Diff for /imach/src/imach.c between versions 1.335 and 1.358

version 1.335, 2022/08/31 08:23:16 version 1.358, 2023/06/14 14:57:02
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.358  2023/06/14 14:57:02  brouard
     * imach.c (Module): Testing if conjugate gradient could be quicker when lot of variables POWELLORIGINCONJUGATE
   
     Revision 1.357  2023/06/14 14:55:52  brouard
     * imach.c (Module): Testing if conjugate gradient could be quicker when lot of variables POWELLORIGINCONJUGATE
   
     Revision 1.356  2023/05/23 12:08:43  brouard
     Summary: 0.99r46
   
     * imach.c (Module): Fixed PROB_r
   
     Revision 1.355  2023/05/22 17:03:18  brouard
     Summary: 0.99r46
   
     * imach.c (Module): In the ILK....txt file, the number of columns
     before the covariates values is dependent of the number of states (16+nlstate): 0.99r46
   
     Revision 1.354  2023/05/21 05:05:17  brouard
     Summary: Temporary change for imachprax
   
     Revision 1.353  2023/05/08 18:48:22  brouard
     *** empty log message ***
   
     Revision 1.352  2023/04/29 10:46:21  brouard
     *** empty log message ***
   
     Revision 1.351  2023/04/29 10:43:47  brouard
     Summary: 099r45
   
     Revision 1.350  2023/04/24 11:38:06  brouard
     *** empty log message ***
   
     Revision 1.349  2023/01/31 09:19:37  brouard
     Summary: Improvements in models with age*Vn*Vm
   
     Revision 1.347  2022/09/18 14:36:44  brouard
     Summary: version 0.99r42
   
     Revision 1.346  2022/09/16 13:52:36  brouard
     * src/imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
   
     Revision 1.345  2022/09/16 13:40:11  brouard
     Summary: Version 0.99r41
   
     * imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you  Feinuo
   
     Revision 1.344  2022/09/14 19:33:30  brouard
     Summary: version 0.99r40
   
     * imach.c (Module): Fixing names of variables in T_ (thanks to Feinuo)
   
     Revision 1.343  2022/09/14 14:22:16  brouard
     Summary: version 0.99r39
   
     * imach.c (Module): Version 0.99r39 with colored dummy covariates
     (fixed or time varying), using new last columns of
     ILK_parameter.txt file.
   
     Revision 1.342  2022/09/11 19:54:09  brouard
     Summary: 0.99r38
   
     * imach.c (Module): Adding timevarying products of any kinds,
     should work before shifting cotvar from ncovcol+nqv columns in
     order to have a correspondance between the column of cotvar and
     the id of column.
     (Module): Some cleaning and adding covariates in ILK.txt
   
     Revision 1.341  2022/09/11 07:58:42  brouard
     Summary: Version 0.99r38
   
     After adding change in cotvar.
   
     Revision 1.340  2022/09/11 07:53:11  brouard
     Summary: Version imach 0.99r37
   
     * imach.c (Module): Adding timevarying products of any kinds,
     should work before shifting cotvar from ncovcol+nqv columns in
     order to have a correspondance between the column of cotvar and
     the id of column.
   
     Revision 1.339  2022/09/09 17:55:22  brouard
     Summary: version 0.99r37
   
     * imach.c (Module): Many improvements for fixing products of fixed
     timevarying as well as fixed * fixed, and test with quantitative
     covariate.
   
     Revision 1.338  2022/09/04 17:40:33  brouard
     Summary: 0.99r36
   
     * imach.c (Module): Now the easy runs i.e. without result or
     model=1+age only did not work. The defautl combination should be 1
     and not 0 because everything hasn't been tranformed yet.
   
     Revision 1.337  2022/09/02 14:26:02  brouard
     Summary: version 0.99r35
   
     * src/imach.c: Version 0.99r35 because it outputs same results with
     1+age+V1+V1*age for females and 1+age for females only
     (education=1 noweight)
   
     Revision 1.336  2022/08/31 09:52:36  brouard
     *** empty log message ***
   
   Revision 1.335  2022/08/31 08:23:16  brouard    Revision 1.335  2022/08/31 08:23:16  brouard
   Summary: improvements...    Summary: improvements...
   
Line 1194  Important routines Line 1298  Important routines
 /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
 /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */  /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
 /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */  /* #define FLATSUP  *//* Suppresses directions where likelihood is flat */
   #define POWELLORIGINCONJUGATE  /* Don't use conjugate but biggest decrease if valuable */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 1245  typedef struct { Line 1350  typedef struct {
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 16384 /* Was 256 and 1024 and 2048. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
   #define GNUPLOTVERSION 5.1
   double gnuplotversion=GNUPLOTVERSION;
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FILENAMELENGTH 256  #define FILENAMELENGTH 256
   
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 128 /**< Maximum number of parameters for the optimization */  #define MAXPARM 216 /**< Maximum number of parameters for the optimization was 128 */
 #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 #define NINTERVMAX 8  #define NINTERVMAX 8
Line 1288  typedef struct { Line 1395  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="August 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[]="Testing conjugate April 2023,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 */
Line 1301  int cptcovt=0; /**< cptcovt: total numbe Line 1409  int cptcovt=0; /**< cptcovt: total numbe
 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 cptcovprodage=0; /**< Number of fixed covariates with age: V3*age or V2*V3*age 1 */
   int cptcovprodvage=0; /**< Number of varying covariates with age: V7*age or V7*V6*age */
   int cptcovdageprod=0; /**< Number of doubleproducts with age, since 0.99r44 only: age*Vn*Vm for gnuplot printing*/
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of single dummy covariates (fixed or time varying) 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 ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */  int ncovvt=0; /* Total number of effective (wave) varying covariates (dummy or quantitative or products [without age]) in the model */
   int ncovvta=0; /*  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
   int ncovta=0; /*age*V3*V2 +age*V2+agev3+ageV4  +age*V6 + age*V7+ age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of expandend products [with age]) in the model */
   int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
   int ncovva=0; /* +age*V6 + age*V7+ge*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
 int nsd=0; /**< Total number of single dummy variables (output) */  int nsd=0; /**< Total number of single dummy variables (output) */
 int nsq=0; /**< Total number of single quantitative variables (output) */  int nsq=0; /**< Total number of single quantitative variables (output) */
 int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */  int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
Line 1320  int npar=NPARMAX; /* Number of parameter Line 1435  int npar=NPARMAX; /* Number of parameter
 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 1391  extern time_t time(); Line 1507  extern time_t time();
   
 struct tm start_time, end_time, curr_time, last_time, forecast_time;  struct tm start_time, end_time, curr_time, last_time, forecast_time;
 time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */  time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   time_t   rlast_btime; /* raw time */
 struct tm tm;  struct tm tm;
   
 char strcurr[80], strfor[80];  char strcurr[80], strfor[80];
Line 1469  double  **covar; /**< covar[j,i], value Line 1586  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 1481  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1598  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[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:         *       covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
Line 1494  int **nbcode, *Tvar; /**< model=V2 => Tv Line 1611  int **nbcode, *Tvar; /**< model=V2 => Tv
   # States 1=Coresidence, 2 Living alone, 3 Institution    # States 1=Coresidence, 2 Living alone, 3 Institution
   # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi    # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
 */  */
 /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  /*           V5+V4+ V3+V4*V3 +V5*age+V2 +V1*V2+V1*age+V1+V4*V3*age */
 /*    k        1  2   3   4     5    6    7     8    9 */  /*    kmodel  1  2   3    4     5     6    7     8     9    10 */
 /*Typevar[k]=  0  0   0   2     1    0    2     1    0 *//*0 for simple covariate (dummy, quantitative,*/  /*Typevar[k]=  0  0   0   2     1    0    2     1     0    3 *//*0 for simple covariate (dummy, quantitative,*/
                                                          /* fixed or varying), 1 for age product, 2 for*/                                                                 /* fixed or varying), 1 for age product, 2 for*/
                                                          /* product */                                                                 /* product without age, 3 for age and double product   */
 /*Dummy[k]=    1  0   0   1     3    1    1     2    0 *//*Dummy[k] 0=dummy (0 1), 1 quantitative */  /*Dummy[k]=    1  0   0   1     3    1    1     2     0     3  *//*Dummy[k] 0=dummy (0 1), 1 quantitative */
                                                          /*(single or product without age), 2 dummy*/                                                                  /*(single or product without age), 2 dummy*/
                                                          /* with age product, 3 quant with age product*/                                                                 /* with age product, 3 quant with age product*/
 /*Tvar[k]=     5  4   3   6     5    2    7     1    1 */  /*Tvar[k]=     5  4   3   6     5    2    7     1     1     6 */
 /*    nsd         1   2                              3 */ /* Counting single dummies covar fixed or tv */  /*    nsd         1   2                               3 */ /* Counting single dummies covar fixed or tv */
 /*TnsdVar[Tvar]   1   2                              3 */   /*TnsdVar[Tvar]   1   2                               3 */ 
 /*TvarsD[nsd]     4   3                              1 */ /* ID of single dummy cova fixed or timevary*/  /*Tvaraff[nsd]    4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
 /*TvarsDind[k]    2   3                              9 */ /* position K of single dummy cova */  /*TvarsD[nsd]     4   3                               1 */ /* ID of single dummy cova fixed or timevary*/
 /*    nsq      1                     2                 */ /* Counting single quantit tv */  /*TvarsDind[nsd]  2   3                               9 */ /* position K of single dummy cova */
 /* TvarsQ[k]   5                     2                 */ /* Number of single quantitative cova */  /*    nsq      1                     2                  */ /* Counting single quantit tv */
 /* TvarsQind   1                     6                 */ /* position K of single quantitative cova */  /* TvarsQ[k]   5                     2                  */ /* Number of single quantitative cova */
 /* Tprod[i]=k             1               2            */ /* Position in model of the ith prod without age */  /* TvarsQind   1                     6                  */ /* position K of single quantitative cova */
 /* cptcovage                    1               2      */ /* Counting cov*age in the model equation */  /* Tprod[i]=k             1               2             */ /* Position in model of the ith prod without age */
 /* Tage[cptcovage]=k            5               8      */ /* Position in the model of ith cov*age */  /* cptcovage                    1               2         3 */ /* Counting cov*age in the model equation */
 /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2              */ /* Position in model of the ith prod without age */  /* Tage[cptcovage]=k            5               8         10 */ /* Position in the model of ith cov*age */
   /* model="V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
   /*  p Tvard[1][1]@21 = {6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0}*/
   /*  p Tvard[2][1]@21 = {7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0 <repeats 11 times>} */
   /* p Tvardk[1][1]@24 = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0}*/
   /* p Tvardk[1][1]@22 = {0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0} */
   /* Tvard[1][1]@4={4,3,1,2}    V4*V3 V1*V2               */ /* Position in model of the ith prod without age */
 /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/  /* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 */ /* Variables of a prod at position in the model equation*/
 /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */  /* TvarF TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
 /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */  /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
Line 1561  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3 Line 1684  int *TvarVD; /* TvarVD[1]=V5 in V5+V4+V3
 int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */  int *TvarVDind; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
 int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */  int *TvarVQ; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
 int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */  int *TvarVQind; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
   int *TvarVV; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarVVind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarVVA; /* We count ncovvt time varying covariates (single or products with age) and put their name into TvarVVA */
   int *TvarVVAind; /* We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
   int *TvarAVVA; /* We count ALL ncovta time varying covariates (single or products with age) and put their name into TvarVVA */
   int *TvarAVVAind; /* We count ALL ncovta time varying covariates (single or products without age) and put their name into TvarVV */
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age */
         /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         /* TvarVV={3,1,3,1,3}, for V3 and then the product V1*V3 is decomposed into V1 and V3 */         
         /* TvarVVind={2,5,5,6,6}, for V3 and then the product V1*V3 is decomposed into V1 and V3 and V1*V3*age into 6,6 */               
 int *Tvarsel; /**< Selected covariates for output */  int *Tvarsel; /**< Selected covariates for output */
 double *Tvalsel; /**< Selected modality value of covariate for output */  double *Tvalsel; /**< Selected modality value of covariate for output */
 int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 age*Vn*Vm */
 int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
 int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
 int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */  int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
Line 1701  char *trimbb(char *out, char *in) Line 1834  char *trimbb(char *out, char *in)
   return s;    return s;
 }  }
   
   char *trimbtab(char *out, char *in)
   { /* Trim  blanks or tabs in line but keeps first blanks if line starts with blanks */
     char *s;
     s=out;
     while (*in != '\0'){
       while( (*in == ' ' || *in == '\t')){ /* && *(in+1) != '\0'){*/
         in++;
       }
       *out++ = *in++;
     }
     *out='\0';
     return s;
   }
   
 /* char *substrchaine(char *out, char *in, char *chain) */  /* char *substrchaine(char *out, char *in, char *chain) */
 /* { */  /* { */
 /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */  /*   /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
Line 1727  char *trimbb(char *out, char *in) Line 1874  char *trimbb(char *out, char *in)
 char *substrchaine(char *out, char *in, char *chain)  char *substrchaine(char *out, char *in, char *chain)
 {  {
   /* Substract chain 'chain' from 'in', return and output 'out' */    /* Substract chain 'chain' from 'in', return and output 'out' */
   /* in="V1+V1*age+age*age+V2", chain="age*age" */    /* in="V1+V1*age+age*age+V2", chain="+age*age" out="V1+V1*age+V2" */
   
   char *strloc;    char *strloc;
   
   strcpy (out, in);     strcpy (out, in);                   /* out="V1+V1*age+age*age+V2" */
   strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */    strloc = strstr(out, chain); /* strloc points to out at "+age*age+V2"  */
   printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);    printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); /* strloc=+age*age+V2 chain="+age*age", out="V1+V1*age+age*age+V2" */
   if(strloc != NULL){     if(strloc != NULL){ 
     /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */      /* will affect out */ /* strloc+strlen(chain)=|+V2 = "V1+V1*age+age*age|+V2" */ /* Will also work in Unicodek */
     memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);      memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); /* move number of bytes corresponding to the length of "+V2" which is 3, plus one is 4 (including the null)*/
     /* strcpy (strloc, strloc +strlen(chain));*/      /* equivalent to strcpy (strloc, strloc +strlen(chain)) if no overlap; Copies from "+V2" to V1+V1*age+ */
   }    }
   printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);    printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);  /* strloc=+V2 chain="+age*age", in="V1+V1*age+age*age+V2", out="V1+V1*age+V2" */
   return out;    return out;
 }  }
   
Line 1747  char *substrchaine(char *out, char *in, Line 1894  char *substrchaine(char *out, char *in,
 char *cutl(char *blocc, char *alocc, char *in, char occ)  char *cutl(char *blocc, char *alocc, char *in, char occ)
 {  {
   /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'     /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ' 
      and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')       and alocc starts after first occurence of char 'occ' : ex cutl(blocc,alocc,"abcdef2ghi2j",'2')
      gives alocc="abcdef" and blocc="ghi2j".       gives alocc="abcdef" and blocc="ghi2j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
Line 1813  int nbocc(char *s, char occ) Line 1960  int nbocc(char *s, char occ)
   return j;    return j;
 }  }
   
   int nboccstr(char *textin, char *chain)
   {
     /* Counts the number of occurence of "chain"  in string textin */
     /*  in="+V7*V4+age*V2+age*V3+age*V4"  chain="age" */
     char *strloc;
     
     int i,j=0;
   
     i=0;
   
     strloc=textin; /* strloc points to "^+V7*V4+age+..." in textin */
     for(;;) {
       strloc= strstr(strloc,chain); /* strloc points to first character of chain in textin if found. Example strloc points^ to "+V7*V4+^age" in textin  */
       if(strloc != NULL){
         strloc = strloc+strlen(chain); /* strloc points to "+V7*V4+age^" in textin */
         j++;
       }else
         break;
     }
     return j;
     
