Diff for /imach/src/imach.c between versions 1.331 and 1.343

version 1.331, 2022/08/07 05:40:09 version 1.343, 2022/09/14 14:22:16
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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    Revision 1.331  2022/08/07 05:40:09  brouard
   *** empty log message ***    *** empty log message ***
   
Line 1202  typedef struct { Line 1301  typedef struct {
 #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 2048 /* Was 256 and 1024. 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 256  #define FILENAMELENGTH 256
   
Line 1242  typedef struct { Line 1343  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[]="September 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 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 (1)=V2+V1+ V3*age+V2*V4 */  /* Number of covariates model (1)=V2+V1+ V3*age+V2*V4 */
 /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */  /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
 int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age */  int cptcovn=0; /**< cptcovn decodemodel: number of covariates k of the models excluding age*products =6 and age*age but including products */
 int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */  int cptcovt=0; /**< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
 int cptcovs=0; /**< cptcovs number of simple covariates in the model V2+V1 =2 (dummy or quantit or time varying) */  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 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 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 (2**cptcoveff combinations of dummies)(computed in tricode as cptcov) */  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 ncovvt=0; /* Total number of effective (wave) varying covariates (dummy or quantitative or products [without age]) in the model */
 int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of 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 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) */
Line 1267  int nqfveff=0; /**< nqfveff Number of Qu Line 1370  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 */
Line 1406  int *ncodemaxwundef;  /* ncodemax[j]= Nu Line 1511  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 1421  double  **covar; /**< covar[j,i], value Line 1527  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 1433  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1539  int **nbcode, *Tvar; /**< model=V2 => Tv
        *  cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 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 1446  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1552  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 */
 /*    k        1  2   3   4     5    6    7     8    9 */  /*    kmodel  1  2   3   4     5    6    7     8    9 */
 /*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 *//*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 */
Line 1457  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1563  int **nbcode, *Tvar; /**< model=V2 => Tv
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */
 /*TnsdVar[Tvar]   1   2                              3 */   /*TnsdVar[Tvar]   1   2                              3 */ 
   /*Tvaraff[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  /*TvarsDind[nsd]  2   3                              9 */ /* position K of single dummy cova */
 /*    nsq      1                     2                 */ /* Counting single quantit tv */  /*    nsq      1                     2                 */ /* Counting single quantit tv */
 /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */  /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */
 /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */  /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */
Line 1483  int *TvarsQind; Line 1590  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 resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */  int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
 int Tresult[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 Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */  int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
 int TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable or quanti value (output) */  int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line  */
 int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */  double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
 double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */  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 1512  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3 Line 1620  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 */
         /*#  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 */
         /* TvarVV={3,1,3}, for V3 and then the product V1*V3 is decomposed into V1 and V3 */             
         /* TvarVVind={2,5,5}, for V3 and then the product V1*V3 is decomposed into V1 and V3 */          
 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 */
Line 2450  void powell(double p[], double **xi, int Line 2564  void powell(double p[], double **xi, int
   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; 
Line 2458  void powell(double p[], double **xi, int Line 2573  void powell(double p[], double **xi, int
     /* (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); */
       printf("\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,*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); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*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++) {
Line 2762  void powell(double p[], double **xi, int Line 2879  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 2787  void powell(double p[], double **xi, int Line 2904  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 2818  void powell(double p[], double **xi, int Line 2935  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,TvarsD[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){ /* 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,Tvar[Tage[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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])];      /*    *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,Tvard[k][1])] * 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,Tvard[k][2])] * 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 2951  void powell(double p[], double **xi, int Line 3107  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;
   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 2991  void powell(double p[], double **xi, int Line 3147  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){ /* A product with age */
       cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[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,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{        }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,Tvard[k][2])] * 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 3161  double **pmij(double **ps, double *cov, Line 3327  double **pmij(double **ps, double *cov,
   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 3410  double **matprod2(double **out, double * Line 3576  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 3448  double ***hpxij(double ***po, int nhstep Line 3615  double ***hpxij(double ***po, int nhstep
       /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */        /* Model(2)  V1 + V2 + V3 + V8 + V7*V8 + V5*V6 + V8*age + V3*age + age*age */
       /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */        /* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age */
       for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */         for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */ 
         if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy  */          if(Typevar[k1]==1){ /* A product with age */
 /*         V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
 /*       for (k=1; k<=nsd;k++) { /\* For single dummy covariates only *\/ */          }else{
 /* /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates *\/ */            cov[2+nagesqr+k1]=precov[nres][k1];
         /* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 */          }
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        }/* End of loop on model equation */
 /*    k        1  2   3   4     5    6    7     8    9 */          /* Old code */ 
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy  *\/ */
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  /* /\*     V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) *\/ */
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  /* /\*       for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only *\\/ *\/ */
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  /* /\* /\\* 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,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] */  /*      /\* codtabm(ij,k)  (1 & (ij-1) >> (k-1))+1 *\/ */
           cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];  /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
           /* 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]])); */  /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
           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);  /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
         }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative variables  */  /* /\*    nsd         1   2                              3 *\/ /\* Counting single dummies covar fixed or tv *\/ */
           /* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline */  /* /\*TvarsD[nsd]     4   3                              1 *\/ /\* ID of single dummy cova fixed or timevary*\/ */
           cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];   /* /\*TvarsDind[k]    2   3                              9 *\/ /\* position K of single dummy cova *\/ */
           /* for (k=1; k<=nsq;k++) { /\* For single varying covariates only *\/ */  /*        /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] *\/ */
           /*    /\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\/ */  /*        cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
           /*    cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; */  /*        /\* 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 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 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); */
         }else if( Dummy[k1]==2 ){ /* For dummy with age product */  /*        printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
           /* Tvar[k1] Variable in the age product age*V1 is 1 */  /*      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables  *\/ */
