[i] = s;
          qd1 = qd1 + (s-l)*(s-l);
      }
      s = 0.0; qd1 = sqrt(qd1); l = qd1;
   #ifdef DEBUGPRAX
     printf("  QUAD after sqrt qd1=%14.8e \n",qd1);
   #endif
    
      if (qd0>0.0 && qd1>0.0 &&nl>=3*n*n) {
   #ifdef DEBUGPRAX
        printf(" QUAD before min value=%14.8e \n",qf1);
   #endif
         /* min(-1, 2, &s, &l, qf1, 1); */
         minny(0, 2, &s, &l, qf1, 1);
         qa = l*(l-qd1)/(qd0*(qd0+qd1));
         qb = (l+qd0)*(qd1-l)/(qd0*qd1);
         qc = l*(l+qd0)/(qd1*(qd0+qd1));
      }
      else {
         fx = qf1; qa = qb = 0.0; qc = 1.0;
      }
   #ifdef DEBUGPRAX
     printf("after eventual min qd0=%14.8e qd1=%14.8e nl=%d\n",qd0, qd1,nl);
   #endif
      qd0 = qd1;
      /* for (i=0; i<n; i++) { */
      for (i=1; i<=n; i++) {
          s = q0[i]; q0[i] = x[i];
          x[i] = qa*s + qb*x[i] + qc*q1[i];
      }
   #ifdef DEBUGQUAD
      vecprint ( " X after QUAD:" , x, n );
   #endif
   }
   
   /* void minfit(int n, double eps, double tol, double ab[N][N], double q[]) */
   void minfit(int n, double eps, double tol, double **ab, double q[])
   /* int n; */
   /* double eps, tol, ab[N][N], q[N]; */
   {
      int l, kt, l2, i, j, k;
      double c, f, g, h, s, x, y, z;
      /* double eps; */
   /* #ifndef MSDOS */
   /*    double e[N];              /\* plenty of stack on a vax *\/ */
   /* #endif */
      /* double *e; */
      /* e=vector(0,n-1); /\* should be freed somewhere but gotos *\/ */
      
      /* householder's reduction to bidiagonal form */
   
      if(n==1){
        /* q[1-1]=ab[1-1][1-1]; */
        /* ab[1-1][1-1]=1.0; */
        q[1]=ab[1][1];
        ab[1][1]=1.0;
        return; /* added from hardt */
      }
      /* eps=macheps; */ /* added */
      x = g = 0.0;
   #ifdef DEBUGPRAX
      matprint (" HOUSE holder:", ab, n, n);
   #endif
   
      /* for (i=0; i<n; i++) {  /\* FOR I := 1 UNTIL N DO *\/ */
      for (i=1; i<=n; i++) {  /* FOR I := 1 UNTIL N DO */
        e[i] = g; s = 0.0; l = i+1;
        /* for (j=i; j<n; j++)  /\* FOR J := I UNTIL N DO S := S*AB(J,I)**2; *\/ /\* not correct *\/ */
        for (j=i; j<=n; j++)  /* FOR J := I UNTIL N DO S := S*AB(J,I)**2; */ /* not correct */
          s += ab[j][i] * ab[j][i];
   #ifdef DEBUGPRAXFIN
        printf("i=%d s=%d %.7g tol=%.7g",i,s,tol);
   #endif
        if (s < tol) {
          g = 0.0;
        }
        else {
          /* f = ab[i][i]; */
          f = ab[i][i];
          if (f < 0.0) 
            g = sqrt(s);
          else
            g = -sqrt(s);
          /* h = f*g - s; ab[i][i] = f - g; */
          h = f*g - s; ab[i][i] = f - g;
          /* for (j=l; j<n; j++) { */ /* FOR J := L UNTIL N DO */ /* wrong */
          for (j=l; j<=n; j++) {
            f = 0.0;
            /* for (k=i; k<n; k++) /\* FOR K := I UNTIL N DO *\/ /\* wrong *\/ */
            for (k=i; k<=n; k++) /* FOR K := I UNTIL N DO */
              /* f += ab[k][i] * ab[k][j]; */
              f += ab[k][i] * ab[k][j];
            f /= h;
            for (k=i; k<=n; k++) /* FOR K := I UNTIL N DO */
              /* for (k=i; k<n; k++)/\* FOR K := I UNTIL N DO *\/ /\* wrong *\/ */
              ab[k][j] += f * ab[k][i];
            /* ab[k][j] += f * ab[k][i]; */
   #ifdef DEBUGPRAX
            printf("Holder J=%d F=%.7g",j,f);
   #endif
          }
        } /* end s */
        /* q[i] = g; s = 0.0; */
        q[i] = g; s = 0.0;
   #ifdef DEBUGPRAX
        printf(" I Q=%d %.7g",i,q[i]);
   #endif   
          
        /* if (i < n) */
        /* if (i <= n)  /\* I is always lower or equal to n wasn't in golub reinsch*\/ */
        /* for (j=l; j<n; j++) */
        for (j=l; j<=n; j++)
          s += ab[i][j] * ab[i][j];
        /* s += ab[i][j] * ab[i][j]; */
        if (s < tol) {
          g = 0.0;
        }
        else {
          if(i<n)
            /* f = ab[i][i+1]; */ /* Brent golub overflow */
            f = ab[i][i+1];
          if (f < 0.0)
            g = sqrt(s);
          else 
            g = - sqrt(s);
          h = f*g - s;
          /* h = f*g - s; ab[i][i+1] = f - g; */ /* Overflow for i=n Error in Golub too but not Burkardt*/
          /* for (j=l; j<n; j++) */
          /*     e[j] = ab[i][j]/h; */
          if(i<n){
            ab[i][i+1] = f - g;
            for (j=l; j<=n; j++)
              e[j] = ab[i][j]/h;
            /* for (j=l; j<n; j++) { */
            for (j=l; j<=n; j++) {
              s = 0.0;
              /* for (k=l; k<n; k++) s += ab[j][k]*ab[i][k]; */
              for (k=l; k<=n; k++) s += ab[j][k]*ab[i][k];
              /* for (k=l; k<n; k++) ab[j][k] += s * e[k]; */
              for (k=l; k<=n; k++) ab[j][k] += s * e[k];
            } /* END J */
          } /* END i <n */
        } /* end s */
          /* y = fabs(q[i]) + fabs(e[i]); */
        y = fabs(q[i]) + fabs(e[i]);
        if (y > x) x = y;
   #ifdef DEBUGPRAX
        printf(" I Y=%d %.7g",i,y);
   #endif
   #ifdef DEBUGPRAX
        printf(" i=%d e(i) %.7g",i,e[i]);
   #endif
      } /* end i */
      /*
        Accumulation of right hand transformations */
      /* for (i=n-1; i >= 0; i--) { */ /* FOR I := N STEP -1 UNTIL 1 DO */
      /* We should avoid the overflow in Golub */
      /* ab[n-1][n-1] = 1.0; */
      /* g = e[n-1]; */
      ab[n][n] = 1.0;
      g = e[n];
      l = n;
   
      /* for (i=n; i >= 1; i--) { */
      for (i=n-1; i >= 1; i--) { /* n-1 loops, different from brent and golub*/
        if (g != 0.0) {
          /* h = ab[i-1][i]*g; */
          h = ab[i][i+1]*g;
          for (j=l; j<=n; j++) ab[j][i] = ab[i][j] / h;
          for (j=l; j<=n; j++) {
            /* h = ab[i][i+1]*g; */
            /* for (j=l; j<n; j++) ab[j][i] = ab[i][j] / h; */
            /* for (j=l; j<n; j++) { */
            s = 0.0;
            /* for (k=l; k<n; k++) s += ab[i][k] * ab[k][j]; */
            /* for (k=l; k<n; k++) ab[k][j] += s * ab[k][i]; */
            for (k=l; k<=n; k++) s += ab[i][k] * ab[k][j];
            for (k=l; k<=n; k++) ab[k][j] += s * ab[k][i];
          }/* END J */
        }/* END G */
        /* for (j=l; j<n; j++) */
        /*     ab[i][j] = ab[j][i] = 0.0; */
        /* ab[i][i] = 1.0; g = e[i]; l = i; */
        for (j=l; j<=n; j++)
          ab[i][j] = ab[j][i] = 0.0;
        ab[i][i] = 1.0; g = e[i]; l = i;
      }/* END I */
   #ifdef DEBUGPRAX
      matprint (" HOUSE accumulation:",ab,n, n );
   #endif
   
      /* diagonalization to bidiagonal form */
      eps *= x;
      /* for (k=n-1; k>= 0; k--) { */
      for (k=n; k>= 1; k--) {
        kt = 0;
   TestFsplitting:
   #ifdef DEBUGPRAX
        printf(" TestFsplitting: k=%d kt=%d\n",k,kt);
        /* for(i=1;i<=n;i++)printf(" e(%d)=%.14f",i,e[i]);printf("\n"); */
   #endif     
        kt = kt+1; 
   /* TestFsplitting: */
        /* if (++kt > 30) { */
        if (kt > 30) { 
          e[k] = 0.0;
          fprintf(stderr, "\n+++ MINFIT - Fatal error\n");
          fprintf ( stderr, "  The QR algorithm failed to converge.\n" );
        }
        /* for (l2=k; l2>=0; l2--) { */
        for (l2=k; l2>=1; l2--) {
          l = l2;
   #ifdef DEBUGPRAX
          printf(" l e(l)< eps %d %.7g %.7g ",l,e[l], eps);
   #endif
          /* if (fabs(e[l]) <= eps) */
          if (fabs(e[l]) <= eps)
            goto TestFconvergence;
          /* if (fabs(q[l-1]) <= eps)*/ /* missing if ( 1 < l ){ *//* printf(" q(l-1)< eps %d %.7g %.7g ",l-1,q[l-2], eps); */
          if (fabs(q[l-1]) <= eps)
            break; /* goto Cancellation; */
        }
      Cancellation:
   #ifdef DEBUGPRAX
        printf(" Cancellation:\n");
   #endif     
        c = 0.0; s = 1.0;
        for (i=l; i<=k; i++) {
          f = s * e[i]; e[i] *= c;
          /* f = s * e[i]; e[i] *= c; */
          if (fabs(f) <= eps)
            goto TestFconvergence;
          /* g = q[i]; */
          g = q[i];
          if (fabs(f) < fabs(g)) {
            double fg = f/g;
            h = fabs(g)*sqrt(1.0+fg*fg);
          }
          else {
            double gf = g/f;
            h = (f!=0.0 ? fabs(f)*sqrt(1.0+gf*gf) : 0.0);
          }
          /*    COMMENT: THE ABOVE REPLACES Q(I):=H:=LONGSQRT(G*G+F*F) */
          /* WHICH MAY GIVE INCORRECT RESULTS IF THE */
          /* SQUARES UNDERFLOW OR IF F = G = 0; */
          
          /* q[i] = h; */
          q[i] = h;
          if (h == 0.0) { h = 1.0; g = 1.0; }
          c = g/h; s = -f/h;
        }
   TestFconvergence:
    #ifdef DEBUGPRAX
        printf(" TestFconvergence: l=%d k=%d\n",l,k);
   #endif     
        /* z = q[k]; */
        z = q[k];
        if (l == k)
          goto Convergence;
        /* shift from bottom 2x2 minor */
        /* x = q[l]; y = q[k-l]; g = e[k-1]; h = e[k]; */ /* Error */
        x = q[l]; y = q[k-1]; g = e[k-1]; h = e[k];
        f = ((y-z)*(y+z) + (g-h)*(g+h)) / (2.0*h*y);
        g = sqrt(f*f+1.0);
        if (f <= 0.0)
          f = ((x-z)*(x+z) + h*(y/(f-g)-h))/x;
        else
          f = ((x-z)*(x+z) + h*(y/(f+g)-h))/x;
        /* next qr transformation */
        s = c = 1.0;
        for (i=l+1; i<=k; i++) {
   #ifdef DEBUGPRAXQR
          printf(" Before Mid TestFconvergence: l+1=%d i=%d k=%d h=%.6e e(i)=%14.8f e(i-1)=%14.8f\n",l+1,i,k, h, e[i],e[i-1]);
   #endif     
          /* g = e[i]; y = q[i]; h = s*g; g *= c; */
          g = e[i]; y = q[i]; h = s*g; g *= c;
          if (fabs(f) < fabs(h)) {
            double fh = f/h;
            z = fabs(h) * sqrt(1.0 + fh*fh);
          }
          else {
            double hf = h/f;
            z = (f!=0.0 ? fabs(f)*sqrt(1.0+hf*hf) : 0.0);
          }
          /* e[i-1] = z; */
          e[i-1] = z;
   #ifdef DEBUGPRAXQR
          printf(" Mid TestFconvergence: l+1=%d i=%d k=%d h=%.6e e(i)=%14.8f e(i-1)=%14.8f\n",l+1,i,k, h, e[i],e[i-1]);
   #endif     
          if (z == 0.0) 
            f = z = 1.0;
          c = f/z; s = h/z;
          f = x*c + g*s; g = - x*s + g*c; h = y*s;
          y *= c;
          /* for (j=0; j<n; j++) { */
          /*     x = ab[j][i-1]; z = ab[j][i]; */
          /*     ab[j][i-1] = x*c + z*s; */
          /*     ab[j][i] = - x*s + z*c; */
          /* } */
          for (j=1; j<=n; j++) {
            x = ab[j][i-1]; z = ab[j][i];
            ab[j][i-1] = x*c + z*s;
            ab[j][i] = - x*s + z*c;
          }
          if (fabs(f) < fabs(h)) {
            double fh = f/h;
            z = fabs(h) * sqrt(1.0 + fh*fh);
          }
          else {
            double hf = h/f;
            z = (f!=0.0 ? fabs(f)*sqrt(1.0+hf*hf) : 0.0);
          }
   #ifdef DEBUGPRAXQR
          printf(" qr transformation z f h=%.7g %.7g %.7g i=%d k=%d\n",z,f,h, i, k);
   #endif
          q[i-1] = z;
          if (z == 0.0)
            z = f = 1.0;
          c = f/z; s = h/z;
          f = c*g + s*y;  /* f can be very small */
          x = - s*g + c*y;
        }
        /* e[l] = 0.0; e[k] = f; q[k] = x; */
        e[l] = 0.0; e[k] = f; q[k] = x;
   #ifdef DEBUGPRAXQR
        printf(" aftermid loop l=%d k=%d e(l)=%7g e(k)=%.7g q(k)=%.7g x=%.7g\n",l,k,e[l],e[k],q[k],x);
   #endif
        goto TestFsplitting;
      Convergence:
   #ifdef DEBUGPRAX
        printf(" Convergence:\n");
   #endif     
        if (z < 0.0) {
          /* q[k] = - z; */
          /* for (j=0; j<n; j++) ab[j][k] = - ab[j][k]; */
          q[k] = - z;
          for (j=1; j<=n; j++) ab[j][k] = - ab[j][k];
        }/* END Z */
      }/* END K */
   } /* END MINFIT */
   
   
   double praxis(double tol, double macheps, double h0, int _n, int _prin, double *_x, double (*_fun)(double *_x))
   /* double praxis(double tol, double macheps, double h0, int _n, int _prin, double *_x, double (*_fun)(double *_x, int _n)) */
   /* double praxis(double (*_fun)(), double _x[], int _n) */
   /* double (*_fun)(); */
   /* double _x[N]; */
   /* double (*_fun)(); */
   /* double _x[N]; */
   {
      /* init global extern variables and parameters */
      /* double *d, *y, *z, */
      /*   *q0, *q1, **v; */
      /* double *tflin; /\* used in flin: return (*fun)(tflin, n); *\/ */
      /* double *e; /\* used in minfit, don't konw how to free memory and thus made global *\/ */
   
     
     int seed; /* added */
     int biter=0;
     double r;
     double randbrent( int (*));
     double s, sf;
     
      h = h0; /* step; */
      t = tol;
      scbd = 1.0;
      illc = 0;
      ktm = 1;
   
      macheps = DBL_EPSILON;
      /* prin=4; */
   #ifdef DEBUGPRAX
      printf("Praxis macheps=%14g h=%14g step=%14g tol=%14g\n",macheps,h, h0,tol); 
   #endif
      n = _n;
      x = _x;
      prin = _prin;
      fun = _fun;
      d=vector(1, n);
      y=vector(1, n);
      z=vector(1, n);
      q0=vector(1, n);
      q1=vector(1, n);
      e=vector(1, n);
      tflin=vector(1, n);
      v=matrix(1, n, 1, n);
      for(i=1;i<=n;i++){d[i]=y[i]=z[i]=q0[0]=e[i]=tflin[i]=0.;}
      small_windows = (macheps) * (macheps); vsmall = small_windows*small_windows;
      large = 1.0/small_windows; vlarge = 1.0/vsmall;
      m2 = sqrt(macheps); m4 = sqrt(m2);
      seed = 123456789; /* added */
      ldfac = (illc ? 0.1 : 0.01);
      for(i=1;i<=n;i++) z[i]=0.; /* Was missing in Gegenfurtner as well as Brent's algol or fortran  */
      nl = kt = 0; nf = 1;
   #ifdef NR_SHIFT
      fx = (*fun)((x-1), n);
   #else
      fx = (*fun)(x);
   #endif
      qf1 = fx;
      t2 = small_windows + fabs(t); t = t2; dmin = small_windows;
   #ifdef DEBUGPRAX
      printf("praxis2 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t); 
   #endif
      if (h < 100.0*t) h = 100.0*t;
   #ifdef DEBUGPRAX
      printf("praxis3 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t); 
   #endif
      ldt = h;
      /* for (i=0; i<n; i++) for (j=0; j<n; j++) */
      for (i=1; i<=n; i++) for (j=1; j<=n; j++)
          v[i][j] = (i == j ? 1.0 : 0.0);
      d[1] = 0.0; qd0 = 0.0;
      /* for (i=0; i<n; i++) q1[i] = x[i]; */
      for (i=1; i<=n; i++) q1[i] = x[i];
      if (prin > 1) {
         printf("\n------------- enter function praxis -----------\n");
         printf("... current parameter settings ...\n");
         printf("... scaling ... %20.10e\n", scbd);
         printf("...   tol   ... %20.10e\n", t);
         printf("... maxstep ... %20.10e\n", h);
         printf("...   illc  ... %20u\n", illc);
         printf("...   ktm   ... %20u\n", ktm);
         printf("... maxfun  ... %20u\n", maxfun);
      }
      if (prin) print2();
   
   mloop:
       biter++;  /* Added to count the loops */
      /* sf = d[0]; */
      /* s = d[0] = 0.0; */
       printf("\n Big iteration %d \n",biter);
       fprintf(ficlog,"\n Big iteration %d \n",biter);
       sf = d[1];
      s = d[1] = 0.0;
   
      /* minimize along first direction V(*,1) */
   #ifdef DEBUGPRAX
      printf("  Minimize along the first direction V(*,1). illc=%d\n",illc);
      /* fprintf(ficlog,"  Minimize along the first direction V(*,1).\n"); */
   #endif
   #ifdef DEBUGPRAX2
      printf("praxis4 macheps=%14g h=%14g step=%14g small=%14g t=%14g\n",macheps,h, h0,small_windows, t); 
   #endif
      /* min(0, 2, &d[0], &s, fx, 0); /\* mac heps not global *\/ */
      minny(1, 2, &d[1], &s, fx, 0); /* mac heps not global it seems that fx doesn't correspond to f(s=*x1) */
   #ifdef DEBUGPRAX
      printf("praxis5 macheps=%14g h=%14g looks at sign of s=%14g fx=%14g\n",macheps,h, s,fx); 
   #endif
      if (s <= 0.0)
         /* for (i=0; i < n; i++) */
         for (i=1; i <= n; i++)
             v[i][1] = -v[i][1];
      /* if ((sf <= (0.9 * d[0])) || ((0.9 * sf) >= d[0])) */
      if ((sf <= (0.9 * d[1])) || ((0.9 * sf) >= d[1]))
         /* for (i=1; i<n; i++) */
         for (i=2; i<=n; i++)
             d[i] = 0.0;
      /* for (k=1; k<n; k++) { */
      for (k=2; k<=n; k++) {
       /*
         The inner loop starts here.
       */
   #ifdef DEBUGPRAX
         printf("      The inner loop  here from k=%d to n=%d.\n",k,n);
         /* fprintf(ficlog,"      The inner loop  here from k=%d to n=%d.\n",k,n); */
   #endif
          /* for (i=0; i<n; i++) */
          for (i=1; i<=n; i++)
              y[i] = x[i];
          sf = fx;
   #ifdef DEBUGPRAX
          printf(" illc=%d and kt=%d and ktm=%d\n", illc, kt, ktm);
   #endif
          illc = illc || (kt > 0);
   next:
          kl = k;
          df = 0.0;
          if (illc) {        /* random step to get off resolution valley */
   #ifdef DEBUGPRAX
             printf("  A random step follows, to avoid resolution valleys.\n");
             matprint("  before rand, vectors:",v,n,n);
   #endif
             for (i=1; i<=n; i++) {
   #ifdef NOBRENTRAND
               r = drandom();
   #else
               seed=i;
               /* seed=i+1; */
   #ifdef DEBUGRAND
               printf(" Random seed=%d, brent i=%d",seed,i); /* YYYY i=5 j=1 vji= -0.0001170073 */
   #endif
               r = randbrent ( &seed );
   #endif
   #ifdef DEBUGRAND
               printf(" Random r=%.7g \n",r);
   #endif      
               z[i] = (0.1 * ldt + t2 * pow(10.0,(double)kt)) * (r - 0.5);
               /* z[i] = (0.1 * ldt + t2 * pow(10.0,(double)kt)) * (drandom() - 0.5); */
   
               s = z[i];
                 for (j=1; j <= n; j++)
                     x[j] += s * v[j][i];
             }
   #ifdef DEBUGRAND
             matprint("  after rand, vectors:",v,n,n);
   #endif
   #ifdef NR_SHIFT
             fx = (*fun)((x-1), n);
   #else
             fx = (*fun)(x, n);
   #endif
             /* fx = (*func) ( (x-1) ); *//* This for func which is computed from x[1] and not from x[0] xm1=(x-1)*/
             nf++;
          }
          /* minimize along non-conjugate directions */
   #ifdef DEBUGPRAX
           printf(" Minimize along the 'non-conjugate' directions (dots printed) V(*,%d),...,V(*,%d).\n",k,n);
           /* fprintf(ficlog," Minimize along the 'non-conjugate' directions  (dots printed) V(*,%d),...,V(*,%d).\n",k,n); */
   #endif
           /* for (k2=k; k2<n; k2++) {  /\* Be careful here k2 <=n ? *\/ */
           for (k2=k; k2<=n; k2++) {  /* Be careful here k2 <=n ? */
              sl = fx;
              s = 0.0;
   #ifdef DEBUGPRAX
              printf(" Minimize along the 'NON-CONJUGATE' true direction k2=%14d fx=%14.7f\n",k2, fx);
      matprint("  before min vectors:",v,n,n);
   #endif
              /* min(k2, 2, &d[k2], &s, fx, 0); */
      /*     jsearch=k2-1; */
      /* min(jsearch, 2, &d[jsearch], &s, fx, 0); */
      minny(k2, 2, &d[k2], &s, fx, 0);
   #ifdef DEBUGPRAX
              printf(" . D(%d)=%14.7f d[k2]=%14.7f z[k2]=%14.7f illc=%14d fx=%14.7f\n",k2,d[k2],d[k2],z[k2],illc,fx);
   #endif
             if (illc) {
                 /* double szk = s + z[k2]; */
                 /* s = d[k2] * szk*szk; */
                 double szk = s + z[k2];
                 s = d[k2] * szk*szk;
              }
              else 
                 s = sl - fx;
              /* if (df < s) { */
              if (df <= s) {
                 df = s;
                 kl = k2;
   #ifdef DEBUGPRAX
               printf(" df=%.7g and choose kl=%d \n",df,kl); /* UUUU */
   #endif
              }
           } /* end loop k2 */
           /*
             If there was not much improvement on the first try, set
             ILLC = true and start the inner loop again.
           */
   #ifdef DEBUGPRAX
           printf(" If there was not much improvement on the first try, set ILLC = true and start the inner loop again. illc=%d\n",illc);
           /* fprintf(ficlog,"  If there was not much improvement on the first try, set ILLC = true and start the inner loop again.\n"); */
   #endif
           if (!illc && (df < fabs(100.0 * (macheps) * fx))) {
   #ifdef DEBUGPRAX
             printf("\n NO SUCCESS because DF is small, starts inner loop with same K(=%d), fabs(  100.0 * machep(=%.10e) * fx(=%.9e) )=%.9e > df(=%.9e) break illc=%d\n", k, macheps, fx, fabs ( 100.0 * macheps * fx ), df, illc);         
   #endif
             illc = 1;
             goto next;
           }
   #ifdef DEBUGPRAX
           printf("\n SUCCESS, BREAKS inner loop K(=%d) because DF is big, fabs(  100.0 * machep(=%.10e) * fx(=%.9e) )=%.9e <= df(=%.9e) break illc=%d\n", k, macheps, fx, fabs ( 100.0 * macheps * fx ), df, illc);
   #endif
           
          /* if ((k == 1) && (prin > 1)){ /\* be careful k=2 *\/ */
          if ((k == 2) && (prin > 1)){ /* be careful k=2 */
   #ifdef DEBUGPRAX
           printf("  NEW D The second difference array d:\n" );
           /* fprintf(ficlog, " NEW D The second difference array d:\n" ); */
   #endif
            vecprint(" NEW D The second difference array d:",d,n);
          }
          /* minimize along conjugate directions */ 
          /*
            Minimize along the "conjugate" directions V(*,1),...,V(*,K-1).
          */
   #ifdef DEBUGPRAX
         printf("Minimize along the 'conjugate' directions V(*,1),...,V(*,K-1=%d).\n",k-1);
         /* fprintf(ficlog,"Minimize along the 'conjugate' directions V(*,1),...,V(*,K-1=%d).\n",k-1); */
   #endif
         /* for (k2=0; k2<=k-1; k2++) { */
         for (k2=1; k2<=k-1; k2++) {
              s = 0.0;
              /* min(k2-1, 2, &d[k2-1], &s, fx, 0); */
              minny(k2, 2, &d[k2], &s, fx, 0);
          }
          f1 = fx;
          fx = sf;
          lds = 0.0;
          /* for (i=0; i<n; i++) { */
          for (i=1; i<=n; i++) {
              sl = x[i];
              x[i] = y[i];
              y[i] = sl - y[i];
              sl = y[i];
              lds = lds + sl*sl;
          }
          lds = sqrt(lds);
   #ifdef DEBUGPRAX
          printf("Minimization done 'conjugate', shifted all points, computed lds=%.8f\n",lds);
   #endif      
         /*
           Discard direction V(*,kl).
           
           If no random step was taken, V(*,KL) is the "non-conjugate"
           direction along which the greatest improvement was made.
         */
          if (lds > small_windows) {
   #ifdef DEBUGPRAX
          printf("lds big enough to throw direction  V(*,kl=%d). If no random step was taken, V(*,KL) is the 'non-conjugate' direction along which the greatest improvement was made.\n",kl);
            matprint("  before shift new conjugate vectors:",v,n,n);
   #endif
            for (i=kl-1; i>=k; i--) {
              /* for (j=0; j < n; j++) */
              for (j=1; j <= n; j++)
                /* v[j][i+1] = v[j][i]; */ /* This is v[j][i+1]=v[j][i] i=kl-1 to k */
                v[j][i+1] = v[j][i]; /* This is v[j][i+1]=v[j][i] i=kl-1 to k */
              /* v[j][i+1] = v[j][i]; */
              /* d[i+1] = d[i];*/  /* last  is d[k+1]= d[k] */
              d[i+1] = d[i];  /* last  is d[k]= d[k-1] */
            }
   #ifdef DEBUGPRAX
            matprint("  after shift new conjugate vectors:",v,n,n);         
   #endif   /* d[k] = 0.0; */
            d[k] = 0.0;
            for (i=1; i <= n; i++)
              v[i][k] = y[i] / lds;
            /* v[i][k] = y[i] / lds; */
   #ifdef DEBUGPRAX
            printf("Minimize along the new 'conjugate' direction V(*,k=%d), which is the normalized vector:  (new x) - (old x). d2=%14.7g lds=%.10f\n",k,d[k],lds);
            /* fprintf(ficlog,"Minimize along the new 'conjugate' direction V(*,k=%d), which is the normalized vector:  (new x) - (old x).\n",k); */
       matprint("  before min new conjugate vectors:",v,n,n);       
   #endif
            /* min(k-1, 4, &d[k-1], &lds, f1, 1); */
            minny(k, 4, &d[k], &lds, f1, 1);
   #ifdef DEBUGPRAX
            printf(" after min d(k)=%d %.7g lds=%14f\n",k,d[k],lds);
      matprint("  after min vectors:",v,n,n);
   #endif
            if (lds <= 0.0) {
              lds = -lds;
   #ifdef DEBUGPRAX
             printf(" lds changed sign lds=%.14f k=%d\n",lds,k);
   #endif     
              /* for (i=0; i<n; i++) */
              /*   v[i][k] = -v[i][k]; */
              for (i=1; i<=n; i++)
                v[i][k] = -v[i][k];
            }
          }
          ldt = ldfac * ldt;
          if (ldt < lds)
             ldt = lds;
          if (prin > 0){
   #ifdef DEBUGPRAX
           printf(" k=%d",k);
           /* fprintf(ficlog," k=%d",k); */
   #endif
           print2();/* n, x, prin, fx, nf, nl ); */
          }
          t2 = 0.0;
          /* for (i=0; i<n; i++) */
          for (i=1; i<=n; i++)
              t2 += x[i]*x[i];
          t2 = m2 * sqrt(t2) + t;
          /*
           See whether the length of the step taken since starting the
           inner loop exceeds half the tolerance.
         */
   #ifdef DEBUGPRAX
          printf("See if step length exceeds half the tolerance.\n"); /* ZZZZZ */
         /* fprintf(ficlog,"See if step length exceeds half the tolerance.\n"); */
   #endif
          if (ldt > (0.5 * t2))
             kt = 0;
          else 
             kt++;
   #ifdef DEBUGPRAX
          printf("if kt=%d >? ktm=%d gotoL2 loop\n",kt,ktm);
   #endif
          if (kt > ktm){
            if ( 0 < prin ){
              /* printf("\nr8vec_print\n X:\n"); */
              /* fprintf(ficlog,"\nr8vec_print\n X:\n"); */
              vecprint ("END  X:", x, n );
            }
              goto fret;
          }
   #ifdef DEBUGPRAX
      matprint("  end of L2 loop vectors:",v,n,n);
   #endif
          
      }
      /* printf("The inner loop ends here.\n"); */
      /* fprintf(ficlog,"The inner loop ends here.\n"); */
      /*
        The inner loop ends here.
        