   }
 /* void cutv(char *u,char *v, char*t, char occ) */  /* void cutv(char *u,char *v, char*t, char occ) */
 /* { */  /* { */
 /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */  /*   /\* cuts string t into u and v where u ends before last occurence of char 'occ'  */
Line 2492  void powell(double p[], double **xi, int Line 2661  void powell(double p[], double **xi, int
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
   int niterf, itmp;    int niterf, itmp;
     int Bigter=0, nBigterf=1;
     
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
   xit=vector(1,n);     xit=vector(1,n); 
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
   rcurr_time = time(NULL);      rcurr_time = time(NULL);
     fp=(*fret); /* Initialisation */
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     rlast_time=rcurr_time;      rlast_time=rcurr_time;
       rlast_btime=rcurr_time;
     /* (void) gettimeofday(&curr_time,&tzp); */      /* (void) gettimeofday(&curr_time,&tzp); */
     rcurr_time = time(NULL);        rcurr_time = time(NULL);  
     curr_time = *localtime(&rcurr_time);      curr_time = *localtime(&rcurr_time);
     printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);      /* printf("\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout); */
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",*iter,*fret, fp-*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); */
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */      Bigter=(*iter - *iter % ncovmodel)/ncovmodel +1; /* Big iteration, i.e on ncovmodel cycle */
       printf("\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d Big Iter=%d -2*LL=%.12f gain=%.3lg %ld sec. %ld sec.",*iter,Bigter,*fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
       fprintf(ficrespow,"%d %d %.12f %d",*iter,Bigter, *fret,curr_time.tm_sec-start_time.tm_sec);
     fp=(*fret); /* From former iteration or initial value */      fp=(*fret); /* From former iteration or initial value */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
Line 2531  void powell(double p[], double **xi, int Line 2706  void powell(double p[], double **xi, int
       }else if(Typevar[j]==2) {        }else if(Typevar[j]==2) {
         printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }else if(Typevar[j]==3) {
           printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
       }        }
     }      }
     printf("\n");      printf("\n");
Line 2561  void powell(double p[], double **xi, int Line 2739  void powell(double p[], double **xi, int
         strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(nBigterf=1;nBigterf<=31;nBigterf+=10){
           niterf=nBigterf*ncovmodel;
           /* rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time); */
         rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         forecast_time = *localtime(&rforecast_time);          forecast_time = *localtime(&rforecast_time);
         strcpy(strfor,asctime(&forecast_time));          strcpy(strfor,asctime(&forecast_time));
         itmp = strlen(strfor);          itmp = strlen(strfor);
         if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';            strfor[itmp-1]='\0';
         printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          printf("   - if your program needs %d BIG iterations (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
         fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d BIG iterations  (%d iterations) to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i */
Line 2582  void powell(double p[], double **xi, int Line 2762  void powell(double p[], double **xi, int
       printf("%d",i);fflush(stdout); /* print direction (parameter) i */        printf("%d",i);fflush(stdout); /* print direction (parameter) i */
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
       linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func); /* New point i minimizing in direction i has coordinates p[j].*/
         /* xit[j] gives the n coordinates of direction i as input.*/
         /* *fret gives the maximum value on direction xit */
 #else  #else
       linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/        linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
                         flatdir[i]=flat; /* Function is vanishing in that direction i */                          flatdir[i]=flat; /* Function is vanishing in that direction i */
Line 2612  void powell(double p[], double **xi, int Line 2794  void powell(double p[], double **xi, int
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     } /* end loop on each direction i */      } /* end loop on each direction i */
     /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */       /* Convergence test will use last linmin estimation (fret) and compare to former iteration (fp) */ 
     /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */      /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit  */
     /* New value of last point Pn is not computed, P(n-1) */  
     for(j=1;j<=n;j++) {      for(j=1;j<=n;j++) {
       if(flatdir[j] >0){        if(flatdir[j] >0){
         printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);          printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
Line 2752  void powell(double p[], double **xi, int Line 2933  void powell(double p[], double **xi, int
           }            }
         }          }
 #endif  #endif
   #ifdef POWELLORIGINCONJUGATE
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
           xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
         }          }
   #else
           for (j=1;j<=n-1;j++) { 
             xi[j][1]=xi[j][j+1]; /* Standard method of conjugate directions */
             xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
           }
   #endif
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
         for (j=1, flatd=0;j<=n;j++) {          for (j=1, flatd=0;j<=n;j++) {
Line 2784  void powell(double p[], double **xi, int Line 2972  void powell(double p[], double **xi, int
 #endif  #endif
         printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
     /* The minimization in direction $\xi_1$ gives $P_1$. From $P_1$ minimization in direction $\xi_2$ gives */
     /* $P_2$. Minimization of line $P_2-P_1$ gives new starting point $P^{(1)}_0$ and direction $\xi_1$ is dropped and replaced by second */
     /* direction $\xi_1^{(1)}=\xi_2$. Also second direction is replaced by new direction $\xi^{(1)}_2=P_2-P_0$. */
   
     /* At the second iteration, starting from $P_0^{(1)}$, minimization amongst $\xi^{(1)}_1$ gives point $P^{(1)}_1$. */
     /* Minimization amongst $\xi^{(1)}_2=(P_2-P_0)$ gives point $P^{(1)}_2$.  As $P^{(2)}_1$ and */
     /* $P^{(1)}_0$ are minimizing in the same direction $P^{(1)}_2 - P^{(1)}_1= P_2-P_0$, directions $P^{(1)}_2-P^{(1)}_0$ */
     /* and $P_2-P_0$ (parallel to $\xi$ and $\xi^c$) are conjugate.  } */
   
                   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 2811  void powell(double p[], double **xi, int Line 3008  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 2870  void powell(double p[], double **xi, int Line 3067  void powell(double p[], double **xi, int
      /* 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(Typevar[k1]==1){ /* A product with age */         if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
        }else{         }else{
          cov[2+nagesqr+k1]=precov[nres][k1];           cov[2+nagesqr+k1]=precov[nres][k1];
Line 3080  void powell(double p[], double **xi, int Line 3277  void powell(double p[], double **xi, int
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     }      }
     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(Typevar[k1]==1){ /* A product with age */        if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
         cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];          cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
       }else{        }else{
         cov[2+nagesqr+k1]=precov[nres][k1];          cov[2+nagesqr+k1]=precov[nres][k1];
Line 3259  double **pmij(double **ps, double *cov, Line 3456  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 3508  double **matprod2(double **out, double * Line 3705  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 dummies values in each resultline (loop on ij to find the corresponding combination) to 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 3546  double ***hpxij(double ***po, int nhstep Line 3744  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(Typevar[k1]==1){ /* A product with age */          if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
         }else{          }else{
           cov[2+nagesqr+k1]=precov[nres][k1];            cov[2+nagesqr+k1]=precov[nres][k1];
Line 3732  double ***hbxij(double ***po, int nhstep Line 3930  double ***hbxij(double ***po, int nhstep
       }        }
       /** New code */        /** New code */
       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(Typevar[k1]==1){ /* A product with age */          if(Typevar[k1]==1 || Typevar[k1]==3){ /* A product with age */
           cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
         }else{          }else{
           cov[2+nagesqr+k1]=precov[nres][k1];            cov[2+nagesqr+k1]=precov[nres][k1];
Line 3839  double ***hbxij(double ***po, int nhstep Line 4037  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 3871  double func( double *x) Line 4073  double func( double *x)
       */        */
       ioffset=2+nagesqr ;        ioffset=2+nagesqr ;
    /* Fixed */     /* Fixed */
       for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */        for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummy or quant or prod */
         /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */          /* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
         /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */          /*             V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */          /*  TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  ID of fixed covariates or product V2, V1*V2, V1 */
         /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */          /* TvarFind;  TvarFind[1]=6,  TvarFind[2]=7, TvarFind[3]=9 *//* Inverse V2(6) is first fixed (single or prod)  */
         cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/          cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (TvarFind[1]=6)*/
         /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */          /* V1*V2 (7)  TvarFind[2]=7, TvarFind[3]=9 */
       }        }
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
Line 3887  double func( double *x) Line 4089  double func( double *x)
          mw[mi][i] is real wave of the mi th effectve wave */           mw[mi][i] is real wave of the mi th effectve wave */
       /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];        /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
          s2=s[mw[mi+1][i]][i];           s2=s[mw[mi+1][i]][i];
          And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i] because now is moved after nvocol+nqv 
          But if the variable is not in the model TTvar[iv] is the real variable effective in the model:           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
       */        */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
         for(k=1; k <= ncovv ; k++){ /* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/        /* Wave varying (but not age varying) */
           /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */          /* for(k=1; k <= ncovv ; k++){ /\* Varying  covariates in the model (single and product but no age )"V5+V4+V3+V4*V3+V5*age+V1*age+V1" +TvarVind 1,2,3,4(V4*V3)  Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*\/ */
           cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];          /*   /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? *\/ */
           /*   cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
           /* } */
           for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age )*/
             itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
             ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             if(FixedV[itv]!=0){ /* Not a fixed covariate */
               cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* cotvar[wav][ncovcol+nqv+iv][i] */
             }else{ /* fixed covariate */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               cotvarv=cotvarv*cotvarvold;
             }
             iposold=ipos;
             cov[ioffset+ipos]=cotvarv;
         }          }
           /* for products of time varying to be done */
         for (ii=1;ii<=nlstate+ndeath;ii++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){            for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
   
           agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
           ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
         for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
           newm=savm;            newm=savm;
           agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agexact;            cov[2]=agexact;
           if(nagesqr==1)            if(nagesqr==1)
             cov[3]= agexact*agexact;  /* Should be changed here */              cov[3]= agexact*agexact;  /* Should be changed here */
           for (kk=1; kk<=cptcovage;kk++) {            /* for (kk=1; kk<=cptcovage;kk++) { */
             if(!FixedV[Tvar[Tage[kk]]])            /*   if(!FixedV[Tvar[Tage[kk]]]) */
               cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */            /*     cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /\* Tage[kk] gives the data-covariate associated with age *\/ */
             else            /*   else */
               cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;            /*     cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact; /\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
             /* } */
             for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
               itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
               ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
               if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
                 cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
               }else{ /* fixed covariate */
                 cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
               }
               if(ipos!=iposold){ /* Not a product or first of a product */
                 cotvarvold=cotvarv;
               }else{ /* A second product */
                 cotvarv=cotvarv*cotvarvold;
               }
               iposold=ipos;
               cov[ioffset+ipos]=cotvarv*agexact;
               /* For products */
           }            }
             
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;            savm=oldm;
Line 3991  double func( double *x) Line 4232  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 4024  double func( double *x) Line 4265  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 4071  double func( double *x) Line 4312  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 4127  double func( double *x) Line 4371  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 4146  double func( double *x) Line 4390  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 4175  double func( double *x) Line 4422  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, kf=0;    int i, ii, j, k, mi, d, kk, kv=0, kf=0;
   int ioffset=0;    int ioffset=0;
     int ipos=0,iposold=0,ncovv=0;
   
     double cotvarv, cotvarvold;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
Line 4198  double funcone( double *x) Line 4448  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 (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */      for (kf=1; kf<=ncovf;kf++){ /*  V2  +  V3  +  V4  Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
         /* 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[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];  */
Line 4215  double funcone( double *x) Line 4473  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 4224  double funcone( double *x) Line 4493  double funcone( double *x)
           