           /* [Tinvresult[nres][V1] is its value in the resultline nres */  /*        /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline *\/ */
           cov[2+nagesqr+k1]=Tinvresult[nres][Tvar[k1]];  /*        cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]];  */
           printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d Tinvresult[nres][%d]=%d,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],Tinvresult[nres][Tvar[k1]],nagesqr,k1,cov[2+nagesqr+k1]);  /*        /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only *\\/ *\/ */
           /* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];     */  /*        /\*   /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates *\\/ *\/ */
           /* for (k=1; k<=cptcovage;k++){ /\* For product with age V1+V1*age +V4 +age*V3 *\/ */  /*        /\*   cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; *\/ */
           /* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/  /*        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]); */
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  /*      }else if( Dummy[k1]==2 ){ /\* For dummy with age product *\/ */
 /*    k        1  2   3   4     5    6    7     8    9 */  /*        /\* Tvar[k1] Variable in the age product age*V1 is 1 *\/ */
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*        /\* [Tinvresult[nres][V1] is its value in the resultline nres *\/ */
 /*cptcovage=2                   1               2      */  /*        cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]*cov[2]; */
 /*Tage[k]=                      5               8      */         /*        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]); */
         }else if( Dummy[k1]==3 ){ /* For quant with age product */  /*        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]];         
           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]]);  /*        /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]];    *\/ */
           /* if(Dummy[Tage[k]]== 2){ /\* dummy with age *\/ */  /*        /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1*age +V4 +age*V3 *\\/ *\/ */
           /* /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age *\\/ *\/ */  /*        /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*\/ */
           /*   /\* 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 *\/ */  /* /\*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
 /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */  /* /\*    k        1  2   3   4     5    6    7     8    9 *\/ */
 /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */  /* /\*Tvar[k]=     5  4   3   6     5    2    7     1    1 *\/ */
 /* /\*cptcovprod=1            1               2            *\/ */  /* /\*cptcovage=2                   1               2      *\/ */
 /* /\*Tprod[]=                4               7            *\/ */  /* /\*Tage[k]=                      5               8      *\/   */
 /* /\*Tvard[][1]             4               1             *\/ */  /*      }else if( Dummy[k1]==3 ){ /\* For quant with age product *\/ */
 /* /\*Tvard[][2]               3               2           *\/ */  /*        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])]); */  /*        /\* 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+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]];      /*        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,Tvard[k1][1], k1,Tvard[k1][2], 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]]); */
           /* if(Dummy[Tvardk[k1][1]]==0){ */  /*        printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
           /*   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)]; */  /*        /\* if(Dummy[Tvardk[k1][1]]==0){ *\/ */
               /* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]];    */  /*        /\*   if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies *\\/ *\/ */
               /* 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]])]; */  /*            /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; *\/ */
             /* }else{ /\* Product of dummy by quantitative *\/ */  /*            /\* 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]])] * Tqresult[nres][k]; */  /*            /\* 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]])]; *\/ */
               /* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][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]; *\/ */
           /* }else{ /\* Product of quantitative by...*\/ */  /*            /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; *\/ */
           /*   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]]; *\/ */  /*        /\* }else{ /\\* Product of quantitative by...*\\/ *\/ */
           /*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; */  /*        /\*   if(Dummy[Tvard[k][2]]==0){  /\\* quant by dummy *\\/ *\/ */
           /*   }else{ /\* Product of two quant *\/ */  /*        /\*     /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; *\\/ *\/ */
           /*     /\* 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]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
           /*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[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]]; *\\/ *\/ */
           /* }/\*end of products quantitative *\/ */  /*        /\*     cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]  ; *\/ */
         }/*end of products */  /*        /\*   } *\/ */
       } /* End of loop on model equation */  /*        /\* }/\\*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 3576  double ***hpxij(double ***po, int nhstep Line 3757  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 3588  double ***hbxij(double ***po, int nhstep Line 3770  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, k, k1;
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
   double **newm, ***newmm;    double **newm, ***newmm;
   double agexact;    double agexact;
Line 3614  double ***hbxij(double ***po, int nhstep Line 3796  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,TvarsD[k])];/* Bug valgrind */          if(Typevar[k1]==1){ /* 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,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{          }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,Tvard[k][2])] * 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 3714  double ***hbxij(double ***po, int nhstep Line 3908  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 3746  double func( double *x) Line 3944  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 dummu 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 3762  double func( double *x) Line 3960  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(TvarFind[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[Tvar[TvarFind[itv]]][i];
             }
             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(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 *\/ */
           /*   cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
           /*   k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
           /*   cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
           /*   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]); */
           /* } */
           /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
           /*   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]); *\/ */
           /*   cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
           /* } */
           /* 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;
Line 3786  double func( double *x) Line 4017  double func( double *x)
             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) */ 
           }            }
           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 3866  double func( double *x) Line 4097  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 3899  double func( double *x) Line 4130  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 3946  double func( double *x) Line 4177  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 4002  double func( double *x) Line 4236  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 4021  double func( double *x) Line 4255  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 4050  double func( double *x) Line 4287  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, 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 */
Line 4073  double funcone( double *x) Line 4313  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++){ /* 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 4090  double funcone( double *x) Line 4338  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 4099  double funcone( double *x) Line 4358  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
         */
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age) including individual from products */
           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(TvarFind[itv]==0){ /* Not a fixed covariate */
             cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */ 
           }else{ /* fixed covariate */
             cotvarv=covar[Tvar[TvarFind[itv]]][i];
           }
           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 */
         }
         /* 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 4136  double funcone( double *x) Line 4436  double funcone( double *x)
           if(!FixedV[Tvar[Tage[kk]]])            if(!FixedV[Tvar[Tage[kk]]])
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
           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) */ 
         }          }
         /* 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); */
Line 4147  double funcone( double *x) Line 4447  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 4179  double funcone( double *x) Line 4491  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) *\/  */
             }
           }
           /* 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 4211  void likelione(FILE *ficres,double p[], Line 4558  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 4221  void likelione(FILE *ficres,double p[], Line 4569  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 4239  void likelione(FILE *ficres,double p[], Line 4617  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): <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)  */
               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 4790  void  freqsummary(char fileres[], double Line 5220  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 4858  Title=%s <br>Datafile=%s Firstpass=%d La Line 5288  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 *\/ */    /* 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 4879  Title=%s <br>Datafile=%s Firstpass=%d La Line 5309  Title=%s <br>Datafile=%s Firstpass=%d La
   