        Try quadratic extrapolation in case we are in a curved valley.
      */
   #ifdef DEBUGPRAX
      printf("Try QUAD ratic extrapolation in case we are in a curved valley.\n");
   #endif
      /*  try quadratic extrapolation in case    */
      /*  we are stuck in a curved valley        */
      quad();
      dn = 0.0;
      /* for (i=0; i<n; i++) { */
      for (i=1; i<=n; i++) {
          d[i] = 1.0 / sqrt(d[i]);
          if (dn < d[i])
             dn = d[i];
      }
      if (prin > 2)
        matprint("  NEW DIRECTIONS vectors:",v,n,n);
      /* for (j=0; j<n; j++) { */
      for (j=1; j<=n; j++) {
          s = d[j] / dn;
          /* for (i=0; i < n; i++) */
          for (i=1; i <= n; i++)
              v[i][j] *= s;
      }
      
      if (scbd > 1.0) {       /* scale axis to reduce condition number */
   #ifdef DEBUGPRAX
        printf("Scale the axes to try to reduce the condition number.\n");
   #endif
        /* fprintf(ficlog,"Scale the axes to try to reduce the condition number.\n"); */
         s = vlarge;
         /* for (i=0; i<n; i++) { */
         for (i=1; i<=n; i++) {
             sl = 0.0;
             /* for (j=0; j < n; j++) */
             for (j=1; j <= n; j++)
                 sl += v[i][j]*v[i][j];
             z[i] = sqrt(sl);
             if (z[i] < m4)
                z[i] = m4;
             if (s > z[i])
                s = z[i];
         }
         /* for (i=0; i<n; i++) { */
         for (i=1; i<=n; i++) {
             sl = s / z[i];
             z[i] = 1.0 / sl;
             if (z[i] > scbd) {
                sl = 1.0 / scbd;
                z[i] = scbd;
             }
         }
      }
      for (i=1; i<=n; i++)
          /* for (j=0; j<=i-1; j++) { */
          /* for (j=1; j<=i; j++) { */
          for (j=1; j<=i-1; j++) {
              s = v[i][j];
              v[i][j] = v[j][i];
              v[j][i] = s;
          }
   #ifdef DEBUGPRAX
       printf(" Calculate a new set of orthogonal directions before repeating  the main loop.\n  Transpose V for MINFIT:...\n");
   #endif
         /*
         MINFIT finds the singular value decomposition of V.
   
         This gives the principal values and principal directions of the
         approximating quadratic form without squaring the condition number.
       */
    #ifdef DEBUGPRAX
       printf(" MINFIT finds the singular value decomposition of V. \n This gives the principal values and principal directions of the\n  approximating quadratic form without squaring the condition number...\n");
   #endif
   
      minfit(n, macheps, vsmall, v, d);
       /* for(i=0; i<n;i++)printf(" %14.7g",d[i]); */
       /* v is overwritten with R. */
       /*
         Unscale the axes.
       */
      if (scbd > 1.0) {
   #ifdef DEBUGPRAX
         printf(" Unscale the axes.\n");
   #endif
         /* for (i=0; i<n; i++) { */
         for (i=1; i<=n; i++) {
             s = z[i];
             /* for (j=0; j<n; j++) */
             for (j=1; j<=n; j++)
                 v[i][j] *= s;
         }
         /* for (i=0; i<n; i++) { */
         for (i=1; i<=n; i++) {
             s = 0.0;
             /* for (j=0; j<n; j++) */
             for (j=1; j<=n; j++)
                 s += v[j][i]*v[j][i];
             s = sqrt(s);
             d[i] *= s;
             s = 1.0 / s;
             /* for (j=0; j<n; j++) */
             for (j=1; j<=n; j++)
                 v[j][i] *= s;
         }
      }
      /* for (i=0; i<n; i++) { */
      double dni; /* added for compatibility with buckhardt but not brent */
      for (i=1; i<=n; i++) {
        dni=dn*d[i]; /* added for compatibility with buckhardt but not brent */
          if ((dn * d[i]) > large)
             d[i] = vsmall;
          else if ((dn * d[i]) < small_windows)
             d[i] = vlarge;
          else 
           d[i] = 1.0 / dni / dni; /* added for compatibility with buckhardt but not brent */
             /* d[i] = pow(dn * d[i],-2.0); */
      }
   #ifdef DEBUGPRAX
      vecprint ("\n Before sort Eigenvalues of a:",d,n );
   #endif
      
      sort();               /* the new eigenvalues and eigenvectors */
   #ifdef DEBUGPRAX
      vecprint( " After sort the eigenvalues ....\n", d, n);
      matprint( " After sort the eigenvectors....\n", v, n,n);
   #endif
   #ifdef DEBUGPRAX
       printf("  Determine the smallest eigenvalue.\n");
   #endif
      /* dmin = d[n-1]; */
      dmin = d[n];
      if (dmin < small_windows)
         dmin = small_windows;
       /*
        The ratio of the smallest to largest eigenvalue determines whether
        the system is ill conditioned.
      */
     
      /* illc = (m2 * d[0]) > dmin; */
      illc = (m2 * d[1]) > dmin;
   #ifdef DEBUGPRAX
       printf("  The ratio of the smallest to largest eigenvalue determines whether\n  the system is ill conditioned=%d . dmin=%.10lf < m2=%.10lf * d[1]=%.10lf \n",illc, dmin,m2, d[1]);
   #endif
      
      if ((prin > 2) && (scbd > 1.0))
         vecprint("\n The scale factors:",z,n);
      if (prin > 2)
         vecprint("  Principal values (EIGEN VALUES OF A) of the quadratic form:",d,n);
      if (prin > 2)
        matprint("  The principal axes (EIGEN VECTORS OF A:",v,n, n);
   
      if ((maxfun > 0) && (nf > maxfun)) {
         if (prin)
            printf("\n... maximum number of function calls reached ...\n");
         goto fret;
      }
   #ifdef DEBUGPRAX
      printf("Goto main loop\n");
   #endif
      goto mloop;   /* back to main loop */
   
   fret:
      if (prin > 0) {
            vecprint("\n  X:", x, n);
            /* printf("\n... ChiSq reduced to %20.10e ...\n", fx); */
            /* printf("... after %20u function calls.\n", nf); */
      }
      free_vector(d, 1, n);
      free_vector(y, 1, n);
      free_vector(z, 1, n);
      free_vector(q0, 1, n);
      free_vector(q1, 1, n);
      free_matrix(v, 1, n, 1, n);
      /*   double *d, *y, *z, */
      /* *q0, *q1, **v; */
      free_vector(tflin, 1, n);
      /* double *tflin; /\* used in flin: return (*fun)(tflin, n); *\/ */
      free_vector(e, 1, n);
      /* double *e; /\* used in minfit, don't konw how to free memory and thus made global *\/ */
      
      return(fx);
   }
   
   /* end praxis gegen */
   
 /*************** powell ************************/  /*************** powell ************************/
 /*  /*
Line 2425  void powell(double p[], double **xi, int Line 4193  void powell(double p[], double **xi, int
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
     int Bigter=0, nBigterf=1;
     
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
   xit=vector(1,n);     xit=vector(1,n); 
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
   rcurr_time = time(NULL);      rcurr_time = time(NULL);
     fp=(*fret); /* Initialisation */
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     rlast_time=rcurr_time;      rlast_time=rcurr_time;
       rlast_btime=rcurr_time;
     /* (void) gettimeofday(&curr_time,&tzp); */      /* (void) gettimeofday(&curr_time,&tzp); */
     rcurr_time = time(NULL);        rcurr_time = time(NULL);  
     curr_time = *localtime(&rcurr_time);      curr_time = *localtime(&rcurr_time);
     printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      /* printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); */
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */      /* Bigter=(*iter - *iter % ncovmodel)/ncovmodel +1; /\* Big iteration, i.e on ncovmodel cycle *\/ */
       Bigter=(*iter - (*iter-1) % n)/n +1; /* Big iteration, i.e on ncovmodel cycle */
       printf("\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       fprintf(ficrespow,"%d %d %.12f %d",*iter,Bigter, *fret,curr_time.tm_sec-start_time.tm_sec);
     fp=(*fret); /* From former iteration or initial value */      fp=(*fret); /* From former iteration or initial value */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 2454  void powell(double p[], double **xi, int Line 4229  void powell(double p[], double **xi, int
         printf("  + age*age  ");          printf("  + age*age  ");
         fprintf(ficlog,"  + age*age  ");          fprintf(ficlog,"  + age*age  ");
     }      }
     for(j=1;j <=ncovmodel-2;j++){      for(j=1;j <=ncovmodel-2-nagesqr;j++){
       if(Typevar[j]==0) {        if(Typevar[j]==0) {
         printf("  +      V%d  ",Tvar[j]);          printf("  +      V%d  ",Tvar[j]);
         fprintf(ficlog,"  +      V%d  ",Tvar[j]);          fprintf(ficlog,"  +      V%d  ",Tvar[j]);
Line 2464  void powell(double p[], double **xi, int Line 4239  void powell(double p[], double **xi, int
       }else if(Typevar[j]==2) {        }else if(Typevar[j]==2) {
         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }else if(Typevar[j]==3) {
           printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
       }        }
     }      }
     printf("\n");      printf("\n");
Line 2494  void powell(double p[], double **xi, int Line 4272  void powell(double p[], double **xi, int
         strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(nBigterf=1;nBigterf<=31;nBigterf+=10){
           niterf=nBigterf*ncovmodel;
           /* rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); */
         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         forecast_time = *localtime(&rforecast_time);          forecast_time = *localtime(&rforecast_time);
         strcpy(strfor,asctime(&forecast_time));          strcpy(strfor,asctime(&forecast_time));
         itmp = strlen(strfor);          itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';            strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          printf("   - if your program needs %d BIG iterations (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d BIG iterations  (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i, maximisation after loading directions */
       for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales. xi is not changed but one dim xit  */
       fptt=(*fret);   
         fptt=(*fret); /* Computes likelihood for parameters xit */
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);        fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
Line 2515  void powell(double p[], double **xi, int Line 4296  void powell(double p[], double **xi, int
       printf("%d",i);fflush(stdout); /* print direction (parameter) i */        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func); /* New point i minimizing in direction xit, i has coordinates p[j].*/
         /* xit[j] gives the n coordinates of direction i as input.*/
         /* *fret gives the maximum value on direction xit */
 #else  #else
       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                         flatdir[i]=flat; /* Function is vanishing in that direction i */        flatdir[i]=flat; /* Function is vanishing in that direction i */
 #endif  #endif
                         /* Outputs are fret(new point p) p is updated and xit rescaled */        /* Outputs are fret(new point p) p is updated and xit rescaled */
       if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */        if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
                                 /* because that direction will be replaced unless the gain del is small */          /* because that direction will be replaced unless the gain del is small */
                                 /* in comparison with the 'probable' gain, mu^2, with the last average direction. */          /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
                                 /* Unless the n directions are conjugate some gain in the determinant may be obtained */          /* Unless the n directions are conjugate some gain in the determinant may be obtained */
                                 /* with the new direction. */          /* with the new direction. */
                                 del=fabs(fptt-(*fret));           del=fabs(fptt-(*fret)); 
                                 ibig=i;           ibig=i; 
       }         } 
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %.12e",i,(*fret));        printf("%d %.12e",i,(*fret));
       fprintf(ficlog,"%d %.12e",i,(*fret));        fprintf(ficlog,"%d %.12e",i,(*fret));
       for (j=1;j<=n;j++) {        for (j=1;j<=n;j++) {
                                 xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
                                 printf(" x(%d)=%.12e",j,xit[j]);          printf(" x(%d)=%.12e",j,xit[j]);
                                 fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
                                 printf(" p(%d)=%.12e",j,p[j]);          printf(" p(%d)=%.12e",j,p[j]);
                                 fprintf(ficlog," p(%d)=%.12e",j,p[j]);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     } /* end loop on each direction i */      } /* end loop on each direction i */
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* Convergence test will use last linmin estimation (fret) and compare to former iteration (fp) */ 
     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
     /* New value of last point Pn is not computed, P(n-1) */      /* New value of last point Pn is not computed, P(n-1) */
     for(j=1;j<=n;j++) {      for(j=1;j<=n;j++) {
Line 2600  void powell(double p[], double **xi, int Line 4383  void powell(double p[], double **xi, int
       return;         return; 
     } /* enough precision */       } /* enough precision */ 
     if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      for (j=1;j<=n;j++) { /* Computes the extrapolated point and value f3, P_0 + 2 (P_n-P_0)=2Pn-P0 and xit is direction Pn-P0 */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; /* Coordinate j of last direction xi_n=P_n-P_0 */
       pt[j]=p[j];   #ifdef DEBUG
     }         printf("\n %d xit=%12.7g p=%12.7g pt=%12.7g ",j,xit[j],p[j],pt[j]);
   #endif
         pt[j]=p[j]; /* New P0 is Pn */
       }
   #ifdef DEBUG
       printf("\n");
   #endif
     fptt=(*func)(ptt); /* f_3 */      fptt=(*func)(ptt); /* f_3 */
 #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in directions until some iterations are done */
                 if (*iter <=4) {                  if (*iter <=4) {
 #else  #else
 #endif  #endif
Line 2625  void powell(double p[], double **xi, int Line 4414  void powell(double p[], double **xi, int
       /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */        /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
       /*  Even if f3 <f1, directest can be negative and t >0 */        /*  Even if f3 <f1, directest can be negative and t >0 */
       /* mu² and del² are equal when f3=f1 */        /* mu² and del² are equal when f3=f1 */
                         /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */        /* f3 < f1 : mu² < del <= lambda^2 both test are equivalent */
                         /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */        /* f3 < f1 : mu² < lambda^2 < del then directtest is negative and powell t is positive */
                         /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */        /* f3 > f1 : lambda² < mu^2 < del then t is negative and directest >0  */
                         /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */        /* f3 > f1 : lambda² < del < mu^2 then t is positive and directest >0  */
 #ifdef NRCORIGINAL  #ifdef NRCORIGINAL
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
 #else  #else
Line 2648  void powell(double p[], double **xi, int Line 4437  void powell(double p[], double **xi, int
 #endif  #endif
 #ifdef POWELLORIGINAL  #ifdef POWELLORIGINAL
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else  /* Not POWELLOriginal but Brouard's */
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
                                 printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);          printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
         printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
         fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);          fprintf(ficlog,"directest= %.12lf (if directest<0 or t<0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
         fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);          fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       }         } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use (P0, Pn) for new direction Xi_n or Xi_iBig */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
         printf("Before linmin in direction P%d-P0\n",n);          printf("Before linmin in direction P%d-P0\n",n);
Line 2689  void powell(double p[], double **xi, int Line 4478  void powell(double p[], double **xi, int
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
         }          }
   
   /* #else */
   /*      for (i=1;i<=n-1;i++) {  */
   /*        for (j=1;j<=n;j++) {  */
   /*          xi[j][i]=xi[j][i+1]; /\* Standard method of conjugate directions, not Powell who changes the nth direction by p0 pn . *\/ */
   /*        } */
   /*      } */
   /*      for (j=1;j<=n;j++) {  */
   /*        xi[j][n]=xit[j];      /\* and this nth direction by the by the average p_0 p_n *\/ */
   /*      } */
   /*      /\* for (j=1;j<=n-1;j++) {  *\/ */
   /*      /\*   xi[j][1]=xi[j][j+1]; /\\* Standard method of conjugate directions *\\/ *\/ */
   /*      /\*   xi[j][n]=xit[j];      /\\* and this nth direction by the by the average p_0 p_n *\\/ *\/ */
   /*      /\* } *\/ */
   /* #endif */
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
         for (j=1, flatd=0;j<=n;j++) {          for (j=1, flatd=0;j<=n;j++) {
Line 2713  void powell(double p[], double **xi, int Line 4517  void powell(double p[], double **xi, int
           free_vector(pt,1,n);             free_vector(pt,1,n); 
           return;            return;
 #endif  #endif
         }          }  /* endif(flatd >0) */
 #endif  #endif /* LINMINORIGINAL */
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                   
Line 2729  void powell(double p[], double **xi, int Line 4533  void powell(double p[], double **xi, int
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t or directest negative */        } /* end of t or directest negative */
         printf(" Directest is positive, P_n-P_0 does not increase the conjugacy. n=%d\n",n);
         fprintf(ficlog," Directest is positive, P_n-P_0 does not increase the conjugacy. n=%d\n",n);
 #ifdef POWELLNOF3INFF1TEST  #ifdef POWELLNOF3INFF1TEST
 #else  #else
       } /* end if (fptt < fp)  */        } /* end if (fptt < fp)  */
Line 2744  void powell(double p[], double **xi, int Line 4550  void powell(double p[], double **xi, int
       
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)    double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
   {    {
     /**< Computes the prevalence limit in each live state at age x and for covariate combination ij       /**< Computes the prevalence limit in each live state at age x and for covariate combination ij . Nicely done
      *   (and selected quantitative values in nres)       *   (and selected quantitative values in nres)
      *  by left multiplying the unit       *  by left multiplying the unit
      *  matrix by transitions matrix until convergence is reached with precision ftolpl        *  matrix by transitions matrix until convergence is reached with precision ftolpl 
Line 2769  void powell(double p[], double **xi, int Line 4575  void powell(double p[], double **xi, int
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
           
   int i, ii,j,k;      int i, ii,j,k, k1;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */    double **out, cov[NCOVMAX+1], **pmij(); /* **pmmij is a global variable feeded with oldms etc */
Line 2800  void powell(double p[], double **xi, int Line 4606  void powell(double p[], double **xi, int
      if(nagesqr==1){       if(nagesqr==1){
       cov[3]= agefin*agefin;        cov[3]= agefin*agefin;
      }       }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
       /* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */         if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
       /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
     }         }else{
     for (k=1; k<=nsq;k++) { /* For single varying covariates only */           cov[2+nagesqr+k1]=precov[nres][k1];
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */         }
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];       }/* End of loop on model equation */
       /* cov[++k1]=Tqresult[nres][k];  */       
       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  /* Start of old code (replaced by a loop on position in the model equation */
     }      /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model *\/ */
     for (k=1; k<=cptcovage;k++){  /* For product with age */      /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
       if(Dummy[Tage[k]]==2){ /* dummy with age */      /*   /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; *\/ */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];      /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
         /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */      /*   /\* model = 1 +age + V1*V3 + age*V1 + V2 + V1 + age*V2 + V3 + V3*age + V1*V2  */
       } else if(Dummy[Tage[k]]==3){ /* quantitative with age */      /*    * k                  1        2      3    4      5      6     7        8 */
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];      /*    *cov[]   1    2      3        4      5    6      7      8     9       10 */
         /* cov[++k1]=Tqresult[nres][k];  */      /*    *TypeVar[k]          2        1      0    0      1      0     1        2 */
       }      /*    *Dummy[k]            0        2      0    0      2      0     2        0 */
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */      /*    *Tvar[k]             4        1      2    1      2      3     3        5 */
     }      /*    *nsd=3                              (1)  (2)           (3) */
     for (k=1; k<=cptcovprod;k++){ /* For product without age */      /*    *TvarsD[nsd]                      [1]=2    1             3 */
       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */      /*    *TnsdVar                          [2]=2 [1]=1         [3]=3 */
       if(Dummy[Tvard[k][1]==0]){      /*    *TvarsDind[nsd](=k)               [1]=3 [2]=4         [3]=6 */
         if(Dummy[Tvard[k][2]==0]){      /*    *Tage[]                  [1]=1                  [2]=2      [3]=3 */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];      /*    *Tvard[]       [1][1]=1                                           [2][1]=1 */
           /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */      /*    *                   [1][2]=3                                           [2][2]=2 */
         }else{      /*    *Tprod[](=k)     [1]=1                                              [2]=8 */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];      /*    *TvarsDp(=Tvar)   [1]=1            [2]=2             [3]=3          [4]=5 */
           /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */      /*    *TvarD (=k)       [1]=1            [2]=3 [3]=4       [3]=6          [4]=6 */
         }      /*    *TvarsDpType */
       }else{      /*    *si model= 1 + age + V3 + V2*age + V2 + V3*age */
         if(Dummy[Tvard[k][2]==0]){      /*    * nsd=1              (1)           (2) */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];      /*    *TvarsD[nsd]          3             2 */
           /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */      /*    *TnsdVar           (3)=1          (2)=2 */
         }else{      /*    *TvarsDind[nsd](=k)  [1]=1        [2]=3 */
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];      /*    *Tage[]                  [1]=2           [2]= 3    */
           /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */      /*    *\/ */
         }      /*   /\* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; *\/ */
       }      /*   /\* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
     }      /* } */
       /* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model *\/ */
       /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
       /*   /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 *\/ */
       /*   /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
       /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
       /*   /\* cov[++k1]=Tqresult[nres][k];  *\/ */
       /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
       /*   if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       /*  /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
       /*   } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
       /*  /\* cov[++k1]=Tqresult[nres][k];  *\/ */
       /*   } */
       /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
       /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
       /*   if(Dummy[Tvard[k][1]]==0){ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
       /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
       /*    /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; *\/ */
       /*  } */
       /*   }else{ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
       /*    /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
       /*    /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
       /*  } */
       /*   } */
       /* } /\* End product without age *\/ */
   /* ENd of old code */
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
Line 2898  void powell(double p[], double **xi, int Line 4743  void powell(double p[], double **xi, int
     first++;      first++;
   }    }
   
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl,
      * (int)age, (int)delaymax, (int)agefin, ncvloop,
      * (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
   free_vector(max,1,nlstate);    free_vector(max,1,nlstate);
   free_vector(meandiff,1,nlstate);    free_vector(meandiff,1,nlstate);
Line 2933  void powell(double p[], double **xi, int Line 4780  void powell(double p[], double **xi, int
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j, k1;
   int first=0;    int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
Line 2973  void powell(double p[], double **xi, int Line 4820  void powell(double p[], double **xi, int
     if(nagesqr==1){      if(nagesqr==1){
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     }      }
     for (k=1; k<=nsd;k++) { /* For single dummy covariates only */      for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
                         /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */        if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
       /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */  
     }  
     /* for (k=1; k<=cptcovn;k++) { */  
     /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */  
     /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */  
     /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */  
     /* } */  
     for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
                         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
       cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];   
       /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
     }  
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */  
     /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */  
     /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */  
     /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
     for (k=1; k<=cptcovage;k++){  /* For product with age */  
       /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ ERROR ???*/  
       if(Dummy[Tage[k]]== 2){ /* dummy with age */  
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
       } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
         cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  
       }  
       /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
     }  
     for (k=1; k<=cptcovprod;k++){ /* For product without age */  
       /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */  
       if(Dummy[Tvard[k][1]==0]){  
         if(Dummy[Tvard[k][2]==0]){  
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
         }else{  
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
         }  
       }else{        }else{
         if(Dummy[Tvard[k][2]==0]){          cov[2+nagesqr+k1]=precov[nres][k1];
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
         }else{  
           cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
         }  
       }        }
     }      }/* End of loop on model equation */
   
   /* Old code */ 
   
       /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
       /*                  /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */
       /*   cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; */
       /*   /\* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
       /* } */
       /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
       /* /\*   /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
       /* /\*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
       /* /\*   /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\\/ *\/ */
       /* /\* } *\/ */
       /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
       /*                  /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
       /*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
       /*   /\* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* /\* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; *\/ */
       /* /\* for (k=1; k<=cptcovprod;k++) /\\* Useless *\\/ *\/ */
       /* /\*   /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\\/ *\/ */
       /* /\*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
       /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
       /*   /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ ERROR ???*\/ */
       /*   if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       /*   } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
       /*  cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
       /*   } */
       /*   /\* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
       /* } */
       /* for (k=1; k<=cptcovprod;k++){ /\* For product without age *\/ */
       /*   /\* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); *\/ */
       /*   if(Dummy[Tvard[k][1]]==0){ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
       /*  } */
       /*   }else{ */
       /*  if(Dummy[Tvard[k][2]]==0){ */
       /*    cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
       /*  }else{ */
       /*    cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
       /*  } */
       /*   } */
       /* } */
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 3127  double **pmij(double **ps, double *cov, Line 4984  double **pmij(double **ps, double *cov,
         /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
       }        }
       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
       /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
     }      }
     for(j=i+1; j<=nlstate+ndeath;j++){      for(j=i+1; j<=nlstate+ndeath;j++){
       for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
Line 3136  double **pmij(double **ps, double *cov, Line 4993  double **pmij(double **ps, double *cov,
         /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
       }        }
       ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
         /* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
     }      }
   }    }
       
   for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
     s1=0;      s1=0;
     for(j=1; j<i; j++){      for(j=1; j<i; j++){
         /* printf("debug1 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[i][j])); */
       s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */  
     }      }
     for(j=i+1; j<=nlstate+ndeath; j++){      for(j=i+1; j<=nlstate+ndeath; j++){
         /* printf("debug2 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[i][j])); */
       s1+=exp(ps[i][j]); /* In fact sums pij/pii */        s1+=exp(ps[i][j]); /* In fact sums pij/pii */
       /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */  
     }      }
     /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
     ps[i][i]=1./(s1+1.);      ps[i][i]=1./(s1+1.);
Line 3189  double **pmij(double **ps, double *cov, Line 5047  double **pmij(double **ps, double *cov,
   /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.    /* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
    * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
    */     */
   int i, ii, j,k;    int ii, j;
       
   double **out, **pmij();    double  **pmij();
   double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
   double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */    double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
Line 3391  double **matprod2(double **out, double * Line 5249  double **matprod2(double **out, double *
   
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
 {  {
   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over     /* Already optimized with precov.
        Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to over 
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      nhstepm*hstepm matrices.        nhstepm*hstepm matrices. 
Line 3403  double ***hpxij(double ***po, int nhstep Line 5262  double ***hpxij(double ***po, int nhstep
   
      */       */
   
   int i, j, d, h, k;    int i, j, d, h, k1;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1];
   double **newm;    double **newm;
   double agexact;    double agexact;
   double agebegin, ageend;    /*double agebegin, ageend;*/
   
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
Line 3426  double ***hpxij(double ***po, int nhstep Line 5285  double ***hpxij(double ***po, int nhstep
       if(nagesqr==1){        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       }        }
       for (k=1; k<=nsd;k++) { /* For single dummy covariates only */        /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */        /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
         /* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 */        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */          if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
 /*    k        1  2   3   4     5    6    7     8    9 */            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];  
         /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */  
       }  
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1*age +V4 +age*V3 */  
         /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/  
         /* */  
         if(Dummy[Tage[k]]== 2){ /* dummy with age */  
         /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age *\/ */  
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  
         }  
         /* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovprod;k++){ /*  For product without age */  
         /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */  
         /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
         if(Dummy[Tvard[k][1]==0]){  
           if(Dummy[Tvard[k][2]==0]){  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
           }  
         }else{          }else{
           if(Dummy[Tvard[k][2]==0]){            cov[2+nagesqr+k1]=precov[nres][k1];
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
           }  
         }          }
       }        }/* End of loop on model equation */
           /* Old code */ 
   /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
   /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
   /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
   /* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\\/ *\/ */
   /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
   /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
   /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
   /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
   /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
   /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
   /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
   /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
   /*        /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); *\/ */
   /*        printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
   /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
   /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
   /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
   /*        /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only *\\/ *\/ */
   /*        /\*   /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
   /*        printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
   /*        printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
   /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
   /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
   /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
   /*        printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
   /*        printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
   
   /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
   /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
   /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
   /*        /\* *\/ */
   /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
   /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
   /* /\*cptcovage=2                   1               2      *\/ */
   /* /\*Tage[k]=                      5               8      *\/   */
   /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
   /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];        */
   /*        printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
   /*        printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
   /*        /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age *\\/ *\/ */
   /*        /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age *\\\/ *\\/ *\/ */
   /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\\/ *\/ */
   /*        /\*   /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]*cov[2]; *\/ */
   /*        /\*   printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); *\/ */
   /*        /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age *\\/ *\/ */
   /*        /\*   cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; *\/ */
   /*        /\* } *\/ */
   /*        /\* printf("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
   /*      }else if(Typevar[k1]==2 ){ /\* For product (not with age) *\/ */
   /* /\*       for (k=1; k<=cptcovprod;k++){ /\\*  For product without age *\\/ *\/ */
   /* /\* /\\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\\/ *\/ */
   /* /\* /\\*    k        1  2   3   4     5    6    7     8    9 *\\/ *\/ */
   /* /\* /\\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\\/ *\/ */
   /* /\* /\\*cptcovprod=1            1               2            *\\/ *\/ */
   /* /\* /\\*Tprod[]=                4               7            *\\/ *\/ */
   /* /\* /\\*Tvard[][1]             4               1             *\\/ *\/ */
   /* /\* /\\*Tvard[][2]               3               2           *\\/ *\/ */
             
   /*        /\* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])],nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]); *\/ */
   /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
   /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];     */
   /*        printf("hPxij Prod ij=%d k1=%d  cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
   /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
   