   
     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
     /* Wave varying (but not age varying) */        /* Wave varying (but not age varying) *//* V1+V3+age*V1+age*V3+V1*V3 with V4 tv and V5 tvq k= 1 to 5 and extra at V(5+1)=6 for V1*V3 */
       for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/        /* for(k=1; k <= ncovv ; k++){ /\* Varying  covariates (single and product but no age )*\/ */
         /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */        /*        /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; *\/ */
         cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];        /*        cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
       }        /* } */
       /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */        
       /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */        /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
       /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */        /* model V1+V3+age*V1+age*V3+V1*V3 */
       /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */        /*  Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
       /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */        /*  TvarVV[1]=V3 (first time varying in the model equation, TvarVV[2]=V1 (in V1*V3) TvarVV[3]=3(V3)  */
       /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */        /* We need the position of the time varying or product in the model */
         /* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1*V3 is decomposed into V1 and V3 but at same position 5 */             
         /* TvarVV gives the variable name */
         /* Other example V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5 
         *      k=         1   2     3     4         5        6        7       8        9
         *  varying            1     2                                 3       4        5
         *  ncovv              1     2                                3 4     5 6      7 8
         * TvarVV[ncovv]      V3     5                                1 3     3 5      1 5
         * TvarVVind           2     3                                7 7     8 8      9 9
         * TvarFind[k]     1   0     0     0         0        0        0       0        0
         */
         /* Other model ncovcol=5 nqv=0 ntv=3 nqtv=0 nlstate=3
          * V2 V3 V4 are fixed V6 V7 are timevarying so V8 and V5 are not in the model and product column will start at 9 Tvar[(v6*V2)6]=9
           * FixedV[ncovcol+qv+ntv+nqtv]       V5
           * 3           V1  V2     V3    V4   V5 V6     V7  V8 V3*V2 V7*V2  V6*V3 V7*V3 V6*V4 V7*V4
           *             0   0      0      0    0  1      1   1  0, 0, 1,1,   1, 0, 1, 0, 1, 0, 1, 0}
           * 3           0   0      0      0    0  1      1   1  0,     1      1    1      1    1}
           * model=          V2  +  V3  +  V4  +  V6  +  V7  +  V6*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +age*V6*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * model2=          V2  +  V3  +  V4  +  V6  +  V7  +  V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +age*V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * model3=          V2  +  V3  +  V4  +  V6  +  V7  + age*V3*V2  +  V7*V2  +  V6*V3  +  V7*V3  +  V6*V4  +  V7*V4  
           *                +age*V2 +age*V3 +age*V4 +age*V6 + age*V7
           *                +V3*V2 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * kmodel           1     2      3      4      5        6         7         8         9        10        11    
           *                  12       13      14      15       16
           *                    17        18         19        20         21
           * Tvar[kmodel]     2     3      4      6      7        9        10        11        12        13        14
           *                   2       3        4       6        7
           *                     9         11          12        13         14            
           * cptcovage=5+5 total of covariates with age 
           * Tage[cptcovage] age*V2=12      13      14      15       16
           *1                   17            18         19        20         21 gives the position in model of covariates associated with age
           *3 Tage[cptcovage] age*V3*V2=6  
           *3                age*V2=12         13      14      15       16
           *3                age*V6*V3=18      19    20   21
           * Tvar[Tage[cptcovage]]    Tvar[12]=2      3      4       6         Tvar[16]=7(age*V7)
           *     Tvar[17]age*V6*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 2   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 3 Tvar[Tage[cptcovage]]    Tvar[6]=9      Tvar[12]=2      3     4       6         Tvar[16]=7(age*V7)
           * 3     Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * 3 Tage[cptcovage] age*V3*V2=6   age*V2=12 age*V3 13    14      15       16
           *                    age*V6*V3=18         19        20         21 gives the position in model of covariates associated with age
           * 3   Tvar[17]age*V3*V2=9      Tvar[18]age*V6*V3=11  age*V7*V3=12         age*V6*V4=13        Tvar[21]age*V7*V4=14
           * Tvar=                {2, 3, 4, 6, 7,
           *                       9, 10, 11, 12, 13, 14,
           *              Tvar[12]=2, 3, 4, 6, 7,
           *              Tvar[17]=9, 11, 12, 13, 14}
           * Typevar[1]@21 = {0, 0, 0, 0, 0,
           *                  2, 2, 2, 2, 2, 2,
           * 3                3, 2, 2, 2, 2, 2,
           *                  1, 1, 1, 1, 1, 
           *                  3, 3, 3, 3, 3}
           * 3                 2, 3, 3, 3, 3}
           * p Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6} Id of the prod at position k in the model
           * p Tprod[1]@21 {6, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
           * 3 Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6}
           * 3 Tprod[1]@21 {17, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
           * cptcovprod=11 (6+5)
           * FixedV[Tvar[Tage[cptcovage]]]]  FixedV[2]=0      FixedV[3]=0      0      1          (age*V7)Tvar[16]=1 FixedV[absolute] not [kmodel]
           *   FixedV[Tvar[17]=FixedV[age*V6*V2]=FixedV[9]=1        1         1          1         1  
           * 3 FixedV[Tvar[17]=FixedV[age*V3*V2]=FixedV[9]=0        [11]=1         1          1         1  
           * FixedV[]          V1=0     V2=0   V3=0  v4=0    V5=0  V6=1    V7=1 v8=1  OK then model dependent
           *                   9=1  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
           * 3                 9=0  [V7*V2]=[10]=1 11=1  12=1  13=1  14=1
           * cptcovdageprod=5  for gnuplot printing
           * cptcovprodvage=6 
           * ncova=15           1        2       3       4       5
           *                      6 7        8 9      10 11        12 13     14 15
           * TvarA              2        3       4       6       7
           *                      6 2        6 7       7 3          6 4       7 4
           * TvaAind             12 12      13 13     14 14      15 15       16 16        
           * ncovf            1     2      3
           *                                    V6       V7      V6*V2     V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
           * ncovvt=14                            1      2        3 4       5 6       7 8       9 10     11 12     13 14     
           * TvarVV[1]@14 = itv               {V6=6,     7, V6*V2=6, 2,     7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           * TvarVVind[1]@14=                    {4,     5,       6, 6,     7, 7,     8, 8,      9, 9,   10, 10,   11, 11}
           * 3 ncovvt=12                        V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4
           * 3 TvarVV[1]@12 = itv                {6,     7, V7*V2=7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           * 3                                    1      2        3  4      5  6      7  8      9 10     11 12
           * TvarVVind[1]@12=         {V6 is in k=4,     5,  7,(4isV2)=7,   8, 8,      9, 9,   10,10,    11,11}TvarVVind[12]=k=11
           * TvarV              6, 7, 9, 10, 11, 12, 13, 14
           * 3 cptcovprodvage=6
           * 3 ncovta=15    +age*V3*V2+age*V2+agev3+ageV4 +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * 3 TvarAVVA[1]@15= itva 3 2    2      3    4        6       7        6 3         7 3         6 4         7 4 
           * 3 ncovta             1 2      3      4    5        6       7        8 9       10 11       12 13        14 15
           *?TvarAVVAind[1]@15= V3 is in k=2 1 1  2    3        4       5        4,2         5,2,      4,3           5 3}TvarVVAind[]
           * TvarAVVAind[1]@15= V3 is in k=6 6 12  13   14      15      16       18 18       19,19,     20,20        21,21}TvarVVAind[]
           * 3 ncovvta=10     +age*V6 + age*V7 + age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4
           * 3 we want to compute =cotvar[mw[mi][i]][TvarVVA[ncovva]][i] at position TvarVVAind[ncovva]
           * 3 TvarVVA[1]@10= itva   6       7        6 3         7 3         6 4         7 4 
           * 3 ncovva                1       2        3 4         5 6         7 8         9 10
           * TvarVVAind[1]@10= V6 is in k=4  5        8,8         9, 9,      10,10        11 11}TvarVVAind[]
           * TvarVVAind[1]@10=       15       16     18,18        19,19,      20,20        21 21}TvarVVAind[]
           * TvarVA              V3*V2=6 6 , 1, 2, 11, 12, 13, 14
           * TvarFind[1]@14= {1,    2,     3,     0 <repeats 12 times>}
           * Tvar[1]@21=     {2,    3,     4,    6,      7,      9,      10,        11,       12,      13,       14,
           *                   2, 3, 4, 6, 7,
           *                     6, 8, 9, 10, 11}
           * TvarFind[itv]                        0      0       0
           * FixedV[itv]                          1      1       1  0      1 0       1 0       1 0       0
           *? FixedV[itv]                          1      1       1  0      1 0       1 0       1 0      1 0     1 0
           * Tvar[TvarFind[ncovf]]=[1]=2 [2]=3 [4]=4
           * Tvar[TvarFind[itv]]                [0]=?      ?ncovv 1 à ncovvt]
           *   Not a fixed cotvar[mw][itv][i]     6       7      6  2      7, 2,     6, 3,     7, 3,     6, 4,     7, 4}
           *   fixed covar[itv]                  [6]     [7]    [6][2] 
           */
   
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /*  V6       V7      V7*V2     V6*V3     V7*V3     V6*V4     V7*V4 Time varying  covariates (single and extended product but no age) including individual from products, product is computed dynamically */
           itv=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, or fixed covariate of a varying product after exploding product Vn*Vm into Vn and then Vm  */
           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
           /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
           if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
             /* printf("DEBUG ncovv=%d, Varying TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
             cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             /* printf("DEBUG Varying cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
           }else{ /* fixed covariate */
             /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
             /* printf("DEBUG ncovv=%d, Fixed TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
             cotvarv=covar[itv][i];  /* Good: In V6*V3, 3 is fixed at position of the data */
             /* printf("DEBUG Fixed cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
           }
           if(ipos!=iposold){ /* Not a product or first of a product */
             cotvarvold=cotvarv;
           }else{ /* A second product */
             cotvarv=cotvarv*cotvarvold;
           }
           iposold=ipos;
           cov[ioffset+ipos]=cotvarv;
           /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
           /* For products */
         }
         /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single *\/ */
         /*        iv=TvarVDind[itv]; /\* iv, position in the model equation of time varying covariate itv *\/ */
         /*        /\*         "V1+V3+age*V1+age*V3+V1*V3" with V3 time varying *\/ */
         /*        /\*           1  2   3      4      5                         *\/ */
         /*        /\*itv           1                                           *\/ */
         /*        /\* TvarVInd[1]= 2                                           *\/ */
         /*        /\* iv= Tvar[Tmodelind[itv]]-ncovcol-nqv;  /\\* Counting the # varying covariate from 1 to ntveff *\\/ *\/ */
         /*        /\* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; *\/ */
         /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; *\/ */
         /*        /\* k=ioffset-2-nagesqr-cptcovage+itv; /\\* position in simple model *\\/ *\/ */
         /*        /\* cov[ioffset+iv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; *\/ */
         /*        cov[ioffset+iv]=cotvar[mw[mi][i]][itv][i]; */
         /*        /\* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][itv][i]=%f\n", i, mi, itv, TvarVDind[itv],cotvar[mw[mi][i]][itv][i]); *\/ */
         /* } */
       /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */        /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
       /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */        /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
       /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */        /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
Line 4257  double funcone( double *x) Line 4673  double funcone( double *x)
         cov[2]=agexact;          cov[2]=agexact;
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= agexact*agexact;            cov[3]= agexact*agexact;
         for (kk=1; kk<=cptcovage;kk++) {          for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
           if(!FixedV[Tvar[Tage[kk]]])            itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
             cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;            ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
           else            /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
             cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;            if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
               /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             }else{ /* fixed covariate */
               /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
               /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               /* printf("DEBUG * \n"); */
               cotvarv=cotvarv*cotvarvold;
             }
             iposold=ipos;
             /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
             cov[ioffset+ipos]=cotvarv*agexact;
             /* For products */
         }          }
   
         /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */          /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
         /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 4272  double funcone( double *x) Line 4706  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 4304  double funcone( double *x) Line 4750  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("Funcone 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],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: 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\ */          /*      printf("%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])); */
         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); */            /* printf(" %10.6f",-ll[k]*gipmx/gsw); */
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f ", -llt);
         /* printf(" %10.6f\n", -llt); */          /* printf(" %10.6f\n", -llt); */
       }          /* if(debugILK){ /\* debugILK is set by a #d in a comment line *\/ */
           /* fprintf(ficresilk,"%09ld ", num[i]); */ /* not necessary */
           for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products *//* Missing values are set to -1 but should be dropped */
             fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
           }
           for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying  covariates (single and product but no age) including individual from products */
             ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             if(ipos!=iposold){ /* Not a product or first of a product */
               fprintf(ficresilk," %g",cov[ioffset+ipos]);
               /* printf(" %g",cov[ioffset+ipos]); */
             }else{
               fprintf(ficresilk,"*");
               /* printf("*"); */
             }
             iposold=ipos;
           }
           /* for (kk=1; kk<=cptcovage;kk++) { */
           /*   if(!FixedV[Tvar[Tage[kk]]]){ */
           /*     fprintf(ficresilk," %g*age",covar[Tvar[Tage[kk]]][i]); */
           /*     /\* printf(" %g*age",covar[Tvar[Tage[kk]]][i]); *\/ */
           /*   }else{ */
           /*     fprintf(ficresilk," %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\/  */
           /*     /\* printf(" %g*age",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\\* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) *\\/  *\/ */
           /*   } */
           /* } */
           for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying  covariates with age including individual from products, product is computed dynamically */
             itv=TvarAVVA[ncovva]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product Vn*Vm into Vn and then Vm  */
             ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
             /* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv *\/ */
             if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
               /* printf("DEBUG  ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i];  /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */ 
             }else{ /* fixed covariate */
               /* cotvarv=covar[Tvar[TvarFind[itv]]][i];  /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model *\/ */
               /* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
               cotvarv=covar[itv][i];  /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
             }
             if(ipos!=iposold){ /* Not a product or first of a product */
               cotvarvold=cotvarv;
             }else{ /* A second product */
               /* printf("DEBUG * \n"); */
               cotvarv=cotvarv*cotvarvold;
             }
             cotvarv=cotvarv*agexact;
             fprintf(ficresilk," %g*age",cotvarv);
             iposold=ipos;
             /* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
             cov[ioffset+ipos]=cotvarv;
             /* For products */
           }
           /* printf("\n"); */
           /* } /\*  End debugILK *\/ */
           fprintf(ficresilk,"\n");
         } /* End if globpr */
     } /* end of wave */      } /* end of wave */
   } /* end of individual */    } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
Line 4331  double funcone( double *x) Line 4831  double funcone( double *x)
     gipmx=ipmx;      gipmx=ipmx;
     gsw=sw;      gsw=sw;
   }    }
 return -l;    return -l;
 }  }
   
   
Line 4342  void likelione(FILE *ficres,double p[], Line 4842  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 4352  void likelione(FILE *ficres,double p[], Line 4853  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 4370  void likelione(FILE *ficres,double p[], Line 4901  void likelione(FILE *ficres,double p[],
     fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));      fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);       fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model); 
               
     for (k=1; k<= nlstate ; k++) {  
       fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \  
 <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);  
     }  
     fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \      fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
 <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  <img src=\"%s-ori.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
     fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \      fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
 <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));  <img src=\"%s-dest.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
       
       for (k=1; k<= nlstate ; k++) {
         fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br>\n \
   <img src=\"%s-p%dj.png\">\n",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
         for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
            kvar=Tvar[TvarFind[kf]];  /* variable */
            fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): ",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]]);
            fprintf(fichtm,"<a href=\"%s-p%dj-%d.png\">%s-p%dj-%d.png</a><br>",subdirf2(optionfilefiname,"ILK_"),k,kvar,subdirf2(optionfilefiname,"ILK_"),k,kvar);
            fprintf(fichtm,"<img src=\"%s-p%dj-%d.png\">",subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]);
         }
         for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Loop on the time varying extended covariates (with extension of Vn*Vm */
           ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
           kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
           /* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
           if(ipos!=iposold){ /* Not a product or first of a product */
             /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
             /* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); */
             if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
               fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored time varying dummy covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
   <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar);
             } /* End only for dummies time varying (single?) */
           }else{ /* Useless product */
             /* printf("*"); */
             /* fprintf(ficresilk,"*"); */ 
           }
           iposold=ipos;
         } /* For each time varying covariate */
       } /* End loop on states */
   
   /*     if(debugILK){ */
   /*       for(kf=1; kf <= ncovf; kf++){ /\* For each simple dummy covariate of the model *\/ */
   /*      /\* kvar=Tvar[TvarFind[kf]]; *\/ /\* variable *\/ */
   /*      for (k=1; k<= nlstate ; k++) { */
   /*        fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
   /* <img src=\"%s-p%dj-%d.png\">",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]); */
   /*      } */
   /*       } */
   /*       for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /\* Loop on the time varying extended covariates (with extension of Vn*Vm *\/ */
   /*      ipos=TvarVVind[ncovv]; /\* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate *\/ */
   /*      kvar=TvarVV[ncovv]; /\*  TvarVV={3, 1, 3} gives the name of each varying covariate *\/ */
   /*      /\* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); *\/ */
   /*      if(ipos!=iposold){ /\* Not a product or first of a product *\/ */
   /*        /\* fprintf(ficresilk," V%d",TvarVV[ncovv]); *\/ */
   /*        /\* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); *\/ */
   /*        if(Dummy[ipos]==0 && Typevar[ipos]==0){ /\* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  *\/ */
   /*          for (k=1; k<= nlstate ; k++) { */
   /*            fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
   /* <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar); */
   /*          } /\* End state *\/ */
   /*        } /\* End only for dummies time varying (single?) *\/ */
   /*      }else{ /\* Useless product *\/ */
   /*        /\* printf("*"); *\/ */
   /*        /\* fprintf(ficresilk,"*"); *\/  */
   /*      } */
   /*      iposold=ipos; */
   /*       } /\* For each time varying covariate *\/ */
   /*     }/\* End debugILK *\/ */
     fflush(fichtm);      fflush(fichtm);
   }    }/* End globpri */
   return;    return;
 }  }
   
Line 4393  void mlikeli(FILE *ficres,double p[], in Line 4977  void mlikeli(FILE *ficres,double p[], in
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
   /*  char filerespow[FILENAMELENGTH];*/    /*  char filerespow[FILENAMELENGTH];*/
     
     double * p1; /* Shifted parameters from 0 instead of 1 */
 #ifdef NLOPT  #ifdef NLOPT
   int creturn;    int creturn;
   nlopt_opt opt;    nlopt_opt opt;
   /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */    /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
   double *lb;    double *lb;
   double minf; /* the minimum objective value, upon return */    double minf; /* the minimum objective value, upon return */
   double * p1; /* Shifted parameters from 0 instead of 1 */  
   myfunc_data dinst, *d = &dinst;    myfunc_data dinst, *d = &dinst;
 #endif  #endif
   