   /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */    /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
   /* Loop on nj=1 or 2 if dummy covariates j!=0    /* Loop on nj=1 or 2 if dummy covariates j!=0
    *   Loop on j1(1 to 2**cptcovn) covariate combination     *   Loop on j1(1 to 2**cptcoveff) covariate combination
    *     freq[s1][s2][iage] =0.     *     freq[s1][s2][iage] =0.
    *     Loop on iind     *     Loop on iind
    *       ++freq[s1][s2][iage] weighted     *       ++freq[s1][s2][iage] weighted
Line 4904  Title=%s <br>Datafile=%s Firstpass=%d La Line 5334  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=cptcovs; /* 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("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);        /*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
Line 4940  Title=%s <br>Datafile=%s Firstpass=%d La Line 5370  Title=%s <br>Datafile=%s Firstpass=%d La
         bool=1;          bool=1;
         if(j !=0){          if(j !=0){
           if(anyvaryingduminmodel==0){ /* If All fixed covariates */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                 /* if(Tvaraff[z1] ==-20){ */                  /* if(Tvaraff[z1] ==-20){ */
                 /*       /\* 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  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/                  /* }else  */ /* TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[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 4965  Title=%s <br>Datafile=%s Firstpass=%d La Line 5398  Title=%s <br>Datafile=%s Firstpass=%d La
             m=mw[mi][iind];              m=mw[mi][iind];
             if(j!=0){              if(j!=0){
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                 for (z1=1; z1<=cptcovn; 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,Tvaraff[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,Tvaraff[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 5001  Title=%s <br>Datafile=%s Firstpass=%d La Line 5440  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 5034  Title=%s <br>Datafile=%s Firstpass=%d La Line 5473  Title=%s <br>Datafile=%s Firstpass=%d La
               