   /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
   /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
   /*            /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];   *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; *\/ */
   /*          /\* }else{ /\\* Product of dummy by quantitative *\\/ *\/ */
   /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; *\/ */
   /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
   /*        /\*   } *\/ */
   /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
   /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
   /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
   /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
   /*        /\*   }else{ /\\* Product of two quant *\\/ *\/ */
   /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\\/ *\/ */
   /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
   /*        /\*   } *\/ */
   /*        /\* }/\\*end of products quantitative *\\/ *\/ */
   /*      }/\*end of products *\/ */
         /* } /\* End of loop on model equation *\/ */
       /* for (k=1; k<=cptcovn;k++)  */        /* for (k=1; k<=cptcovn;k++)  */
       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
       /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */        /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
Line 3516  double ***hpxij(double ***po, int nhstep Line 5430  double ***hpxij(double ***po, int nhstep
 /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
 double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
 {  {
   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over    /* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
        computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
      nhstepm*hstepm matrices.       nhstepm*hstepm matrices.
Line 3528  double ***hbxij(double ***po, int nhstep Line 5443  double ***hbxij(double ***po, int nhstep
      The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output       The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
   */    */
   
   int i, j, d, h, k;    int i, j, d, h, k1;
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
   double **newm, ***newmm;    double **newm, ***newmm;
   double agexact;    double agexact;
   double agebegin, ageend;    /*double agebegin, ageend;*/
   double **oldm, **savm;    double **oldm, **savm;
   
   newmm=po; /* To be saved */    newmm=po; /* To be saved */
Line 3554  double ***hbxij(double ***po, int nhstep Line 5469  double ***hbxij(double ***po, int nhstep
         /* Debug */          /* Debug */
       /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */        /* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1){
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=nsd;k++){ /* For single dummy covariates only *//* cptcovn error */        }
       /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */        /** New code */
       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */        for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];/* Bug valgrind */          if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
         /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
       }  
       for (k=1; k<=nsq;k++) { /* For single varying covariates only */  
         /* Here comes the value of quantitative after renumbering k with single quantitative covariates */  
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];   
         /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 *//* For product with age */  
         /* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!*\/ */  
         if(Dummy[Tage[k]]== 2){ /* dummy with age */  
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];  
         } else if(Dummy[Tage[k]]== 3){ /* quantitative with age */  
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];   
         }  
         /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */  
       }  
       for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */  
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];  
         if(Dummy[Tvard[k][1]==0]){  
           if(Dummy[Tvard[k][2]==0]){  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];  
           }  
         }else{          }else{
           if(Dummy[Tvard[k][2]==0]){            cov[2+nagesqr+k1]=precov[nres][k1];
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];  
           }else{  
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
           }  
         }          }
       }                         }/* End of loop on model equation */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /** End of new code */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    /** This was old code */
         /* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only *\//\* cptcovn error *\/ */
         /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; *\/ */
         /* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\\/ *\/ */
         /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind *\/ */
         /*   /\* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); *\/ */
         /* } */
         /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */
         /*        /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */
         /*        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];  */
         /*        /\* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); *\/ */
         /* } */
         /* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 *\//\* For product with age *\/ */
         /*        /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!*\\/ *\/ */
         /*        if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */
         /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
         /*        } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age *\/ */
         /*          cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];  */
         /*        } */
         /*        /\* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); *\/ */
         /* } */
         /* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn *\/ */
         /*        cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
         /*        if(Dummy[Tvard[k][1]]==0){ */
         /*          if(Dummy[Tvard[k][2]]==0){ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
         /*          }else{ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
         /*          } */
         /*        }else{ */
         /*          if(Dummy[Tvard[k][2]]==0){ */
         /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
         /*          }else{ */
         /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */
         /*          } */
         /*        } */
         /* }                       */
         /* /\*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*\/ */
         /* /\*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*\/ */
   /** End of old code */
         
       /* Careful transposed matrix */        /* Careful transposed matrix */
       /* age is in cov[2], prevacurrent at beginning of transition. */        /* age is in cov[2], prevacurrent at beginning of transition. */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
Line 3654  double ***hbxij(double ***po, int nhstep Line 5581  double ***hbxij(double ***po, int nhstep
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk, kf=0;
   int ioffset=0;    int ioffset=0;
     int ipos=0,iposold=0,ncovv=0;
   
     double cotvarv, cotvarvold;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   int s1, s2;    int s1, s2;
   int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   
   double bbh, survp;    double bbh, survp;
   long ipmx;  
   double agexact;    double agexact;
     double agebegin, ageend;
   /*extern weight */    /*extern weight */
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 3686  double func( double *x) Line 5617  double func( double *x)
       */        */
       ioffset=2+nagesqr ;        ioffset=2+nagesqr ;
    /* Fixed */     /* Fixed */
       for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */        for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummy or quant or prod */
         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */          /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */          /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */          /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */          /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/          cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */          /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
       }        }
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
Line 3702  double func( double *x) Line 5633  double func( double *x)
          mw[mi][i] is real wave of the mi th effectve wave */           mw[mi][i] is real wave of the mi th effectve wave */
       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];        /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
          s2=s[mw[mi+1][i]][i];           s2=s[mw[mi+1][i]][i];
          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i] because now is moved after nvocol+nqv 
          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
       */        */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/        /* Wave varying (but not age varying) */
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */          /* for(k=1; k <= ncovv ; k++){ /\* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*\/ */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];          /*   /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? *\/ */
           /*   cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
           /* } */
           for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age )*/
             itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
             ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             if(FixedV[itv]!=0){ /* Not a fixed covariate */
               cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* cotvar[wav][ncovcol+nqv+iv][i] */
             }else{ /* fixed covariate */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               cotvarv=cotvarv*cotvarvold;
             }
             iposold=ipos;
             cov[ioffset+ipos]=cotvarv;
         }          }
           /* for products of time varying to be done */
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
   
           agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
           ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;            cov[2]=agexact;
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;  /* Should be changed here */              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            /* for (kk=1; kk<=cptcovage;kk++) { */
             if(!FixedV[Tvar[Tage[kk]]])            /*   if(!FixedV[Tvar[Tage[kk]]]) */
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */            /*     cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /\* Tage[kk] gives the data-covariate associated with age *\/ */
             else            /*   else */
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;            /*     cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
             /* } */
             for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
               itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
               ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
               if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
                 cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
               }else{ /* fixed covariate */
                 cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
               }
               if(ipos!=iposold){ /* Not a product or first of a product */
                 cotvarvold=cotvarv;
               }else{ /* A second product */
                 cotvarv=cotvarv*cotvarvold;
               }
               iposold=ipos;
               cov[ioffset+ipos]=cotvarv*agexact;
               /* For products */
           }            }
             
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;            savm=oldm;
Line 3806  double func( double *x) Line 5776  double func( double *x)
           /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
           lli= log(survp);            lli= log(survp);
         }          }
         else if  (s2==-4) {           /* else if  (s2==-4) {  */
           for (j=3,survp=0. ; j<=nlstate; j++)            /*   for (j=3,survp=0. ; j<=nlstate; j++)   */
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];          /*     survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; */
           lli= log(survp);           /*   lli= log(survp);  */
         }           /* }  */
         else if  (s2==-5) {           /* else if  (s2==-5) {  */
           for (j=1,survp=0. ; j<=2; j++)            /*   for (j=1,survp=0. ; j<=2; j++)   */
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];          /*     survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j]; */
           lli= log(survp);           /*   lli= log(survp);  */
         }           /* }  */
         else{          else{
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         }           } 
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         /*if(lli ==000.0)*/          /*if(lli ==000.0)*/
         /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */          /* printf("num[i], i=%d, bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         ipmx +=1;          ipmx +=1;
         sw += weight[i];          sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
Line 3839  double func( double *x) Line 5809  double func( double *x)
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];          cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
         for(k=1; k <= ncovv ; k++){          for(k=1; k <= ncovv ; k++){
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
         }          }
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
Line 3886  double func( double *x) Line 5856  double func( double *x)
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              if(!FixedV[Tvar[Tage[kk]]])
                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
               else
                 cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
           }            }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 3942  double func( double *x) Line 5915  double func( double *x)
         ipmx +=1;          ipmx +=1;
         sw += weight[i];          sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */          /* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
Line 3961  double func( double *x) Line 5934  double func( double *x)
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
           for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              if(!FixedV[Tvar[Tage[kk]]])
                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
               else
                 cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
           }            }
                   
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 3990  double func( double *x) Line 5966  double func( double *x)
 double funcone( double *x)  double funcone( double *x)
 {  {
   /* Same as func but slower because of a lot of printf and if */    /* Same as func but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kv=0, kf=0;
   int ioffset=0;    int ioffset=0;
     int ipos=0,iposold=0,ncovv=0;
   
     double cotvarv, cotvarvold;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
Line 4013  double funcone( double *x) Line 5992  double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;    ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /* Computes the values of the ncovmodel covariates of the model
          depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
          to be observed in j being in i according to the model.
       */
     /* ioffset=2+nagesqr+cptcovage; */      /* ioffset=2+nagesqr+cptcovage; */
     ioffset=2+nagesqr;      ioffset=2+nagesqr;
     /* Fixed */      /* Fixed */
     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
     /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
     for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */      for (kf=1; kf<=ncovf;kf++){ /*  V2  +  V3  +  V4  Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
       cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/        /* printf("Debug3 TvarFind[%d]=%d",kf, TvarFind[kf]); */
         /* printf(" Tvar[TvarFind[kf]]=%d", Tvar[TvarFind[kf]]); */
         /* printf(" i=%d covar[Tvar[TvarFind[kf]]][i]=%f\n",i,covar[Tvar[TvarFind[kf]]][i]); */
         cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
 /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
 /*    cov[2+6]=covar[Tvar[6]][i];  */  /*    cov[2+6]=covar[Tvar[6]][i];  */
 /*    cov[2+6]=covar[2][i]; V2  */  /*    cov[2+6]=covar[2][i]; V2  */
Line 4030  double funcone( double *x) Line 6017  double funcone( double *x)
 /*    cov[2+9]=covar[Tvar[9]][i];  */  /*    cov[2+9]=covar[Tvar[9]][i];  */
 /*    cov[2+9]=covar[1][i]; V1  */  /*    cov[2+9]=covar[1][i]; V1  */
     }      }
         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
            is 5, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]=6 
            has been calculated etc */
         /* For an individual i, wav[i] gives the number of effective waves */
         /* We compute the contribution to Likelihood of each effective transition
            mw[mi][i] is real wave of the mi th effectve wave */
         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
            s2=s[mw[mi+1][i]][i];
            And the iv th varying covariate in the DATA is the cotvar[mw[mi+1][i]][ncovcol+nqv+iv][i]
         */
       /* This part may be useless now because everythin should be in covar */
     /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */      /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
     /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */      /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
     /* } */      /* } */
Line 4039  double funcone( double *x) Line 6037  double funcone( double *x)
           
   
     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
     /* Wave varying (but not age varying) */        /* Wave varying (but not age varying) *//* V1+V3+age*V1+age*V3+V1*V3 with V4 tv and V5 tvq k= 1 to 5 and extra at V(5+1)=6 for V1*V3 */
       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/        /* for(k=1; k <= ncovv ; k++){ /\* Varying  covariates (single and product but no age )*\/ */
         /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */        /*        /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; *\/ */
         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];        /*        cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
       }        /* } */
       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */        
       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */        /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */        /* model V1+V3+age*V1+age*V3+V1*V3 */
       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */        /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */        /*  TvarVV[1]=V3 (first time varying in the model equation, TvarVV[2]=V1 (in V1*V3) TvarVV[3]=3(V3)  */
       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */        /* We need the position of the time varying or product in the model */
         /* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1*V3 is decomposed into V1 and V3 but at same position 5 */             
         /* TvarVV gives the variable name */
         /* Other example V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5 
         *      k=         1   2     3     4         5        6        7       8        9
         *  varying            1     2                                 3       4        5
         *  ncovv              1     2                                3 4     5 6      7 8
         * TvarVV[ncovv]      V3     5                                1 3     3 5      1 5
         * TvarVVind           2     3                                7 7     8 8      9 9
         * TvarFind[k]     1   0     0     0         0        0        0       0        0
         */
         /* Other model ncovcol=5 nqv=0 ntv=3 nqtv=0 nlstate=3
          * V2 V3 V4 are fixed V6 V7 are timevarying so V8 and V5 are not in the model and product column will start at 9 Tvar[(v6*V2)6]=9
           * FixedV[ncovcol+qv+ntv+nqtv]       V5
           * 3           V1  V2     V3    V4   V5 V6     V7  V8 V3*V2 V7*V2  V6*V3 V7*V3 V6*V4 V7*V4
           *             0   0      0      0    0  1      1   1  0, 0, 1,1,   1, 0, 1, 0, 1, 0, 1, 0}
           * 3           0   0      0      0    0  1      1   1  0,     1      1    1      1    1}
           * model=          V2  +  V3  +  V4  +  V6  +  V7  +  V6*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +age*V6*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * model2=          V2  +  V3  +  V4  +  V6  +  V7  +  V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +age*V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * model3=          V2  +  V3  +  V4  +  V6  +  V7  + age*V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * kmodel           1     2      3      4      5        6         7         8         9        10        11    
           *                  12       13      14      15       16
           *                    17        18         19        20         21
           * Tvar[kmodel]     2     3      4      6      7        9        10        11        12        13        14
           *                   2       3        4       6        7
           *                     9         11          12        13         14            
           * cptcovage=5+5 total of covariates with age 
           * Tage[cptcovage] age*V2=12      13      14      15       16
           *1                   17            18         19        20         21 gives the position in model of covariates associated with age
           *3 Tage[cptcovage] age*V3*V2=6  
           *3                age*V2=12         13      14      15       16
           *3                age*V6*V3=18      19    20   21
           * Tvar[Tage[cptcovage]]    Tvar[12]=2      3      4       6         Tvar[16]=7(age*V7)
           *     Tvar[17]age*V6*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 2   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 3 Tvar[Tage[cptcovage]]    Tvar[6]=9      Tvar[12]=2      3     4       6         Tvar[16]=7(age*V7)
           * 3     Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 3 Tage[cptcovage] age*V3*V2=6   age*V2=12 age*V3 13    14      15       16
           *                    age*V6*V3=18         19        20         21 gives the position in model of covariates associated with age
           * 3   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * Tvar=                {2, 3, 4, 6, 7,
           *                       9, 10, 11, 12, 13, 14,
           *              Tvar[12]=2, 3, 4, 6, 7,
           *              Tvar[17]=9, 11, 12, 13, 14}
           * Typevar[1]@21 = {0, 0, 0, 0, 0,
           *                  2, 2, 2, 2, 2, 2,
           * 3                3, 2, 2, 2, 2, 2,
           *                  1, 1, 1, 1, 1, 
           *                  3, 3, 3, 3, 3}
           * 3                 2, 3, 3, 3, 3}
           * p Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6} Id of the prod at position k in the model
           * p Tprod[1]@21 {6, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
           * 3 Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6}
           * 3 Tprod[1]@21 {17, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
           * cptcovprod=11 (6+5)
           * FixedV[Tvar[Tage[cptcovage]]]]  FixedV[2]=0      FixedV[3]=0      0      1          (age*V7)Tvar[16]=1 FixedV[absolute] not [kmodel]
           *   FixedV[Tvar[17]=FixedV[age*V6*V2]=FixedV[9]=1        1         1          1         1  
           * 3 FixedV[Tvar[17]=FixedV[age*V3*V2]=FixedV[9]=0        [11]=1         1          1         1  
           * FixedV[]          V1=0     V2=0   V3=0  v4=0    V5=0  V6=1    V7=1 v8=1  OK then model dependent
           *                   9=1  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
           * 3                 9=0  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
           * cptcovdageprod=5  for gnuplot printing
           * cptcovprodvage=6 
           * ncova=15           1        2       3       4       5
           *                      6 7        8 9      10 11        12 13     14 15
           * TvarA              2        3       4       6       7
           *                      6 2        6 7       7 3          6 4       7 4
           * TvaAind             12 12      13 13     14 14      15 15       16 16        
           * ncovf            1     2      3
           *                                    V6       V7      V6*V2     V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
           * ncovvt=14                            1      2        3 4       5 6       7 8       9 10     11 12     13 14     
           * TvarVV[1]@14 = itv               {V6=6,     7, V6*V2=6, 2,     7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           * TvarVVind[1]@14=                    {4,     5,       6, 6,     7, 7,     8, 8,      9, 9,   10, 10,   11, 11}
           * 3 ncovvt=12                        V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
           * 3 TvarVV[1]@12 = itv                {6,     7, V7*V2=7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           * 3                                    1      2        3  4      5  6      7  8      9 10     11 12
           * TvarVVind[1]@12=         {V6 is in k=4,     5,  7,(4isV2)=7,   8, 8,      9, 9,   10,10,    11,11}TvarVVind[12]=k=11
           * TvarV              6, 7, 9, 10, 11, 12, 13, 14
           * 3 cptcovprodvage=6
           * 3 ncovta=15    +age*V3*V2+age*V2+agev3+ageV4 +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * 3 TvarAVVA[1]@15= itva 3 2    2      3    4        6       7        6 3         7 3         6 4         7 4 
           * 3 ncovta             1 2      3      4    5        6       7        8 9       10 11       12 13        14 15
           *?TvarAVVAind[1]@15= V3 is in k=2 1 1  2    3        4       5        4,2         5,2,      4,3           5 3}TvarVVAind[]
           * TvarAVVAind[1]@15= V3 is in k=6 6 12  13   14      15      16       18 18       19,19,     20,20        21,21}TvarVVAind[]
           * 3 ncovvta=10     +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * 3 we want to compute =cotvar[mw[mi][i]][TvarVVA[ncovva]][i] at position TvarVVAind[ncovva]
           * 3 TvarVVA[1]@10= itva   6       7        6 3         7 3         6 4         7 4 
           * 3 ncovva                1       2        3 4         5 6         7 8         9 10
           * TvarVVAind[1]@10= V6 is in k=4  5        8,8         9, 9,      10,10        11 11}TvarVVAind[]
           * TvarVVAind[1]@10=       15       16     18,18        19,19,      20,20        21 21}TvarVVAind[]
           * TvarVA              V3*V2=6 6 , 1, 2, 11, 12, 13, 14
           * TvarFind[1]@14= {1,    2,     3,     0 <repeats 12 times>}
           * Tvar[1]@21=     {2,    3,     4,    6,      7,      9,      10,        11,       12,      13,       14,
           *                   2, 3, 4, 6, 7,
           *                     6, 8, 9, 10, 11}
           * TvarFind[itv]                        0      0       0
           * FixedV[itv]                          1      1       1  0      1 0       1 0       1 0       0
           *? FixedV[itv]                          1      1       1  0      1 0       1 0       1 0      1 0     1 0
           * Tvar[TvarFind[ncovf]]=[1]=2 [2]=3 [4]=4
           * Tvar[TvarFind[itv]]                [0]=?      ?ncovv 1 à ncovvt]
           *   Not a fixed cotvar[mw][itv][i]     6       7      6  2      7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           *   fixed covar[itv]                  [6]     [7]    [6][2] 
           */
   
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /*  V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4 Time varying  covariates (single and extended product but no age) including individual from products, product is computed dynamically */
           itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, or fixed covariate of a varying product after exploding product Vn*Vm into Vn and then Vm  */
           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
           /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
           if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
             /* printf("DEBUG ncovv=%d, Varying TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
             cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             /* printf("DEBUG Varying cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
           }else{ /* fixed covariate */
             /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
             /* printf("DEBUG ncovv=%d, Fixed TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
             cotvarv=covar[itv][i];  /* Good: In V6*V3, 3 is fixed at position of the data */
             /* printf("DEBUG Fixed cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
           }
           if(ipos!=iposold){ /* Not a product or first of a product */
             cotvarvold=cotvarv;
           }else{ /* A second product */
             cotvarv=cotvarv*cotvarvold;
           }
           iposold=ipos;
           cov[ioffset+ipos]=cotvarv;
           /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
           /* For products */
         }
         /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single *\/ */
         /*        iv=TvarVDind[itv]; /\* iv, position in the model equation of time varying covariate itv *\/ */
         /*        /\*         "V1+V3+age*V1+age*V3+V1*V3" with V3 time varying *\/ */
         /*        /\*           1  2   3      4      5                         *\/ */
         /*        /\*itv           1                                           *\/ */
         /*        /\* TvarVInd[1]= 2                                           *\/ */
         /*        /\* iv= Tvar[Tmodelind[itv]]-ncovcol-nqv;  /\\* Counting the # varying covariate from 1 to ntveff *\\/ *\/ */
         /*        /\* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; *\/ */
         /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; *\/ */
         /*        /\* k=ioffset-2-nagesqr-cptcovage+itv; /\\* position in simple model *\\/ *\/ */
         /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; *\/ */
         /*        cov[ioffset+iv]=cotvar[mw[mi][i]][itv][i]; */
         /*        /\* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][itv][i]=%f\n", i, mi, itv, TvarVDind[itv],cotvar[mw[mi][i]][itv][i]); *\/ */
         /* } */
       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */        /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */        /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */        /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
Line 4072  double funcone( double *x) Line 6217  double funcone( double *x)
         cov[2]=agexact;          cov[2]=agexact;
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {          for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
           if(!FixedV[Tvar[Tage[kk]]])            itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;            ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
           else            /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;            if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
               /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             }else{ /* fixed covariate */
               /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
               /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               /* printf("DEBUG * \n"); */
               cotvarv=cotvarv*cotvarvold;
             }
             iposold=ipos;
             /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
             cov[ioffset+ipos]=cotvarv*agexact;
             /* For products */
         }          }
   
         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */          /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 4087  double funcone( double *x) Line 6250  double funcone( double *x)
         savm=oldm;          savm=oldm;
         oldm=newm;          oldm=newm;
       } /* end mult */        } /* end mult */
                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           /* But now since version 0.9 we anticipate for bias at large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
            * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
                                    * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                                    * -stepm/2 to stepm/2 .
                                    * For stepm=1 the results are the same as for previous versions of Imach.
                                    * For stepm > 1 the results are less biased than in previous versions. 
                                    */
       s1=s[mw[mi][i]][i];        s1=s[mw[mi][i]][i];
       s2=s[mw[mi+1][i]][i];        s2=s[mw[mi+1][i]][i];
       /* if(s2==-1){ */        /* if(s2==-1){ */
Line 4119  double funcone( double *x) Line 6294  double funcone( double *x)
       ipmx +=1;        ipmx +=1;
       sw += weight[i];        sw += weight[i];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /* Printing covariates values for each contribution for checking */
         /* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\          fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
  %11.6f %11.6f %11.6f ", \   %11.6f %11.6f %11.6f ", \
                 num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,                  num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
                 2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));                  2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
           /*      printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
           /* %11.6f %11.6f %11.6f ", \ */
           /*              num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw, */
           /*              2*weight[i]*lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
         for(k=1,llt=0.,l=0.; k<=nlstate; k++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           llt +=ll[k]*gipmx/gsw;            llt +=ll[k]*gipmx/gsw;
           fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
             /* printf(" %10.6f",-ll[k]*gipmx/gsw); */
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f ", -llt);
       }          /* printf(" %10.6f\n", -llt); */
         } /* end of wave */          /* if(debugILK){ /\* debugILK is set by a #d in a comment line *\/ */
 } /* end of individual */          /* fprintf(ficresilk,"%09ld ", num[i]); */ /* not necessary */
 for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
             fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
           }
           for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age) including individual from products */
             ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             if(ipos!=iposold){ /* Not a product or first of a product */
               fprintf(ficresilk," %g",cov[ioffset+ipos]);
               /* printf(" %g",cov[ioffset+ipos]); */
             }else{
               fprintf(ficresilk,"*");
               /* printf("*"); */
             }
             iposold=ipos;
           }
           /* for (kk=1; kk<=cptcovage;kk++) { */
           /*   if(!FixedV[Tvar[Tage[kk]]]){ */
           /*     fprintf(ficresilk," %g*age",covar[Tvar[Tage[kk]]][i]); */
           /*     /\* printf(" %g*age",covar[Tvar[Tage[kk]]][i]); *\/ */
           /*   }else{ */
           /*     fprintf(ficresilk," %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
           /*     /\* printf(" %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\\/  *\/ */
           /*   } */
           /* } */
           for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
             itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
             ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
             if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
               /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             }else{ /* fixed covariate */
               /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
               /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               /* printf("DEBUG * \n"); */
               cotvarv=cotvarv*cotvarvold;
             }
             cotvarv=cotvarv*agexact;
             fprintf(ficresilk," %g*age",cotvarv);
             iposold=ipos;
             /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
             cov[ioffset+ipos]=cotvarv;
             /* For products */
           }
           /* printf("\n"); */
           /* } /\*  End debugILK *\/ */
           fprintf(ficresilk,"\n");
         } /* End if globpr */
       } /* end of wave */
     } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 if(globpr==0){ /* First time we count the contributions and weights */    if(globpr==0){ /* First time we count the contributions and weights */
         gipmx=ipmx;      gipmx=ipmx;
         gsw=sw;      gsw=sw;
 }    }
 return -l;    return -l;
 }  }
   
   
Line 4151  void likelione(FILE *ficres,double p[], Line 6386  void likelione(FILE *ficres,double p[],
      the selection of individuals/waves and       the selection of individuals/waves and
      to check the exact contribution to the likelihood.       to check the exact contribution to the likelihood.
      Plotting could be done.       Plotting could be done.
    */    */
   int k;    void pstamp(FILE *ficres);
     int k, kf, kk, kvar, ncovv, iposold, ipos;
   
   if(*globpri !=0){ /* Just counts and sums, no printings */    if(*globpri !=0){ /* Just counts and sums, no printings */
     strcpy(fileresilk,"ILK_");       strcpy(fileresilk,"ILK_"); 
Line 4161  void likelione(FILE *ficres,double p[], Line 6397  void likelione(FILE *ficres,double p[],
       printf("Problem with resultfile: %s\n", fileresilk);        printf("Problem with resultfile: %s\n", fileresilk);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     }      }
       pstamp(ficresilk);fprintf(ficresilk,"# model=1+age+%s\n",model);
     fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");      fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");      fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
     /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for(k=1; k<=nlstate; k++)       for(k=1; k<=nlstate; k++) 
       fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total) ");
   }  
       /* if(debugILK){ /\* debugILK is set by a #d in a comment line *\/ */
         for(kf=1;kf <= ncovf; kf++){
           fprintf(ficresilk,"V%d",Tvar[TvarFind[kf]]);
           /* printf("V%d",Tvar[TvarFind[kf]]); */
         }
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){
           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
           if(ipos!=iposold){ /* Not a product or first of a product */
             /* printf(" %d",ipos); */
             fprintf(ficresilk," V%d",TvarVV[ncovv]);
           }else{
             /* printf("*"); */
             fprintf(ficresilk,"*");
           }
           iposold=ipos;
         }
         for (kk=1; kk<=cptcovage;kk++) {
           if(!FixedV[Tvar[Tage[kk]]]){
             /* printf(" %d*age(Fixed)",Tvar[Tage[kk]]); */
             fprintf(ficresilk," %d*age(Fixed)",Tvar[Tage[kk]]);
           }else{
             fprintf(ficresilk," %d*age(Varying)",Tvar[Tage[kk]]);/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
             /* printf(" %d*age(Varying)",Tvar[Tage[kk]]);/\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
           }
         }
       /* } /\* End if debugILK *\/ */
       /* printf("\n"); */
       fprintf(ficresilk,"\n");
     } /* End glogpri */
   
   *fretone=(*func)(p);    *fretone=(*func)(p);
   if(*globpri !=0){    if(*globpri !=0){
Line 4179  void likelione(FILE *ficres,double p[], Line 6445  void likelione(FILE *ficres,double p[],
     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);       fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
               
     for (k=1; k<= nlstate ; k++) {  
       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \  
 <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);  
     }  
     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \      fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
 <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  <img src=\"%s-ori.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \      fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
 <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  <img src=\"%s-dest.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br>\n \
   <img src=\"%s-p%dj.png\">\n",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
         for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
            kvar=Tvar[TvarFind[kf]];  /* variable */
            fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): ",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]]);
            fprintf(fichtm,"<a href=\"%s-p%dj-%d.png\">%s-p%dj-%d.png</a><br>",subdirf2(optionfilefiname,"ILK_"),k,kvar,subdirf2(optionfilefiname,"ILK_"),k,kvar);
            fprintf(fichtm,"<img src=\"%s-p%dj-%d.png\">",subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]);
         }
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Loop on the time varying extended covariates (with extension of Vn*Vm */
           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
           kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
           /* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
           if(ipos!=iposold){ /* Not a product or first of a product */
             /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
             /* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); */
             if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
               fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored time varying dummy covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar);
             } /* End only for dummies time varying (single?) */
           }else{ /* Useless product */
             /* printf("*"); */
             /* fprintf(ficresilk,"*"); */ 
           }
           iposold=ipos;
         } /* For each time varying covariate */
       } /* End loop on states */
   
   /*     if(debugILK){ */
   /*       for(kf=1; kf <= ncovf; kf++){ /\* For each simple dummy covariate of the model *\/ */
   /*      /\* kvar=Tvar[TvarFind[kf]]; *\/ /\* variable *\/ */
   /*      for (k=1; k<= nlstate ; k++) { */
   /*        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
   /* <img src=\"%s-p%dj-%d.png\">",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]); */
   /*      } */
   /*       } */
   /*       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /\* Loop on the time varying extended covariates (with extension of Vn*Vm *\/ */
   /*      ipos=TvarVVind[ncovv]; /\* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate *\/ */
   /*      kvar=TvarVV[ncovv]; /\*  TvarVV={3, 1, 3} gives the name of each varying covariate *\/ */
   /*      /\* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); *\/ */
   /*      if(ipos!=iposold){ /\* Not a product or first of a product *\/ */
   /*        /\* fprintf(ficresilk," V%d",TvarVV[ncovv]); *\/ */
   /*        /\* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); *\/ */
   /*        if(Dummy[ipos]==0 && Typevar[ipos]==0){ /\* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  *\/ */
   /*          for (k=1; k<= nlstate ; k++) { */
   /*            fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
   /* <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar); */
   /*          } /\* End state *\/ */
   /*        } /\* End only for dummies time varying (single?) *\/ */
   /*      }else{ /\* Useless product *\/ */
   /*        /\* printf("*"); *\/ */
   /*        /\* fprintf(ficresilk,"*"); *\/  */
   /*      } */
   /*      iposold=ipos; */
   /*       } /\* For each time varying covariate *\/ */
   /*     }/\* End debugILK *\/ */
     fflush(fichtm);      fflush(fichtm);
   }    }/* End globpri */
   return;    return;
 }  }
   
Line 4197  void likelione(FILE *ficres,double p[], Line 6516  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j,k, jk, jkk=0, iter=0;    int i,j,  jkk=0, iter=0;
   double **xi;    double **xi;
   double fret;    /*double fret;*/
   double fretone; /* Only one call to likelihood */    /*double fretone;*/ /* Only one call to likelihood */
   /*  char filerespow[FILENAMELENGTH];*/    /*  char filerespow[FILENAMELENGTH];*/
     
     /*double * p1;*/ /* Shifted parameters from 0 instead of 1 */
 #ifdef NLOPT  #ifdef NLOPT
   int creturn;    int creturn;
   nlopt_opt opt;    nlopt_opt opt;
   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   double *lb;    double *lb;
   double minf; /* the minimum objective value, upon return */    double minf; /* the minimum objective value, upon return */
   double * p1; /* Shifted parameters from 0 instead of 1 */  
   myfunc_data dinst, *d = &dinst;    myfunc_data dinst, *d = &dinst;
 #endif  #endif
   