   
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)  /* Starting with canonical directions j=1,n xi[i=1,n][j] */
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
       xi[i][j]=(i==j ? 1.0 : 0.0);        xi[i][j]=(i==j ? 1.0 : 0.0);
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
Line 4735  double hessij( double x[], double **hess Line 5320  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
         /* What are the thetai and thetaj? thetai/ncovmodel thetai=(thetai-thetai%ncovmodel)/ncovmodel +thetai%ncovmodel=(line,pos)  */
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
Line 5080  Title=%s <br>Datafile=%s Firstpass=%d La Line 5666  Title=%s <br>Datafile=%s Firstpass=%d La
                 /* }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( 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( 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)                  if(Tvaraff[z1]<1 || Tvaraff[z1]>=NCOVMAX)
                   printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);                    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 */                  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 */
Line 5101  Title=%s <br>Datafile=%s Firstpass=%d La Line 5687  Title=%s <br>Datafile=%s Firstpass=%d La
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                 for (z1=1; z1<=cptcoveff; z1++) {                  for (z1=1; z1<=cptcoveff; z1++) {
                   if( Fixed[Tmodelind[z1]]==1){                    if( Fixed[Tmodelind[z1]]==1){
                     iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;                      /* iv= Tvar[Tmodelind[z1]]-ncovcol-nqv; /\* Good *\/ */
                       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                       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. */
Line 5182  Title=%s <br>Datafile=%s Firstpass=%d La Line 5769  Title=%s <br>Datafile=%s Firstpass=%d La
         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 5390  Title=%s <br>Datafile=%s Firstpass=%d La Line 5977  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 5638  void prevalence(double ***probs, double Line 6225  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,TnsdVar[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 */
Line 5947  void  concatwav(int wav[], int **dh, int Line 6534  void  concatwav(int wav[], int **dh, int
    /* 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++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */     for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and age*age */
      for (j=-1; (j < maxncov); j++) Ndum[j]=0;       for (j=-1; (j < maxncov); j++) Ndum[j]=0;
      if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */        /* printf("Testing k=%d, cptcovt=%d\n",k, cptcovt); */
        if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 3  && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */ 
        switch(Fixed[k]) {         switch(Fixed[k]) {
        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
          modmaxcovj=0;           modmaxcovj=0;
          modmincovj=0;           modmincovj=0;
          for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
              /* printf("Waiting for error tricode Tvar[%d]=%d i=%d (int)(covar[Tvar[k]][i]=%d\n",k,Tvar[k], i, (int)(covar[Tvar[k]][i])); */
            ij=(int)(covar[Tvar[k]][i]);             ij=(int)(covar[Tvar[k]][i]);
            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
             * If product of Vn*Vm, still boolean *:              * If product of Vn*Vm, still boolean *:
Line 6043  void  concatwav(int wav[], int **dh, int Line 6632  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){ /* Quantitative covariate and not age product */        if(Dummy[k]==1 && Typevar[k] !=1 && Typevar[k] !=3 && Fixed ==0){ /* Fixed Quantitative covariate and not age product */ 
        for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/         for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
          if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){           if(Tvar[k]<=0 || Tvar[k]>=NCOVMAX){
            printf("Error k=%d \n",k);             printf("Error k=%d \n",k);
Line 6234  void  concatwav(int wav[], int **dh, int Line 6823  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 6502  void  concatwav(int wav[], int **dh, int Line 7092  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 */ /* To be done*/  
      fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);     /* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
      /* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value *\/ /\* To be done*\/ */
      /*   fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
      /* } */
      for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */ /* To be done*/
        /* fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); */
        fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
    }     }
    for(j=1;j<=cptcoveff;j++)      /* for(j=1;j<=cptcoveff;j++)  */
      fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[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 7062  void varprob(char optionfilefiname[], do Line 7658  void varprob(char optionfilefiname[], do
    double ***varpij;     double ***varpij;
   
    strcpy(fileresprob,"PROB_");      strcpy(fileresprob,"PROB_"); 
    strcat(fileresprob,fileres);     strcat(fileresprob,fileresu);
    if((ficresprob=fopen(fileresprob,"w"))==NULL) {     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
      printf("Problem with resultfile: %s\n", fileresprob);       printf("Problem with resultfile: %s\n", fileresprob);
      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
Line 7137  To be simple, these graphs help to under Line 7733  To be simple, these graphs help to under
   
    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 */     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);       /* 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)       if(tj != 1 && TKresult[nres]!= j1)
        continue;         continue;
   
Line 7153  To be simple, these graphs help to under Line 7749  To be simple, these graphs help to under
   
        /* Including quantitative variables of the resultline to be done */         /* Including quantitative variables of the resultline to be done */
        for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */         for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline  */
          printf("Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);           /* 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=%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=%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */           /* 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(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 */             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(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  */
Line 7177  To be simple, these graphs help to under Line 7773  To be simple, these graphs help to under
            }             }
          }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */           }else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
            /* For each selected (single) quantitative value */             /* For each selected (single) quantitative value */
            fprintf(ficresprob," V%d=%f ",Tvqresult[nres][z1],Tqresult[nres][z1]);             fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
            if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */             if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
              fprintf(ficresprob,"fixed ");               fprintf(ficresprob,"fixed ");
              fprintf(ficresprobcov,"fixed ");               fprintf(ficresprobcov,"fixed ");
Line 7219  To be simple, these graphs help to under Line 7815  To be simple, these graphs help to under
          cov[3]= age*age;           cov[3]= age*age;
        /* New code end of combination but for each resultline */         /* New code end of combination but for each resultline */
        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(Typevar[k1]==1){ /* A product with age */           if(Typevar[k1]==1 || Typevar[k1] ==3){ /* A product with age */
            cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];             cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
          }else{           }else{
            cov[2+nagesqr+k1]=precov[nres][k1];             cov[2+nagesqr+k1]=precov[nres][k1];
Line 7524  void printinghtml(char fileresu[], char Line 8120  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 7558  void printinghtml(char fileresu[], char Line 8164  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 7624  divided by h: <sub>h</sub>P<sub>ij</sub> Line 8228  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 7661  with weights corresponding to observed p Line 8266  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 7708  See page 'Matrix of variance-covariance Line 8313  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 7719  See page 'Matrix of variance-covariance Line 8324  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 7748  See page 'Matrix of variance-covariance Line 8349  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 7800  true period expectancies (those weighted Line 8398  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 7809  true period expectancies (those weighted Line 8406  true period expectancies (those weighted
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[256],optfileres[256];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[256], gplotlabel[256];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,kf=0,kvar=0,kk=0,ipos=0,iposold=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
Line 7837  void printinggnuplot(char fileresu[], ch Line 8434  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 7874  void printinggnuplot(char fileresu[], ch Line 8471  void printinggnuplot(char fileresu[], ch
   fprintf(ficgp,"\nset out;unset log\n");    fprintf(ficgp,"\nset out;unset log\n");
   /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */    /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
     /* Plot the probability implied in the likelihood by covariate value */
     fprintf(ficgp,"\nset ter pngcairo size 640, 480");
     /* if(debugILK==1){ */
     for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
       kvar=Tvar[TvarFind[kf]]; /* variable name */
       /* k=18+Tvar[TvarFind[kf]];/\*offset because there are 18 columns in the ILK_ file but could be placed else where *\/ */
       /* k=18+kf;/\*offset because there are 18 columns in the ILK_ file *\/ */
       /* k=19+kf;/\*offset because there are 19 columns in the ILK_ file *\/ */
       k=16+nlstate+kf;/*offset because there are 19 columns in the ILK_ file, first cov Vn on col 21 with 4 living states */
       for (i=1; i<= nlstate ; i ++) {
         fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
         fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
         if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
           fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
           for (j=2; j<= nlstate+ndeath ; j ++) {
             fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
           }
         }else{
           fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
           for (j=2; j<= nlstate+ndeath ; j ++) {
             fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
           }
         }
         fprintf(ficgp,";\nset out; unset ylabel;\n"); 
       }
     } /* End of each covariate dummy */
     for(ncovv=1, iposold=0, kk=0; ncovv <= ncovvt ; ncovv++){
       /* Other example        V1 + V3 + V5 + age*V1  + age*V3 + age*V5 + V1*V3  + V3*V5  + V1*V5 
        *     kmodel       =     1   2     3     4         5        6        7       8        9
        *  varying                   1     2                                 3       4        5
        *  ncovv                     1     2                                3 4     5 6      7 8
        * TvarVV[ncovv]             V3     5                                1 3     3 5      1 5
        * TvarVVind[ncovv]=kmodel    2     3                                7 7     8 8      9 9
        * TvarFind[kmodel]       1   0     0     0         0        0        0       0        0
        * kdata     ncovcol=[V1 V2] nqv=0 ntv=[V3 V4] nqtv=V5
        * Dummy[kmodel]          0   0     1     2         2        3        1       1        1
        */
       ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
       kvar=TvarVV[ncovv]; /*  TvarVV={3, 1, 3} gives the name of each varying covariate */
       /* printf("DebugILK ficgp ncovv=%d, kvar=TvarVV[ncovv]=%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
       if(ipos!=iposold){ /* Not a product or first of a product */
         /* printf(" %d",ipos); */
         /* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
         /* printf(" DebugILK ficgp suite ipos=%d != iposold=%d\n", ipos, iposold); */
         kk++; /* Position of the ncovv column in ILK_ */
         k=18+ncovf+kk; /*offset because there are 18 columns in the ILK_ file plus ncovf fixed covariate */
         if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummy*age, 3quant*age) Typevar (0 single, 1=*age,2=Vn*vm)  */
           for (i=1; i<= nlstate ; i ++) {
             fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
             fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot  \"%s\"",subdirf(fileresilk));
   
               /* printf("Before DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
             if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
               /* printf("DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
               fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
               for (j=2; j<= nlstate+ndeath ; j ++) {
                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
               }
             }else{
               /* printf("DebugILK gnuplotversion=%g <5.2\n",gnuplotversion); */
               fprintf(ficgp,"  u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
               for (j=2; j<= nlstate+ndeath ; j ++) {
                 fprintf(ficgp,",\\\n \"\" u  2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
               }
             }
             fprintf(ficgp,";\nset out; unset ylabel;\n"); 
           }
         }/* End if dummy varying */
       }else{ /*Product */
         /* printf("*"); */
         /* fprintf(ficresilk,"*"); */
       }
       iposold=ipos;
     } /* For each time varying covariate */
     /* } /\* debugILK==1 *\/ */
     /* unset log; plot  "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u  2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */                
     /* fprintf(ficgp,"\nset log y;plot  \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
     /* fprintf(ficgp,"\nreplot  \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
     fprintf(ficgp,"\nset out;unset log\n");
     /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
   
   
     