               
       /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       if(cptcovn==0 && nj==1) /* no covariate and first pass */        if(cptcoveff==0 && nj==1) /* no covariate and first pass */
         pstamp(ficresp);          pstamp(ficresp);
       if  (cptcovn>0 && j!=0){        if  (cptcoveff>0 && j!=0){
         pstamp(ficresp);          pstamp(ficresp);
         printf( "\n#********** Variable ");           printf( "\n#********** Variable "); 
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");           fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
         fprintf(ficlog, "\n#********** Variable ");           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcovs; 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,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[z1]])]);              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
Line 5089  Title=%s <br>Datafile=%s Firstpass=%d La Line 5528  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((cptcovn==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<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[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((cptcovn==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);
       }        }
       if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
       fprintf(ficresphtm, "\n");        fprintf(ficresphtm, "\n");
               
       /* Header of frequency table by age */        /* Header of frequency table by age */
Line 5164  Title=%s <br>Datafile=%s Firstpass=%d La Line 5606  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
                   
         /* Writing ficresp */          /* Writing ficresp */
         if(cptcovn==0 && nj==1){ /* no covariate and first pass */          if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
           if( iage <= iagemax){            if( iage <= iagemax){
             fprintf(ficresp," %d",iage);              fprintf(ficresp," %d",iage);
           }            }
         }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<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,Tvaraff[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 5186  Title=%s <br>Datafile=%s Firstpass=%d La Line 5628  Title=%s <br>Datafile=%s Firstpass=%d La
           }            }
           if( iage <= iagemax){            if( iage <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               if(cptcovn==0 && nj==1){ /* no covariate and first pass */                if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
               }else if( nj==2){                }else if( nj==2){
                 fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);                  fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
Line 5195  Title=%s <br>Datafile=%s Firstpass=%d La Line 5637  Title=%s <br>Datafile=%s Firstpass=%d La
               /*probs[iage][s1][j1]= pp[s1]/pos;*/                /*probs[iage][s1][j1]= pp[s1]/pos;*/
               /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/                /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
             } else{              } else{
               if((cptcovn==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);                if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);                fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
             }              }
           }            }
Line 5221  Title=%s <br>Datafile=%s Firstpass=%d La Line 5663  Title=%s <br>Datafile=%s Firstpass=%d La
         }          }
         fprintf(ficresphtmfr,"</tr>\n ");          fprintf(ficresphtmfr,"</tr>\n ");
         fprintf(ficresphtm,"</tr>\n");          fprintf(ficresphtm,"</tr>\n");
         if((cptcovn==0 && nj==1)|| nj==2 ) {          if((cptcoveff==0 && nj==1)|| nj==2 ) {
           if(iage <= iagemax)            if(iage <= iagemax)
             fprintf(ficresp,"\n");              fprintf(ficresp,"\n");
         }          }
Line 5248  Title=%s <br>Datafile=%s Firstpass=%d La Line 5690  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 5479  void prevalence(double ***probs, double Line 5921  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 5496  void prevalence(double ***probs, double Line 5938  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,Tvaraff[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,Tvaraff[z1])]) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
               bool=0;                bool=0;
             }              }
         }          }
Line 5803  void  concatwav(int wav[], int **dh, int Line 6245  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] != 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 5901  void  concatwav(int wav[], int **dh, int Line 6345  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 && 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 5910  void  concatwav(int wav[], int **dh, int Line 6358  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 5924  void  concatwav(int wav[], int **dh, int Line 6372  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 5946  void  concatwav(int wav[], int **dh, int Line 6403  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; /* cptcov= Number of total real effective covariates: effective (used as cptcoveff in other functions)     *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 6079  void  concatwav(int wav[], int **dh, int Line 6536  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 6347  void  concatwav(int wav[], int **dh, int Line 6805  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]]);
    }     }
    for(j=1;j<=cptcoveff;j++)      /* for(j=1;j<=cptcoveff;j++)  */
      fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,Tvaraff[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 6979  To be simple, these graphs help to under Line 7442  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,Tvaraff[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,Tvaraff[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,Tvaraff[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,Tvaraff[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,Tvaraff[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 7013  To be simple, these graphs help to under Line 7521  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){ /* 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,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,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]);  
            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,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(j1,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,Tvard[k][1])] * 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,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]]; */  
            }  
          }           }
          /* 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 7249  To be simple, these graphs help to under Line 7766  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 7281  void printinghtml(char fileresu[], char Line 7798  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 7315  void printinghtml(char fileresu[], char Line 7832  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 7349  void printinghtml(char fileresu[], char Line 7876  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 7415  divided by h: <sub>h</sub>P<sub>ij</sub> Line 7940  divided by h: <sub>h</sub>P<sub>ij</sub>
      /* 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>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);         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>", cpt, nlstate, cpt, 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,"P_"),subdirf2(optionfilefiname,"P_"));         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);        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 7452  with weights corresponding to observed p Line 7978  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 7499  See page 'Matrix of variance-covariance Line 8025  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 7510  See page 'Matrix of variance-covariance Line 8036  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 7539  See page 'Matrix of variance-covariance Line 8061  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 7591  true period expectancies (those weighted Line 8110  true period expectancies (those weighted
      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 7602  void printinggnuplot(char fileresu[], ch Line 8120  void printinggnuplot(char fileresu[], ch
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[132], gplotlabel[132];
   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 7628  void printinggnuplot(char fileresu[], ch Line 8146  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 7665  void printinggnuplot(char fileresu[], ch Line 8183  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 */
       k=18+Tvar[TvarFind[kf]];/*offset because there are 18 columns in the ILK_ file */
       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));
         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);
         }
         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));
   