   
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)  /* Starting with canonical directions j=1,n xi[i=1,n][j] */
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell-prax\n");  fprintf(ficlog,"Powell-prax\n");
   strcpy(filerespow,"POW_");     strcpy(filerespow,"POW_"); 
   strcat(filerespow,fileres);    strcat(filerespow,fileres);
   if((ficrespow=fopen(filerespow,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
Line 4282  void mlikeli(FILE *ficres,double p[], in Line 6602  void mlikeli(FILE *ficres,double p[], in
   }    }
   powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);    powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
 #else  /* FLATSUP */  #else  /* FLATSUP */
   powell(p,xi,npar,ftol,&iter,&fret,func);  /*  powell(p,xi,npar,ftol,&iter,&fret,func);*/
   /*   praxis ( t0, h0, n, prin, x, beale_f ); */
     /* int prin=1; */
     /* double h0=0.25; */
     /* double macheps; */
     /* double fmin; */
     macheps=pow(16.0,-13.0);
   /* #include "praxis.h" */
     /* Be careful that praxis start at x[0] and powell start at p[1] */
      /* praxis ( ftol, h0, npar, prin, p, func ); */
   /* p1= (p+1); */ /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
   printf("Praxis Gegenfurtner \n");
   fprintf(ficlog, "Praxis  Gegenfurtner\n");fflush(ficlog);
   /* praxis ( ftol, h0, npar, prin, p1, func ); */
     /* fmin = praxis(1.e-5,macheps, h, n, prin, x, func); */
     ffmin = praxis(ftol,macheps, h0, npar, prin, p, func);
   printf("End Praxis\n");
 #endif  /* FLATSUP */  #endif  /* FLATSUP */
   
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
Line 4544  double hessij( double x[], double **hess Line 6880  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
         /* What are the thetai and thetaj? thetai/ncovmodel thetai=(thetai-thetai%ncovmodel)/ncovmodel +thetai%ncovmodel=(line,pos)  */
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
Line 4730  void  freqsummary(char fileres[], double Line 7067  void  freqsummary(char fileres[], double
                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies as well as proposing some starting values */  {  /* Some frequencies as well as proposing some starting values */
       /* Frequencies of any combination of dummy covariate used in the model equation */ 
   int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
Line 4798  Title=%s <br>Datafile=%s Firstpass=%d La Line 7135  Title=%s <br>Datafile=%s Firstpass=%d La
   j1=0;    j1=0;
       
   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
   j=cptcoveff;  /* Only dummy covariates of the model */    j=cptcoveff;  /* Only simple dummy covariates used in the model */
     /* j=cptcovn;  /\* Only dummy covariates of the model *\/ */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
       
Line 4806  Title=%s <br>Datafile=%s Firstpass=%d La Line 7144  Title=%s <br>Datafile=%s Firstpass=%d La
      reference=low_education V1=0,V2=0       reference=low_education V1=0,V2=0
      med_educ                V1=1 V2=0,        med_educ                V1=1 V2=0, 
      high_educ               V1=0 V2=1       high_educ               V1=0 V2=1
      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn 
   */    */
   dateintsum=0;    dateintsum=0;
   k2cpt=0;    k2cpt=0;
Line 4843  Title=%s <br>Datafile=%s Firstpass=%d La Line 7181  Title=%s <br>Datafile=%s Firstpass=%d La
     if(nj==1)      if(nj==1)
       j=0;  /* First pass for the constant */        j=0;  /* First pass for the constant */
     else{      else{
       j=cptcoveff; /* Other passes for the covariate values */        j=cptcoveff; /* Other passes for the covariate values number of simple covariates in the model V2+V1 =2 (simple dummy fixed or time varying) */
     }      }
     first=1;      first=1;
     for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
       posproptt=0.;        posproptt=0.;
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
       for (i=-5; i<=nlstate+ndeath; i++)          for (i=-5; i<=nlstate+ndeath; i++)  
         for (s2=-5; s2<=nlstate+ndeath; s2++)            for (s2=-5; s2<=nlstate+ndeath; s2++)  
Line 4885  Title=%s <br>Datafile=%s Firstpass=%d La Line 7223  Title=%s <br>Datafile=%s Firstpass=%d La
                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                 /* }else  if(Tvaraff[z1] ==-10){ */                  /* }else  if(Tvaraff[z1] ==-10){ */
                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                 /* }else  */                  /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */                  /* if( iind >=imx-3) printf("Searching error iind=%d Tvaraff[z1]=%d covar[Tvaraff[z1]][iind]=%.f TnsdVar[Tvaraff[z1]]=%d, cptcoveff=%d, cptcovs=%d \n",iind, Tvaraff[z1], covar[Tvaraff[z1]][iind],TnsdVar[Tvaraff[z1]],cptcoveff, cptcovs); */
                   if(Tvaraff[z1]<1 || Tvaraff[z1]>=NCOVMAX)
                     printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=1+age+%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);
                   if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
                   /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */                    /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                   bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */                    bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                   /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",                     /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
                      bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                    /*   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
                      j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                    /*   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                   /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                    /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                 } /* Onlyf fixed */                  } /* Onlyf fixed */
               } /* end z1 */                } /* end z1 */
             } /* cptcovn > 0 */              } /* cptcoveff > 0 */
           } /* end any */            } /* end any */
         }/* end j==0 */          }/* end j==0 */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
Line 4906  Title=%s <br>Datafile=%s Firstpass=%d La Line 7247  Title=%s <br>Datafile=%s Firstpass=%d La
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                 for (z1=1; z1<=cptcoveff; z1++) {                  for (z1=1; z1<=cptcoveff; z1++) {
                   if( Fixed[Tmodelind[z1]]==1){                    if( Fixed[Tmodelind[z1]]==1){
                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;                      /* iv= Tvar[Tmodelind[z1]]-ncovcol-nqv; /\* Good *\/ */
                     if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's                       iv= Tvar[Tmodelind[z1]]; /* Good *//* because cotvar starts now at first at ncovcol+nqv+ntv */ 
                       if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's 
                                                                                       value is -1, we don't select. It differs from the                                                                                         value is -1, we don't select. It differs from the 
                                                                                       constant and age model which counts them. */                                                                                        constant and age model which counts them. */
                       bool=0; /* not selected */                        bool=0; /* not selected */
                   }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */                    }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                     if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {                      /* i1=Tvaraff[z1]; */
                       /* i2=TnsdVar[i1]; */
                       /* i3=nbcode[i1][i2]; */
                       /* i4=covar[i1][iind]; */
                       /* if(i4 != i3){ */
                       if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) { /* Bug valgrind */
                       bool=0;                        bool=0;
                     }                      }
                   }                    }
Line 4940  Title=%s <br>Datafile=%s Firstpass=%d La Line 7287  Title=%s <br>Datafile=%s Firstpass=%d La
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                   for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */                    for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
                     if(!isnan(covar[ncovcol+z1][iind])){                      if(!isnan(covar[ncovcol+z1][iind])){
                         idq[z1]=idq[z1]+weight[iind];                        idq[z1]=idq[z1]+weight[iind];
                         meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */                        meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                         /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/                        /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; *//*error*/
                         stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */                        stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                     }                      }
                   }                    }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
Line 4984  Title=%s <br>Datafile=%s Firstpass=%d La Line 7331  Title=%s <br>Datafile=%s Firstpass=%d La
         fprintf(ficlog, "\n#********** Variable ");           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++){          for (z1=1; z1<=cptcoveff; z1++){
           if(!FixedV[Tvaraff[z1]]){            if(!FixedV[Tvaraff[z1]]){
             printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }else{            }else{
             printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
             fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }            }
         }          }
         printf( "**********\n#");          printf( "**********\n#");
Line 5030  Title=%s <br>Datafile=%s Firstpass=%d La Line 7377  Title=%s <br>Datafile=%s Firstpass=%d La
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");          fprintf(ficresp, " Age");
       if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        if(nj==2) for (z1=1; z1<=cptcoveff; z1++) {
             printf(" V%d=%d, z1=%d, Tvaraff[z1]=%d, j1=%d, TnsdVar[Tvaraff[%d]]=%d |",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])], z1, Tvaraff[z1], j1,z1,TnsdVar[Tvaraff[z1]]);
             fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }
       for(i=1; i<=nlstate;i++) {        for(i=1; i<=nlstate;i++) {
         if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);          if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
         fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
Line 5110  Title=%s <br>Datafile=%s Firstpass=%d La Line 7460  Title=%s <br>Datafile=%s Firstpass=%d La
         }else if( nj==2){          }else if( nj==2){
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
             for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
           }            }
         }          }
         for(s1=1; s1 <=nlstate ; s1++){          for(s1=1; s1 <=nlstate ; s1++){
Line 5187  Title=%s <br>Datafile=%s Firstpass=%d La Line 7537  Title=%s <br>Datafile=%s Firstpass=%d La
         printf("#  This combination (%d) is not valid and no result will be produced\n",j1);          printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
         invalidvarcomb[j1]=1;          invalidvarcomb[j1]=1;
       }else{        }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced (or no resultline).</p>",j1);
         invalidvarcomb[j1]=0;          invalidvarcomb[j1]=0;
       }        }
       fprintf(ficresphtmfr,"</table>\n");        fprintf(ficresphtmfr,"</table>\n");
Line 5399  void prevalence(double ***probs, double Line 7749  void prevalence(double ***probs, double
   int i, m, jk, j1, bool, z1,j, iv;    int i, m, jk, j1, bool, z1,j, iv;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int iage;    int iage;
   double agebegin, ageend;    double agebegin; /*, ageend;*/
   
   double **prop;    double **prop;
   double posprop;     double posprop; 
Line 5418  void prevalence(double ***probs, double Line 7768  void prevalence(double ***probs, double
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=0;    first=0;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of simple dummy covariates */
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
         prop[i][iage]=0.0;          prop[i][iage]=0.0;
Line 5435  void prevalence(double ***probs, double Line 7785  void prevalence(double ***probs, double
         /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */          /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
         for (z1=1; z1<=cptcoveff; z1++){          for (z1=1; z1<=cptcoveff; z1++){
           if( Fixed[Tmodelind[z1]]==1){            if( Fixed[Tmodelind[z1]]==1){
             iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;              iv= Tvar[Tmodelind[z1]];/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
             if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */              if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
               bool=0;                bool=0;
           }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
               bool=0;                bool=0;
             }              }
         }          }
Line 5638  void  concatwav(int wav[], int **dh, int Line 7988  void  concatwav(int wav[], int **dh, int
             if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
             else if(j<0){              else if(j<0){
               nberr++;                nberr++;
               printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               j=1; /* Temporary Dangerous patch */                j=1; /* Temporary Dangerous patch */
               printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
             }              }
             k=k+1;              k=k+1;
Line 5675  void  concatwav(int wav[], int **dh, int Line 8025  void  concatwav(int wav[], int **dh, int
           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           if(j<0){            if(j<0){
             nberr++;              nberr++;
             printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld (around line %d) who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }            }
           sum=sum+j;            sum=sum+j;
         }          }
Line 5742  void  concatwav(int wav[], int **dh, int Line 8092  void  concatwav(int wav[], int **dh, int
        nbcode[k][j]=0; /* Valgrind */         nbcode[k][j]=0; /* Valgrind */
   
    /* Loop on covariates without age and products and no quantitative variable */     /* Loop on covariates without age and products and no quantitative variable */
    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */     for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */        /* printf("Testing k=%d, cptcovt=%d\n",k, cptcovt); */
        if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 3  && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */ 
        switch(Fixed[k]) {         switch(Fixed[k]) {
        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
          modmaxcovj=0;           modmaxcovj=0;
          modmincovj=0;           modmincovj=0;
          for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
              /* printf("Waiting for error tricode Tvar[%d]=%d i=%d (int)(covar[Tvar[k]][i]=%d\n",k,Tvar[k], i, (int)(covar[Tvar[k]][i])); */
            ij=(int)(covar[Tvar[k]][i]);             ij=(int)(covar[Tvar[k]][i]);
            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
             * If product of Vn*Vm, still boolean *:              * If product of Vn*Vm, still boolean *:
Line 5840  void  concatwav(int wav[], int **dh, int Line 8192  void  concatwav(int wav[], int **dh, int
          break;           break;
        } /* end switch */         } /* end switch */
      } /* end dummy test */       } /* end dummy test */
      if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */        if(Dummy[k]==1 && Typevar[k] !=1 && Typevar[k] !=3 && Fixed ==0){ /* Fixed Quantitative covariate and not age product */ 
        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/         for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
            if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){
              printf("Error k=%d \n",k);
              exit(1);
            }
          if(isnan(covar[Tvar[k]][i])){           if(isnan(covar[Tvar[k]][i])){
            printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);             printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
            fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);             fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
Line 5849  void  concatwav(int wav[], int **dh, int Line 8205  void  concatwav(int wav[], int **dh, int
            exit(1);             exit(1);
          }           }
        }         }
      }       } /* end Quanti */
    } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/       } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
       
    for (k=-1; k< maxncov; k++) Ndum[k]=0;      for (k=-1; k< maxncov; k++) Ndum[k]=0; 
Line 5863  void  concatwav(int wav[], int **dh, int Line 8219  void  concatwav(int wav[], int **dh, int
       
    ij=0;     ij=0;
    /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */     /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
    for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */     for (k=1; k<=  cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
        /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
      /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */       /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
      if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */       if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy simple and non empty in the model */
          /* Typevar[k] =0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
          /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product*/
        /* If product not in single variable we don't print results */         /* If product not in single variable we don't print results */
        /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */         ++ij;/*    V5 + V4 + V3 + V4*V3 + V5*age + V2 +  V1*V2 + V1*age + V1, *//* V5 quanti, V2 quanti, V4, V3, V1 dummies */
          /* k=       1    2   3     4       5       6      7       8        9  */
          /* Tvar[k]= 5    4    3    6       5       2      7       1        1  */
          /* ij            1    2                                            3  */  
          /* Tvaraff[ij]=  4    3                                            1  */
          /* Tmodelind[ij]=2    3                                            9  */
          /* TmodelInvind[ij]=2 1                                            1  */
        Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/         Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */         Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
        TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */         TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
Line 5885  void  concatwav(int wav[], int **dh, int Line 8250  void  concatwav(int wav[], int **dh, int
    } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
    /* ij--; */     /* ij--; */
    /* cptcoveff=ij; /\*Number of total covariates*\/ */     /* cptcoveff=ij; /\*Number of total covariates*\/ */
    *cptcov=ij; /*Number of total real effective covariates: effective     *cptcov=ij; /* cptcov= Number of total real effective simple dummies (fixed or time  arying) effective (used as cptcoveff in other functions)
                 * because they can be excluded from the model and real                  * because they can be excluded from the model and real
                 * if in the model but excluded because missing values, but how to get k from ij?*/                  * if in the model but excluded because missing values, but how to get k from ij?*/
    for(j=ij+1; j<= cptcovt; j++){     for(j=ij+1; j<= cptcovt; j++){
Line 5906  void  concatwav(int wav[], int **dh, int Line 8271  void  concatwav(int wav[], int **dh, int
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
     /* cij is the combination in the list of combination of dummy covariates */
     /* strstart is a string of time at start of computing */
   int i, j, nhstepm, hstepm, h, nstepm;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
Line 5974  void  concatwav(int wav[], int **dh, int Line 8341  void  concatwav(int wav[], int **dh, int
     /* If stepm=6 months */      /* If stepm=6 months */
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           /* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
Line 6016  void  concatwav(int wav[], int **dh, int Line 8383  void  concatwav(int wav[], int **dh, int
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .       to initial status i, ei. .
   */    */
     /* Very time consuming function, but already optimized with precov */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
Line 6226  void  concatwav(int wav[], int **dh, int Line 8594  void  concatwav(int wav[], int **dh, int
 /************ Variance ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
  {   {
    /** Variance of health expectancies      /** Computes the matrix of variance covariance of health expectancies e.j= sum_i w_i e_ij where w_i depends of popbased,
       * either cross-sectional or implied.
       * return vareij[i][j][(int)age]=cov(e.i,e.j)=sum_h sum_k trgrad(h_p.i) V(theta) grad(k_p.k) Equation 20
     *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);      *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
     * double **newm;      * double **newm;
     * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)       * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) 
Line 6243  void  concatwav(int wav[], int **dh, int Line 8613  void  concatwav(int wav[], int **dh, int
    double ***gradg, ***trgradg; /**< for var eij */     double ***gradg, ***trgradg; /**< for var eij */
    double **gradgp, **trgradgp; /**< for var p point j */     double **gradgp, **trgradgp; /**< for var p point j */
    double *gpp, *gmp; /**< for var p point j */     double *gpp, *gmp; /**< for var p point j */
    double **varppt; /**< for var p point j nlstate to nlstate+ndeath */     double **varppt; /**< for var p.3 p.death nlstate+1 to nlstate+ndeath */
    double ***p3mat;     double ***p3mat;
    double age,agelim, hf;     double age,agelim, hf;
    /* double ***mobaverage; */     /* double ***mobaverage; */
Line 6284  void  concatwav(int wav[], int **dh, int Line 8654  void  concatwav(int wav[], int **dh, int
    pstamp(ficresprobmorprev);     pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
    fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");     fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
    for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */  
      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);     /* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
      /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ /\* To be done*\/ */
      /*   fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
      /* } */
      for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */ /* To be done*/
        /* fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); */
        fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
    }     }
    for(j=1;j<=cptcoveff;j++)      /* for(j=1;j<=cptcoveff;j++)  */
      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);     /*   fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]); */
    fprintf(ficresprobmorprev,"\n");     fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
Line 6305  void  concatwav(int wav[], int **dh, int Line 8681  void  concatwav(int wav[], int **dh, int
    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); /* In fact, currently a double */
    pstamp(ficresvij);     pstamp(ficresvij);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
    if(popbased==1)     if(popbased==1)
Line 6374  void  concatwav(int wav[], int **dh, int Line 8750  void  concatwav(int wav[], int **dh, int
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.         /**< Computes the shifted plus (gp) transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
         */                                */                      
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
        /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability         /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
Line 6383  void  concatwav(int wav[], int **dh, int Line 8759  void  concatwav(int wav[], int **dh, int
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];               gp[h][j] += prlim[i][i]*p3mat[i][j][h]; /* gp[h][j]= w_i h_pij */
          }           }
        }         }
        /* Next for computing shifted+ probability of death (h=1 means         /* Next for computing shifted+ probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .            as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){ /* Currently only once for theta plus  p.3(age) Sum_i wi pi3*/
          for(i=1,gpp[j]=0.; i<= nlstate; i++)           for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];             gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }         }
Line 6412  void  concatwav(int wav[], int **dh, int Line 8788  void  concatwav(int wav[], int **dh, int
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);           hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Still minus */
                                                   
        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */         for(j=1; j<= nlstate; j++){  /* gm[h][j]= Sum_i of wi * pij =  h_p.j */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gm[h][j]=0.;i<=nlstate;i++)             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
              gm[h][j] += prlim[i][i]*p3mat[i][j][h];               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 6422  void  concatwav(int wav[], int **dh, int Line 8798  void  concatwav(int wav[], int **dh, int
        }         }
        /* This for computing probability of death (h=1 means         /* This for computing probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim.            as a weighted average of prlim. j is death. gmp[3]=sum_i w_i*p_i3=p.3 minus theta
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){  /* Currently only once theta_minus  p.3=Sum_i wi pi3*/
          for(i=1,gmp[j]=0.; i<= nlstate; i++)           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];             gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }    
        /* end shifting computations */         /* end shifting computations */
   
        /**< Computing gradient matrix at horizon h          /**< Computing gradient of p.j matrix at horizon h and still for one parameter of vector theta
           * equation 31 and 32
         */          */
        for(j=1; j<= nlstate; j++) /* vareij */         for(j=1; j<= nlstate; j++) /* computes grad p.j(x, over each  h) where p.j is Sum_i w_i*pij(x over h)
                                     * equation 24 */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }           }
        /**< Gradient of overall mortality p.3 (or p.j)          /**< Gradient of overall mortality p.3 (or p.death) 
         */          */
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* computes grad of p.3 from wi+pi3 grad p.3 (theta) */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }         }
                                                   
      } /* End theta */       } /* End theta */
             
      /* We got the gradient matrix for each theta and state j */                       /* We got the gradient matrix for each theta and each state j of gradg(h]theta][j)=grad(_hp.j(theta) */            
      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);
                                   
      for(h=0; h<=nhstepm; h++) /* veij */       for(h=0; h<=nhstepm; h++) /* veij */ /* computes the transposed of grad  (_hp.j(theta)*/
        for(j=1; j<=nlstate;j++)         for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)           for(theta=1; theta <=npar; theta++)
            trgradg[h][j][theta]=gradg[h][theta][j];             trgradg[h][j][theta]=gradg[h][theta][j];
                                   
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* computes transposed of grad p.3 (theta)*/
        for(theta=1; theta <=npar; theta++)         for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];           trgradgp[j][theta]=gradgp[theta][j];
      /**< as well as its transposed matrix        /**< as well as its transposed matrix 
Line 6464  void  concatwav(int wav[], int **dh, int Line 8842  void  concatwav(int wav[], int **dh, int
          vareij[i][j][(int)age] =0.;           vareij[i][j][(int)age] =0.;
   
      /* Computing trgradg by matcov by gradg at age and summing over h       /* Computing trgradg by matcov by gradg at age and summing over h
       * and k (nhstepm) formula 15 of article        * and k (nhstepm) formula 32 of article
       * Lievre-Brouard-Heathcote        * Lievre-Brouard-Heathcote so that for each j, computes the cov(e.j,e.k) (formula 31).
         * for given h and k computes trgradg[h](i,j) matcov (theta) gradg(k)(i,j) into vareij[i][j] which is
         cov(e.i,e.j) and sums on h and k
         * including the covariances.
       */        */
             
      for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm;h++){
Line 6474  void  concatwav(int wav[], int **dh, int Line 8855  void  concatwav(int wav[], int **dh, int
          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
          for(i=1;i<=nlstate;i++)           for(i=1;i<=nlstate;i++)
            for(j=1;j<=nlstate;j++)             for(j=1;j<=nlstate;j++)
              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;               vareij[i][j][(int)age] += doldm[i][j]*hf*hf; /* This is vareij=sum_h sum_k trgrad(h_pij) V(theta) grad(k_pij)
                                                                including the covariances of e.j */
        }         }
      }       }
                                   
      /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of       /* Mortality: pptj is p.3 or p.death = trgradgp by cov by gradgp, variance of
       * p.j overall mortality formula 49 but computed directly because        * p.3=1-p..=1-sum i p.i  overall mortality computed directly because
       * we compute the grad (wix pijx) instead of grad (pijx),even if        * we compute the grad (wix pijx) instead of grad (pijx),even if
       * wix is independent of theta.        * wix is independent of theta. 
       */        */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(j=nlstate+1;j<=nlstate+ndeath;j++)
        for(i=nlstate+1;i<=nlstate+ndeath;i++)         for(i=nlstate+1;i<=nlstate+ndeath;i++)
          varppt[j][i]=doldmp[j][i];           varppt[j][i]=doldmp[j][i];  /* This is the variance of p.3 */
      /* end ppptj */       /* end ppptj */
      /*  x centered again */       /*  x centered again */
                                   
Line 6510  void  concatwav(int wav[], int **dh, int Line 8892  void  concatwav(int wav[], int **dh, int
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);         hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
      for(j=nlstate+1;j<=nlstate+ndeath;j++){       for(j=nlstate+1;j<=nlstate+ndeath;j++){
        for(i=1,gmp[j]=0.;i<= nlstate; i++)          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
          gmp[j] += prlim[i][i]*p3mat[i][j][1];            gmp[j] += prlim[i][i]*p3mat[i][j][1]; /* gmp[j] is p.3 */
      }           }    
      /* end probability of death */       /* end probability of death */
                                   
      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));/* p.3 (STD p.3) */
        for(i=1; i<=nlstate;i++){         for(i=1; i<=nlstate;i++){
          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]); /* wi, pi3 */
        }         }
      }        } 
      fprintf(ficresprobmorprev,"\n");       fprintf(ficresprobmorprev,"\n");
Line 6844  void varprob(char optionfilefiname[], do Line 9226  void varprob(char optionfilefiname[], do
    double ***varpij;     double ***varpij;
   
    strcpy(fileresprob,"PROB_");      strcpy(fileresprob,"PROB_"); 
    strcat(fileresprob,fileres);     strcat(fileresprob,fileresu);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);       printf("Problem with resultfile: %s\n", fileresprob);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
Line 6916  To be simple, these graphs help to under Line 9298  To be simple, these graphs help to under
    tj = (int) pow(2,cptcoveff);     tj = (int) pow(2,cptcoveff);
    if (cptcovn<1) {tj=1;ncodemax[1]=1;}     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
    j1=0;     j1=0;
    for(j1=1; j1<=tj;j1++){  /* For each valid combination of covariates or only once*/  
      for(nres=1;nres <=1; nres++){ /* For each resultline */     for(nres=1;nres <=nresult; nres++){ /* For each resultline */
      /* for(nres=1;nres <=nresult; nres++){ /\* For each resultline *\/ */     for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
        /* printf("Varprob  TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n",  TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs); */
        if(tj != 1 && TKresult[nres]!= j1)
          continue;
   
      /* for(j1=1; j1<=tj;j1++){  /\* For each valid combination of covariates or only once*\/ */
        /* for(nres=1;nres <=1; nres++){ /\* For each resultline *\/ */
        /* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline *\\/ *\/ */
      if  (cptcovn>0) {       if  (cptcovn>0) {
        fprintf(ficresprob, "\n#********** Variable ");          fprintf(ficresprob, "\n#********** Variable ");
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
        fprintf(ficresprob, "**********\n#\n");  
        fprintf(ficresprobcov, "\n#********** Variable ");          fprintf(ficresprobcov, "\n#********** Variable "); 
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);         fprintf(ficgp, "\n#********** Variable ");
          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
          fprintf(ficresprobcor, "\n#********** Variable ");    
   
          /* Including quantitative variables of the resultline to be done */
          for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */
            /* printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model); */
            fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
            /* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
            if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline  */
              if(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */
                fprintf(ficresprob,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprobcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficgp,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(fichtmcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprobcor,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
                fprintf(ficresprob,"fixed ");
                fprintf(ficresprobcov,"fixed ");
                fprintf(ficgp,"fixed ");
                fprintf(fichtmcov,"fixed ");
                fprintf(ficresprobcor,"fixed ");
              }else{
                fprintf(ficresprob,"varyi ");
                fprintf(ficresprobcov,"varyi ");
                fprintf(ficgp,"varyi ");
                fprintf(fichtmcov,"varyi ");
                fprintf(ficresprobcor,"varyi ");
              }
            }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
              /* For each selected (single) quantitative value */
              fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
              if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
                fprintf(ficresprob,"fixed ");
                fprintf(ficresprobcov,"fixed ");
                fprintf(ficgp,"fixed ");
                fprintf(fichtmcov,"fixed ");
                fprintf(ficresprobcor,"fixed ");
              }else{
                fprintf(ficresprob,"varyi ");
                fprintf(ficresprobcov,"varyi ");
                fprintf(ficgp,"varyi ");
                fprintf(fichtmcov,"varyi ");
                fprintf(ficresprobcor,"varyi ");
              }
            }else{
              printf("Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
              fprintf(ficlog,"Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff);  /* end if dummy  or quanti */
              exit(1);
            }
          } /* End loop on variable of this resultline */
          /* for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); */
          fprintf(ficresprob, "**********\n#\n");
        fprintf(ficresprobcov, "**********\n#\n");         fprintf(ficresprobcov, "**********\n#\n");
                           
        fprintf(ficgp, "\n#********** Variable ");   
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
        fprintf(ficgp, "**********\n#\n");         fprintf(ficgp, "**********\n#\n");
                           