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
     for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */      /* for (k1=1; k1<= m ; k1 ++){ /\* For each valid combination of covariate *\/ */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
           k1=TKresult[nres];
           if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
         if(m != 1 && TKresult[nres]!= k1)          /* if(m != 1 && TKresult[nres]!= k1) */
           continue;          /*   continue; */
         /* We are interested in selected combination by the resultline */          /* We are interested in selected combination by the resultline */
         /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);          fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         strcpy(gplotlabel,"(");          strcpy(gplotlabel,"(");
         for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the value of the covariate corresponding to k1 combination *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][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 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate k get corresponding value lv for combination k1 *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination *\\/ *\/ */
           vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           /* printf(" V%d=%d ",Tvaraff[k],vlv); */          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 *\/ */
         }          /*   /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv *\/ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   /\* printf(" V%d=%d ",Tvaraff[k],vlv); *\/ */
           /* 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 (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 7916  void printinggnuplot(char fileresu[], ch Line 8602  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 8015  void printinggnuplot(char fileresu[], ch Line 8701  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]]);
         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       }        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
       /* for(k=1; k <= ncovds; k++){ */        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* } */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* /\* for(k=1; k <= ncovds; k++){ *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," 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(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 8083  void printinggnuplot(char fileresu[], ch Line 8774  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 ++) { /* Fragile no verification of covariate values */        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]]);
           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* 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]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
         }                 /* 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 8140  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 8836  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=codtabm(k1,TnsdVar[Tvaraff[k]]);            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* 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]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* 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 8193  set ter svg size 640, 480\nunset log y\n Line 8894  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=codtabm(k1,TnsdVar[Tvaraff[k]]);            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination *\/ */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* 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]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* 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]]);
         lv=codtabm(k1,TnsdVar[Tvaraff[k]]);          sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */        /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        /*        lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
       }        /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /* } */
         /* 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]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate and each value *\/ */
           /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /*   /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* 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]]);
           lv=codtabm(k1,TnsdVar[Tvaraff[k]]);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* 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 k1 combination and kth covariate *\\/ *\/ */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /*   lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
           /* vlv= nbcode[Tvaraff[k]][lv]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */                /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
               lv=codtabm(k1,TnsdVar[Tvaraff[k]]);              for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
                 /* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
                 lv=Tvresult[nres][k];
                 vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
               /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
               /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */                /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];                /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
               kl++;                kl++;
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,lv, kl+1, vlv );
               kl++;                kl++;
               if(k <cptcoveff && cptcoveff>1)                if(k <cptcovs && cptcovs>1)
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
             }              }
             strcpy(gplotcondition+strlen(gplotcondition),")");              strcpy(gplotcondition+strlen(gplotcondition),")");
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   if(prevbcast==1){    if(prevbcast==1){
     /* Back projection from cross-sectional to stable (mixed) for each covariate */      /* Back projection from cross-sectional to stable (mixed) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */      /* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       k1=TKresult[nres];
         continue;       if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
          /* if(m != 1 && TKresult[nres]!= k1) */
          /*       continue; */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
         for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */          for (k=1; k<=cptcovs; k++){    /* For each covariate k get corresponding value lv for combination k1 */
           /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */            fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
           /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
           /* 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 k1 combination and kth covariate *\\/ *\/ */
           /* 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]; */          /*   /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
           vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];          /*   /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          /*   /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);          /*   /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         }          /*   vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          /*   fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);          /* } */
           /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
           /*   fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
           /*   sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         }                 }       
         strcpy(gplotlabel+strlen(gplotlabel),")");          strcpy(gplotlabel+strlen(gplotlabel),")");
         fprintf(ficgp,"\n#\n");          fprintf(ficgp,"\n#\n");
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           }else{            }else{
             fprintf(ficgp,",\\\n '' ");              fprintf(ficgp,",\\\n '' ");
           }            }
           if(cptcoveff ==0){ /* No covariate */            /* if(cptcoveff ==0){ /\* No covariate *\/ */
             if(cptcovs ==0){ /* No covariate */
             ioffset=2; /* Age is in 2 */              ioffset=2; /* Age is in 2 */
             /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
             /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
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             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
             for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              for (k=1; k<=cptcovs; k++){    /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
               /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */                if(Dummy[modelresult[nres][k]]==0){  /* To be verified */
               lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */                  /* for (k=1; k<=cptcoveff; k++){    /\* For each covariate writing the chain of conditions *\/ */
               /* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                  /* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* 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=Tvresult[nres][k];
               /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */                  vlv=TinvDoQresult[nres][Tvresult[nres][k]];
               vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];                  /* 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 */
               sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                  /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
               kl++;                  /* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] *\/ */
               if(k <cptcoveff && cptcoveff>1)                  /* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  kl++;
                   /* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
                   sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
                   kl++;
                   if(k <cptcovs && cptcovs>1)
                     sprintf(gplotcondition+strlen(gplotcondition)," && ");
                 }
             }              }
             strcpy(gplotcondition+strlen(gplotcondition),")");              strcpy(gplotcondition+strlen(gplotcondition),")");
             /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
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   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
     fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#model=%s \n",model);      fprintf(ficgp,"#model=1+age+%s \n",model);
     fprintf(ficgp,"# Type of graphic ng=%d\n",ng);      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
     fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */      /* fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/\* to be checked *\/ */
     for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcovs,m);/* to be checked */
       /* for(k1=1; k1 <=m; k1++)  /\* For each combination of covariate *\/ */
     for(nres=1; nres <= nresult; nres++){ /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       if(m != 1 && TKresult[nres]!= k1)       /* k1=nres; */
         continue;        k1=TKresult[nres];
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);        if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
         fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
       strcpy(gplotlabel,"(");        strcpy(gplotlabel,"(");
       /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/        /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
       for (k=1; k<=cptcoveff; k++){    /* For each correspondig covariate value  */        for (k=1; k<=cptcovs; k++){  /**< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) */
         /* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate *\/ */          /* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
         lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */             TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
         /* decodtabm(1,2,4) = 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(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */        }
         /* vlv= nbcode[Tvaraff[k]][lv]; */        /* if(m != 1 && TKresult[nres]!= k1) */
         vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];        /*        continue; */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        /* fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1); */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);        /* strcpy(gplotlabel,"("); */
       }        /* /\*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*\/ */
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */        /* for (k=1; k<=cptcoveff; k++){    /\* For each correspondig covariate value  *\/ */
         fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate *\\/ *\/ */
         sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);        /*        lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k *\/ */
       }         /*        /\* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 *\/ */
         /*        /\* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 *\/ */
         /*        /\* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 *\/ */
         /*        /\* vlv= nbcode[Tvaraff[k]][lv]; *\/ */
         /*        vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
         /*        fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
         /* } */
         /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         /*        fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /*        sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
         /* }       */
       strcpy(gplotlabel+strlen(gplotlabel),")");        strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
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                   } /* end Tprod */                    } /* end Tprod */
                 }                  }
                 break;                  break;
                 case 3:
                   if(cptcovdageprod >0){
                     /* if(j==Tprod[ijp]) { */ /* not necessary */ 
                       /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                       if(ijp <=cptcovprod) { /* Product Vn*Vm and age*VN*Vm*/
                         if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
                           if(DummyV[Tvardk[ijp][2]]==0){/* Vn and Vm are dummy */
                             /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                             fprintf(ficgp,"+p%d*%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
                           }else{ /* Vn is dummy and Vm is quanti */
                             /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                             fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                           }
                         }else{ /* age* Vn*Vm Vn is quanti HERE */
                           if(DummyV[Tvard[ijp][2]]==0){
                             fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
                           }else{ /* Both quanti */
                             fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                           }
                         }
                         ijp++;
                       }
                       /* } */ /* end Tprod */
                   }
                   break;
               case 0:                case 0:
                 /* simple covariate */                  /* simple covariate */
                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */                  /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
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                     } /* end Tprod */                      } /* end Tprod */
                   } /* end if */                    } /* end if */
                   break;                    break;
                   case 3:
                     if(cptcovdageprod >0){
                       /* if(j==Tprod[ijp]) { /\* *\/  */
                         /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                         if(ijp <=cptcovprod) { /* Product */
                           if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
                             if(DummyV[Tvardk[ijp][2]]==0){/* Vn and Vm are dummy */
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                               fprintf(ficgp,"+p%d*%d*%d*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
                             }else{ /* Vn is dummy and Vm is quanti */
                               /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
                               fprintf(ficgp,"+p%d*%d*%f*x",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             }
                           }else{ /* Vn*Vm Vn is quanti */
                             if(DummyV[Tvardk[ijp][2]]==0){
                               fprintf(ficgp,"+p%d*%d*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
                               /* fprintf(ficgp,"+p%d*%d*%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
                             }else{ /* Both quanti */
                               fprintf(ficgp,"+p%d*%f*%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
                               /* fprintf(ficgp,"+p%d*%f*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
                             } 
                           }
                           ijp++;
                         }
                       /* } /\* end Tprod *\/ */
                     } /* end if */
                     break;
                 case 0:                   case 0: 
                   /* simple covariate */                    /* simple covariate */
                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */                    /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
Line 8878  set ter svg size 640, 480\nunset log y\n Line 9682  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 9192  void prevforecast(char fileres[], double Line 9996  void prevforecast(char fileres[], double
   /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */    /* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
   /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */    /* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
   /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */    /* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
   i1=pow(2,cptcoveff);    /* i1=pow(2,cptcoveff); */
   if (cptcovn < 1){i1=1;}    /* if (cptcovn < 1){i1=1;} */
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */      k=TKresult[nres];
     if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
       continue;      /*  for(k=1; k<=i1;k++){ /\* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) *\/ */
     if(invalidvarcomb[k]){      /* if(i1 != 1 && TKresult[nres]!= k) */
       printf("\nCombination (%d) projection ignored because no cases \n",k);       /*   continue; */
       continue;      /* if(invalidvarcomb[k]){ */
     }      /*   printf("\nCombination (%d) projection ignored because no cases \n",k);  */
       /*   continue; */
       /* } */
     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcovs;j++){
       /* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */        /* for(j=1;j<=cptcoveff;j++) { */
       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[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 */      /* } */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);      /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
       /*   fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
       /* } */
         fprintf(ficresf," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
     }      }
    
     fprintf(ficresf," yearproj age");      fprintf(ficresf," yearproj age");
     for(j=1; j<=nlstate+ndeath;j++){       for(j=1; j<=nlstate+ndeath;j++){ 
       for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)        
Line 9240  void prevforecast(char fileres[], double Line 10050  void prevforecast(char fileres[], double
           }            }
         }          }
         fprintf(ficresf,"\n");          fprintf(ficresf,"\n");
         for(j=1;j<=cptcoveff;j++)           /* for(j=1;j<=cptcoveff;j++)  */
           for(j=1;j<=cptcovs;j++) 
             fprintf(ficresf,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
           /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */            /* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct *\/ */
           fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff]  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 9334  void prevforecast(char fileres[], double Line 10146  void prevforecast(char fileres[], double
   /* if(jintmean==0) jintmean=1; */    /* if(jintmean==0) jintmean=1; */
   /* if(mintmean==0) jintmean=1; */    /* if(mintmean==0) jintmean=1; */
       
   i1=pow(2,cptcoveff);    /* i1=pow(2,cptcoveff); */
   if (cptcovn < 1){i1=1;}    /* if (cptcovn < 1){i1=1;} */
       
   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
   printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
       
   fprintf(ficresfb,"#****** Routine prevbackforecast **\n");    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
       
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
   for(k=1; k<=i1;k++){      k=TKresult[nres];
     if(i1 != 1 && TKresult[nres]!= k)      if(TKresult[nres]==0) k=1; /* To be checked for noresult */
       continue;    /* for(k=1; k<=i1;k++){ */
     if(invalidvarcomb[k]){    /*   if(i1 != 1 && TKresult[nres]!= k) */
       printf("\nCombination (%d) projection ignored because no cases \n",k);     /*     continue; */
       continue;    /*   if(invalidvarcomb[k]){ */
     }    /*     printf("\nCombination (%d) projection ignored because no cases \n",k);  */
     /*     continue; */
     /*   } */
     fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcovs;j++){
       fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);      /* for(j=1;j<=cptcoveff;j++) { */
     }      /*   fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      /* } */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficresfb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
     }      }
      /*  fprintf(ficrespij,"******\n"); */
      /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
      /*    fprintf(ficresfb," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
      /*  } */
     fprintf(ficresfb," yearbproj age");      fprintf(ficresfb," yearbproj age");
     for(j=1; j<=nlstate+ndeath;j++){      for(j=1; j<=nlstate+ndeath;j++){
       for(i=1; i<=nlstate;i++)        for(i=1; i<=nlstate;i++)
Line 9387  void prevforecast(char fileres[], double Line 10205  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,TnsdVar[Tvaraff[j]])]);          for(j=1;j<=cptcovs;j++)
             fprintf(ficresfb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
             /* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
         fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);          fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-h*hstepm/YEARM*stepm);
         for(i=1; i<=nlstate+ndeath;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
           ppij=0.;ppi=0.;            ppij=0.;ppi=0.;
Line 9447  void prevforecast(char fileres[], double Line 10267  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++){ /* We find the combination equivalent to result line values of dummies */         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,TnsdVar[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,TnsdVar[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,TnsdVar[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]])]); */
           /* 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][resultmodel[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(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(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 9504  void prevforecast(char fileres[], double Line 10328  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,TnsdVar[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,TnsdVar[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,TnsdVar[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][resultmodel[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][resultmodel[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][resultmodel[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 9979  int readdata(char datafile[], int firsto Line 10809  int readdata(char datafile[], int firsto
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   
   DummyV=ivector(1,NCOVMAX); /* 1 to 3 */    /* DummyV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
   FixedV=ivector(1,NCOVMAX); /* 1 to 3 */    /* FixedV=ivector(-1,NCOVMAX); /\* 1 to 3 *\/ */
   for(v=1;v<NCOVMAX;v++){    
     DummyV[v]=0;    ncovcolt=ncovcol+nqv+ntv+nqtv; /* total of covariates in the data, not in the model equation */
     FixedV[v]=0;    
   }  
   
   for(v=1; v <=ncovcol;v++){  
     DummyV[v]=0;  
     FixedV[v]=0;  
   }  
   for(v=ncovcol+1; v <=ncovcol+nqv;v++){  
     DummyV[v]=1;  
     FixedV[v]=0;  
   }  
   for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){  
     DummyV[v]=0;  
     FixedV[v]=1;  
   }  
   for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){  
     DummyV[v]=1;  
     FixedV[v]=1;  
   }  
   for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){  
     printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);  
     fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);  
   }  
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;      fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
Line 10084  int readdata(char datafile[], int firsto Line 10891  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 10104  int readdata(char datafile[], int firsto Line 10911  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 10144  int readdata(char datafile[], int firsto Line 10951  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 10156  int readdata(char datafile[], int firsto Line 10963  int readdata(char datafile[], int firsto
         errno=0;          errno=0;
         lval=strtol(strb,&endptr,10);           lval=strtol(strb,&endptr,10); 
         /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/          /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){          if( strb[0]=='\0' || (*endptr != '\0' )){
           printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);            printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
           fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);            fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
             return 1;
           }else if( lval==0 || lval > nlstate+ndeath){
             printf("Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile);fflush(stdout);
             fprintf(ficlog,"Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'!  Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile); fflush(ficlog);
           return 1;            return 1;
         }          }
       }        }
Line 10357  int decoderesult( char resultline[], int Line 11168  int decoderesult( char resultline[], int
   printf("decoderesult:%s\n",resultline);    printf("decoderesult:%s\n",resultline);
   
   strcpy(resultsav,resultline);    strcpy(resultsav,resultline);
   printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);    /* printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline); */
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' in this resultline */
   }    }
   if(j == 0){ /* Resultline but no = */    if(j == 0 && cptcovs== 0){ /* Resultline but no =  and no covariate in the model */
     TKresult[nres]=0; /* Combination for the nresult and the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     return (0);      return (0);
   }    }
   if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */    if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
     printf("ERROR: the number of variables in 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 which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(ficlog);
     fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);      printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(stdout);
     /* return 1;*/      if(j==0)
         return 1;
   }    }
   for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */    for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */
     if(nbocc(resultsav,'=') >1){      if(nbocc(resultsav,'=') >1){
Line 10406  int decoderesult( char resultline[], int Line 11218  int decoderesult( char resultline[], int
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);          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 (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[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*/      }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*/
Line 10417  int decoderesult( char resultline[], int Line 11229  int decoderesult( char resultline[], int
         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[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 */            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 */            resultmodel[nres][k1]=k2; /* Added here */
           printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);            /* 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 */            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 (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);          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=%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;        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*/      }else if(Typevar[k1]==2 || Typevar[k1]==3){ /* Product with or without age. We want to get the position in the resultline of the product in the model line*/
       /* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */         /* 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;        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]);        /* 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 */        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   */          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; */            /* modelresult[k2]=k1; */
           printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);            /* 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 */            match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
         }          }
       }        }
       if(match == 0){        if(match == 0){
         printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);          printf("Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
         fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);          fprintf(ficlog,"Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
         return 1;          return 1;
       }        }
       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(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5   */          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;*/            /* modelresult[k2]=k1;*/
           printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);            /* 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 */            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 (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);          printf("Error in result line (Product without age second variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
         fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",Tvardk[k1][2], resultline, model);          fprintf(ficlog,"Error in result line (Product without age second variable or double product with age): V%d is missing in result : %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
         return 1;          return 1;
       }        }
     }/* End of testing */      }/* End of testing */
Line 10466  int decoderesult( char resultline[], int Line 11278  int decoderesult( char resultline[], int
     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 only */        if(Typevar[k1]==0){ /* Single only */
         if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */          if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4  What if a product?  */
           resultmodel[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 */            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;
Line 10474  int decoderesult( char resultline[], int Line 11286  int decoderesult( char resultline[], int
       }        }
     }      }
     if(match == 0){      if(match == 0){
       printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], 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: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], 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;
     }      }
   }    }
Line 10507  int decoderesult( char resultline[], int Line 11319  int decoderesult( char resultline[], int
     /* 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, k1 is sorting according to MODEL, but k3 to resultline */      if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, fixed or timevarying, k1 is sorting according to MODEL, but k3 to resultline */
        /* 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) */         /* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
       /* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/        /* 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 */
Line 10531  int decoderesult( char resultline[], int Line 11343  int decoderesult( char resultline[], int
       Tvresult[nres][k3]=(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 */
       precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */        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);        /* 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                                 */
Line 10549  int decoderesult( char resultline[], int Line 11361  int decoderesult( char resultline[], int
       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 */
       precov[nres][k1]=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]);        /* 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 "V2+V3+V4+V6+V7+V6*V2+V7*V2+V6*V3+V7*V3+V6*V4+V7*V4+age*V2+age*V3+age*V4+age*V6+age*V7+age*V6*V2+age*V6*V3+age*V7*V3+age*V6*V4+age*V7*V4\r"*/
       /* Tvar[k1]; */ /* Age variable */        /* Tvar[k1]; */ /* Age variable */ /* 17 age*V6*V2 ?*/
       /* Wrong we want the value of variable name Tvar[k1] */        /* Wrong we want the value of variable name Tvar[k1] */
               if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
       k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/          precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
       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)*/        /* 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]]); */
       TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */        }else{
       precov[nres][k1]=Tvalsel[k3];          k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=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]);          k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
           TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
           precov[nres][k1]=Tvalsel[k3];
         }
         /* printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]); */
     }else if( Dummy[k1]==3 ){ /* For quant with age product */      }else if( Dummy[k1]==3 ){ /* For quant with age product */
       k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */        if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
       k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */          precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];      
       TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */        /* 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]]); */
       precov[nres][k1]=Tvalsel[k3q];        }else{
       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]);          k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
     }else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */          k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
           TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
           precov[nres][k1]=Tvalsel[k3q];
         }
         /* printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1,  Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
       }else if(Typevar[k1]==2 || Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
       precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];              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]]);        /* 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 Decoderesult 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 Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);        fprintf(ficlog,"Error Decoderesult probably a product  Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
Line 10587  int decodemodel( char model[], int lasto Line 11408  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 10597  int decodemodel( char model[], int lasto Line 11419  int decodemodel( char model[], int lasto
 /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1, Tage[1]=2 */
 {  {
   int i, j, k, ks, v;    int i, j, k, ks, v;
   int  j1, k1, k2, k3, k4;    int n,m;
   char modelsav[80];    int  j1, k1, k11, k12, k2, k3, k4;
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char modelsav[300];
     char stra[300], strb[300], strc[300], strd[300],stre[300],strf[300];
   char *strpt;    char *strpt;
     int  **existcomb;
     
     existcomb=imatrix(1,NCOVMAX,1,NCOVMAX);
     for(i=1;i<=NCOVMAX;i++)
       for(j=1;j<=NCOVMAX;j++)
         existcomb[i][j]=0;
       