             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 7706  void printinggnuplot(char fileresu[], ch Line 8303  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 7732  void printinggnuplot(char fileresu[], ch Line 8329  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 7760  void printinggnuplot(char fileresu[], ch Line 8358  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 7774  void printinggnuplot(char fileresu[], ch Line 8374  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 7802  void printinggnuplot(char fileresu[], ch Line 8402  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 7868  void printinggnuplot(char fileresu[], ch Line 8475  void printinggnuplot(char fileresu[], ch
       } /* 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 7923  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 8537  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");
Line 7974  set ter svg size 640, 480\nunset log y\n Line 8595  set ter svg size 640, 480\nunset log y\n
         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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             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 *\/ */
                 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]; /* 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]);
               kl++;                kl++;
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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");
Line 8330  set ter svg size 640, 480\nunset log y\n Line 8988  set ter svg size 640, 480\nunset log y\n
             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 *\/ */
Line 8405  set ter svg size 640, 480\nunset log y\n Line 9071  set ter svg size 640, 480\nunset log y\n
   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 */      /* 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);
Line 8643  set ter svg size 640, 480\nunset log y\n Line 9323  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 8966  void prevforecast(char fileres[], double Line 9646  void prevforecast(char fileres[], double
       
 /*            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++){      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(i1 != 1 && TKresult[nres]!= k)      if(i1 != 1 && TKresult[nres]!= k)
       continue;        continue;
     if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
Line 8975  void prevforecast(char fileres[], double Line 9655  void prevforecast(char fileres[], double
     }      }
     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<=cptcoveff;j++) {
       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]);        /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
         fprintf(ficresf," 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 */      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=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 9005  void prevforecast(char fileres[], double Line 9686  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,Tvaraff[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 9115  void prevforecast(char fileres[], double Line 9797  void prevforecast(char fileres[], double
     }      }
     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<=cptcoveff;j++) {
       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[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 */      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=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 9151  void prevforecast(char fileres[], double Line 9833  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,Tvaraff[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 9210  void prevforecast(char fileres[], double Line 9892  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,Tvaraff[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,Tvaraff[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,Tvaraff[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 9267  void prevforecast(char fileres[], double Line 9953  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,Tvaraff[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,Tvaraff[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,Tvaraff[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 9769  int readdata(char datafile[], int firsto Line 10461  int readdata(char datafile[], int firsto
     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[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]);      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]);
   }    }
     
     ncovcolt=ncovcol+nqv+ntv+nqtv; /* total of covariates in the data, not in the model equation */
     