                           
        fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");   
        /* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */  
        for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
        fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                           
        fprintf(ficresprobcor, "\n#********** Variable ");      
        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
        fprintf(ficresprobcor, "**********\n#");             fprintf(ficresprobcor, "**********\n#");    
        if(invalidvarcomb[j1]){         if(invalidvarcomb[j1]){
          fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);            fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1); 
Line 6950  To be simple, these graphs help to under Line 9377  To be simple, these graphs help to under
      trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
      gp=vector(1,(nlstate)*(nlstate+ndeath));       gp=vector(1,(nlstate)*(nlstate+ndeath));
      gm=vector(1,(nlstate)*(nlstate+ndeath));       gm=vector(1,(nlstate)*(nlstate+ndeath));
      for (age=bage; age<=fage; age ++){        for (age=bage; age<=fage; age ++){ /* Fo each age we feed the model equation with covariates, using precov as in hpxij() ? */
        cov[2]=age;         cov[2]=age;
        if(nagesqr==1)         if(nagesqr==1)
          cov[3]= age*age;           cov[3]= age*age;
        /* for (k=1; k<=cptcovn;k++) { */         /* New code end of combination but for each resultline */
        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */         for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
        for (k=1; k<=nsd;k++) { /* For single dummy covariates only */           if(Typevar[k1]==1 || Typevar[k1] ==3){ /* A product with age */
          /* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */             cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,k)];  
          /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4  
                                                                     * 1  1 1 1 1  
                                                                     * 2  2 1 1 1  
                                                                     * 3  1 2 1 1  
                                                                     */  
          /* nbcode[1][1]=0 nbcode[1][2]=1;*/  
        }  
        /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */  
        /* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */  
        /*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */  
        for (k=1; k<=cptcovage;k++){  /* For product with age */  
          if(Dummy[Tage[k]]==2){ /* dummy with age */  
            cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,k)]*cov[2];  
            /* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */  
          } else if(Dummy[Tage[k]]==3){ /* quantitative with age */  
            printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);  
            exit(1);  
              /* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\* Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; *\/ */  
            /* cov[++k1]=Tqresult[nres][k];  */  
          }  
          /* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */  
        }  
        for (k=1; k<=cptcovprod;k++){/* For product without age */  
          if(Dummy[Tvard[k][1]==0]){  
            if(Dummy[Tvard[k][2]==0]){  
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)];  
              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */  
            }else{ /* Should we use the mean of the quantitative variables? */  
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * Tqresult[nres][k];  
              /* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */  
            }  
          }else{           }else{
            if(Dummy[Tvard[k][2]==0]){             cov[2+nagesqr+k1]=precov[nres][k1];
              cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,k)] * Tqinvresult[nres][Tvard[k][1]];  
              /* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */  
            }else{  
              cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];  
              /* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; */  
            }  
          }           }
          /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; */         }/* End of loop on model equation */
        }                          /* Old code */
          /* /\* for (k=1; k<=cptcovn;k++) { *\/ */
          /* /\*    cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; *\/ */
          /* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */
          /*        /\* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates *\/ */
          /*        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])]; */
          /*        /\*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*\//\* j1 1 2 3 4 */
          /*                                                                   * 1  1 1 1 1 */
          /*                                                                   * 2  2 1 1 1 */
          /*                                                                   * 3  1 2 1 1 */
          /*                                                                   *\/ */
          /*        /\* nbcode[1][1]=0 nbcode[1][2]=1;*\/ */
          /* } */
          /* /\* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
          /* /\* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] *\/ */
          /* /\*for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; *\/ */
          /* for (k=1; k<=cptcovage;k++){  /\* For product with age *\/ */
          /*        if(Dummy[Tage[k]]==2){ /\* dummy with age *\/ */
          /*          cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2]; */
          /*          /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
          /*        } else if(Dummy[Tage[k]]==3){ /\* quantitative with age *\/ */
          /*          printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]); */
          /*          /\* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]*cov[2];/\\* Using the mean of quantitative variable Tvar[Tage[k]] /\\* Tqresult[nres][k]; *\\/ *\/ */
          /*          /\* exit(1); *\/ */
          /*          /\* cov[++k1]=Tqresult[nres][k];  *\/ */
          /*        } */
          /*        /\* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; *\/ */
          /* } */
          /* for (k=1; k<=cptcovprod;k++){/\* For product without age *\/ */
          /*        if(Dummy[Tvard[k][1]]==0){ */
          /*          if(Dummy[Tvard[k][2]]==0){ */
          /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])]; */
          /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
          /*          }else{ /\* Should we use the mean of the quantitative variables? *\/ */
          /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]]; */
          /*            /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; *\/ */
          /*          } */
          /*        }else{ */
          /*          if(Dummy[Tvard[k][2]]==0){ */
          /*            cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]]; */
          /*            /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; *\/ */
          /*          }else{ */
          /*            cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]*  Tqinvresult[nres][TnsdVar[Tvard[k][2]]]; */
          /*            /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]]; *\/ */
          /*          } */
          /*        } */
          /*        /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
          /* } */                  
 /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/                       /* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/                     
        for(theta=1; theta <=npar; theta++){         for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++)           for(i=1; i<=npar; i++)
Line 7186  To be simple, these graphs help to under Line 9622  To be simple, these graphs help to under
          } /* k12 */           } /* k12 */
        } /*l1 */         } /*l1 */
      }/* k1 */       }/* k1 */
    } /* loop on nres */  
    }  /* loop on combination of covariates j1 */     }  /* loop on combination of covariates j1 */
      } /* loop on nres */
    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
Line 7208  void printinghtml(char fileresu[], char Line 9644  void printinghtml(char fileresu[], char
                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, cpt, nres;
   /* In fact some results are already printed in fichtm which is open */    /* In fact some results are already printed in fichtm which is open */
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
Line 7218  void printinghtml(char fileresu[], char Line 9654  void printinghtml(char fileresu[], char
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
    fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",     fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
    fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));     fprintf(fichtm,",  <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
Line 7252  void printinghtml(char fileresu[], char Line 9688  void printinghtml(char fileresu[], char
    jj1=0;     jj1=0;
   
    fprintf(fichtm," \n<ul>");     fprintf(fichtm," \n<ul>");
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0)k1=1; /* To be checked for no result */
      /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
      /*   if(m != 1 && TKresult[nres]!= k1) */
      /*     continue; */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");         fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
          /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
          /*        fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
          /* } */
          /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
          /*        fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
          /* } */
        fprintf(fichtm,"\">");         fprintf(fichtm,"\">");
                 
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm,"************ Results for covariates");         fprintf(fichtm,"************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
          /* fprintf(fichtm,"************ Results for covariates"); */
          /* for (cpt=1; cpt<=cptcoveff;cpt++){  */
          /*        fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
          /* } */
          /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
          /*        fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
          /* } */
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
          continue;           continue;
Line 7286  void printinghtml(char fileresu[], char Line 9732  void printinghtml(char fileresu[], char
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
      /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
      /*   if(m != 1 && TKresult[nres]!= k1) */
      /*     continue; */
   
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<p><a name=\"rescov");         fprintf(fichtm,"\n<p><a name=\"rescov");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
          /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
          /*        fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
          /* } */
        fprintf(fichtm,"\"</a>");         fprintf(fichtm,"\"</a>");
     
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);           printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */           /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
        }         }
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);  
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);  
       }  
          
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);         fprintf(fichtm," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
          printf("\nCombination (%d) ignored because no cases \n",k1);            printf("\nCombination (%d) ignored because no cases \n",k1); 
Line 7337  divided by h: <sub>h</sub>P<sub>ij</sub> Line 9781  divided by h: <sub>h</sub>P<sub>ij</sub>
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. Mean times spent in state (or Life Expectancy or Health Expectancy etc.) are the areas under each curve. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\         fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
  And probability to be observed in various states (up to %d) being in state %d at different ages.       \   And probability to be observed in various states (up to %d) being in state %d at different ages.  Mean times spent in state (or Life Expectancy or Health Expectancy etc.) are the areas under each curve. \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
          fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }       }
      /* Period (forward stable) prevalence in each health state */       /* Period (forward stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be alive in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);         fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
         fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(prevbcast==1){       if(prevbcast==1){
        /* Backward prevalence in each health state */         /* Backward prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJB_"),subdirf2(optionfilefiname,"PIJB_"));
            fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
Line 7371  divided by h: <sub>h</sub>P<sub>ij</sub> Line 9820  divided by h: <sub>h</sub>P<sub>ij</sub>
       /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */        /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \           fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
  from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \   from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d). Randomness in cross-sectional prevalence is not taken into \
  account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \   account but can visually be appreciated. Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
 with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);  with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
          fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));           fprintf(fichtm," (data from text file  <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
          fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);           fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
Line 7385  with weights corresponding to observed p Line 9834  with weights corresponding to observed p
        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );         fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1=nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
   
    fprintf(fichtm,"\     fprintf(fichtm,"\
Line 7432  See page 'Matrix of variance-covariance Line 9881  See page 'Matrix of variance-covariance
 /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=1+age+%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);     fflush(fichtm);
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
Line 7443  See page 'Matrix of variance-covariance Line 9892  See page 'Matrix of variance-covariance
   jj1=0;    jj1=0;
   
    fprintf(fichtm," \n<ul>");     fprintf(fichtm," \n<ul>");
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){ /* For each combination of covariate */       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       /* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate *\/ */
        /* if(m != 1 && TKresult[nres]!= k1) */
        /*   continue; */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");         fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescovsecond");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
        fprintf(fichtm,"\">");         fprintf(fichtm,"\">");
                 
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm,"************ Results for covariates");         fprintf(fichtm,"************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
Line 7472  See page 'Matrix of variance-covariance Line 9917  See page 'Matrix of variance-covariance
        }         }
        fprintf(fichtm,"</a></li>");         fprintf(fichtm,"</a></li>");
      } /* cptcovn >0 */       } /* cptcovn >0 */
    }     } /* End nres */
    fprintf(fichtm," \n</ul>");     fprintf(fichtm," \n</ul>");
   
    jj1=0;     jj1=0;
   
    for(nres=1; nres <= nresult; nres++){ /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){       /* k1=nres; */
      if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
        continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
        /* for(k1=1; k1<=m;k1++){ */
        /* if(m != 1 && TKresult[nres]!= k1) */
        /*   continue; */
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"\n<p><a name=\"rescovsecond");         fprintf(fichtm,"\n<p><a name=\"rescovsecond");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcovs;cpt++){ 
          fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);           fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
        }  
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
          fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);  
        }         }
        fprintf(fichtm,"\"</a>");         fprintf(fichtm,"\"</a>");
                 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){  /**< cptcoveff number of variables */         for (cpt=1; cpt<=cptcovs;cpt++){  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);           fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);           printf(" V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
          /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */           /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
        }         }
        for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */  
         fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);  
       }  
   
        fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);         fprintf(fichtm," (model=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
   
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
          fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);            fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1); 
          continue;           continue;
        }         }
      }       } /* If cptcovn >0 */
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
Line 7517  prevalence (with 95%% confidence interva Line 9959  prevalence (with 95%% confidence interva
        fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);         fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \  health expectancies in each live state (1 to %d) with confidence intervals \
   on left y-scale as well as proportions of time spent in each live state \
   (with confidence intervals) on right y-scale 0 to 100%%.\
    If popbased=1 the smooth (due to the model)                            \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
      fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));       fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
      fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);       fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */  
   }/* End nres */    }/* End nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
    fflush(fichtm);     fflush(fichtm);
Line 7533  true period expectancies (those weighted Line 9977  true period expectancies (those weighted
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[256],optfileres[256];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[256], gplotlabel[256];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,kf=0,kvar=0,kk=0,ipos=0,iposold=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
Line 7561  void printinggnuplot(char fileresu[], ch Line 10005  void printinggnuplot(char fileresu[], ch
   fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);    fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
   fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);    fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   
   fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);    fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] for [j=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0)  ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate, nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   fprintf(ficgp,"\n#show arrow\nunset label\n");    fprintf(ficgp,"\n#show arrow\nunset label\n");
   fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);    fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
   fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);    fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
Line 7598  void printinggnuplot(char fileresu[], ch Line 10042  void printinggnuplot(char fileresu[], ch
   fprintf(ficgp,"\nset out;unset log\n");    fprintf(ficgp,"\nset out;unset log\n");
   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
     /* Plot the probability implied in the likelihood by covariate value */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
     /* if(debugILK==1){ */
     for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
       kvar=Tvar[TvarFind[kf]]; /* variable name */
       /* k=18+Tvar[TvarFind[kf]];/\*offset because there are 18 columns in the ILK_ file but could be placed else where *\/ */
       /* k=18+kf;/\*offset because there are 18 columns in the ILK_ file *\/ */
       /* k=19+kf;/\*offset because there are 19 columns in the ILK_ file *\/ */
       k=16+nlstate+kf;/*offset because there are 19 columns in the ILK_ file, first cov Vn on col 21 with 4 living states */
       for (i=1; i<= nlstate ; i ++) {
         fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
         fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
         if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
           fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
           for (j=2; j<= nlstate+ndeath ; j ++) {
             fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
           }
         }else{
           fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
           for (j=2; j<= nlstate+ndeath ; j ++) {
             fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
           }
         }
         fprintf(ficgp,";\nset out; unset ylabel;\n"); 
       }
     } /* End of each covariate dummy */
     for(ncovv=1, iposold=0, kk=0; ncovv <= ncovvt ; ncovv++){
       /* Other example        V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5 
        *     kmodel       =     1   2     3     4         5        6        7       8        9
        *  varying                   1     2                                 3       4        5
        *  ncovv                     1     2                                3 4     5 6      7 8
        * TvarVV[ncovv]             V3     5                                1 3     3 5      1 5
        * TvarVVind[ncovv]=kmodel    2     3                                7 7     8 8      9 9
        * TvarFind[kmodel]       1   0     0     0         0        0        0       0        0
        * kdata     ncovcol=[V1 V2] nqv=0 ntv=[V3 V4] nqtv=V5
        * Dummy[kmodel]          0   0     1     2         2        3        1       1        1
        */
       ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
       kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
       /* printf("DebugILK ficgp ncovv=%d, kvar=TvarVV[ncovv]=%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
       if(ipos!=iposold){ /* Not a product or first of a product */
         /* printf(" %d",ipos); */
         /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
         /* printf(" DebugILK ficgp suite ipos=%d != iposold=%d\n", ipos, iposold); */
         kk++; /* Position of the ncovv column in ILK_ */
         k=18+ncovf+kk; /*offset because there are 18 columns in the ILK_ file plus ncovf fixed covariate */
         if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
           for (i=1; i<= nlstate ; i ++) {
             fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
             fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
   
               /* printf("Before DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
             if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
               /* printf("DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
               fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
               for (j=2; j<= nlstate+ndeath ; j ++) {
                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
               }
             }else{
               /* printf("DebugILK gnuplotversion=%g <5.2\n",gnuplotversion); */
               fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
               for (j=2; j<= nlstate+ndeath ; j ++) {
                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
               }
             }
             fprintf(ficgp,";\nset out; unset ylabel;\n"); 
           }
         }/* End if dummy varying */
       }else{ /*Product */
         /* printf("*"); */
         /* fprintf(ficresilk,"*"); */
       }
       iposold=ipos;
     } /* For each time varying covariate */
     /* } /\* debugILK==1 *\/ */
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   
     
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */      /* for (k1=1; k1<= m ; k1 ++){ /\* For each valid combination of covariate *\/ */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
           k1=TKresult[nres];
           if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         if(m != 1 && TKresult[nres]!= k1)          /* if(m != 1 && TKresult[nres]!= k1) */
           continue;          /*   continue; */
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */  
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* printf(" V%d=%d ",Tvaraff[k],vlv); */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
           /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */          /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   /\* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         }          }
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         /* printf("\n#\n"); */          /* printf("\n#\n"); */
Line 7639  void printinggnuplot(char fileresu[], ch Line 10173  void printinggnuplot(char fileresu[], ch
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
         fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
         fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);          fprintf(ficgp,"set title \"Alive state %d %s model=1+age+%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */          /* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
       /* k1-1 error should be nres-1*/        /* k1-1 error should be nres-1*/
Line 7665  void printinggnuplot(char fileresu[], ch Line 10199  void printinggnuplot(char fileresu[], ch
         }else{          }else{
           kl=0;            kl=0;
           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */              /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
             /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */              /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
             /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */              /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
             /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */              /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
Line 7693  void printinggnuplot(char fileresu[], ch Line 10228  void printinggnuplot(char fileresu[], ch
           }else{            }else{
             kl=0;              kl=0;
             for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */              for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */                /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */
                 lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv];                /* vlv= nbcode[Tvaraff[k]][lv]; */
                 vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
               kl++;                kl++;
               /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */                /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
Line 7707  void printinggnuplot(char fileresu[], ch Line 10244  void printinggnuplot(char fileresu[], ch
                 fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \                  fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                         2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/                          2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
               }else{                }else{
                 fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);                  fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
                 kl++;                  kl++;
               }                }
             } /* end covariate */              } /* end covariate */
Line 7735  void printinggnuplot(char fileresu[], ch Line 10272  void printinggnuplot(char fileresu[], ch
         /* fprintf(ficgp,"\nset out ;unset label;\n"); */          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
         fprintf(ficgp,"\nset out ;unset title;\n");          fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
     } /* k1 */      /* } /\* k1 *\/ */
   } /* cpt */    } /* cpt */
   
       
   /*2 eme*/    /*2 eme*/
   for (k1=1; k1<= m ; k1 ++){      /* for (k1=1; k1<= m ; k1 ++){   */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         vlv= nbcode[Tvaraff[k]][lv];        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
       }        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
       /* for(k=1; k <= ncovds; k++){ */        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* } */
         /* /\* for(k=1; k <= ncovds; k++){ *\/ */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       }        }
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
Line 7772  void printinggnuplot(char fileresu[], ch Line 10316  void printinggnuplot(char fileresu[], ch
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);          fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
         if(vpopbased==0){          if(vpopbased==0){
           fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nunset ytics; unset y2tics; set ytics nomirror; set y2tics 0,10,100;set y2range [0:100];\nplot [%.f:%.f] ",ageminpar,fage);
         }else          }else
           fprintf(ficgp,"\nreplot ");            fprintf(ficgp,"\nreplot ");
         for (i=1; i<= nlstate+1 ; i ++) {          for (i=1; i<= nlstate+1 ; i ++) { /* For state i-1=0 is LE, while i-1=1 to nlstate are origin state */
           k=2*i;            k=2*i;
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased); /* for fixed variables age, popbased, mobilav */
           for (j=1; j<= nlstate+1 ; j ++) {            for (j=1; j<= nlstate+1 ; j ++) { /* e.. e.1 e.2 again j-1 is the state of end, wlim_i eij*/
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)"); /* We want to read e.. i=1,j=1, e.1 i=2,j=2, e.2 i=3,j=3 */
             else fprintf(ficgp," %%*lf (%%*lf)");              else fprintf(ficgp," %%*lf (%%*lf)");  /* skipping that field with a star */
           }               }   
           if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
           else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);            else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1); /* state=i-1=1 to nlstate  */
           fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
           for (j=1; j<= nlstate+1 ; j ++) {            for (j=1; j<= nlstate+1 ; j ++) {
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)");
Line 7795  void printinggnuplot(char fileresu[], ch Line 10339  void printinggnuplot(char fileresu[], ch
             if (j==i) fprintf(ficgp," %%lf (%%lf)");              if (j==i) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");              else fprintf(ficgp," %%*lf (%%*lf)");
           }               }   
           if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");            if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0,\\\n"); /* ,\\\n added for th percentage graphs */
           else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");            else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
         } /* state */          } /* state */
           /* again for the percentag spent in state i-1=1 to i-1=nlstate */
           for (i=2; i<= nlstate+1 ; i ++) { /* For state i-1=0 is LE, while i-1=1 to nlstate are origin state */
             k=2*i;
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d &&  ($4)<=1 && ($4)>=0 ?($4)*100. : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased); /* for fixed variables age, popbased, mobilav */
             for (j=1; j<= nlstate ; j ++)
               fprintf(ficgp," %%*lf (%%*lf)"); /* Skipping TLE and LE to read %LE only */
             for (j=1; j<= nlstate+1 ; j ++) { /* e.. e.1 e.2 again j-1 is the state of end, wlim_i eij*/
               if (j==i) fprintf(ficgp," %%lf (%%lf)"); /* We want to read e.. i=1,j=1, e.1 i=2,j=2, e.2 i=3,j=3 */
               else fprintf(ficgp," %%*lf (%%*lf)");  /* skipping that field with a star */
             }   
             if (i== 1) fprintf(ficgp,"\" t\"%%TLE\" w l lt %d axis x1y2, \\\n",i); /* Not used */
             else fprintf(ficgp,"\" t\"%%LE in state (%d)\" w l lw 2 lt %d axis x1y2, \\\n",i-1,i+1); /* state=i-1=1 to nlstate  */
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && ($4-$5*2)<=1 && ($4-$5*2)>=0? ($4-$5*2)*100. : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate ; j ++)
               fprintf(ficgp," %%*lf (%%*lf)"); /* Skipping TLE and LE to read %LE only */
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             fprintf(ficgp,"\" t\"\" w l lt 0 axis x1y2,");
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && ($4+$5*2)<=1 && ($4+$5*2)>=0 ? ($4+$5*2)*100. : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate ; j ++)
               fprintf(ficgp," %%*lf (%%*lf)"); /* Skipping TLE and LE to read %LE only */
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0 axis x1y2");
             else fprintf(ficgp,"\" t\"\" w l lt 0 axis x1y2,\\\n");
           } /* state for percent */
       } /* vpopbased */        } /* vpopbased */
       fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */        fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
     } /* end nres */      } /* end nres */
   } /* k1 end 2 eme*/    /* } /\* k1 end 2 eme*\/ */
                   
                   
   /*3eme*/    /*3eme*/
   for (k1=1; k1<= m ; k1 ++){    /* for (k1=1; k1<= m ; k1 ++){ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
   
       for (cpt=1; cpt<= nlstate ; cpt ++) {        for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
         fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);          fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         }                 /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
           }
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
Line 7856  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 10437  plot [%.f:%.f] \"%s\" every :::%d::%d u
       }        }
       fprintf(ficgp,"\nunset label;\n");        fprintf(ficgp,"\nunset label;\n");
     } /* end nres */      } /* end nres */
   } /* end kl 3eme */    /* } /\* end kl 3eme *\/ */
       
   /* 4eme */    /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<=m; k1++){    /* For each covariate and each value */    /* for (k1=1; k1<=m; k1++){    /\* For each covariate and each value *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state %d : 'LIJ_' files, cov=%d state=%d", cpt, k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           vlv= nbcode[Tvaraff[k]][lv];          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end nres */      } /* end nres */
   } /* end covariate k1 */      /* } /\* end covariate k1 *\/   */
   
 /* 5eme */  /* 5eme */
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */    /* for (k1=1; k1<= m ; k1++){ /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           vlv= nbcode[Tvaraff[k]][lv];          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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         }          }
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        /* } /\* end covariate *\/   */
   } /* end nres */    } /* end nres */
       
 /* 6eme */  /* 6eme */
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */    /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
       continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
        /* if(m != 1 && TKresult[nres]!= k1) */
        /*  continue; */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
       strcpy(gplotlabel,"(");              strcpy(gplotlabel,"(");      
       fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         vlv= nbcode[Tvaraff[k]][lv];        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
       }        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         /* } */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
       }         } 
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
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 /* 7eme */  /* 7eme */
   if(prevbcast == 1){    if(prevbcast == 1){
     /* CV backward prevalence  for each covariate */      /* CV backward prevalence  for each covariate */
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */      /* Projection from cross-sectional to forward stable (period) prevalence for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)        k1=TKresult[nres];
         continue;        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* if(m != 1 && TKresult[nres]!= k1) */
         /*        continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
               for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                 /* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
                 lv=Tvresult[nres][k];
                 vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */                /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
                 /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
               kl++;                kl++;
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,lv, kl+1, vlv );
               kl++;                kl++;
               if(k <cptcoveff && cptcoveff>1)                if(k <cptcovs && cptcovs>1)
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
             }              }
             strcpy(gplotcondition+strlen(gplotcondition),")");              strcpy(gplotcondition+strlen(gplotcondition),")");
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   if(prevbcast==1){    if(prevbcast==1){
     /* Back projection from cross-sectional to stable (mixed) for each covariate */      /* Back projection from cross-sectional to stable (mixed) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
         continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
          /* if(m != 1 && TKresult[nres]!= k1) */
          /*       continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv];          /*   lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         }          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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           }else{            }else{
             fprintf(ficgp,",\\\n '' ");              fprintf(ficgp,",\\\n '' ");
           }            }
           if(cptcoveff ==0){ /* No covariate */            /* if(cptcoveff ==0){ /\* No covariate *\/ */
             if(cptcovs ==0){ /* No covariate */
             ioffset=2; /* Age is in 2 */              ioffset=2; /* Age is in 2 */
             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
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             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              for (k=1; k<=cptcovs; k++){    /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
               lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                if(Dummy[modelresult[nres][k]]==0){  /* To be verified */
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                  /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                  /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                  /* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
               vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */                  lv=Tvresult[nres][k];
               kl++;                  vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                  /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               kl++;                  /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               if(k <cptcoveff && cptcoveff>1)                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
                   /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
                   kl++;
                   /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
                   sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
                   kl++;
                   if(k <cptcovs && cptcovs>1)
                     sprintf(gplotcondition+strlen(gplotcondition)," && ");
                 }
             }              }
             strcpy(gplotcondition+strlen(gplotcondition),")");              strcpy(gplotcondition+strlen(gplotcondition),")");
             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
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   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#model=%s \n",model);      fprintf(ficgp,"#model=1+age+%s \n",model);
     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      /* fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/\* to be checked *\/ */
     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcovs,m);/* to be checked */
       /* for(k1=1; k1 <=m; k1++)  /\* For each combination of covariate *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       /* k1=nres; */
         continue;        k1=TKresult[nres];
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/        /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */        for (k=1; k<=cptcovs; k++){  /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          /* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */             TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         vlv= nbcode[Tvaraff[k]][lv];        }
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /* if(m != 1 && TKresult[nres]!= k1) */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        continue; */
       }        /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /* strcpy(gplotlabel,"("); */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
       }         /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
         /*        lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
         /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         /* } */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /* }       */
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
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             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */              /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */              for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                switch(Typevar[j]){
                 if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */                case 1:
                   if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                  if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     if(DummyV[j]==0){/* Bug valgrind */                    if(j==Tage[ij]) { /* Product by age  To be looked at!!*//* Bug valgrind */
                       fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;                      if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     }else{ /* quantitative */                        if(DummyV[j]==0){/* Bug valgrind */
                       fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */                          fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                        }else{ /* quantitative */
                           fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                           /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                         }
                         ij++;
                     }                      }
                     ij++;  
                   }                    }
                 }                   }
               }else if(cptcovprod >0){                  break;
                 if(j==Tprod[ijp]) { /* */                 case 2:
                   /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */                  if(cptcovprod >0){
                   if(ijp <=cptcovprod) { /* Product */                    if(j==Tprod[ijp]) { /* */ 
                     if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */                      /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                       if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */                      if(ijp <=cptcovprod) { /* Product */
                         /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */                        if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);                          if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                       }else{ /* Vn is dummy and Vm is quanti */                            /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                         /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */                            fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                          }else{ /* Vn is dummy and Vm is quanti */
                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                             fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                           }
                         }else{ /* Vn*Vm Vn is quanti */
                           if(DummyV[Tvard[ijp][2]]==0){
                             fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                           }else{ /* Both quanti */
                             fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                           }
                       }                        }
                     }else{ /* Vn*Vm Vn is quanti */                        ijp++;
                       if(DummyV[Tvard[ijp][2]]==0){                      }
                         fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);                    } /* end Tprod */
                       }else{ /* Both quanti */                  }
                         fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                  break;
                 case 3:
                   if(cptcovdageprod >0){
                     /* if(j==Tprod[ijp]) { */ /* not necessary */ 
                       /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                       if(ijp <=cptcovprod) { /* Product Vn*Vm and age*VN*Vm*/
                         if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
                           if(DummyV[Tvardk[ijp][2]]==0){/* Vn and Vm are dummy */
                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                             fprintf(ficgp,"+p%d*%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                           }else{ /* Vn is dummy and Vm is quanti */
                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                             fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                           }
                         }else{ /* age* Vn*Vm Vn is quanti HERE */
                           if(DummyV[Tvard[ijp][2]]==0){
                             fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
                           }else{ /* Both quanti */
                             fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                           }
                       }                        }
                         ijp++;
                     }                      }
                     ijp++;                      /* } */ /* end Tprod */
                   }                  }
                 } /* end Tprod */                  break;
               } else{  /* simple covariate */                case 0:
                   /* simple covariate */
                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */                  /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                 if(Dummy[j]==0){                  if(Dummy[j]==0){
                   fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */                    fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
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                   fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */                    fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                   /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                    /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                 }                  }
               } /* end simple */                 /* end simple */
                   break;
                 default:
                   break;
                 } /* end switch */
             } /* end j */              } /* end j */
           }else{            }else{ /* k=k2 */
             i=i-ncovmodel;              if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */                fprintf(ficgp," (1.");i=i-ncovmodel;
               fprintf(ficgp," (1.");              }else
                 i=i-ncovmodel;
           }            }
                       
           if(ng != 1){            if(ng != 1){
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                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                                 
               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                ijp=1;
                  if(cptcovage >0){                 /* for(j=3; j <=ncovmodel-nagesqr; j++){ */
                    if((j-2)==Tage[ij]) { /* Bug valgrind */                for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
                      if(ij <=cptcovage) { /* Bug valgrind */                  switch(Typevar[j]){
                        fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);                  case 1:
                        /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                    if(cptcovage >0){ 
                        ij++;                      if(j==Tage[ij]) { /* Bug valgrind */
                      }                        if(ij <=cptcovage) { /* Bug valgrind */
                    }                          if(DummyV[j]==0){/* Bug valgrind */
                  }else                            /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); */
                    fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */                            /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); */
                             fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
                             /* fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
                             /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                           }else{ /* quantitative */
                             /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
                             fprintf(ficgp,"+p%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                             /* fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult *\/ */
                             /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                           }
                           ij++;
                         }
                       }
                     }
                     break;
                   case 2:
                     if(cptcovprod >0){
                       if(j==Tprod[ijp]) { /* */ 
                         /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                         if(ijp <=cptcovprod) { /* Product */
                           if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                             if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                               fprintf(ficgp,"+p%d*%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
                             }else{ /* Vn is dummy and Vm is quanti */
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             }
                           }else{ /* Vn*Vm Vn is quanti */
                             if(DummyV[Tvard[ijp][2]]==0){
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
                             }else{ /* Both quanti */
                               fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             } 
                           }
                           ijp++;
                         }
                       } /* end Tprod */
                     } /* end if */
                     break;
                   case 3:
                     if(cptcovdageprod >0){
                       /* if(j==Tprod[ijp]) { /\* *\/  */
                         /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                         if(ijp <=cptcovprod) { /* Product */
                           if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
                             if(DummyV[Tvardk[ijp][2]]==0){/* Vn and Vm are dummy */
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                               fprintf(ficgp,"+p%d*%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
                             }else{ /* Vn is dummy and Vm is quanti */
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                               fprintf(ficgp,"+p%d*%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             }
                           }else{ /* Vn*Vm Vn is quanti */
                             if(DummyV[Tvardk[ijp][2]]==0){
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
                               /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
                             }else{ /* Both quanti */
                               fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             } 
                           }
                           ijp++;
                         }
                       /* } /\* end Tprod *\/ */
                     } /* end if */
                     break;
                   case 0: 
                     /* simple covariate */
                     /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                     if(Dummy[j]==0){
                       /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
                       fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /*  */
                       /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\*  *\/ */
                     }else{ /* quantitative */
                       fprintf(ficgp,"+p%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
                       /* fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* *\/ */
                       /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                     }
                     /* end simple */
                     /* fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode *\/ */
                     break;
                   default:
                     break;
                   } /* end switch */
               }                }
               fprintf(ficgp,")");                fprintf(ficgp,")");
             }              }
Line 8489  set ter svg size 640, 480\nunset log y\n Line 11270  set ter svg size 640, 480\nunset log y\n
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             else /* ng= 3 */              else /* ng= 3 */
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
             if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
               fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }            }
Line 8502  set ter svg size 640, 480\nunset log y\n Line 11283  set ter svg size 640, 480\nunset log y\n
       } /* end k2 */        } /* end k2 */
       /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
       fprintf(ficgp,"\n set out; unset title;set key default;\n");        fprintf(ficgp,"\n set out; unset title;set key default;\n");
     } /* end k1 */      } /* end resultline */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
   fflush(ficgp);     fflush(ficgp); 
Line 8760  void prevforecast(char fileres[], double Line 11541  void prevforecast(char fileres[], double
   */    */
   /* double anprojd, mprojd, jprojd; */    /* double anprojd, mprojd, jprojd; */
   /* double anprojf, mprojf, jprojf; */    /* double anprojf, mprojf, jprojf; */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, i, h,  nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2;    double agelim, ppij;
   double *popeffectif,*popcount;    /*double *popcount;*/
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
Line 8816  void prevforecast(char fileres[], double Line 11597  void prevforecast(char fileres[], double
   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */    /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */    /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */    /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
   i1=pow(2,cptcoveff);    /* i1=pow(2,cptcoveff); */
   if (cptcovn < 1){i1=1;}    /* if (cptcovn < 1){i1=1;} */
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
   for(k=1; k<=i1;k++){      k=TKresult[nres];
     if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
       continue;      /*  for(k=1; k<=i1;k++){ /\* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) *\/ */
     if(invalidvarcomb[k]){      /* if(i1 != 1 && TKresult[nres]!= k) */
       printf("\nCombination (%d) projection ignored because no cases \n",k);       /*   continue; */
       continue;      /* if(invalidvarcomb[k]){ */
     }      /*   printf("\nCombination (%d) projection ignored because no cases \n",k);  */
       /*   continue; */
       /* } */
     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcovs;j++){
       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        /* for(j=1;j<=cptcoveff;j++) { */
     }      /*   /\* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); *\/ */
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      /*   fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);      /* } */
       /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
       /*   fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       /* } */
         fprintf(ficresf," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
     }      }
    
     fprintf(ficresf," yearproj age");      fprintf(ficresf," yearproj age");
     for(j=1; j<=nlstate+ndeath;j++){       for(j=1; j<=nlstate+ndeath;j++){ 
       for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)        
Line 8863  void prevforecast(char fileres[], double Line 11651  void prevforecast(char fileres[], double
           }            }
         }          }
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         for(j=1;j<=cptcoveff;j++)           /* for(j=1;j<=cptcoveff;j++)  */
           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          for(j=1;j<=cptcovs;j++) 
             fprintf(ficresf,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
             /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
             /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* TnsdVar[Tvaraff]  correct *\/ */
         fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);          fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+h*hstepm/YEARM*stepm);
                   
         for(j=1; j<=nlstate+ndeath;j++) {          for(j=1; j<=nlstate+ndeath;j++) {
Line 8901  void prevforecast(char fileres[], double Line 11692  void prevforecast(char fileres[], double
      anback2 year of end of backprojection (same day and month as back1).       anback2 year of end of backprojection (same day and month as back1).
      prevacurrent and prev are prevalences.       prevacurrent and prev are prevalences.
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k,  i, h, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/    double agelim, ppij, ppi; /* ,jintmean,mintmean,aintmean;*/
   double *popeffectif,*popcount;    /*double *popcount;*/
   double ***p3mat;    double ***p3mat;
   /* double ***mobaverage; */    /* double ***mobaverage; */
   char fileresfb[FILENAMELENGTH];    char fileresfb[FILENAMELENGTH];
Line 8956  void prevforecast(char fileres[], double Line 11747  void prevforecast(char fileres[], double
   /* if(jintmean==0) jintmean=1; */    /* if(jintmean==0) jintmean=1; */
   /* if(mintmean==0) jintmean=1; */    /* if(mintmean==0) jintmean=1; */
       
   i1=pow(2,cptcoveff);    /* i1=pow(2,cptcoveff); */
   if (cptcovn < 1){i1=1;}    /* if (cptcovn < 1){i1=1;} */
       