   /*removespace(model);*/    /*removespace(model);*/
   if (strlen(model) >1){ /* If there is at least 1 covariate */    if (strlen(model) >1){ /* If there is at least 1 covariate */
     j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;      j=0, j1=0, k1=0, k12=0, k2=-1, ks=0, cptcovn=0;
     if (strstr(model,"AGE") !=0){      if (strstr(model,"AGE") !=0){
       printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);        printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
       fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);        fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     if (strstr(model,"v") !=0){      if (strstr(model,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' model=%s ",model);        printf("Error. 'v' must be in upper case 'V' model=1+age+%s ",model);
       fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);        fprintf(ficlog,"Error. 'v' must be in upper case model=1+age+%s ",model);fflush(ficlog);
       return 1;        return 1;
     }      }
     strcpy(modelsav,model);       strcpy(modelsav,model); 
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=1+age+%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
         printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
         fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
         return 1;          return 1;
Line 10636  int decodemodel( char model[], int lasto Line 11465  int decodemodel( char model[], int lasto
         substrchaine(modelsav, model, "age*age");          substrchaine(modelsav, model, "age*age");
     }else      }else
       nagesqr=0;        nagesqr=0;
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){ /* V2 +V3 +V4 +V6 +V7 +V6*V2 +V7*V2 +V6*V3 +V7*V3 +V6*V4 +V7*V4 +age*V2 +age*V3 +age*V4 +age*V6 +age*V7 +age*V6*V2 +V7*V2 +age*V6*V3 +age*V7*V3 +age*V6*V4 +age*V7*V4 */
       j=nbocc(modelsav,'+'); /**< j=Number of '+' */        j=nbocc(modelsav,'+'); /**< j=Number of '+' */
       j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */        j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
       cptcovs=j+1-j1; /**<  Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =5-3=2  */        cptcovs=0; /**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age => V1 + V3 =4+1-3=2  Wrong */
       cptcovt= j+1; /* Number of total covariates in the model, not including        cptcovt= j+1; /* Number of total covariates in the model, not including
                      * cst, age and age*age                        * cst, age and age*age 
                      * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/                       * V1+V1*age+ V3 + V3*V4+age*age=> 3+1=4*/
       /* including age products which are counted in cptcovage.        /* including age products which are counted in cptcovage.
        * but the covariates which are products must be treated          * but the covariates which are products must be treated 
        * separately: ncovn=4- 2=2 (V1+V3). */         * separately: ncovn=4- 2=2 (V1+V3). */
       cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */        cptcovprod=0; /**< Number of products  V1*V2 +v3*age = 2 */
         cptcovdageprod=0; /* Number of doouble products with age age*Vn*VM or Vn*age*Vm or Vn*Vm*age */
       cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */        cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
               cptcovprodage=0;
         /* cptcovprodage=nboccstr(modelsav,"age");*/
               
       /*   Design        /*   Design
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight         *  V1   V2   V3   V4  V5  V6  V7  V8  V9 Weight
Line 10656  int decodemodel( char model[], int lasto Line 11487  int decodemodel( char model[], int lasto
        * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8         * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
        *   k=  1    2      3       4     5       6      7        8         *   k=  1    2      3       4     5       6      7        8
        *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8         *  cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
        *  covar[k,i], value of kth covariate if not including age for individual i:         *  covar[k,i], are for fixed covariates, value of kth covariate if not including age for individual i:
        *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)         *       covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
        *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8         *  Tvar[k] # of the kth covariate:  Tvar[1]=2  Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
        *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and          *       if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and 
        *  Tage[++cptcovage]=k         *  Tage[++cptcovage]=k
        *       if products, new covar are created after ncovcol with k1         *       if products, new covar are created after ncovcol + nqv (quanti fixed) with k1
        *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11         *  Tvar[k]=ncovcol+k1; # of the kth covariate product:  Tvar[5]=ncovcol+1=10  Tvar[6]=ncovcol+1=11
        *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product         *  Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
        *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8         *  Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
        *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];         *  Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
        *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted         *  Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
        *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11         *  V1   V2   V3   V4  V5  V6  V7  V8  V9  V10  V11
        *  <          ncovcol=8                >         *  <          ncovcol=8  8 fixed covariate. Additional starts at 9 (V5*V6) and 10(V7*V8)              >
        *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2         *       Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8    d1   d1   d2  d2
        *          k=  1    2      3       4     5       6      7        8    9   10   11  12         *          k=  1    2      3       4     5       6      7        8    9   10   11  12
        *     Tvar[k]= 2    1      3       3    10      11      8        8    5    6    7   8         *     Tvard[k]= 2    1      3       3    10      11      8        8    5    6    7   8
        * p Tvar[1]@12={2,   1,     3,      3,  11,     10,     8,       8,   7,   8,   5,  6}         * p Tvar[1]@12={2,   1,     3,      3,   9,     10,     8,       8}
        * p Tprod[1]@2={                         6, 5}         * p Tprod[1]@2={                         6, 5}
        *p Tvard[1][1]@4= {7, 8, 5, 6}         *p Tvard[1][1]@4= {7, 8, 5, 6}
        * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8            * covar[k][i]= V2   V1      ?      V3    V5*V6?   V7*V8?  ?       V8   
Line 10702  int decodemodel( char model[], int lasto Line 11533  int decodemodel( char model[], int lasto
         Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
       }        }
       cptcovage=0;        cptcovage=0;
   
         /* First loop in order to calculate */
         /* for age*VN*Vm
          * Provides, Typevar[k], Tage[cptcovage], existcomb[n][m], FixedV[ncovcolt+k12]
          * Tprod[k1]=k  Tposprod[k]=k1;    Tvard[k1][1] =m;
         */
         /* Needs  FixedV[Tvardk[k][1]] */
         /* For others:
          * Sets   Typevar[k];
          * Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
          *        Tposprod[k]=k11;
          *        Tprod[k11]=k;
          *        Tvardk[k][1] =m;
          * Needs FixedV[Tvardk[k][1]] == 0
         */
         
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right          cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
                                          modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */                                           modelsav==V2+V1+V5*age+V4+V3*age strb=V3*age stra=V2+V1V5*age+V4 */    /* <model> "V5+V4+V3+V4*V3+V5*age+V1*age+V1" strb="V5" stra="V4+V3+V4*V3+V5*age+V1*age+V1" */
Line 10709  int decodemodel( char model[], int lasto Line 11556  int decodemodel( char model[], int lasto
           strcpy(strb,modelsav); /* and analyzes it */            strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/          /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age */          if (strchr(strb,'*')) {  /**< Model includes a product V2+V1+V5*age+ V4+V3*age strb=V3*age OR double product with age strb=age*V6*V2 or V6*V2*age or V6*age*V2 */
           cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */            cutl(strc,strd,strb,'*'); /**< k=1 strd*strc  Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 OR strb=age*V6*V2 strc=V6*V2 strd=age OR c=V2*age OR c=age*V2  */
           if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */            if(strchr(strc,'*')) { /**< Model with age and DOUBLE product: allowed since 0.99r44, strc=V6*V2 or V2*age or age*V2, strd=age or V6 or V6   */
             /* covar is not filled and then is empty */              Typevar[k]=3;  /* 3 for age and double product age*Vn*Vm varying of fixed */
             cptcovprod--;              if(strstr(strc,"age")!=0) { /* It means that strc=V2*age or age*V2 and thus that strd=Vn */
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */                cutl(stre,strf,strc,'*') ; /* strf=age or Vm, stre=Vm or age. If strc=V6*V2 then strf=V6 and stre=V2 */
             Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */                strcpy(strc,strb); /* save strb(=age*Vn*Vm) into strc */
             Typevar[k]=1;  /* 1 for age product */                /* We want strb=Vn*Vm */
             cptcovage++; /* Counts the number of covariates which include age as a product */                if(strcmp(strf,"age")==0){ /* strf is "age" so that stre=Vm =V2 . */
             Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */                  strcpy(strb,strd);
             /*printf("stre=%s ", stre);*/                  strcat(strb,"*");
           } else if (strcmp(strd,"age")==0) { /* or age*Vn */                  strcat(strb,stre);
             cptcovprod--;                }else{  /* strf=Vm  If strf=V6 then stre=V2 */
             cutl(stre,strb,strc,'V');                  strcpy(strb,strf);
             Tvar[k]=atoi(stre);                  strcat(strb,"*");
             Typevar[k]=1;  /* 1 for age product */                  strcat(strb,stre);
             cptcovage++;                  strcpy(strd,strb); /* in order for strd to not be "age"  for next test (will be Vn*Vm */
             Tage[cptcovage]=k;                }
           } else {  /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2  strb=V3*V2*/                /* printf("DEBUG FIXED k=%d, Tage[k]=%d, Tvar[Tage[k]=%d,FixedV[Tvar[Tage[k]]]=%d\n",k,Tage[k],Tvar[Tage[k]],FixedV[Tvar[Tage[k]]]); */
             /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */                /* FixedV[Tvar[Tage[k]]]=0; /\* HERY not sure if V7*V4*age Fixed might not exist  yet*\/ */
             cptcovn++;              }else{  /* strc=Vn*Vm (and strd=age) and should be strb=Vn*Vm but want to keep original strb double product  */
             cptcovprodnoage++;k1++;                strcpy(stre,strb); /* save full b in stre */
                 strcpy(strb,strc); /* save short c in new short b for next block strb=Vn*Vm*/
                 strcpy(strf,strc); /* save short c in new short f */
                 cutl(strc,strd,strf,'*'); /* We get strd=Vn and strc=Vm for next block (strb=Vn*Vm)*/
                 /* strcpy(strc,stre);*/ /* save full e in c for future */
               }
               cptcovdageprod++; /* double product with age  Which product is it? */
               /* strcpy(strb,strc);  /\* strb was age*V6*V2 or V6*V2*age or V6*age*V2 IS now V6*V2 or V2*age or age*V2 *\/ */
               /* cutl(strc,strd,strb,'*'); /\* strd=  V6    or   V2     or    age and  strc=  V2 or    age or    V2 *\/ */
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but              n=atoi(stre);
                                                 because this model-covariate is a construction we invent a new column  
                                                 which is after existing variables ncovcol+nqv+ntv+nqtv + k1  
                                                 If already ncovcol=4 and model= V2 + V1 + V1*V4 + age*V3 + V3*V2  
                                                 thus after V4 we invent V5 and V6 because age*V3 will be computed in 4  
                                                 Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=4 etc */  
             /* 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 double fixed dummy covariates */  
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              m=atoi(strc);
             Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */              cptcovage++; /* Counts the number of covariates which include age as a product */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tage[cptcovage]=k; /* For age*V3*V2 gives the position in model of covariates associated with age Tage[1]=6 HERY too*/
             Tvardk[k][1] =atoi(strc); /* m 1 for V1*/              if(existcomb[n][m] == 0){
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/                /*  r /home/brouard/Documents/Recherches/REVES/Zachary/Zach-2022/Feinuo_Sun/Feinuo-threeway/femV12V15_3wayintNBe.imach */
             Tvardk[k][2] =atoi(stre); /* n 4 for V4*/                printf("Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */                fprintf(ficlog,"Warning in model combination V%d*V%d should exist in the model before adding V%d*V%d*age !\n",n,m,n,m);
             /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */                fflush(ficlog);
             /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */                k1++;  /* The combination Vn*Vm will be in the model so we create it at k1 */
             /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */                k12++;
             /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */                existcomb[n][m]=k1;
             for (i=1; i<=lastobs;i++){                existcomb[m][n]=k1;
               /* Computes the new covariate which is a product of                Tvar[k]=ncovcol+nqv+ntv+nqtv+k1;
                  covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */                Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2+ age*V6*V3 Gives the k position of the k1 double product Vn*Vm or age*Vn*Vm*/
               covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];                Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 Gives the k1 double product  Vn*Vm or age*Vn*Vm at the k position */
                 Tvard[k1][1] =m; /* m 1 for V1*/
                 Tvardk[k][1] =m; /* m 1 for V1*/
                 Tvard[k1][2] =n; /* n 4 for V4*/
                 Tvardk[k][2] =n; /* n 4 for V4*/
   /*            Tvar[Tage[cptcovage]]=k1;*/ /* Tvar[6=age*V3*V2]=9 (new fixed covariate) */ /* We don't know about Fixed yet HERE */
                 if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                   for (i=1; i<=lastobs;i++){/* For fixed product */
                     /* Computes the new covariate which is a product of
                        covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                     covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                   }
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                   FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=0;
                 }else{ /*End of FixedV */
                   cptcovprodvage++; /* Counting the number of varying covariate with age */
                   FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=1;
                 }
               }else{  /* k1 Vn*Vm already exists */
                 k11=existcomb[n][m];
                 Tposprod[k]=k11; /* OK */
                 Tvar[k]=Tvar[Tprod[k11]]; /* HERY */
                 Tvardk[k][1]=m;
                 Tvardk[k][2]=n;
                 if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                   /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                   /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
                   Tvar[Tage[cptcovage]]=k1;
                   FixedV[ncovcolt+k12]=0; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=0;
                 }else{ /* Already exists but time varying (and age) */
                   /*cptcovage++;*/ /* Counts the number of covariates which include age as a product */
                   /*Tage[cptcovage]=k;*/ /* For age*V3*V2 Tage[1]=V3*V3=9 HERY too*/
                   /* Tvar[Tage[cptcovage]]=k1; */
                   cptcovprodvage++;
                   FixedV[ncovcolt+k12]=1; /* We expand Vn*Vm */
                   k12++;
                   FixedV[ncovcolt+k12]=1;
                 }
             }              }
           } /* End age is not in the model */              /* Tage[cptcovage]=k;  /\*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 *\/ */
         } /* End if model includes a product */              /* Tvar[k]=k11; /\* HERY *\/ */
         else { /* not a product */            } else {/* simple product strb=age*Vn so that c=Vn and d=age, or strb=Vn*age so that c=age and d=Vn, or b=Vn*Vm so that c=Vm and d=Vn */
               cptcovprod++;
               if (strcmp(strc,"age")==0) { /**< Model includes age: strb= Vn*age c=age d=Vn*/
                 /* covar is not filled and then is empty */
                 cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
                 Tvar[k]=atoi(stre);  /* V2+V1+V5*age+V4+V3*age Tvar[5]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
                 Typevar[k]=1;  /* 1 for age product */
                 cptcovage++; /* Counts the number of covariates which include age as a product */
                 Tage[cptcovage]=k;  /*  V2+V1+V4+V3*age Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
                 if( FixedV[Tvar[k]] == 0){
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                 }else{
                   cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
                 }
                 /*printf("stre=%s ", stre);*/
               } else if (strcmp(strd,"age")==0) { /* strb= age*Vn c=Vn */
                 cutl(stre,strb,strc,'V');
                 Tvar[k]=atoi(stre);
                 Typevar[k]=1;  /* 1 for age product */
                 cptcovage++;
                 Tage[cptcovage]=k;
                 if( FixedV[Tvar[k]] == 0){
                   cptcovprodage++; /* Counting the number of fixed covariate with age */
                 }else{
                   cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
                 }
               }else{ /*  for product Vn*Vm */
                 Typevar[k]=2;  /* 2 for product Vn*Vm */
                 cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
                 n=atoi(stre);
                 cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
                 m=atoi(strc);
                 k1++;
                 cptcovprodnoage++;
                 if(existcomb[n][m] != 0 || existcomb[m][n] != 0){
                   printf("Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
                   fprintf(ficlog,"Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
                   fflush(ficlog);
                   k11=existcomb[n][m];
                   Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
                   Tposprod[k]=k11;
                   Tprod[k11]=k;
                   Tvardk[k][1] =m; /* m 1 for V1*/
                   /* Tvard[k11][1] =m; /\* n 4 for V4*\/ */
                   Tvardk[k][2] =n; /* n 4 for V4*/                
                   /* Tvard[k11][2] =n; /\* n 4 for V4*\/ */
                 }else{ /* combination Vn*Vm doesn't exist we create it (no age)*/
                   existcomb[n][m]=k1;
                   existcomb[m][n]=k1;
                   Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* ncovcolt+k1; For model-covariate k tells which data-covariate to use but
                                                       because this model-covariate is a construction we invent a new column
                                                       which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                                       If already ncovcol=4 and model= V2 + V1 + V1*V4 + age*V3 + V3*V2
                                                       thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
                                                       Tvar[3=V1*V4]=4+1=5 Tvar[5=V3*V2]=4 + 2= 6, Tvar[4=age*V3]=3 etc */
                   /* Please remark that the new variables are model dependent */
                   /* If we have 4 variable but the model uses only 3, like in
                    * model= V1 + age*V1 + V2 + V3 + age*V2 + age*V3 + V1*V2 + V1*V3
                    *  k=     1     2      3   4     5        6        7       8
                    * Tvar[k]=1     1       2   3     2        3       (5       6) (and not 4 5 because of V4 missing)
                    * Tage[kk]    [1]= 2           [2]=5      [3]=6                  kk=1 to cptcovage=3
                    * Tvar[Tage[kk]][1]=2          [2]=2      [3]=3
                    */
                   /* We need to feed some variables like TvarVV, but later on next loop because of ncovv (k2) is not correct */
                   Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 +V6*V2*age  */
                   Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
                   Tvard[k1][1] =m; /* m 1 for V1*/
                   Tvardk[k][1] =m; /* m 1 for V1*/
                   Tvard[k1][2] =n; /* n 4 for V4*/
                   Tvardk[k][2] =n; /* n 4 for V4*/
                   k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
                   /* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) *\/ */
                   /* Tvar[cptcovt+k2+1]=Tvard[k1][2];  /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) *\/ */
                   /*ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
                   /*                     1  2   3      4     5 | Tvar[5+1)=1, Tvar[7]=2   */
                   if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with Vn*Vm */
                     for (i=1; i<=lastobs;i++){/* For fixed product */
                       /* Computes the new covariate which is a product of
                          covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
                       covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
                     }
                     /* TvarVV[k2]=n; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                     /* TvarVV[k2+1]=m; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                   }else{ /* not FixedV */
                     /* TvarVV[k2]=n; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                     /* TvarVV[k2+1]=m; */
                     /* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE *\/ */
                   }                 
                 }  /* End of creation of Vn*Vm if not created by age*Vn*Vm earlier  */
               } /*  End of product Vn*Vm */
             } /* End of age*double product or simple product */
           }else { /* not a product */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
Line 10779  int decodemodel( char model[], int lasto Line 11758  int decodemodel( char model[], int lasto
                                 /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);                                  /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
                                   scanf("%d",i);*/                                    scanf("%d",i);*/
       } /* end of loop + on total covariates */        } /* end of loop + on total covariates */
   