   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 9847  int readdata(char datafile[], int firsto Line 10541  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 9867  int readdata(char datafile[], int firsto Line 10561  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 9907  int readdata(char datafile[], int firsto Line 10601  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 10113  int decoderesult( char resultline[], int Line 10807  int decoderesult( char resultline[], int
   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){ /* Resultline but no = */
     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);      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, %s.\n",j, cptcovs, model);
     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);      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, %s.\n",j, cptcovs, model);
       /* 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 10151  int decoderesult( char resultline[], int Line 10850  int decoderesult( char resultline[], int
       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){ /* Product No 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): 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): 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): 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): 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   */
           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 */            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 */
   /* nres=1st 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 */
Line 10208  int decoderesult( char resultline[], int Line 10959  int decoderesult( char resultline[], int
   /* 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 k1 on position in the model line (excluding product) */    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.
                                                      * loop on position k1 in the MODEL LINE */
     /* k counting number of combination of single dummies in the equation model */      /* k counting number of combination of single dummies in the equation model */
     /* k4 counting single dummies in the equation model */      /* k4 counting single dummies in the equation model */
     /* k4q counting single quantitatives in the equation model */      /* k4q counting single quantitatives in the equation model */
     if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */
        /* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */         /* 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 correspond to the k1 position in the model line */        /* 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 */        /* 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 */        /* 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                                          */        /*      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.                                                          */        /* 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.                                                         */        /* 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                                 */        /* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline                   */
       /* Tvresult[nres][result_position]= id 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                                                      */        /* 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                                                      */        /* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line                                                      */
       k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/        k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
       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)*/        /* 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) */        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]; /* Tinvresult[nres][4]=1 */        TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
       Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1)  Tresult[nres=2][2]=0(V3=0) */        /* Tinvresult[nres][4]=1 */
       Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=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 ){ /* Quantitative and single */      }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
       /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */        /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline                                 */
       /* Tqvresult[nres][result_position]= id of the 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                                 */
       /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */        /* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line                                                      */
       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        k2q=(int)Tvarsel[k3q]; /*  Name of variable at k3q th position in the resultline */
       Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */        /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */        /* 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 */
       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        TinvDoQresult[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]);        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 */      }else if( Dummy[k1]==2 ){ /* For dummy with age product */
       /* Tvar[k1]; */ /* Age variable */        /* Tvar[k1]; */ /* Age variable */
       k3= resultmodel[nres][Tvar[k1]]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/        /* Wrong we want the value of variable name Tvar[k1] */
         
         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)*/        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]; /* Tinvresult[nres][4]=1 */        TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
       printf("Decoderesult Dummy with age k=%d, k1=%d Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);        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 */      }else if( Dummy[k1]==3 ){ /* For quant with age product */
       k3q= resultmodel[nres][Tvar[k1]]; /* resultmodel[1(V5)] = 25.1=k3q */        k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */        k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */        TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
       printf("Decoderesult Quantitative with age nres=%d, k1=%d, Tvar[%d]=V%d V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k1, k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);        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 ){ /* For product quant or dummy (not with age) */      }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
       printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d Tvar[%d]=%d \n",nres, k1, k1, Tvar[k1]);        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{      }else{
       printf("Error Decodemodel probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);        printf("Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
       fprintf(ficlog,"Error Decodemodel 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 10276  int decodemodel( char model[], int lasto Line 11044  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 10300  int decodemodel( char model[], int lasto Line 11069  int decodemodel( char model[], int lasto
       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 10421  int decodemodel( char model[], int lasto Line 11190  int decodemodel( char model[], int lasto
             cptcovn++;              cptcovn++;
             cptcovprodnoage++;k1++;              cptcovprodnoage++;k1++;
             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              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                                                  because this model-covariate is a construction we invent a new column
                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                                 If already ncovcol=4 and model=V2 + V1 +V1*V4 +age*V3 +V3*V2                                                  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                                                  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 */                                                  Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=3 etc */
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */              /* 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
                */
               Typevar[k]=2;  /* 2 for product */
             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  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */              Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
Line 10440  int decodemodel( char model[], int lasto Line 11217  int decodemodel( char model[], int lasto
             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */              /* 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 */              /*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   */              /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
             for (i=1; i<=lastobs;i++){              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                /* 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[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];                covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
             }                }
               } /*End of FixedV */
           } /* End age is not in the model */            } /* End age is not in the model */
         } /* End if model includes a product */          } /* End if model includes a product */
         else { /* not a product */          else { /* not a product */
Line 10495  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11274  Dummy[k] 0=dummy (0 1), 1 quantitative (
 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 \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;}
     for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=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 10511  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11291  Dummy[k] 0=dummy (0 1), 1 quantitative (
       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 *\/ */
       }else if( Tposprod[k]>0  &&  Typevar[k]==2 && 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 */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 0;        Dummy[k]= 0;
       ncoveff++;        ncoveff++;
Line 10529  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11310  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 10554  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11342  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 10561  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11356  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=%d,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];
Line 10600  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11395  Dummy[k] 0=dummy (0 1), 1 quantitative (
         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
       }        }
     }else if (Typevar[k] == 2) {  /* product without age */      }else if (Typevar[k] == 2) {  /* product 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  */
       k1=Tposprod[k];        /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
       if(Tvard[k1][1] <=ncovcol){        /* model V1+V3+age*V1+age*V3+V1*V3 */
         if(Tvard[k1][2] <=ncovcol){        /*  Tvar={1, 3, 1, 3, 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} 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 */
   