   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
       
   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
       
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
   for(k=1; k<=i1;k++){      k=TKresult[nres];
     if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
       continue;    /* for(k=1; k<=i1;k++){ */
     if(invalidvarcomb[k]){    /*   if(i1 != 1 && TKresult[nres]!= k) */
       printf("\nCombination (%d) projection ignored because no cases \n",k);     /*     continue; */
       continue;    /*   if(invalidvarcomb[k]){ */
     }    /*     printf("\nCombination (%d) projection ignored because no cases \n",k);  */
     /*     continue; */
     /*   } */
     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcovs;j++){
       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      /* for(j=1;j<=cptcoveff;j++) { */
     }      /*   fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      /* } */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficresfb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
     }      }
      /*  fprintf(ficrespij,"******\n"); */
      /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
      /*    fprintf(ficresfb," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
      /*  } */
     fprintf(ficresfb," yearbproj age");      fprintf(ficresfb," yearbproj age");
     for(j=1; j<=nlstate+ndeath;j++){      for(j=1; j<=nlstate+ndeath;j++){
       for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++)
Line 9009  void prevforecast(char fileres[], double Line 11806  void prevforecast(char fileres[], double
           }            }
         }          }
         fprintf(ficresfb,"\n");          fprintf(ficresfb,"\n");
         for(j=1;j<=cptcoveff;j++)          /* for(j=1;j<=cptcoveff;j++) */
           fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          for(j=1;j<=cptcovs;j++)
             fprintf(ficresfb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
             /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);          fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
         for(i=1; i<=nlstate+ndeath;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
           ppij=0.;ppi=0.;            ppij=0.;ppi=0.;
Line 9069  void prevforecast(char fileres[], double Line 11868  void prevforecast(char fileres[], double
     i1=pow(2,cptcoveff);      i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){         k=TKresult[nres];
          if(TKresult[nres]==0) k=1; /* To be checked for noresult */
        /* for(k=1; k<=i1;k++){ /\* We find the combination equivalent to result line values of dummies *\/ */
       if(i1 != 1 && TKresult[nres]!= k)        if(i1 != 1 && TKresult[nres]!= k)
         continue;          continue;
       fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       fprintf(ficlog,"\n#****** ");        fprintf(ficlog,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++) {
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvpl,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }          /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */          /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        }
         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
       }         /*        fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* }       */
       fprintf(ficresvpl,"******\n");        fprintf(ficresvpl,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 9126  void prevforecast(char fileres[], double Line 11929  void prevforecast(char fileres[], double
    i1=pow(2,cptcoveff);     i1=pow(2,cptcoveff);
    if (cptcovn < 1){i1=1;}     if (cptcovn < 1){i1=1;}
         
    for(nres=1; nres <= nresult; nres++) /* For each resultline */     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
      for(k=1; k<=i1;k++){       k=TKresult[nres];
        if(i1 != 1 && TKresult[nres]!= k)       if(TKresult[nres]==0) k=1; /* To be checked for noresult */
          continue;      /* for(k=1; k<=i1;k++){ */
       /*    if(i1 != 1 && TKresult[nres]!= k) */
       /*   continue; */
        fprintf(ficresvbl,"\n#****** ");         fprintf(ficresvbl,"\n#****** ");
        printf("\n#****** ");         printf("\n#****** ");
        fprintf(ficlog,"\n#****** ");         fprintf(ficlog,"\n#****** ");
        for(j=1;j<=cptcoveff;j++) {         for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */
          fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           fprintf(ficresvbl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);           fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
        }         /* for(j=1;j<=cptcoveff;j++) { */
        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */         /*        fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);         /*        fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);         /*        printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
          fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);         /* } */
          /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
          /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
          /*        fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
          /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
        }         }
        fprintf(ficresvbl,"******\n");         fprintf(ficresvbl,"******\n");
        printf("******\n");         printf("******\n");
Line 9485  double gompertz(double x[]) Line 12294  double gompertz(double x[])
          A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
        } else if (cens[i] == 0){         } else if (cens[i] == 0){
         A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))          A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
           +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);            +log(fabs(x[1])/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
           /* +log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM); */  /* To be seen */
       } else        } else
          printf("Gompertz cens[%d] neither 1 nor 0\n",i);           printf("Gompertz cens[%d] neither 1 nor 0\n",i);
       /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */        /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
Line 9569  void printinggnuplotmort(char fileresu[] Line 12379  void printinggnuplotmort(char fileresu[]
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   
   int ng;    /*int ng;*/
   
   
   /*#ifdef windows */    /*#ifdef windows */
Line 9593  int readdata(char datafile[], int firsto Line 12403  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0, iv=0, v;    int i = 0, j = 0, n = 0, iv = 0;/* , v;*/
   int lstra;    int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   int noffset=0; /* This is the offset if BOM data file */    int noffset=0; /* This is the offset if BOM data file */
Line 9601  int readdata(char datafile[], int firsto Line 12411  int readdata(char datafile[], int firsto
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   
   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */    /* DummyV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */    /* FixedV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
   for(v=1;v<NCOVMAX;v++){    
     DummyV[v]=0;    ncovcolt=ncovcol+nqv+ntv+nqtv; /* total of covariates in the data, not in the model equation */
     FixedV[v]=0;    
   }  
   
   for(v=1; v <=ncovcol;v++){  
     DummyV[v]=0;  
     FixedV[v]=0;  
   }  
   for(v=ncovcol+1; v <=ncovcol+nqv;v++){  
     DummyV[v]=1;  
     FixedV[v]=0;  
   }  
   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){  
     DummyV[v]=0;  
     FixedV[v]=1;  
   }  
   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){  
     DummyV[v]=1;  
     FixedV[v]=1;  
   }  
   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){  
     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);  
     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);  
   }  
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
Line 9706  int readdata(char datafile[], int firsto Line 12493  int readdata(char datafile[], int firsto
         if(strb[0]=='.') { /* Missing value */          if(strb[0]=='.') { /* Missing value */
           lval=-1;            lval=-1;
           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */            cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
           cotvar[j][ntv+iv][i]=-1; /* For performance reasons */            cotvar[j][ncovcol+nqv+ntv+iv][i]=-1; /* For performance reasons */
           if(isalpha(strb[1])) { /* .m or .d Really Missing value */            if(isalpha(strb[1])) { /* .m or .d Really Missing value */
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);              printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);              fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
Line 9726  int readdata(char datafile[], int firsto Line 12513  int readdata(char datafile[], int firsto
             return 1;              return 1;
           }            }
           cotqvar[j][iv][i]=dval;             cotqvar[j][iv][i]=dval; 
           cotvar[j][ntv+iv][i]=dval;             cotvar[j][ncovcol+nqv+ntv+iv][i]=dval; /* because cotvar starts now at first ntv */ 
         }          }
         strcpy(line,stra);          strcpy(line,stra);
       }/* end loop ntqv */        }/* end loop ntqv */
Line 9766  int readdata(char datafile[], int firsto Line 12553  int readdata(char datafile[], int firsto
  Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);   Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
           return 1;            return 1;
         }          }
         cotvar[j][iv][i]=(double)(lval);          cotvar[j][ncovcol+nqv+iv][i]=(double)(lval);
         strcpy(line,stra);          strcpy(line,stra);
       }/* end loop ntv */        }/* end loop ntv */
               
Line 9778  int readdata(char datafile[], int firsto Line 12565  int readdata(char datafile[], int firsto
         errno=0;          errno=0;
         lval=strtol(strb,&endptr,10);           lval=strtol(strb,&endptr,10); 
         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/          /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){          if( strb[0]=='\0' || (*endptr != '\0' )){
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }else if( lval==0 || lval > nlstate+ndeath){
             printf("Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile);fflush(stdout);
             fprintf(ficlog,"Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile); fflush(ficlog);
           return 1;            return 1;
         }          }
       }        }
Line 9966  void removefirstspace(char **stri){/*, c Line 12757  void removefirstspace(char **stri){/*, c
   *stri=p2;     *stri=p2; 
 }  }
   
 int decoderesult ( char resultline[], int nres)  int decoderesult( char resultline[], int nres)
 /**< This routine decode one result line and returns the combination # of dummy covariates only **/  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
 {  {
   int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;    int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
   char resultsav[MAXLINE];    char resultsav[MAXLINE];
   int resultmodel[MAXLINE];    /* int resultmodel[MAXLINE]; */
   int modelresult[MAXLINE];    /* int modelresult[MAXLINE]; */
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   removefirstspace(&resultline);    removefirstspace(&resultline);
     printf("decoderesult:%s\n",resultline);
   
   if (strstr(resultline,"v") !=0){    strcpy(resultsav,resultline);
     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);    /* printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline); */
     fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);  
     return 1;  
   }  
   trimbb(resultsav, resultline);  
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */
   }    }
   if(j == 0){ /* Resultline but no = */    if(j == 0 && cptcovs== 0){ /* Resultline but no =  and no covariate in the model */
     TKresult[nres]=0; /* Combination for the nresult and the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     return (0);      return (0);
   }    }
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);      fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(ficlog);
     fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);      printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(stdout);
       if(j==0)
         return 1;
   }    }
   for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */    for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */
     if(nbocc(resultsav,'=') >1){      if(nbocc(resultsav,'=') >1){
       cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */        cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop *//*     resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
         /* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
       cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */        cutl(strc,strd,strb,'=');  /* strb:"V4=1" strc="1" strd="V4" */
         /* If a blank, then strc="V4=" and strd='\0' */
         if(strc[0]=='\0'){
         printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
           fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
           return 1;
         }
     }else      }else
       cutl(strc,strd,resultsav,'=');        cutl(strc,strd,resultsav,'=');
     Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */      Tvalsel[k]=atof(strc); /* 1 */ /* Tvalsel of k is the float value of the kth covariate appearing in this result line */
Line 10010  int decoderesult ( char resultline[], in Line 12807  int decoderesult ( char resultline[], in
       strcpy(resultsav,stra); /* and analyzes it */        strcpy(resultsav,stra); /* and analyzes it */
   }    }
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */    /* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
     if(Typevar[k1]==0){ /* Single covariate in model *//*0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */    for(k1=1; k1<= cptcovt ;k1++){ /* Loop on MODEL LINE V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single covariate in model */
         /* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
       match=0;        match=0;
       for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */        for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
         if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */          if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
           modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */            modelresult[nres][k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
           match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */            match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
           break;            break;
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);          printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
         fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);          fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%s\n",Tvar[k1], resultline, model);
         return 1;          return 1;
       }        }
     }      }else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
   }        /* We feed resultmodel[k1]=k2; */
         match=0;
         for(k2=1; k2 <=j;k2++){/* Loop on resultline.  jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
             modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vn*age in the model modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
             resultmodel[nres][k1]=k2; /* Added here */
             /* printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]); */
             match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
             break;
           }
         }
         if(match == 0){
           printf("Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
           fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
         return 1;
         }
       }else if(Typevar[k1]==2 || Typevar[k1]==3){ /* Product with or without age. We want to get the position in the resultline of the product in the model line*/
         /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */ 
         match=0;
         /* printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]); */
         for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
             /* modelresult[k2]=k1; */
             /* printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]); */
             match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
           }
         }
         if(match == 0){
           printf("Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
           fprintf(ficlog,"Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
           return 1;
         }
         match=0;
         for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */
             /* modelresult[k2]=k1;*/
             /* printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]); */
             match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
             break;
           }
         }
         if(match == 0){
           printf("Error in result line (Product without age second variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
           fprintf(ficlog,"Error in result line (Product without age second variable or double product with age): V%d is missing in result : %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
           return 1;
         }
       }/* End of testing */
     }/* End loop cptcovt */
   /* Checking for missing or useless values in comparison of current model needs */    /* Checking for missing or useless values in comparison of current model needs */
   for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    /* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
     for(k2=1; k2 <=j;k2++){ /* j or cptcovs is the number of single covariates used either in the model line as well as in the result line (dummy or quantitative)
                              * Loop on resultline variables: result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     match=0;      match=0;
     for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */      for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single */        if(Typevar[k1]==0){ /* Single only */
         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */          if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4  What if a product?  */
           resultmodel[k1]=k2;  /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */            resultmodel[nres][k1]=k2;  /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             modelresult[nres][k2]=k1; /* k1th position in the model equation corresponds to k2th position in the result line. modelresult[1]=2 modelresult[2]=1  modelresult[3]=3  remodelresult[4]=6 modelresult[5]=9 */
           ++match;            ++match;
         }          }
       }        }
     }      }
     if(match == 0){      if(match == 0){
       printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);        printf("Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
       fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);        fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
       return 1;        return 1;
     }else if(match > 1){      }else if(match > 1){
       printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);        printf("Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
       fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);        fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
       return 1;        return 1;
     }      }
   }    }
           /* cptcovres=j /\* Number of variables in the resultline is equal to cptcovs and thus useless *\/     */
   /* We need to deduce which combination number is chosen and save quantitative values */    /* We need to deduce which combination number is chosen and save quantitative values */
   /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */    /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */    /* nres=1st result line: V4=1 V5=25.1 V3=0  V2=8 V1=1 */
   /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/    /* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 1*1 + 0*2 + 1*4 = 5 + (1offset) = 6*/
   /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */    /* nres=2nd result line: V4=1 V5=24.1 V3=1  V2=8 V1=0 */
   /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/    /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
   /*    1 0 0 0 */    /*    1 0 0 0 */
   /*    2 1 0 0 */    /*    2 1 0 0 */
   /*    3 0 1 0 */     /*    3 0 1 0 */ 
   /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */    /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 (nres=2)*/
   /*    5 0 0 1 */    /*    5 0 0 1 */
   /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */    /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 (nres=1)*/
   /*    7 0 1 1 */    /*    7 0 1 1 */
   /*    8 1 1 1 */    /*    8 1 1 1 */
   /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */    /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
   /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */    /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
   /* V5*age V5 known which value for nres?  */    /* V5*age V5 known which value for nres?  */
   /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */    /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
   for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */    for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* cptcovt number of covariates (excluding 1 and age or age*age) in the MODEL equation.
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */                                                     * loop on position k1 in the MODEL LINE */
       k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */      /* k counting number of combination of single dummies in the equation model */
       k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */      /* k4 counting single dummies in the equation model */
       k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */      /* k4q counting single quantitatives in the equation model */
       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, fixed or timevarying, k1 is sorting according to MODEL, but k3 to resultline */
       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */         /* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
         /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
         /* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
         /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline                        */
         /*      k3 is the position in the nres result line of the k1th variable of the model equation                                  */
         /* Tvarsel[k3]: Name of the variable at the k3th position in the result line.                                                  */
         /* Tvalsel[k3]: Value of the variable at the k3th position in the result line.                                                 */
         /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
         /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline                     */
         /* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line                                        */
         /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
         k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
         /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
         k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
         k+=Tvalsel[k3]*pow(2,k4);  /* nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
         TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
         /* Tinvresult[nres][4]=1 */
         /* Tresult[nres][k4+1]=Tvalsel[k3];/\* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) *\/ */
         Tresult[nres][k3]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */
         /* Tvresult[nres][k4+1]=(int)Tvarsel[k3];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
         Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
       Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */        Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
       printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);        precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
         /* printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4); */
       k4++;;        k4++;;
     }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
       k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */        /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline                                 */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
         k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
         /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
         /* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 *\/ */
         /* Tvresult[nres][k4q+1]=(int)Tvarsel[k3q];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 *\/ */
         /* Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /\* Tvqresult[nres][1]=5 *\/ */
         Tqresult[nres][k3q]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvresult[nres][k3q]=(int)Tvarsel[k3q];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tvqresult[nres][k3q]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
       Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
       printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);        TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         precov[nres][k1]=Tvalsel[k3q];
         /* printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
       k4q++;;        k4q++;;
       }else if( Dummy[k1]==2 ){ /* For dummy with age product "V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
         /* Tvar[k1]; */ /* Age variable */ /* 17 age*V6*V2 ?*/
         /* Wrong we want the value of variable name Tvar[k1] */
         if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
           precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
         /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
         }else{
           k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
           k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
           TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
           precov[nres][k1]=Tvalsel[k3];
         }
         /* printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]); */
       }else if( Dummy[k1]==3 ){ /* For quant with age product */
         if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
           precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
         /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
         }else{
           k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
           k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
           TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
           precov[nres][k1]=Tvalsel[k3q];
         }
         /* printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
       }else if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
         precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
         /* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
       }else{
         printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
         fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
     }      }
   }    }
       
   TKresult[nres]=++k; /* Combination for the nresult and the model */    TKresult[nres]=++k; /* Number of combinations of dummies for the nresult and the model =Tvalsel[k3]*pow(2,k4) + 1*/
   return (0);    return (0);
 }  }
   
Line 10100  int decodemodel( char model[], int lasto Line 13010  int decodemodel( char model[], int lasto
         * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age          * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
         * - cptcovage number of covariates with age*products =2          * - cptcovage number of covariates with age*products =2
         * - cptcovs number of simple covariates          * - cptcovs number of simple covariates
           * ncovcolt=ncovcol+nqv+ntv+nqtv total of covariates in the data, not in the model equation
         * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10          * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
         *     which is a new column after the 9 (ncovcol) variables.           *     which is a new column after the 9 (ncovcol+nqv+ntv+nqtv) variables. 
         * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual          * - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
         * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage          * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
         *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.          *    Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
Line 10109  int decodemodel( char model[], int lasto Line 13020  int decodemodel( char model[], int lasto
         */          */
 /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
 {  {
   int i, j, k, ks, v;    int i, j, k, ks;/* , v;*/
   int  j1, k1, k2, k3, k4;    int n,m;
   char modelsav[80];    int  j1, k1, k11, k12, k2, k3, k4;
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char modelsav[300];
     char stra[300], strb[300], strc[300], strd[300],stre[300],strf[300];
   char *strpt;    char *strpt;
     int  **existcomb;
     
     existcomb=imatrix(1,NCOVMAX,1,NCOVMAX);
     for(i=1;i<=NCOVMAX;i++)
       for(j=1;j<=NCOVMAX;j++)
         existcomb[i][j]=0;
       
   /*removespace(model);*/    /*removespace(model);*/
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      j=0, j1=0, k1=0, k12=0, k2=-1, ks=0, cptcovn=0;
     if (strstr(model,"AGE") !=0){      if (strstr(model,"AGE") !=0){
       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' model=%s ",model);        printf("Error. 'v' must be in upper case 'V' model=1+age+%s ",model);
       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. 'v' must be in upper case model=1+age+%s ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=1+age+%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;          return 1;
Line 10149  int decodemodel( char model[], int lasto Line 13067  int decodemodel( char model[], int lasto
         substrchaine(modelsav, model, "age*age");          substrchaine(modelsav, model, "age*age");
     }else      }else
       nagesqr=0;        nagesqr=0;
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){ /* V2 +V3 +V4 +V6 +V7 +V6*V2 +V7*V2 +V6*V3 +V7*V3 +V6*V4 +V7*V4 +age*V2 +age*V3 +age*V4 +age*V6 +age*V7 +age*V6*V2 +V7*V2 +age*V6*V3 +age*V7*V3 +age*V6*V4 +age*V7*V4 */
       j=nbocc(modelsav,'+'); /**< j=Number of '+' */        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */        cptcovs=0; /**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age => V1 + V3 =4+1-3=2  Wrong */
       cptcovt= j+1; /* Number of total covariates in the model, not including        cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age                        * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
       /* including age products which are counted in cptcovage.        /* including age products which are counted in cptcovage.
        * but the covariates which are products must be treated          * but the covariates which are products must be treated 
        * separately: ncovn=4- 2=2 (V1+V3). */         * separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */        cptcovprod=0; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovdageprod=0; /* Number of doouble products with age age*Vn*VM or Vn*age*Vm or Vn*Vm*age */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
               cptcovprodage=0;
         /* cptcovprodage=nboccstr(modelsav,"age");*/
               
       /*   Design        /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
Line 10169  int decodemodel( char model[], int lasto Line 13089  int decodemodel( char model[], int lasto
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8         *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:         *  covar[k,i], are for fixed covariates, value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k         *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1         *       if products, new covar are created after ncovcol + nqv (quanti fixed) with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11         *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product         *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8         *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];         *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted         *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11         *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >         *  <          ncovcol=8  8 fixed covariate. Additional starts at 9 (V5*V6) and 10(V7*V8)              >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8         *     Tvard[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}         * p Tvar[1]@12={2,   1,     3,      3,   9,     10,     8,       8}
        * p Tprod[1]@2={                         6, 5}         * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}         *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8            * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
Line 10215  int decodemodel( char model[], int lasto Line 13135  int decodemodel( char model[], int lasto
         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
       }        }
       cptcovage=0;        cptcovage=0;
   
         /* First loop in order to calculate */
         /* for age*VN*Vm
          * Provides, Typevar[k], Tage[cptcovage], existcomb[n][m], FixedV[ncovcolt+k12]
          * Tprod[k1]=k  Tposprod[k]=k1;    Tvard[k1][1] =m;
         */
         /* Needs  FixedV[Tvardk[k][1]] */
         /* For others:
          * Sets   Typevar[k];
          * Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
          *        Tposprod[k]=k11;
          *        Tprod[k11]=k;
          *        Tvardk[k][1] =m;
          * Needs FixedV[Tvardk[k][1]] == 0
         */
         
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right          cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
                                          modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */                                           modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
Line 10222  int decodemodel( char model[], int lasto Line 13158  int decodemodel( char model[], int lasto
           strcpy(strb,modelsav); /* and analyzes it */            strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/          /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */          if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age OR double product with age strb=age*V6*V2 or V6*V2*age or V6*age*V2 */
           cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */            cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 OR strb=age*V6*V2 strc=V6*V2 strd=age OR c=V2*age OR c=age*V2  */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */            if(strchr(strc,'*')) { /**< Model with age and DOUBLE product: allowed since 0.99r44, strc=V6*V2 or V2*age or age*V2, strd=age or V6 or V6   */
             /* covar is not filled and then is empty */              Typevar[k]=3;  /* 3 for age and double product age*Vn*Vm varying of fixed */
             cptcovprod--;              if(strstr(strc,"age")!=0) { /* It means that strc=V2*age or age*V2 and thus that strd=Vn */
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */                cutl(stre,strf,strc,'*') ; /* strf=age or Vm, stre=Vm or age. If strc=V6*V2 then strf=V6 and stre=V2 */
             Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */                strcpy(strc,strb); /* save strb(=age*Vn*Vm) into strc */
             Typevar[k]=1;  /* 1 for age product */                /* We want strb=Vn*Vm */
             cptcovage++; /* Counts the number of covariates which include age as a product */                if(strcmp(strf,"age")==0){ /* strf is "age" so that stre=Vm =V2 . */
             Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */                  strcpy(strb,strd);
             /*printf("stre=%s ", stre);*/                  strcat(strb,"*");
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */                  strcat(strb,stre);
             cptcovprod--;                }else{  /* strf=Vm  If strf=V6 then stre=V2 */
             cutl(stre,strb,strc,'V');                  strcpy(strb,strf);
             Tvar[k]=atoi(stre);                  strcat(strb,"*");
             Typevar[k]=1;  /* 1 for age product */                  strcat(strb,stre);
             cptcovage++;                  strcpy(strd,strb); /* in order for strd to not be "age"  for next test (will be Vn*Vm */
             Tage[cptcovage]=k;                }
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/                /* printf("DEBUG FIXED k=%d, Tage[k]=%d, Tvar[Tage[k]=%d,FixedV[Tvar[Tage[k]]]=%d\n",k,Tage[k],Tvar[Tage[k]],FixedV[Tvar[Tage[k]]]); */
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */                /* FixedV[Tvar[Tage[k]]]=0; /\* HERY not sure if V7*V4*age Fixed might not exist  yet*\/ */
             cptcovn++;              }else{  /* strc=Vn*Vm (and strd=age) and should be strb=Vn*Vm but want to keep original strb double product  */
             cptcovprodnoage++;k1++;                strcpy(stre,strb); /* save full b in stre */
                 strcpy(strb,strc); /* save short c in new short b for next block strb=Vn*Vm*/
                 strcpy(strf,strc); /* save short c in new short f */
                 cutl(strc,strd,strf,'*'); /* We get strd=Vn and strc=Vm for next block (strb=Vn*Vm)*/
                 /* strcpy(strc,stre);*/ /* save full e in c for future */
               }
               cptcovdageprod++; /* double product with age  Which product is it? */
               /* strcpy(strb,strc);  /\* strb was age*V6*V2 or V6*V2*age or V6*age*V2 IS now V6*V2 or V2*age or age*V2 *\/ */
               /* cutl(strc,strd,strb,'*'); /\* strd=  V6    or   V2     or    age and  strc=  V2 or    age or    V2 *\/ */
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but              n=atoi(stre);
                                                 because this model-covariate is a construction we invent a new column  
                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1  
                                                 If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2  
                                                 thus after V4 we invent V5 and V6 because age*V3 will be computed in 4  
                                                 Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */  
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */  
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              m=atoi(strc);
             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */              cptcovage++; /* Counts the number of covariates which include age as a product */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tage[cptcovage]=k; /* For age*V3*V2 gives the position in model of covariates associated with age Tage[1]=6 HERY too*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              if(existcomb[n][m] == 0){
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */                /*  r /home/brouard/Documents/Recherches/REVES/Zachary/Zach-2022/Feinuo_Sun/Feinuo-threeway/femV12V15_3wayintNBe.imach */
             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */                printf("Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */                fprintf(ficlog,"Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */                fflush(ficlog);
             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */                k1++;  /* The combination Vn*Vm will be in the model so we create it at k1 */
             for (i=1; i<=lastobs;i++){                k12++;
               /* Computes the new covariate which is a product of                existcomb[n][m]=k1;
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                existcomb[m][n]=k1;
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];                Tvar[k]=ncovcol+nqv+ntv+nqtv+k1;
                 Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2+ age*V6*V3 Gives the k position of the k1 double product Vn*Vm or age*Vn*Vm*/
                 Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 Gives the k1 double product  Vn*Vm or age*Vn*Vm at the k position */
                 Tvard[k1][1] =m; /* m 1 for V1*/
                 Tvardk[k][1] =m; /* m 1 for V1*/
                 Tvard[k1][2] =n; /* n 4 for V4*/
                 Tvardk[k][2] =n; /* n 4 for V4*/
   /*            Tvar[Tage[cptcovage]]=k1;*/ /* Tvar[6=age*V3*V2]=9 (new fixed covariate) */ /* We don't know about Fixed yet HERE */
                 if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                   for (i=1; i<=lastobs;i++){/* For fixed product */
                     /* Computes the new covariate which is a product of
                        covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                     covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                   }
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                   FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=0;
                 }else{ /*End of FixedV */
                   cptcovprodvage++; /* Counting the number of varying covariate with age */
                   FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=1;
                 }
               }else{  /* k1 Vn*Vm already exists */
                 k11=existcomb[n][m];
                 Tposprod[k]=k11; /* OK */
                 Tvar[k]=Tvar[Tprod[k11]]; /* HERY */
                 Tvardk[k][1]=m;
                 Tvardk[k][2]=n;
                 if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                   /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                   /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
                   Tvar[Tage[cptcovage]]=k1;
                   FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=0;
                 }else{ /* Already exists but time varying (and age) */
                   /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
                   /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
                   /* Tvar[Tage[cptcovage]]=k1; */
                   cptcovprodvage++;
                   FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=1;
                 }
             }              }
           } /* End age is not in the model */              /* Tage[cptcovage]=k;  /\*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
         } /* End if model includes a product */              /* Tvar[k]=k11; /\* HERY *\/ */
         else { /* not a product */            } else {/* simple product strb=age*Vn so that c=Vn and d=age, or strb=Vn*age so that c=age and d=Vn, or b=Vn*Vm so that c=Vm and d=Vn */
               cptcovprod++;
               if (strcmp(strc,"age")==0) { /**< Model includes age: strb= Vn*age c=age d=Vn*/
                 /* covar is not filled and then is empty */
                 cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
                 Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
                 Typevar[k]=1;  /* 1 for age product */
                 cptcovage++; /* Counts the number of covariates which include age as a product */
                 Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
                 if( FixedV[Tvar[k]] == 0){
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                 }else{
                   cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
                 }
                 /*printf("stre=%s ", stre);*/
               } else if (strcmp(strd,"age")==0) { /* strb= age*Vn c=Vn */
                 cutl(stre,strb,strc,'V');
                 Tvar[k]=atoi(stre);
                 Typevar[k]=1;  /* 1 for age product */
                 cptcovage++;
                 Tage[cptcovage]=k;
                 if( FixedV[Tvar[k]] == 0){
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                 }else{
                   cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
                 }
               }else{ /*  for product Vn*Vm */
                 Typevar[k]=2;  /* 2 for product Vn*Vm */
                 cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                 n=atoi(stre);
                 cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
                 m=atoi(strc);
                 k1++;
                 cptcovprodnoage++;
                 if(existcomb[n][m] != 0 || existcomb[m][n] != 0){
                   printf("Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
                   fprintf(ficlog,"Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
                   fflush(ficlog);
                   k11=existcomb[n][m];
                   Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
                   Tposprod[k]=k11;
                   Tprod[k11]=k;
                   Tvardk[k][1] =m; /* m 1 for V1*/
                   /* Tvard[k11][1] =m; /\* n 4 for V4*\/ */
                   Tvardk[k][2] =n; /* n 4 for V4*/                
                   /* Tvard[k11][2] =n; /\* n 4 for V4*\/ */
                 }else{ /* combination Vn*Vm doesn't exist we create it (no age)*/
                   existcomb[n][m]=k1;
                   existcomb[m][n]=k1;
                   Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* ncovcolt+k1; For model-covariate k tells which data-covariate to use but
                                                       because this model-covariate is a construction we invent a new column
                                                       which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                                       If already ncovcol=4 and model= V2 + V1 + V1*V4 + age*V3 + V3*V2
                                                       thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
                                                       Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=3 etc */
                   /* Please remark that the new variables are model dependent */
                   /* If we have 4 variable but the model uses only 3, like in
                    * model= V1 + age*V1 + V2 + V3 + age*V2 + age*V3 + V1*V2 + V1*V3
                    *  k=     1     2      3   4     5        6        7       8
                    * Tvar[k]=1     1       2   3     2        3       (5       6) (and not 4 5 because of V4 missing)
                    * Tage[kk]    [1]= 2           [2]=5      [3]=6                  kk=1 to cptcovage=3
                    * Tvar[Tage[kk]][1]=2          [2]=2      [3]=3
                    */
                   /* We need to feed some variables like TvarVV, but later on next loop because of ncovv (k2) is not correct */
                   Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 +V6*V2*age  */
                   Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
                   Tvard[k1][1] =m; /* m 1 for V1*/
                   Tvardk[k][1] =m; /* m 1 for V1*/
                   Tvard[k1][2] =n; /* n 4 for V4*/
                   Tvardk[k][2] =n; /* n 4 for V4*/
                   k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
                   /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
                   /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
                   /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
                   /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
                   if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                     for (i=1; i<=lastobs;i++){/* For fixed product */
                       /* Computes the new covariate which is a product of
                          covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                       covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                     }
                     /* TvarVV[k2]=n; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                     /* TvarVV[k2+1]=m; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                   }else{ /* not FixedV */
                     /* TvarVV[k2]=n; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                     /* TvarVV[k2+1]=m; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                   }                 
                 }  /* End of creation of Vn*Vm if not created by age*Vn*Vm earlier  */
               } /*  End of product Vn*Vm */
             } /* End of age*double product or simple product */
           }else { /* not a product */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
Line 10282  int decodemodel( char model[], int lasto Line 13360  int decodemodel( char model[], int lasto
                                 /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                   scanf("%d",i);*/                                    scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
   