         
     } /* end if strlen(modelsave == 0) age*age might exist */      } /* end if strlen(modelsave == 0) age*age might exist */
   } /* end if strlen(model == 0) */    } /* end if strlen(model == 0) */
       cptcovs=cptcovt - cptcovdageprod - cptcovprod;/**<  Number of simple covariates V1 +V1*age +V3 +V3*V4 +age*age + age*v4*V3=> V1 + V3 =4+1-3=2  */
   
   /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.    /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
     If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/      If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
       
Line 10807  int decodemodel( char model[], int lasto Line 11789  int decodemodel( char model[], int lasto
   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
         /* Computing effective variables, ie used by the model, that is from the cptcovt variables */          /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
   printf("Model=1+age+%s\n\    printf("Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   fprintf(ficlog,"Model=1+age+%s\n\    fprintf(ficlog,"Model=1+age+%s\n\
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product, 3 for double product with age  \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}    for(k=-1;k<=NCOVMAX; k++){ Fixed[k]=0; Dummy[k]=0;}
   for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */    for(k=1;k<=NCOVMAX; k++){TvarFind[k]=0; TvarVind[k]=0;}
   
   
     /* Second loop for calculating  Fixed[k], Dummy[k]*/
   
     
     for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0,ncovva=0,ncovvta=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt loop on k from model */
     if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 0;        Dummy[k]= 0;
Line 10830  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11818  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 *\/ */
       Fixed[k]= 0;  
       Dummy[k]= 0;  
       ncoveff++;  
       ncovf++;  
       modell[k].maintype= FTYPE;  
       TvarF[ncovf]=Tvar[k];  
       /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */  
       TvarFind[ncovf]=k;  
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  
       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  
     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */      }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 1;        Dummy[k]= 1;
Line 10856  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11834  Dummy[k] 0=dummy (0 1), 1 quantitative (
       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 10873  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11858  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 10888  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 11880  Dummy[k] 0=dummy (0 1), 1 quantitative (
       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */        TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
       TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */        TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
       /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */        /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
       printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);        /* printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%Ad,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); */
       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);        /* printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); */
     }else if (Typevar[k] == 1) {  /* product with age */      }else if (Typevar[k] == 1) {  /* product with age */
       ncova++;        ncova++;
       TvarA[ncova]=Tvar[k];        TvarA[ncova]=Tvar[k];
       TvarAind[ncova]=k;        TvarAind[ncova]=k;
         /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
         /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
         Fixed[k]= 2;          Fixed[k]= 2;
         Dummy[k]= 2;          Dummy[k]= 2;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APFD;          modell[k].subtype= APFD;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*  (2)age*V3 */
           TvarAVVAind[ncovta]=k;
         /* ncoveff++; */          /* ncoveff++; */
       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
         Fixed[k]= 2;          Fixed[k]= 2;
         Dummy[k]= 3;          Dummy[k]= 3;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */          modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*   */
           TvarAVVAind[ncovta]=k;
         /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv ){        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
         Fixed[k]= 3;          Fixed[k]= 3;
         Dummy[k]= 2;          Dummy[k]= 2;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APVD;                /*      Product age * varying dummy */          modell[k].subtype= APVD;                /*      Product age * varying dummy */
           ncovva++;
           TvarVVA[ncovva]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*   */
           TvarAVVAind[ncovta]=k;
         /* ntveff++; /\* Only simple time varying dummy variable *\/ */          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
         Fixed[k]= 3;          Fixed[k]= 3;
         Dummy[k]= 3;          Dummy[k]= 3;
         modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
         modell[k].subtype= APVQ;                /*      Product age * varying quantitative */          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
           ncovva++;
           TvarVVA[ncovva]=Tvar[k]; /*   */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvar[k]; /*  (1)+age*V6 + (2)age*V7 */
           TvarAVVAind[ncovta]=k;
         /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
       }        }
     }else if (Typevar[k] == 2) {  /* product without age */      }else if( Tposprod[k]>0  &&  Typevar[k]==2){  /* Detects if fixed product no age Vm*Vn */
       k1=Tposprod[k];        printf("MEMORY ERRORR k=%d  Tposprod[k]=%d, Typevar[k]=%d\n ",k, Tposprod[k], Typevar[k]);
       if(Tvard[k1][1] <=ncovcol){        if(FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* Needs a fixed product Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol V3*V2 */
         if(Tvard[k1][2] <=ncovcol){        printf("MEMORY ERRORR k=%d Tvardk[k][1]=%d, Tvardk[k][2]=%d, FixedV[Tvardk[k][1]]=%d,FixedV[Tvardk[k][2]]=%d\n ",k,Tvardk[k][1],Tvardk[k][2],FixedV[Tvardk[k][1]],FixedV[Tvardk[k][2]]);
           Fixed[k]= 1;          Fixed[k]= 0;
           Dummy[k]= 0;          Dummy[k]= 0;
           ncoveff++;
           ncovf++;
           /* ncovv++; */
           /* TvarVV[ncovv]=Tvardk[k][1]; */
           /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
           /* ncovv++; */
           /* TvarVV[ncovv]=Tvardk[k][2]; */
           /* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE *\/ */
           modell[k].maintype= FTYPE;
           TvarF[ncovf]=Tvar[k];
           /* TnsdVar[Tvar[k]]=nsd; */ /* To be done */
           TvarFind[ncovf]=k;
           TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
           TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         }else{/* product varying Vn * Vm without age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
           /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
           /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
           /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
           k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
           ncovvt++;
           TvarVV[ncovvt]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
           TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
           ncovvt++;
           TvarVV[ncovvt]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
           TvarVVind[ncovvt]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
           
           /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
           /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
           
           if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
             if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDD;            /*      Product fixed dummy * fixed dummy */
               ncovf++; /* Fixed variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
               Fixed[k]= 0;  /* Fixed product */
               Dummy[k]= 1;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDQ;            /*      Product fixed dummy * fixed quantitative */
               ncovf++; /* Varying variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product fixed dummy * varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
               TvarVind[ncovv]=k;/* TvarVind[1]=5 */ 
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product fixed dummy * varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti  */
             if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
               Fixed[k]= 0;  /*  Fixed product */
               Dummy[k]= 1;
               modell[k].maintype= FTYPE;
               modell[k].subtype= FPDQ;            /*      Product fixed quantitative * fixed dummy */
               ncovf++; /* Fixed variables without age */
               TvarF[ncovf]=Tvar[k];
               TvarFind[ncovf]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product fixed quantitative * varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product fixed quantitative * varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
             if(Tvard[k1][2] <=ncovcol){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product time varying dummy * fixed dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying dummy * fixed quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[k]= 1;
               Dummy[k]= 0;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDD;            /*      Product time varying dummy * time varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying dummy * time varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
             if(Tvard[k1][2] <=ncovcol){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying quantitative * fixed dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product time varying quantitative * fixed quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPDQ;            /*      Product time varying quantitative * time varying dummy */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
               Fixed[k]= 1;
               Dummy[k]= 1;
               modell[k].maintype= VTYPE;
               modell[k].subtype= VPQQ;            /*      Product time varying quantitative * time varying quantitative */
               ncovv++; /* Varying variables without age */
               TvarV[ncovv]=Tvar[k];
               TvarVind[ncovv]=k;
             }
           }else{
             printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
             fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           } /*end k1*/
         }
       }else if(Typevar[k] == 3){  /* product Vn * Vm with age, V1+V3+age*V1+age*V3+V1*V3 looking at V1*V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product  */
         /*#  ID           V1     V2          weight               birth   death   1st    s1      V3      V4      V5       2nd  s2 */
         /* model V1+V3+age*V1+age*V3+V1*V3 + V1*V3*age*/
         /*  Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
         k1=Tposprod[k];  /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
         ncova++;
         TvarA[ncova]=Tvard[k1][1];  /*  TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
         TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
         ncova++;
         TvarA[ncova]=Tvard[k1][2];  /*  TvarVV[3]=V3 */
         TvarAind[ncova]=k;  /*  TvarVVind[2]=5 (because TvarVVind[2] was V1*V3 at position 5 */
   