   
         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;            Fixed[k]= 1;
           Dummy[k]= 0;            Dummy[k]= 0;
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
Line 10611  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11417  Dummy[k] 0=dummy (0 1), 1 quantitative (
           ncovf++; /* Fixed variables without age */            ncovf++; /* Fixed variables without age */
           TvarF[ncovf]=Tvar[k];            TvarF[ncovf]=Tvar[k];
           TvarFind[ncovf]=k;            TvarFind[ncovf]=k;
         }else if(Tvard[k1][2] <=ncovcol+nqv){          }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
           Fixed[k]= 0;  /* or 2 ?*/            Fixed[k]= 0;  /* Fixed product */
           Dummy[k]= 1;            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 */            ncovf++; /* Varying variables without 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 a time varying dummy covariate */
           Fixed[k]= 1;            Fixed[k]= 1;
           Dummy[k]= 0;            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 */            ncovv++; /* Varying variables without age */
           TvarV[ncovv]=Tvar[k];            TvarV[ncovv]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
           TvarVind[ncovv]=k;            TvarVind[ncovv]=k;/* TvarVind[1]=5 */ 
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
           Fixed[k]= 1;            Fixed[k]= 1;
           Dummy[k]= 1;            Dummy[k]= 1;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
Line 10636  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11442  Dummy[k] 0=dummy (0 1), 1 quantitative (
           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]= 0;  /*  Fixed product */
           Dummy[k]= 1;            Dummy[k]= 1;
           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 */            ncovf++; /* Fixed variables without 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]= 1;
           Dummy[k]= 1;            Dummy[k]= 1;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
Line 10653  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11459  Dummy[k] 0=dummy (0 1), 1 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][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
           Fixed[k]= 1;            Fixed[k]= 1;
           Dummy[k]= 1;            Dummy[k]= 1;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
Line 10665  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11471  Dummy[k] 0=dummy (0 1), 1 quantitative (
           TvarV[ncovv]=Tvar[k];            TvarV[ncovv]=Tvar[k];
           TvarVind[ncovv]=k;            TvarVind[ncovv]=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]= 1;
           Dummy[k]= 1;            Dummy[k]= 1;
Line 10699  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11505  Dummy[k] 0=dummy (0 1), 1 quantitative (
           TvarV[ncovv]=Tvar[k];            TvarV[ncovv]=Tvar[k];
           TvarVind[ncovv]=k;            TvarVind[ncovv]=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]= 1;
           Dummy[k]= 1;            Dummy[k]= 1;
Line 10741  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11547  Dummy[k] 0=dummy (0 1), 1 quantitative (
       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]);
   }    }
   /* Searching for doublons in the model */    /* Searching for doublons in the model */
Line 10752  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11558  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 11088  void syscompilerinfo(int logged) Line 11894  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 11116  int prevalence_limit(double *p, double * Line 11923  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,Tvaraff[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,Tvaraff[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,Tvaraff[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 11151  int prevalence_limit(double *p, double * Line 11963  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,Tvaraff[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,Tvaraff[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 11171  int prevalence_limit(double *p, double * Line 11989  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 11214  int back_prevalence_limit(double *p, dou Line 12032  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,Tvaraff[j])]);          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[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,Tvaraff[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 11242  int back_prevalence_limit(double *p, dou Line 12067  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,Tvaraff[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 11266  int back_prevalence_limit(double *p, dou Line 12091  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,Tvaraff[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 11277  int back_prevalence_limit(double *p, dou Line 12102  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 11287  int back_prevalence_limit(double *p, dou Line 12112  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;
Line 11297  int hPijx(double *p, int bage, int fage) Line 12122  int hPijx(double *p, int bage, int fage)
   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,Tvaraff[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 11399  int hPijx(double *p, int bage, int fage) Line 12227  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,Tvaraff[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? */
       /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
       for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        continue;
         /* 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 *\/ */
               for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
         /*        nhstepm=nhstepm*YEARM; aff par mois*/        /* 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 */
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */        nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
         /* and memory limitations if stepm is small */        
         /*          nhstepm=nhstepm*YEARM; aff par mois*/
         /* oldm=oldms;savm=savms; */        
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */        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, k, nres);/* Bug valgrind */        /* and memory limitations if stepm is small */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */        
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");        /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %1d-%1d",i,j);
         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(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");          fprintf(ficrespijb,"\n");
         for (h=0; h<=nhstepm; h++){        }
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );        fprintf(ficrespijb,"\n");
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */      } /* end age deb */
           for(i=1; i<=nlstate;i++)      /* } /\* end combination *\/ */
             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");  
       } /* end age deb */  
     } /* end combination */  
   } /* end nres */    } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
Line 11499  int main(int argc, char *argv[]) Line 12331  int main(int argc, char *argv[])
   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 , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 11842  int main(int argc, char *argv[]) Line 12674  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 11870  int main(int argc, char *argv[]) Line 12702  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 11883  int main(int argc, char *argv[]) Line 12717  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 12126  Please run with mle=-1 to get a correct Line 12961  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 12146  Please run with mle=-1 to get a correct Line 12981  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); /*  */    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 12163  Please run with mle=-1 to get a correct Line 12999  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); /*  */
   