         
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* end if strlen(model == 0) */
       cptcovs=cptcovt - cptcovdageprod - cptcovprod;/**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age + age*v4*V3=> V1 + V3 =4+1-3=2  */
   
   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
       
Line 10310  int decodemodel( char model[], int lasto Line 13391  int decodemodel( char model[], int lasto
   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
         /* Computing effective variables, ie used by the model, that is from the cptcovt variables */          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
   printf("Model=1+age+%s\n\    printf("Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   fprintf(ficlog,"Model=1+age+%s\n\    fprintf(ficlog,"Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age  \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}    for(k=-1;k<=NCOVMAX; k++){ Fixed[k]=0; Dummy[k]=0;}
   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */    for(k=1;k<=NCOVMAX; k++){TvarFind[k]=0; TvarVind[k]=0;}
   
   
     /* Second loop for calculating  Fixed[k], Dummy[k]*/
   
     
     for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0,ncovva=0,ncovvta=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt loop on k from model */
     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 0;        Dummy[k]= 0;
Line 10328  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13415  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
       TvarsD[nsd]=Tvar[k];        TvarsD[nsd]=Tvar[k];
       TvarsDind[nsd]=k;        TvarsDind[nsd]=k;
         TnsdVar[Tvar[k]]=nsd;
       TvarF[ncovf]=Tvar[k];        TvarF[ncovf]=Tvar[k];
       TvarFind[ncovf]=k;        TvarFind[ncovf]=k;
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */      /* }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /\* Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol *\/ */
       Fixed[k]= 0;  
       Dummy[k]= 0;  
       ncoveff++;  
       ncovf++;  
       modell[k].maintype= FTYPE;  
       TvarF[ncovf]=Tvar[k];  
       TvarFind[ncovf]=k;  
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  
       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  
     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */      }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 1;        Dummy[k]= 1;
Line 10349  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13428  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
       modell[k].subtype= FQ;        modell[k].subtype= FQ;
       nsq++;        nsq++;
       TvarsQ[nsq]=Tvar[k];        TvarsQ[nsq]=Tvar[k]; /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary see below */
       TvarsQind[nsq]=k;        TvarsQind[nsq]=k;    /* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
       ncovf++;        ncovf++;
       TvarF[ncovf]=Tvar[k];        TvarF[ncovf]=Tvar[k];
       TvarFind[ncovf]=k;        TvarFind[ncovf]=k;
       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */        TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */        TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */      }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 */
         /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         ncovvt++;
         TvarVV[ncovvt]=Tvar[k];  /*  TvarVV[1]=V3 (first time varying in the model equation  */
         TvarVVind[ncovvt]=k;    /*  TvarVVind[1]=2 (second position in the model equation  */
   
       Fixed[k]= 1;        Fixed[k]= 1;
       Dummy[k]= 0;        Dummy[k]= 0;
       ntveff++; /* Only simple time varying dummy variable */        ntveff++; /* Only simple time varying dummy variable */
Line 10365  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13451  Dummy[k] 0=dummy (0 1), 1 quantitative (
       nsd++;        nsd++;
       TvarsD[nsd]=Tvar[k];        TvarsD[nsd]=Tvar[k];
       TvarsDind[nsd]=k;        TvarsDind[nsd]=k;
         TnsdVar[Tvar[k]]=nsd; /* To be verified */
       ncovv++; /* Only simple time varying variables */        ncovv++; /* Only simple time varying variables */
       TvarV[ncovv]=Tvar[k];        TvarV[ncovv]=Tvar[k];
       TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */        TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
Line 10373  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13460  Dummy[k] 0=dummy (0 1), 1 quantitative (
       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);        printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);        printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/      }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 */
         /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         ncovvt++;
         TvarVV[ncovvt]=Tvar[k];  /*  TvarVV[1]=V3 (first time varying in the model equation  */
         TvarVVind[ncovvt]=k;  /*  TvarVV[1]=V3 (first time varying in the model equation  */
         
       Fixed[k]= 1;        Fixed[k]= 1;
       Dummy[k]= 1;        Dummy[k]= 1;
       nqtveff++;        nqtveff++;
Line 10380  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13474  Dummy[k] 0=dummy (0 1), 1 quantitative (
       modell[k].subtype= VQ;        modell[k].subtype= VQ;
       ncovv++; /* Only simple time varying variables */        ncovv++; /* Only simple time varying variables */
       nsq++;        nsq++;
       TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */        TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */ /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary here) */
       TvarsQind[nsq]=k;        TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate *//* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
       TvarV[ncovv]=Tvar[k];        TvarV[ncovv]=Tvar[k];
       TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */        TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */        TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */        TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */        TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */        /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);        /* printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%Ad,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); */
       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);        /* printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); */
     }else if (Typevar[k] == 1) {  /* product with age */      }else if (Typevar[k] == 1) {  /* product with age */
       ncova++;        ncova++;
       TvarA[ncova]=Tvar[k];        TvarA[ncova]=Tvar[k];
       TvarAind[ncova]=k;        TvarAind[ncova]=k;
         /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
         /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
         Fixed[k]= 2;          Fixed[k]= 2;
         Dummy[k]= 2;          Dummy[k]= 2;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APFD;          modell[k].subtype= APFD;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*  (2)age*V3 */
           TvarAVVAind[ncovta]=k;
         /* ncoveff++; */          /* ncoveff++; */
       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
         Fixed[k]= 2;          Fixed[k]= 2;
         Dummy[k]= 3;          Dummy[k]= 3;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */          modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*   */
           TvarAVVAind[ncovta]=k;
         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv ){        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
         Fixed[k]= 3;          Fixed[k]= 3;
         Dummy[k]= 2;          Dummy[k]= 2;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APVD;                /*      Product age * varying dummy */          modell[k].subtype= APVD;                /*      Product age * varying dummy */
           ncovva++;
           TvarVVA[ncovva]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*   */
           TvarAVVAind[ncovta]=k;
         /* ntveff++; /\* Only simple time varying dummy variable *\/ */          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
         Fixed[k]= 3;          Fixed[k]= 3;
         Dummy[k]= 3;          Dummy[k]= 3;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
           ncovva++;
           TvarVVA[ncovva]=Tvar[k]; /*   */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
           TvarAVVAind[ncovta]=k;
         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
       }        }
     }else if (Typevar[k] == 2) {  /* product without age */      }else if( Tposprod[k]>0  &&  Typevar[k]==2){  /* Detects if fixed product no age Vm*Vn */
       k1=Tposprod[k];        printf("MEMORY ERRORR k=%d  Tposprod[k]=%d, Typevar[k]=%d\n ",k, Tposprod[k], Typevar[k]);
       if(Tvard[k1][1] <=ncovcol){        if(FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* Needs a fixed product Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol V3*V2 */
         if(Tvard[k1][2] <=ncovcol){        printf("MEMORY ERRORR k=%d Tvardk[k][1]=%d, Tvardk[k][2]=%d, FixedV[Tvardk[k][1]]=%d,FixedV[Tvardk[k][2]]=%d\n ",k,Tvardk[k][1],Tvardk[k][2],FixedV[Tvardk[k][1]],FixedV[Tvardk[k][2]]);
           Fixed[k]= 1;          Fixed[k]= 0;
           Dummy[k]= 0;          Dummy[k]= 0;
           ncoveff++;
           ncovf++;
           /* ncovv++; */
           /* TvarVV[ncovv]=Tvardk[k][1]; */
           /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
           /* ncovv++; */
           /* TvarVV[ncovv]=Tvardk[k][2]; */
           /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
           modell[k].maintype= FTYPE;
           TvarF[ncovf]=Tvar[k];
           /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
           TvarFind[ncovf]=k;
           TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
           TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         }else{/* product varying Vn * Vm without age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
           /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
           /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
           /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
           k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
           ncovvt++;
           TvarVV[ncovvt]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
           TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
           ncovvt++;
           TvarVV[ncovvt]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
           TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
           
           /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
           /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
           
           if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
             if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDD;            /*      Product fixed dummy * fixed dummy */
               ncovf++; /* Fixed variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
               Fixed[k]= 0;  /* Fixed product */
               Dummy[k]= 1;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDQ;            /*      Product fixed dummy * fixed quantitative */
               ncovf++; /* Varying variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product fixed dummy * varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
               TvarVind[ncovv]=k;/* TvarVind[1]=5 */ 
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product fixed dummy * varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti  */
             if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
               Fixed[k]= 0;  /*  Fixed product */
               Dummy[k]= 1;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDQ;            /*      Product fixed quantitative * fixed dummy */
               ncovf++; /* Fixed variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product fixed quantitative * varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product fixed quantitative * varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
             if(Tvard[k1][2] <=ncovcol){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product time varying dummy * fixed dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying dummy * fixed quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product time varying dummy * time varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying dummy * time varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
             if(Tvard[k1][2] <=ncovcol){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying quantitative * fixed dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product time varying quantitative * fixed quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying quantitative * time varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product time varying quantitative * time varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else{
             printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
             fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           } /*end k1*/
         }
       }else if(Typevar[k] == 3){  /* product Vn * Vm with age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
         /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
         ncova++;
         TvarA[ncova]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
         TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
         ncova++;
         TvarA[ncova]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
         TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
   
         /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
         /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
         if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
         }else{
           ncovva++;  /* HERY  reached */
           TvarVVA[ncovva]=Tvard[k1][1]; /*  age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4  */
           TvarVVAind[ncovva]=k;
           ncovva++;
           TvarVVA[ncovva]=Tvard[k1][2]; /*   */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
         }
         if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
           if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
             Fixed[k]= 2;
             Dummy[k]= 2;
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
           ncovf++; /* Fixed variables without age */            /* TvarF[ncova]=Tvar[k];   /\* Problem to solve *\/ */
           TvarF[ncovf]=Tvar[k];            /* TvarFind[ncova]=k; */
           TvarFind[ncovf]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
         }else if(Tvard[k1][2] <=ncovcol+nqv){            Fixed[k]= 2;  /* Fixed product */
           Fixed[k]= 0;  /* or 2 ?*/            Dummy[k]= 3;
           Dummy[k]= 1;  
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
           ncovf++; /* Varying variables without age */            /* TvarF[ncova]=Tvar[k]; */
           TvarF[ncovf]=Tvar[k];            /* TvarFind[ncova]=k; */
           TvarFind[ncovf]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            Fixed[k]= 3;
           Fixed[k]= 1;            Dummy[k]= 2;
           Dummy[k]= 0;  
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */            modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
           ncovv++; /* Varying variables without age */            TvarV[ncova]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
           TvarV[ncovv]=Tvar[k];            TvarVind[ncova]=k;/* TvarVind[1]=5 */ 
           TvarVind[ncovv]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            Fixed[k]= 3;
           Fixed[k]= 1;            Dummy[k]= 3;
           Dummy[k]= 1;  
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */            modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncovv++; /\* Varying variables without age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncovv]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncovv]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv){        }else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti  */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
           Fixed[k]= 0;  /* or 2 ?*/            Fixed[k]= 2;  /*  Fixed product */
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
           ncovf++; /* Fixed variables without age */            /* ncova++; /\* Fixed variables with age *\/ */
           TvarF[ncovf]=Tvar[k];            /* TvarF[ncovf]=Tvar[k]; */
           TvarFind[ncovf]=k;            /* TvarFind[ncovf]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */            modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
           ncovv++; /* Varying variables without age */            ncova++; /* Varying variables without age */
           TvarV[ncovv]=Tvar[k];            TvarV[ncova]=Tvar[k];
           TvarVind[ncovv]=k;            TvarVind[ncova]=k;
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables without age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 0;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */            modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */            modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else{        }else{
         printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
       } /*end k1*/        } /*end k1*/
     }else{      } else{
       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
     }      }
     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);      /* printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); */
     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);      /* printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); */
     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);      fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
   }    }
     ncovvta=ncovva;
   /* Searching for doublons in the model */    /* Searching for doublons in the model */
   for(k1=1; k1<= cptcovt;k1++){    for(k1=1; k1<= cptcovt;k1++){
     for(k2=1; k2 <k1;k2++){      for(k2=1; k2 <k1;k2++){
Line 10571  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13887  Dummy[k] 0=dummy (0 1), 1 quantitative (
       if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){        if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
         if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */          if((Typevar[k1] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
           if(Tvar[k1]==Tvar[k2]){            if(Tvar[k1]==Tvar[k2]){
             printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);              printf("Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);              fprintf(ficlog,"Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
             return(1);              return(1);
           }            }
         }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
           k3=Tposprod[k1];            k3=Tposprod[k1];
           k4=Tposprod[k2];            k4=Tposprod[k2];
           if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){            if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
             printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);              printf("Error duplication in the model=1+age+%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
             fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);              fprintf(ficlog,"Error duplication in the model=1+age+%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
             return(1);              return(1);
           }            }
         }          }
Line 10591  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 13907  Dummy[k] 0=dummy (0 1), 1 quantitative (
   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);    printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);    fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
   
     free_imatrix(existcomb,1,NCOVMAX,1,NCOVMAX);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
   printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
Line 10907  void syscompilerinfo(int logged) Line 14225  void syscompilerinfo(int logged)
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
     /* Computes the prevalence limit for each combination of the dummy covariates */
   int i, j, k, i1, k4=0, nres=0 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
Line 10935  int prevalence_limit(double *p, double * Line 14254  int prevalence_limit(double *p, double *
   i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */    i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */    /* for(k=1; k<=i1;k++){ /\* For each combination k of dummy covariates in the model *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(i1 != 1 && TKresult[nres]!= k)        k=TKresult[nres];
         continue;        if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         /* if(i1 != 1 && TKresult[nres]!= k) /\* We found the combination k corresponding to the resultline value of dummies *\/ */
         /*        continue; */
   
       /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
       /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       /* k=k+1; */        /* k=k+1; */
       /* to clean */        /* to clean */
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));        /*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*/
       fprintf(ficrespl,"#******");        fprintf(ficrespl,"#******");
       printf("#******");        printf("#******");
       fprintf(ficlog,"#******");        fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */        for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/          /* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy*\/ */
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }          fprintf(ficrespl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        }
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
       }        /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
         /* } */
       fprintf(ficrespl,"******\n");        fprintf(ficrespl,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 10970  int prevalence_limit(double *p, double * Line 14294  int prevalence_limit(double *p, double *
       }        }
   
       fprintf(ficrespl,"#Age ");        fprintf(ficrespl,"#Age ");
       for(j=1;j<=cptcoveff;j++) {        /* for(j=1;j<=cptcoveff;j++) { */
         fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        /*        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         /* } */
         for(j=1;j<=cptcovs;j++) { /* New the quanti variable is added */
           fprintf(ficrespl,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);        for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
       fprintf(ficrespl,"Total Years_to_converge\n");        fprintf(ficrespl,"Total Years_to_converge\n");
           
       for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
         /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
         prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);          /**< Computes the prevalence limit in each live state at age x and for covariate combination (k and) nres */
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); /* Nicely done */
         fprintf(ficrespl,"%.0f ",age );          fprintf(ficrespl,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          /* for(j=1;j<=cptcoveff;j++) */
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /*   fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           for(j=1;j<=cptcovs;j++)
             fprintf(ficrespl,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         tot=0.;          tot=0.;
         for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
           tot +=  prlim[i][i];            tot +=  prlim[i][i];
Line 10990  int prevalence_limit(double *p, double * Line 14320  int prevalence_limit(double *p, double *
         fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);          fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
       } /* Age */        } /* Age */
       /* was end of cptcod */        /* was end of cptcod */
     } /* cptcov */      } /* nres */
   } /* nres */    /* } /\* for each combination *\/ */
   return 0;    return 0;
 }  }
   
Line 11033  int back_prevalence_limit(double *p, dou Line 14363  int back_prevalence_limit(double *p, dou
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
      if(i1 != 1 && TKresult[nres]!= k)        k=TKresult[nres];
         continue;        if(TKresult[nres]==0) k=1; /* To be checked for noresult */
       //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));       /* if(i1 != 1 && TKresult[nres]!= k) */
        /*         continue; */
        /* /\*printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));*\/ */
       fprintf(ficresplb,"#******");        fprintf(ficresplb,"#******");
       printf("#******");        printf("#******");
       fprintf(ficlog,"#******");        fprintf(ficlog,"#******");
       for(j=1;j<=cptcoveff ;j++) {/* all covariates */        for(j=1;j<=cptcovs ;j++) {/**< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) */
         fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        /* for(j=1;j<=cptcoveff ;j++) {/\* all covariates *\/ */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /*        fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /*        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        /*        fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        /* } */
         /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* } */
       fprintf(ficresplb,"******\n");        fprintf(ficresplb,"******\n");
       printf("******\n");        printf("******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
Line 11061  int back_prevalence_limit(double *p, dou Line 14398  int back_prevalence_limit(double *p, dou
       }        }
           
       fprintf(ficresplb,"#Age ");        fprintf(ficresplb,"#Age ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++) {
         fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        }
       for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
       fprintf(ficresplb,"Total Years_to_converge\n");        fprintf(ficresplb,"Total Years_to_converge\n");
Line 11085  int back_prevalence_limit(double *p, dou Line 14422  int back_prevalence_limit(double *p, dou
           /* exit(1); */            /* exit(1); */
         }          }
         fprintf(ficresplb,"%.0f ",age );          fprintf(ficresplb,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcovs;j++)
           fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficresplb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         tot=0.;          tot=0.;
         for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
           tot +=  bprlim[i][i];            tot +=  bprlim[i][i];
Line 11096  int back_prevalence_limit(double *p, dou Line 14433  int back_prevalence_limit(double *p, dou
       } /* Age */        } /* Age */
       /* was end of cptcod */        /* was end of cptcod */
       /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */        /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
     } /* end of any combination */      /* } /\* end of any combination *\/ */
   } /* end of nres */      } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
   /* fclose(ficrespijb); */    /* fclose(ficrespijb); */
Line 11106  int back_prevalence_limit(double *p, dou Line 14443  int back_prevalence_limit(double *p, dou
     
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /* to be optimized with precov */
   int stepsize;    int stepsize;
   int agelim;    int agelim;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k, k4, nres=0;    int h, i, i1, j, k, nres=0;
   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
   
     strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);    strcpy(filerespij,"PIJ_");  strcat(filerespij,fileresu);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {    if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij); return 1;      printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;      fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
     }    }
     printf("Computing pij: result on file '%s' \n", filerespij);    printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
       
     stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
     
     agelim=AGESUP;    agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */    hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
                     
     /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);    pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");    fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,cptcoveff);    i1= pow(2,cptcoveff);
                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                 /*      k=k+1;  */    /*    k=k+1;  */
     for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){      k=TKresult[nres];
       if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         continue;      /* for(k=1; k<=i1;k++){ */
       fprintf(ficrespij,"\n#****** ");      /* if(i1 != 1 && TKresult[nres]!= k) */
       for(j=1;j<=cptcoveff;j++)       /*  continue; */
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      fprintf(ficrespij,"\n#****** ");
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      for(j=1;j<=cptcovs;j++){
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
       fprintf(ficrespij,"******\n");        /*        printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
               /*        fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      }
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       fprintf(ficrespij,"******\n");
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      
               for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                 nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
         oldm=oldms;savm=savms;        /*          nhstepm=nhstepm*YEARM; aff par mois*/
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);          
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespij," %1d-%1d",i,j);
         fprintf(ficrespij,"\n");
         for (h=0; h<=nhstepm; h++){
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespij," %1d-%1d",i,j);              fprintf(ficrespij," %.5f", p3mat[i][j][h]);
         fprintf(ficrespij,"\n");  
         for (h=0; h<=nhstepm; h++){  
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/  
           fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
           fprintf(ficrespij,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespij,"\n");          fprintf(ficrespij,"\n");
       }        }
       /*}*/        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespij,"\n");
     }      }
     return 0;    }
     /*}*/
     return 0;
 }  }
     
  int hBijx(double *p, int bage, int fage, double ***prevacurrent){   int hBijx(double *p, int bage, int fage, double ***prevacurrent){
     /*------------- h Bij x at various ages ------------*/      /*------------- h Bij x at various ages ------------*/
       /* To be optimized with precov */
   int stepsize;    int stepsize;
   /* int agelim; */    /* int agelim; */
         int ageminl;          int ageminl;
Line 11218  int hPijx(double *p, int bage, int fage) Line 14558  int hPijx(double *p, int bage, int fage)
   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for(nres=1; nres <= nresult; nres++){ /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      k=TKresult[nres];
       if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
         continue;      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
       fprintf(ficrespijb,"\n#****** ");      /*    if(i1 != 1 && TKresult[nres]!= k) */
       for(j=1;j<=cptcoveff;j++)      /*  continue; */
         fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      fprintf(ficrespijb,"\n#****** ");
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */      for(j=1;j<=cptcovs;j++){
         fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        fprintf(ficrespijb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       }        /* for(j=1;j<=cptcoveff;j++) */
       fprintf(ficrespijb,"******\n");        /*        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       if(invalidvarcomb[k]){  /* Is it necessary here? */        /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);         /*        fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         continue;      }
       }      fprintf(ficrespijb,"******\n");
       if(invalidvarcomb[k]){  /* Is it necessary here? */
         fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
         continue;
       }
       
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
               
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        /*          nhstepm=nhstepm*YEARM; aff par mois*/
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        
         /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
         nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm+0.1)-1; /* Typically 20 years = 20*12/6=40 or 55*12/24=27.5-1.1=>27 */        /* and memory limitations if stepm is small */
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/        
                 /* oldm=oldms;savm=savms; */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                 hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */        /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         /* and memory limitations if stepm is small */        fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)
         /* oldm=oldms;savm=savms; */          for(j=1; j<=nlstate+ndeath;j++)
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */            fprintf(ficrespijb," %1d-%1d",i,j);
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */        fprintf(ficrespijb,"\n");
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */        for (h=0; h<=nhstepm; h++){
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");          /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);              fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
         fprintf(ficrespijb,"\n");  
         for (h=0; h<=nhstepm; h++){  
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/  
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );  
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */  
           fprintf(ficrespijb,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       } /* end age deb */        }
     } /* end combination */        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       } /* end age deb */
       /* } /\* end combination *\/ */
   } /* end nres */    } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
Line 11308  int main(int argc, char *argv[]) Line 14652  int main(int argc, char *argv[])
   double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;    double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
   double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */    double ageminout=-AGEOVERFLOW,agemaxout=AGEOVERFLOW; /* Smaller Age range redefined after movingaverage */
   
     double stdpercent; /* for computing the std error of percent e.i: e.i/e.. */
   double fret;    double fret;
   double dum=0.; /* Dummy variable */    double dum=0.; /* Dummy variable */
   double ***p3mat;    /* double*** p3mat;*/
   /* double ***mobaverage; */    /* double ***mobaverage; */
   double wald;    double wald;
   
   char line[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char  modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
   char resultline[MAXLINE];    char resultline[MAXLINE], resultlineori[MAXLINE];
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/    /* int firstobs=1, lastobs=10; /\* nobs = lastobs-firstobs declared globally ;*\/ */
   int c,  h , cpt, c2;    int c, h; /* c2; */
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
   int count=0;    int count=0;
Line 11358  int main(int argc, char *argv[]) Line 14703  int main(int argc, char *argv[])
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    //double **varpl; /* Variances of prevalence limits by age */
   
   double *epj, vepp;    double *epj, vepp;
   
Line 11416  int main(int argc, char *argv[]) Line 14761  int main(int argc, char *argv[])
   getcwd(pathcd, size);    getcwd(pathcd, size);
 #endif  #endif
   syscompilerinfo(0);    syscompilerinfo(0);
   printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);    printf("\nIMaCh prax version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     if(!fgets(pathr,FILENAMELENGTH,stdin)){      if(!fgets(pathr,FILENAMELENGTH,stdin)){
Line 11647  int main(int argc, char *argv[]) Line 14992  int main(int argc, char *argv[])
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=%[^.\n]", model)) !=EOF){ /* Every character after model but dot and  return */
       if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
         model[0]='\0';
         goto end;
       }else{
         trimbtab(linetmp,line); /* Trims multiple blanks in line */
         strcpy(line, linetmp);
       }
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ /* Every character after 1+age but dot and  return */
     if (num_filled != 1){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
Line 11661  int main(int argc, char *argv[]) Line 15017  int main(int argc, char *argv[])
         strcpy(model,modeltemp);           strcpy(model,modeltemp); 
       }        }
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=1+age+%s\n",model, modeltemp, model);fflush(stdout); */
     printf("model=1+age+%s\n",model);fflush(stdout);      printf("model=1+age+%s\n",model);fflush(stdout);
     fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);      fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
     fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);      fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
Line 11689  int main(int argc, char *argv[]) Line 15045  int main(int argc, char *argv[])
     numlinepar++;      numlinepar++;
     if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */      if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
       z[0]=line[1];        z[0]=line[1];
       }else if(line[1]=='d'){ /* For debugging individual values of covariates in ficresilk */
         debugILK=1;printf("DebugILK\n");
     }      }
     /* printf("****line [1] = %c \n",line[1]); */      /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);      fputs(line, stdout);
Line 11702  int main(int argc, char *argv[]) Line 15060  int main(int argc, char *argv[])
   covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */    covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
   if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
   if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
   if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/    /* if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /\**< Time varying covariate (dummy and quantitative)*\/ */
     if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);  /**< Might be better */
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
   /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5    /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
      v1+v2*age+v2*v3 makes cptcovn = 3       v1+v2*age+v2*v3 makes cptcovn = 3
Line 11945  Please run with mle=-1 to get a correct Line 15304  Please run with mle=-1 to get a correct
   mint=matrix(1,maxwav,firstobs,lastobs);    mint=matrix(1,maxwav,firstobs,lastobs);
   anint=matrix(1,maxwav,firstobs,lastobs);    anint=matrix(1,maxwav,firstobs,lastobs);
   s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */    s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
   printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));    /* printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel)); */
   tab=ivector(1,NCOVMAX);    tab=ivector(1,NCOVMAX);
   ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
   ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */    ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
Line 11964  Please run with mle=-1 to get a correct Line 15323  Please run with mle=-1 to get a correct
       
   Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
   TvarsDind=ivector(1,NCOVMAX); /*  */    TvarsDind=ivector(1,NCOVMAX); /*  */
     TnsdVar=ivector(1,NCOVMAX); /*  */
       /* for(i=1; i<=NCOVMAX;i++) TnsdVar[i]=3; */
   TvarsD=ivector(1,NCOVMAX); /*  */    TvarsD=ivector(1,NCOVMAX); /*  */
   TvarsQind=ivector(1,NCOVMAX); /*  */    TvarsQind=ivector(1,NCOVMAX); /*  */
   TvarsQ=ivector(1,NCOVMAX); /*  */    TvarsQ=ivector(1,NCOVMAX); /*  */
Line 11981  Please run with mle=-1 to get a correct Line 15342  Please run with mle=-1 to get a correct
   TvarVDind=ivector(1,NCOVMAX); /*  */    TvarVDind=ivector(1,NCOVMAX); /*  */
   TvarVQ=ivector(1,NCOVMAX); /*  */    TvarVQ=ivector(1,NCOVMAX); /*  */
   TvarVQind=ivector(1,NCOVMAX); /*  */    TvarVQind=ivector(1,NCOVMAX); /*  */
     TvarVV=ivector(1,NCOVMAX); /*  */
     TvarVVind=ivector(1,NCOVMAX); /*  */
     TvarVVA=ivector(1,NCOVMAX); /*  */
     TvarVVAind=ivector(1,NCOVMAX); /*  */
     TvarAVVA=ivector(1,NCOVMAX); /*  */
     TvarAVVAind=ivector(1,NCOVMAX); /*  */
   
   Tvalsel=vector(1,NCOVMAX); /*  */    Tvalsel=vector(1,NCOVMAX); /*  */
   Tvarsel=ivector(1,NCOVMAX); /*  */    Tvarsel=ivector(1,NCOVMAX); /*  */
   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */    Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */    Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */    Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
     DummyV=ivector(-1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(-1,NCOVMAX); /* 1 to 3 */
   
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 12006  Please run with mle=-1 to get a correct Line 15376  Please run with mle=-1 to get a correct
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
     Tvardk=imatrix(0,NCOVMAX,1,2);
   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age    Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
Line 12025  Please run with mle=-1 to get a correct Line 15396  Please run with mle=-1 to get a correct
                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,                                  * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                 * 3, 1, 0, 0, 0, 0, 0, 0},                                  * 3, 1, 0, 0, 0, 0, 0, 0},
                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/                                  * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   
   /* Probably useless zeroes */
     for(i=1;i<NCOVMAX;i++){
       DummyV[i]=0;
       FixedV[i]=0;
     }
   
     for(i=1; i <=ncovcol;i++){
       DummyV[i]=0;
       FixedV[i]=0;
     }
     for(i=ncovcol+1; i <=ncovcol+nqv;i++){
       DummyV[i]=1;
       FixedV[i]=0;
     }
     for(i=ncovcol+nqv+1; i <=ncovcol+nqv+ntv;i++){
       DummyV[i]=0;
       FixedV[i]=1;
     }
     for(i=ncovcol+nqv+ntv+1; i <=ncovcol+nqv+ntv+nqtv;i++){
       DummyV[i]=1;
       FixedV[i]=1;
     }
     for(i=1; i <=ncovcol+nqv+ntv+nqtv;i++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
     }
   
   
   
 /* Main decodemodel */  /* Main decodemodel */
   
   
Line 12085  Please run with mle=-1 to get a correct Line 15486  Please run with mle=-1 to get a correct
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   cptcoveff=0;    cptcoveff=0;
   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; as well as calculate cptcoveff or number of total effective dummy covariates*/
   }    }
       
   ncovcombmax=pow(2,cptcoveff);    ncovcombmax=pow(2,cptcoveff);
   invalidvarcomb=ivector(1, ncovcombmax);     invalidvarcomb=ivector(0, ncovcombmax); 
   for(i=1;i<ncovcombmax;i++)    for(i=0;i<ncovcombmax;i++)
     invalidvarcomb[i]=0;      invalidvarcomb[i]=0;
       
   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
Line 12115  Please run with mle=-1 to get a correct Line 15516  Please run with mle=-1 to get a correct
            * For k=4 covariates, h goes from 1 to m=2**k             * For k=4 covariates, h goes from 1 to m=2**k
            * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;             * codtabm(h,k)=  (1 & (h-1) >> (k-1)) + 1;
            * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1             * #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
            *     h\k   1     2     3     4             *     h\k   1     2     3     4   *  h-1\k-1  4  3  2  1          
            *______________________________               *______________________________   *______________________
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1   *     0     0  0  0  0 
            *     2     2     1     1     1             *     2     2     1     1     1   *     1     0  0  0  1 
            *     3 i=2 1     2     1     1             *     3 i=2 1     2     1     1   *     2     0  0  1  0 
            *     4     2     2     1     1             *     4     2     2     1     1   *     3     0  0  1  1 
            *     5 i=3 1 i=2 1     2     1             *     5 i=3 1 i=2 1     2     1   *     4     0  1  0  0 
            *     6     2     1     2     1             *     6     2     1     2     1   *     5     0  1  0  1 
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1   *     6     0  1  1  0 
            *     8     2     2     2     1             *     8     2     2     2     1   *     7     0  1  1  1 
            *     9 i=5 1 i=3 1 i=2 1     2             *     9 i=5 1 i=3 1 i=2 1     2   *     8     1  0  0  0 
            *    10     2     1     1     2             *    10     2     1     1     2   *     9     1  0  0  1 
            *    11 i=6 1     2     1     2             *    11 i=6 1     2     1     2   *    10     1  0  1  0 
            *    12     2     2     1     2             *    12     2     2     1     2   *    11     1  0  1  1 
            *    13 i=7 1 i=4 1     2     2                 *    13 i=7 1 i=4 1     2     2   *    12     1  1  0  0  
            *    14     2     1     2     2             *    14     2     1     2     2   *    13     1  1  0  1 
            *    15 i=8 1     2     2     2             *    15 i=8 1     2     2     2   *    14     1  1  1  0 
            *    16     2     2     2     2             *    16     2     2     2     2   *    15     1  1  1  1          
            */             */                                     
   /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */    /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
      /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4       /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
      * and the value of each covariate?       * and the value of each covariate?
Line 12224  Title=%s <br>Datafile=%s Firstpass=%d La Line 15625  Title=%s <br>Datafile=%s Firstpass=%d La
           optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);            optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   
   fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br>  \    fprintf(fichtm,"<html><head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n\
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <title>IMaCh %s</title></head>\n\
    <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n\
   <font size=\"3\">Sponsored by Copyright (C)  2002-2015 <a href=http://www.ined.fr>INED</a>\
   -EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 \
   (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - \
   <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \n", optionfilehtm);
     
     fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\
 <font size=\"2\">IMaCh-%s <br> %s</font> \  <font size=\"2\">IMaCh-%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n\
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\  This file: <a href=\"%s\">%s</a></br>Title=%s <br>Datafile=<a href=\"%s\">%s</a> Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
 \n\  \n\
 <hr  size=\"2\" color=\"#EC5E5E\">\  <hr  size=\"2\" color=\"#EC5E5E\">\
  <ul><li><h4>Parameter files</h4>\n\   <ul><li><h4>Parameter files</h4>\n\
Line 12237  Title=%s <br>Datafile=%s Firstpass=%d La Line 15645  Title=%s <br>Datafile=%s Firstpass=%d La
  - Log file of the run: <a href=\"%s\">%s</a><br>\n\   - Log file of the run: <a href=\"%s\">%s</a><br>\n\
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\   - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
  - Date and time at start: %s</ul>\n",\   - Date and time at start: %s</ul>\n",\
           optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\            version,fullversion,optionfilehtm,optionfilehtm,title,datafile,datafile,firstpass,lastpass,stepm, weightopt, model, \
           optionfilefiname,optionfilext,optionfilefiname,optionfilext,\            optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
           fileres,fileres,\            fileres,fileres,\
           filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);            filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
Line 12255  Title=%s <br>Datafile=%s Firstpass=%d La Line 15663  Title=%s <br>Datafile=%s Firstpass=%d La
   /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age 
                  and for any valid combination of covariates                   and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \    freqsummary(fileres, p, pstart, (double)agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
Line 12346  Interval (in months) between two waves: Line 15754  Interval (in months) between two waves:
 #ifdef GSL  #ifdef GSL
     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");      printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
 #else  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell-mort\n");  fprintf(ficlog,"Powell-mort\n");
 #endif  #endif
     strcpy(filerespow,"POW-MORT_");       strcpy(filerespow,"POW-MORT_"); 
     strcat(filerespow,fileresu);      strcat(filerespow,fileresu);
Line 12441  Interval (in months) between two waves: Line 15849  Interval (in months) between two waves:
     gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */      gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1)  */
 #endif  #endif
 #ifdef POWELL  #ifdef POWELL
      powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);  #ifdef LINMINORIGINAL
 #endif    #else /* LINMINORIGINAL */
     
     flatdir=ivector(1,npar); 
     for (j=1;j<=npar;j++) flatdir[j]=0; 
   #endif /*LINMINORIGINAL */
       /* powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); */
     /* double h0=0.25; */
     macheps=pow(16.0,-13.0);
     printf("Praxis Gegenfurtner mle=%d\n",mle);
     fprintf(ficlog, "Praxis  Gegenfurtner mle=%d\n", mle);fflush(ficlog);
      /* ffmin = praxis(ftol,macheps, h0, npar, prin, p, gompertz); */
     /* For the Gompertz we use only two parameters */
     int _npar=2;
      ffmin = praxis(ftol,macheps, h0, _npar, 4, p, gompertz);
     printf("End Praxis\n");
     fclose(ficrespow);      fclose(ficrespow);
   #ifdef LINMINORIGINAL
   #else
         free_ivector(flatdir,1,npar); 
   #endif  /* LINMINORIGINAL*/
           
     hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);       hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz); 
   
     for(i=1; i <=NDIM; i++)      for(i=1; i <=NDIM; i++)
       for(j=i+1;j<=NDIM;j++)        for(j=i+1;j<=NDIM;j++)
                                 matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
           
     printf("\nCovariance matrix\n ");      printf("\nCovariance matrix\n ");
     fprintf(ficlog,"\nCovariance matrix\n ");      fprintf(ficlog,"\nCovariance matrix\n ");
Line 12551  Please run with mle=-1 to get a correct Line 15977  Please run with mle=-1 to get a correct
     globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */      globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
             /* exit(0); */
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
Line 12577  Please run with mle=-1 to get a correct Line 16004  Please run with mle=-1 to get a correct
       fprintf(ficlog,"  + age*age  ");        fprintf(ficlog,"  + age*age  ");
       fprintf(fichtm, "<th>+ age*age</th>");        fprintf(fichtm, "<th>+ age*age</th>");
     }      }
     for(j=1;j <=ncovmodel-2;j++){      for(j=1;j <=ncovmodel-2-nagesqr;j++){
       if(Typevar[j]==0) {        if(Typevar[j]==0) {
         printf("  +      V%d  ",Tvar[j]);          printf("  +      V%d  ",Tvar[j]);
         fprintf(ficres,"  +      V%d  ",Tvar[j]);          fprintf(ficres,"  +      V%d  ",Tvar[j]);
Line 12593  Please run with mle=-1 to get a correct Line 16020  Please run with mle=-1 to get a correct
         fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }else if(Typevar[j]==3) { /* TO VERIFY */
           printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficres,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
       }        }
     }      }
     printf("\n");      printf("\n");
Line 12643  Please run with mle=-1 to get a correct Line 16075  Please run with mle=-1 to get a correct
         fprintf(ficlog,"  + age*age  ");          fprintf(ficlog,"  + age*age  ");
         fprintf(fichtm, "<th>+ age*age</th>");          fprintf(fichtm, "<th>+ age*age</th>");
       }        }
       for(j=1;j <=ncovmodel-2;j++){        for(j=1;j <=ncovmodel-2-nagesqr;j++){
         if(Typevar[j]==0) {          if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);            printf("  +      V%d  ",Tvar[j]);
           fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);            fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
Line 12652  Please run with mle=-1 to get a correct Line 16084  Please run with mle=-1 to get a correct
           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);            fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
         }else if(Typevar[j]==2) {          }else if(Typevar[j]==2) {
           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);            fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           }else if(Typevar[j]==3) { /* TO VERIFY */
             fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }          }
       }        }
       fprintf(fichtm, "</tr>\n");        fprintf(fichtm, "</tr>\n");
Line 12709  Please run with mle=-1 to get a correct Line 16143  Please run with mle=-1 to get a correct
     }      }
           
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle >= 1) /* To big for the screen */      if(mle >= 1) /* Too big for the screen */
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     /* # 121 Var(a12)\n\ */      /* # 121 Var(a12)\n\ */
Line 12895  Please run with mle=-1 to get a correct Line 16329  Please run with mle=-1 to get a correct
     }      }
             
     /* Results */      /* Results */
       /* Value of covariate in each resultine will be computed (if product) and sorted according to model rank */
       /* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */  
       precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
     endishere=0;      endishere=0;
     nresult=0;      nresult=0;
     parameterline=0;      parameterline=0;
Line 12968  Please run with mle=-1 to get a correct Line 16405  Please run with mle=-1 to get a correct
         }          }
         break;          break;
       case 13:        case 13:
         num_filled=sscanf(line,"result:%[^\n]\n",resultline);          num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
         nresult++; /* Sum of resultlines */          nresult++; /* Sum of resultlines */
         printf("Result %d: result:%s\n",nresult, resultline);          /* printf("Result %d: result:%s\n",nresult, resultlineori); */
           /* removefirstspace(&resultlineori); */
           
           if(strstr(resultlineori,"v") !=0){
             printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
             fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
             return 1;
           }
           trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
           /* printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori); */
         if(nresult > MAXRESULTLINESPONE-1){          if(nresult > MAXRESULTLINESPONE-1){
           printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);            printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
           fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);            fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
           goto end;            goto end;
         }          }
           
         if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */          if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
           fprintf(ficparo,"result: %s\n",resultline);            fprintf(ficparo,"result: %s\n",resultline);
           fprintf(ficres,"result: %s\n",resultline);            fprintf(ficres,"result: %s\n",resultline);
Line 13052  Please run with mle=-1 to get a correct Line 16499  Please run with mle=-1 to get a correct
         date2dmy(datebackf,&jbackf, &mbackf, &anbackf);          date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
       }        }
               
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);/* HERE valgrind Tvard*/
     }      }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
Line 13079  Please run with mle=-1 to get a correct Line 16526  Please run with mle=-1 to get a correct
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
       /* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
     prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);      prevalence_limit(p, prlim,  ageminpar, agemaxpar, ftolpl, &ncvyear);
     fclose(ficrespl);      fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
       /** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
       /* calls hpxij with combination k */
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
           
     /* ncovcombmax=  pow(2,cptcoveff); */      /* ncovcombmax=  pow(2,cptcoveff); */
     /*-------------- Variance of one-step probabilities---*/      /*-------------- Variance of one-step probabilities for a combination ij or for nres ?---*/
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
           
Line 13199  Please run with mle=-1 to get a correct Line 16649  Please run with mle=-1 to get a correct
   
     pstamp(ficreseij);      pstamp(ficreseij);
                                   
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */      /* i1=pow(2,cptcoveff); /\* Number of combination of dummy covariates *\/ */
     if (cptcovn < 1){i1=1;}      /* if (cptcovn < 1){i1=1;} */
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
       if(i1 != 1 && TKresult[nres]!= k)        /* if(i1 != 1 && TKresult[nres]!= k) */
         continue;        /*        continue; */
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        /* for(j=1;j<=cptcoveff;j++) { */
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           fprintf(ficreseij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
           printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
           /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        }
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          printf(" V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */
         fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
       printf("******\n");        printf("******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
         /* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
               
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 13231  Please run with mle=-1 to get a correct Line 16685  Please run with mle=-1 to get a correct
   
                                   
     /*---------- State-specific expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                       /* Should be moved in a function */         
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
     strcat(filerest,fileresu);      strcat(filerest,fileresu);
     if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
Line 13270  Please run with mle=-1 to get a correct Line 16724  Please run with mle=-1 to get a correct
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
     if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++) /* For each resultline, find the combination and output results according to the values of dummies and then quanti.  */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying. For each nres and each value at position k
       if(i1 != 1 && TKresult[nres]!= k)                            * we know Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline
                             * Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline 
                             * and Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
         /* */
         if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */
         continue;          continue;
       printf("\n# model %s \n#****** Result for:", model);        printf("\n# model=1+age+%s \n#****** Result for:", model);  /* HERE model is empty */
       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);        fprintf(ficrest,"\n# model=1+age+%s \n#****** Result for:", model);
       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);        fprintf(ficlog,"\n# model=1+age+%s \n#****** Result for:", model);
       for(j=1;j<=cptcoveff;j++){         /* It might not be a good idea to mix dummies and quantitative */
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        /* for(j=1;j<=cptcoveff;j++){ /\* j=resultpos. Could be a loop on cptcovs: number of single dummy covariate in the result line as well as in the model *\/ */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        for(j=1;j<=cptcovs;j++){ /* j=resultpos. Could be a loop on cptcovs: number of single covariate (dummy or quantitative) in the result line as well as in the model */
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* Output by variables in the resultline *\/ */
       }          /* Tvaraff[j] is the name of the dummy variable in position j in the equation model:
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */           * Tvaraff[1]@9={4, 3, 0, 0, 0, 0, 0, 0, 0}, in model=V5+V4+V3+V4*V3+V5*age
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);           * (V5 is quanti) V4 and V3 are dummies
         fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);           * TnsdVar[4] is the position 1 and TnsdVar[3]=2 in codtabm(k,l)(V4  V3)=V4  V3
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);           *                                                              l=1 l=2
       }            *                                                           k=1  1   1   0   0
            *                                                           k=2  2   1   1   0
            *                                                           k=3 [1] [2]  0   1
            *                                                           k=4  2   2   1   1
            * If nres=1 result: V3=1 V4=0 then k=3 and outputs
            * If nres=2 result: V4=1 V3=0 then k=2 and outputs
            * nres=1 =>k=3 j=1 V4= nbcode[4][codtabm(3,1)=1)=0; j=2  V3= nbcode[3][codtabm(3,2)=2]=1
            * nres=2 =>k=2 j=1 V4= nbcode[4][codtabm(2,1)=2)=1; j=2  V3= nbcode[3][codtabm(2,2)=1]=0
            */
           /* Tvresult[nres][j] Name of the variable at position j in this resultline */
           /* Tresult[nres][j] Value of this variable at position j could be a float if quantitative  */
   /* We give up with the combinations!! */
           /* if(debugILK) */
           /*   printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]);  /\* end if dummy  or quanti *\/ */
   
           if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline  */
             /* printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /\* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  *\/ */ /* TinvDoQresult[nres][Name of the variable] */
             printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordered by the covariate values in the resultline  */
             fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
               printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
             }else{
               printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
             }
             /* fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
             /* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           }else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
             /* For each selected (single) quantitative value */
             printf(" V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             fprintf(ficrest," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
             if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
               printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
             }else{
               printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
             }
           }else{
             printf("Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
             fprintf(ficlog,"Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff);  /* end if dummy  or quanti */
             exit(1);
           }
         } /* End loop for each variable in the resultline */
         /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ */
         /*        printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /\* Wrong j is not in the equation model *\/ */
         /*        fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /*        fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
         /* }       */
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
       printf("******\n");        printf("******\n");
               
       fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
       fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
         /* It could have been: for(j=1;j<=cptcoveff;j++) {printf("V=%d=%lg",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);} */
         /* But it won't be sorted and depends on how the resultline is ordered */
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          /* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }          /* fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        }
         fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation  */
         fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
           fprintf(ficrescveij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
       }         } 
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
Line 13307  Please run with mle=-1 to get a correct Line 16815  Please run with mle=-1 to get a correct
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       /* pstamp(ficresvij); */        /* pstamp(ficresvij); */
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
           /* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]); */
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);          /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
           fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
       }         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
Line 13332  Please run with mle=-1 to get a correct Line 16842  Please run with mle=-1 to get a correct
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         oldm=oldms;savm=savms; /* ZZ Segmentation fault */          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
         cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
         printf("varevsij vpopbased=%d \n",vpopbased);          printf("varevsij vpopbased=%d popbased=%d \n",vpopbased,popbased);
         fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);          fprintf(ficlog, "varevsij vpopbased=%d popbased=%d \n",vpopbased,popbased);
           /* Call to varevsij to get cov(e.i, e.j)= vareij[i][j][(int)age]=sum_h sum_k trgrad(h_p.i) V(theta) grad(k_p.k) Equation 20 */
           /* Depending of popbased which changes the prevalences, either cross-sectional or period */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each state\n\
   #  (these are weighted average of eij where weights are ");
         if(vpopbased==1)          if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally)\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
         else          else
           fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific forward period (stable) prevalences in each state) \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# with proportions of time spent in each state with standard error (on the right of the table.\n ");
           fprintf(ficrest,"# Age popbased mobilav e.. (std) "); /* Adding covariate values? */
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           for (i=1;i<=nlstate;i++) fprintf(ficrest," %% e.%d/e.. (std) ",i);
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
         printf("Computing age specific forward period (stable) prevalences in each health state \n");          printf("Computing age specific forward period (stable) prevalences in each health state \n");
Line 13367  Please run with mle=-1 to get a correct Line 16882  Please run with mle=-1 to get a correct
               /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */                /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
             }              }
             epj[nlstate+1] +=epj[j];              epj[nlstate+1] +=epj[j]; /* epp=sum_j epj = sum_j sum_i w_i e_ij */
           }            }
           /* printf(" age %4.0f \n",age); */            /* printf(" age %4.0f \n",age); */
                       
           for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1, vepp=0.;i <=nlstate;i++)  /* Variance of total life expectancy e.. */
             for(j=1;j <=nlstate;j++)              for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];                vepp += vareij[i][j][(int)age]; /* sum_i sum_j cov(e.i, e.j) = var(e..) */
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             /* vareij[i][j] is the covariance  cov(e.i, e.j) and vareij[j][j] is the variance  of e.j  */
           for(j=1;j <=nlstate;j++){            for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }            }
             /* And proportion of time spent in state j */
             /* $$ E[r(X,Y)-E(r(X,Y))]^2=[\frac{1}{\mu_y} -\frac{\mu_x}{{\mu_y}^2}]' Var(X,Y)[\frac{1}{\mu_y} -\frac{\mu_x}{{\mu_y}^2}]$$ */
             /* \frac{\mu_x^2}{\mu_y^2} ( \frac{\sigma^2_x}{\mu_x^2}-2\frac{\sigma_{xy}}{\mu_x\mu_y} +\frac{\sigma^2_y}{\mu_y^2}) */
             /* \frac{e_{.i}^2}{e_{..}^2} ( \frac{\Var e_{.i}}{e_{.i}^2}-2\frac{\Var e_{.i} + \sum_{j\ne i} \Cov e_{.j},e_{.i}}{e_{.i}e_{..}} +\frac{\Var e_{..}}{e_{..}^2})*/
             /*\mu_x = epj[j], \sigma^2_x = vareij[j][j][(int)age] and \mu_y=epj[nlstate+1], \sigma^2_y=vepp \sigmaxy= */
             /* vareij[j][j][(int)age]/epj[nlstate+1]^2 + vepp/epj[nlstate+1]^4 */
             for(j=1;j <=nlstate;j++){
               /* fprintf(ficrest," %7.3f (%7.3f)", epj[j]/epj[nlstate+1], sqrt( vareij[j][j][(int)age]/epj[j]/epj[j] + vepp/epj[j]/epj[j]/epj[j]/epj[j] )); */
               /* fprintf(ficrest," %7.3f (%7.3f)", epj[j]/epj[nlstate+1], sqrt( vareij[j][j][(int)age]/epj[j]/epj[j] + vepp/epj[j]/epj[j]/epj[j]/epj[j] )); */
               
               for(i=1,stdpercent=0.;i<=nlstate;i++){ /* Computing cov(e..,e.j)=cov(sum_i e.i,e.j)=sum_i cov(e.i, e.j) */
                 stdpercent += vareij[i][j][(int)age];
               }
               stdpercent= epj[j]*epj[j]/epj[nlstate+1]/epj[nlstate+1]* (vareij[j][j][(int)age]/epj[j]/epj[j]-2.*stdpercent/epj[j]/epj[nlstate+1]+ vepp/epj[nlstate+1]/epj[nlstate+1]);
               /* stdpercent= epj[j]*epj[j]/epj[nlstate+1]/epj[nlstate+1]*(vareij[j][j][(int)age]/epj[j]/epj[j] + vepp/epj[nlstate+1]/epj[nlstate+1]); */ /* Without covariance */
               /* fprintf(ficrest," %7.3f (%7.3f)", epj[j]/epj[nlstate+1], sqrt( vareij[j][j][(int)age]/epj[nlstate+1]/epj[nlstate+1] + epj[j]*epj[j]*vepp/epj[nlstate+1]/epj[nlstate+1]/epj[nlstate+1]/epj[nlstate+1] )); */
               fprintf(ficrest," %7.3f (%7.3f)", epj[j]/epj[nlstate+1], sqrt(stdpercent));
             }
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
         }          }
       } /* End vpopbased */        } /* End vpopbased */
Line 13387  Please run with mle=-1 to get a correct Line 16921  Please run with mle=-1 to get a correct
       printf("done selection\n");fflush(stdout);        printf("done selection\n");fflush(stdout);
       fprintf(ficlog,"done selection\n");fflush(ficlog);        fprintf(ficlog,"done selection\n");fflush(ficlog);
               
     } /* End k selection */      } /* End k selection or end covariate selection for nres */
   
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /* variance-covariance of forward period prevalence*/      /* variance-covariance of forward period prevalence */
     varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);      varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
           
     free_vector(weight,firstobs,lastobs);      free_vector(weight,firstobs,lastobs);
       free_imatrix(Tvardk,0,NCOVMAX,1,2);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,firstobs,lastobs);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,firstobs,lastobs);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
Line 13418  Please run with mle=-1 to get a correct Line 16953  Please run with mle=-1 to get a correct
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
   /* endfree:*/    /* endfree:*/
     if(mle!=-3) free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
   if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);    /* if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); */
     if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);
   if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
   if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);    if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
   free_matrix(covar,0,NCOVMAX,firstobs,lastobs);    free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
Line 13437  Please run with mle=-1 to get a correct Line 16974  Please run with mle=-1 to get a correct
   free_ivector(ncodemaxwundef,1,NCOVMAX);    free_ivector(ncodemaxwundef,1,NCOVMAX);
   free_ivector(Dummy,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
   free_ivector(Fixed,-1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
   free_ivector(DummyV,1,NCOVMAX);    free_ivector(DummyV,-1,NCOVMAX);
   free_ivector(FixedV,1,NCOVMAX);    free_ivector(FixedV,-1,NCOVMAX);
   free_ivector(Typevar,-1,NCOVMAX);    free_ivector(Typevar,-1,NCOVMAX);
   free_ivector(Tvar,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
   free_ivector(TvarsQ,1,NCOVMAX);    free_ivector(TvarsQ,1,NCOVMAX);
   free_ivector(TvarsQind,1,NCOVMAX);    free_ivector(TvarsQind,1,NCOVMAX);
   free_ivector(TvarsD,1,NCOVMAX);    free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TnsdVar,1,NCOVMAX);
   free_ivector(TvarsDind,1,NCOVMAX);    free_ivector(TvarsDind,1,NCOVMAX);
   free_ivector(TvarFD,1,NCOVMAX);    free_ivector(TvarFD,1,NCOVMAX);
   free_ivector(TvarFDind,1,NCOVMAX);    free_ivector(TvarFDind,1,NCOVMAX);
Line 13459  Please run with mle=-1 to get a correct Line 16997  Please run with mle=-1 to get a correct
   free_ivector(TvarVDind,1,NCOVMAX);    free_ivector(TvarVDind,1,NCOVMAX);
   free_ivector(TvarVQ,1,NCOVMAX);    free_ivector(TvarVQ,1,NCOVMAX);
   free_ivector(TvarVQind,1,NCOVMAX);    free_ivector(TvarVQind,1,NCOVMAX);
     free_ivector(TvarAVVA,1,NCOVMAX);
     free_ivector(TvarAVVAind,1,NCOVMAX);
     free_ivector(TvarVVA,1,NCOVMAX);
     free_ivector(TvarVVAind,1,NCOVMAX);
     free_ivector(TvarVV,1,NCOVMAX);
     free_ivector(TvarVVind,1,NCOVMAX);
     
   free_ivector(Tvarsel,1,NCOVMAX);    free_ivector(Tvarsel,1,NCOVMAX);
   free_vector(Tvalsel,1,NCOVMAX);    free_vector(Tvalsel,1,NCOVMAX);
   free_ivector(Tposprod,1,NCOVMAX);    free_ivector(Tposprod,1,NCOVMAX);
   free_ivector(Tprod,1,NCOVMAX);    free_ivector(Tprod,1,NCOVMAX);
   free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(Tvaraff,1,NCOVMAX);
   free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(invalidvarcomb,0,ncovcombmax);
   free_ivector(Tage,1,NCOVMAX);    free_ivector(Tage,1,NCOVMAX);
   free_ivector(Tmodelind,1,NCOVMAX);    free_ivector(Tmodelind,1,NCOVMAX);
   free_ivector(TmodelInvind,1,NCOVMAX);    free_ivector(TmodelInvind,1,NCOVMAX);
   free_ivector(TmodelInvQind,1,NCOVMAX);    free_ivector(TmodelInvQind,1,NCOVMAX);
     
     /* free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /\* Could be elsewhere ?*\/ */
   
   free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
   /* free_imatrix(codtab,1,100,1,10); */    /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);

Removed from v.1.328  
changed lines
  Added in v.1.362


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