   Tvalsel=vector(1,NCOVMAX); /*  */    Tvalsel=vector(1,NCOVMAX); /*  */
   Tvarsel=ivector(1,NCOVMAX); /*  */    Tvarsel=ivector(1,NCOVMAX); /*  */
Line 12268  Please run with mle=-1 to get a correct Line 13106  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 12407  Title=%s <br>Datafile=%s Firstpass=%d La Line 13245  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 12420  Title=%s <br>Datafile=%s Firstpass=%d La Line 13265  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 12734  Please run with mle=-1 to get a correct Line 13579  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 13078  Please run with mle=-1 to get a correct Line 13924  Please run with mle=-1 to get a correct
     }      }
             
     /* Results */      /* Results */
       /* Value of covariate in each resultine will be compututed (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 13151  Please run with mle=-1 to get a correct Line 14000  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 13262  Please run with mle=-1 to get a correct Line 14121  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 13392  Please run with mle=-1 to get a correct Line 14254  Please run with mle=-1 to get a correct
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]);          fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[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");
Line 13415  Please run with mle=-1 to get a correct Line 14277  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 13454  Please run with mle=-1 to get a correct Line 14316  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 %s \n#****** Result for:", model);
       fprintf(ficrest,"\n# model %s \n#****** Result for:", model);        fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
       fprintf(ficlog,"\n# model %s \n#****** Result for:", model);        fprintf(ficlog,"\n# model %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,Tvaraff[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,Tvaraff[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,Tvaraff[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  */
             fprintf(ficlog,"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  */
             fprintf(ficrest,"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  */
             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,Tvaraff[j])]);          fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[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 13491  Please run with mle=-1 to get a correct Line 14406  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,Tvaraff[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 13524  Please run with mle=-1 to get a correct Line 14441  Please run with mle=-1 to get a correct
           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 health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          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);
         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"); */
Line 13571  Please run with mle=-1 to get a correct Line 14488  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);
   
           
Line 13606  Please run with mle=-1 to get a correct Line 14523  Please run with mle=-1 to get a correct
   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 13645  Please run with mle=-1 to get a correct Line 14563  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(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.1.331  
changed lines
  Added in v.1.343


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