         /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
         /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
         if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
         }else{
           ncovva++;  /* HERY  reached */
           TvarVVA[ncovva]=Tvard[k1][1]; /*  age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4  */
           TvarVVAind[ncovva]=k;
           ncovva++;
           TvarVVA[ncovva]=Tvard[k1][2]; /*   */
           TvarVVAind[ncovva]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][1]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
           ncovta++;
           TvarAVVA[ncovta]=Tvard[k1][2]; /*   age*V6*V3 +age*V7*V3 + age*V6*V4 +age*V7*V4 */
           TvarAVVAind[ncovta]=k;
         }
         if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
           if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
             Fixed[k]= 2;
             Dummy[k]= 2;
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
           ncovf++; /* Fixed variables without age */            /* TvarF[ncova]=Tvar[k];   /\* Problem to solve *\/ */
           TvarF[ncovf]=Tvar[k];            /* TvarFind[ncova]=k; */
           TvarFind[ncovf]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
         }else if(Tvard[k1][2] <=ncovcol+nqv){            Fixed[k]= 2;  /* Fixed product */
           Fixed[k]= 0;  /* or 2 ?*/            Dummy[k]= 3;
           Dummy[k]= 1;  
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
           ncovf++; /* Varying variables without age */            /* TvarF[ncova]=Tvar[k]; */
           TvarF[ncovf]=Tvar[k];            /* TvarFind[ncova]=k; */
           TvarFind[ncovf]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            Fixed[k]= 3;
           Fixed[k]= 1;            Dummy[k]= 2;
           Dummy[k]= 0;  
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */            modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
           ncovv++; /* Varying variables without age */            TvarV[ncova]=Tvar[k];  /* TvarV[1]=Tvar[5]=5 because there is a V4 */
           TvarV[ncovv]=Tvar[k];            TvarVind[ncova]=k;/* TvarVind[1]=5 */ 
           TvarVind[ncovv]=k;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            Fixed[k]= 3;
           Fixed[k]= 1;            Dummy[k]= 3;
           Dummy[k]= 1;  
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */            modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncovv++; /\* Varying variables without age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncovv]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncovv]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv){        }else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti  */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
           Fixed[k]= 0;  /* or 2 ?*/            Fixed[k]= 2;  /*  Fixed product */
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
           modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
           ncovf++; /* Fixed variables without age */            /* ncova++; /\* Fixed variables with age *\/ */
           TvarF[ncovf]=Tvar[k];            /* TvarF[ncovf]=Tvar[k]; */
           TvarFind[ncovf]=k;            /* TvarFind[ncovf]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */            modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
           ncovv++; /* Varying variables without age */            ncova++; /* Varying variables without age */
           TvarV[ncovv]=Tvar[k];            TvarV[ncova]=Tvar[k];
           TvarVind[ncovv]=k;            TvarVind[ncova]=k;
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables without age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 0;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */            modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */            modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
         if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
           Fixed[k]= 1;            Fixed[k]= 2;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 2;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 1;            Fixed[k]= 3;
           Dummy[k]= 1;            Dummy[k]= 3;
           modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
           modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
           ncovv++; /* Varying variables without age */            /* ncova++; /\* Varying variables with age *\/ */
           TvarV[ncovv]=Tvar[k];            /* TvarV[ncova]=Tvar[k]; */
           TvarVind[ncovv]=k;            /* TvarVind[ncova]=k; */
         }          }
       }else{        }else{
         printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
       } /*end k1*/        } /*end k1*/
     }else{      } else{
       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
     }      }
     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);      /* printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); */
     printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);      /* printf("           modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); */
     fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);      fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
   }    }
     ncovvta=ncovva;
   /* Searching for doublons in the model */    /* Searching for doublons in the model */
   for(k1=1; k1<= cptcovt;k1++){    for(k1=1; k1<= cptcovt;k1++){
     for(k2=1; k2 <k1;k2++){      for(k2=1; k2 <k1;k2++){
Line 11071  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 12285  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 11091  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 12305  Dummy[k] 0=dummy (0 1), 1 quantitative (
   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);    printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
   fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);    fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
   
     free_imatrix(existcomb,1,NCOVMAX,1,NCOVMAX);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
   printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
Line 11436  int prevalence_limit(double *p, double * Line 12652  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++){ */
Line 11450  int prevalence_limit(double *p, double * Line 12668  int prevalence_limit(double *p, double *
       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*\/ */
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* Here problem for varying dummy*/          /* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[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,TnsdVar[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]]);
       }          printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
       for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */          fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
         printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        }
         fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value *\/ */
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        /*        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 11472  int prevalence_limit(double *p, double * Line 12692  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,TnsdVar[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,TnsdVar[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 11492  int prevalence_limit(double *p, double * Line 12718  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 11535  int back_prevalence_limit(double *p, dou Line 12761  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,TnsdVar[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,TnsdVar[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,TnsdVar[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][resultmodel[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][resultmodel[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][resultmodel[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 11563  int back_prevalence_limit(double *p, dou Line 12796  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,TnsdVar[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 11587  int back_prevalence_limit(double *p, dou Line 12820  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,TnsdVar[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 11598  int back_prevalence_limit(double *p, dou Line 12831  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 11608  int back_prevalence_limit(double *p, dou Line 12841  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 11618  int hPijx(double *p, int bage, int fage) Line 12851  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,TnsdVar[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 11720  int hPijx(double *p, int bage, int fage) Line 12956  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,TnsdVar[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][resultmodel[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");  
         for (h=0; h<=nhstepm; h++){  
           /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/  
           fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );  
           /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */  
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */  
           fprintf(ficrespijb,"\n");  
         }  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       } /* end age deb */        }
     } /* end combination */        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         fprintf(ficrespijb,"\n");
       } /* end age deb */
       /* } /\* end combination *\/ */
   } /* end nres */    } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
Line 11816  int main(int argc, char *argv[]) Line 13056  int main(int argc, char *argv[])
   /* double ***mobaverage; */    /* double ***mobaverage; */
   double wald;    double wald;
   
   char line[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char  modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
Line 12149  int main(int argc, char *argv[]) Line 13389  int main(int argc, char *argv[])
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=%[^.\n]", model)) !=EOF){ /* Every character after model but dot and  return */
       if (num_filled != 1){
         printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
         model[0]='\0';
         goto end;
       }else{
         trimbtab(linetmp,line); /* Trims multiple blanks in line */
         strcpy(line, linetmp);
       }
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ /* Every character after 1+age but dot and  return */
     if (num_filled != 1){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
Line 12163  int main(int argc, char *argv[]) Line 13414  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 12191  int main(int argc, char *argv[]) Line 13442  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 12204  int main(int argc, char *argv[]) Line 13457  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 12447  Please run with mle=-1 to get a correct Line 13701  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 12485  Please run with mle=-1 to get a correct Line 13739  Please run with mle=-1 to get a correct
   TvarVDind=ivector(1,NCOVMAX); /*  */    TvarVDind=ivector(1,NCOVMAX); /*  */
   TvarVQ=ivector(1,NCOVMAX); /*  */    TvarVQ=ivector(1,NCOVMAX); /*  */
   TvarVQind=ivector(1,NCOVMAX); /*  */    TvarVQind=ivector(1,NCOVMAX); /*  */
     TvarVV=ivector(1,NCOVMAX); /*  */
     TvarVVind=ivector(1,NCOVMAX); /*  */
     TvarVVA=ivector(1,NCOVMAX); /*  */
     TvarVVAind=ivector(1,NCOVMAX); /*  */
     TvarAVVA=ivector(1,NCOVMAX); /*  */
     TvarAVVAind=ivector(1,NCOVMAX); /*  */
   
   Tvalsel=vector(1,NCOVMAX); /*  */    Tvalsel=vector(1,NCOVMAX); /*  */
   Tvarsel=ivector(1,NCOVMAX); /*  */    Tvarsel=ivector(1,NCOVMAX); /*  */
   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */    Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */    Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */    Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
     DummyV=ivector(-1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(-1,NCOVMAX); /* 1 to 3 */
   
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 12510  Please run with mle=-1 to get a correct Line 13773  Please run with mle=-1 to get a correct
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
                             * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.                               * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd. 
                             * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */                              * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
   Tvardk=imatrix(1,NCOVMAX,1,2);    Tvardk=imatrix(0,NCOVMAX,1,2);
   Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age    Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
Line 12530  Please run with mle=-1 to get a correct Line 13793  Please run with mle=-1 to get a correct
                                 * Tmodelqind[1]=1,Tvaraff[1]@9={4,                                  * Tmodelqind[1]=1,Tvaraff[1]@9={4,
                                 * 3, 1, 0, 0, 0, 0, 0, 0},                                  * 3, 1, 0, 0, 0, 0, 0, 0},
                                 * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/                                  * model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
   
   /* Probably useless zeroes */
     for(i=1;i<NCOVMAX;i++){
       DummyV[i]=0;
       FixedV[i]=0;
     }
   
     for(i=1; i <=ncovcol;i++){
       DummyV[i]=0;
       FixedV[i]=0;
     }
     for(i=ncovcol+1; i <=ncovcol+nqv;i++){
       DummyV[i]=1;
       FixedV[i]=0;
     }
     for(i=ncovcol+nqv+1; i <=ncovcol+nqv+ntv;i++){
       DummyV[i]=0;
       FixedV[i]=1;
     }
     for(i=ncovcol+nqv+ntv+1; i <=ncovcol+nqv+ntv+nqtv;i++){
       DummyV[i]=1;
       FixedV[i]=1;
     }
     for(i=1; i <=ncovcol+nqv+ntv+nqtv;i++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",i,i,DummyV[i],i,FixedV[i]);
     }
   
   
   
 /* Main decodemodel */  /* Main decodemodel */
   
   
Line 12594  Please run with mle=-1 to get a correct Line 13887  Please run with mle=-1 to get a correct
   }    }
       
   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 12740  Title=%s <br>Datafile=%s Firstpass=%d La Line 14033  Title=%s <br>Datafile=%s Firstpass=%d La
   fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\    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\
 This file: <a href=\"%s\">%s</a>Title=%s <br>Datafile=<a href=\"%s\">%s</a> 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 13106  Please run with mle=-1 to get a correct Line 14399  Please run with mle=-1 to get a correct
         fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficres,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);          fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }else if(Typevar[j]==3) { /* TO VERIFY */
           printf("  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficres,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d*age ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
       }        }
     }      }
     printf("\n");      printf("\n");
Line 13165  Please run with mle=-1 to get a correct Line 14463  Please run with mle=-1 to get a correct
           fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);            fprintf(fichtm, "<th>+  V%d*age</th>",Tvar[j]);
         }else if(Typevar[j]==2) {          }else if(Typevar[j]==2) {
           fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);            fprintf(fichtm, "<th>+  V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           }else if(Typevar[j]==3) { /* TO VERIFY */
             fprintf(fichtm, "<th>+  V%d*V%d*age</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }          }
       }        }
       fprintf(fichtm, "</tr>\n");        fprintf(fichtm, "</tr>\n");
Line 13222  Please run with mle=-1 to get a correct Line 14522  Please run with mle=-1 to get a correct
     }      }
           
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle >= 1) /* To big for the screen */      if(mle >= 1) /* Too big for the screen */
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");        printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     /* # 121 Var(a12)\n\ */      /* # 121 Var(a12)\n\ */
Line 13486  Please run with mle=-1 to get a correct Line 14786  Please run with mle=-1 to get a correct
       case 13:        case 13:
         num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);          num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
         nresult++; /* Sum of resultlines */          nresult++; /* Sum of resultlines */
         printf("Result %d: result:%s\n",nresult, resultlineori);          /* printf("Result %d: result:%s\n",nresult, resultlineori); */
         /* removefirstspace(&resultlineori); */          /* removefirstspace(&resultlineori); */
                   
         if(strstr(resultlineori,"v") !=0){          if(strstr(resultlineori,"v") !=0){
Line 13495  Please run with mle=-1 to get a correct Line 14795  Please run with mle=-1 to get a correct
           return 1;            return 1;
         }          }
         trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */          trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
         printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);          /* 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);
Line 13578  Please run with mle=-1 to get a correct Line 14878  Please run with mle=-1 to get a correct
         date2dmy(datebackf,&jbackf, &mbackf, &anbackf);          date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
       }        }
               
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);        printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);/* HERE valgrind Tvard*/
     }      }
     printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \      printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
Line 13728  Please run with mle=-1 to get a correct Line 15028  Please run with mle=-1 to get a correct
   
     pstamp(ficreseij);      pstamp(ficreseij);
                                   
     i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */      /* i1=pow(2,cptcoveff); /\* Number of combination of dummy covariates *\/ */
     if (cptcovn < 1){i1=1;}      /* if (cptcovn < 1){i1=1;} */
           
     for(nres=1; nres <= nresult; nres++) /* For each resultline */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */      /* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying *\/ */
       if(i1 != 1 && TKresult[nres]!= k)        /* if(i1 != 1 && TKresult[nres]!= k) */
         continue;        /*        continue; */
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       printf("\n#****** ");        printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcovs;j++){
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);        /* for(j=1;j<=cptcoveff;j++) { */
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);          /* fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
           fprintf(ficreseij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
           printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
           /* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
       }        }
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
         printf(" V%d=%f ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */          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 ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);          fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
       printf("******\n");        printf("******\n");
Line 13761  Please run with mle=-1 to get a correct Line 15064  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 13808  Please run with mle=-1 to get a correct Line 15111  Please run with mle=-1 to get a correct
       /* */        /* */
       if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */        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);  /* HERE model is empty */
       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);
       /* It might not be a good idea to mix dummies and quantitative */        /* It might not be a good idea to mix dummies and quantitative */
Line 13832  Please run with mle=-1 to get a correct Line 15135  Please run with mle=-1 to get a correct
         /* Tvresult[nres][j] Name of the variable at position j in this resultline */          /* 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  */          /* Tresult[nres][j] Value of this variable at position j could be a float if quantitative  */
 /* We give up with the combinations!! */  /* We give up with the combinations!! */
         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(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  */          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=%d ",Tvresult[nres][j],Tresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */            /* printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /\* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  *\/ */ /* TinvDoQresult[nres][Name of the variable] */
           fprintf(ficlog,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */            printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordered by the covariate values in the resultline  */
           fprintf(ficrest,"V%d=%d ",Tvresult[nres][j],Tresult[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][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
             fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline  */
           if(Fixed[modelresult[nres][j]]==0){ /* Fixed */            if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");              printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
           }else{            }else{
Line 13847  Please run with mle=-1 to get a correct Line 15152  Please run with mle=-1 to get a correct
           /* fprintf(ficlog,"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 */          }else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
           /* For each selected (single) quantitative value */            /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);            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 */            if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
             printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");              printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
           }else{            }else{
Line 13870  Please run with mle=-1 to get a correct Line 15177  Please run with mle=-1 to get a correct
               
       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 ",Tvresult[nres][j],Tresult[nres][j]);          fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
         /* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[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]])]); */          /* 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, TvarsQind gives the position of a quantitative in model equation  */        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation  */
         fprintf(ficresstdeij," V%d=%f ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);          fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
         fprintf(ficrescveij," V%d=%f ",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 13889  Please run with mle=-1 to get a correct Line 15198  Please run with mle=-1 to get a correct
         /* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[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]); /\* To solve *\/ */          /* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve *\/ */
         fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */          fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
       }         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
Line 13977  Please run with mle=-1 to get a correct Line 15286  Please run with mle=-1 to get a correct
   
           
     free_vector(weight,firstobs,lastobs);      free_vector(weight,firstobs,lastobs);
     free_imatrix(Tvardk,1,NCOVMAX,1,2);      free_imatrix(Tvardk,0,NCOVMAX,1,2);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,firstobs,lastobs);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,firstobs,lastobs);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
Line 14002  Please run with mle=-1 to get a correct Line 15311  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 14018  Please run with mle=-1 to get a correct Line 15328  Please run with mle=-1 to get a correct
   free_ivector(ncodemaxwundef,1,NCOVMAX);    free_ivector(ncodemaxwundef,1,NCOVMAX);
   free_ivector(Dummy,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
   free_ivector(Fixed,-1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
   free_ivector(DummyV,1,NCOVMAX);    free_ivector(DummyV,-1,NCOVMAX);
   free_ivector(FixedV,1,NCOVMAX);    free_ivector(FixedV,-1,NCOVMAX);
   free_ivector(Typevar,-1,NCOVMAX);    free_ivector(Typevar,-1,NCOVMAX);
   free_ivector(Tvar,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
   free_ivector(TvarsQ,1,NCOVMAX);    free_ivector(TvarsQ,1,NCOVMAX);
Line 14041  Please run with mle=-1 to get a correct Line 15351  Please run with mle=-1 to get a correct
   free_ivector(TvarVDind,1,NCOVMAX);    free_ivector(TvarVDind,1,NCOVMAX);
   free_ivector(TvarVQ,1,NCOVMAX);    free_ivector(TvarVQ,1,NCOVMAX);
   free_ivector(TvarVQind,1,NCOVMAX);    free_ivector(TvarVQind,1,NCOVMAX);
     free_ivector(TvarAVVA,1,NCOVMAX);
     free_ivector(TvarAVVAind,1,NCOVMAX);
     free_ivector(TvarVVA,1,NCOVMAX);
     free_ivector(TvarVVAind,1,NCOVMAX);
     free_ivector(TvarVV,1,NCOVMAX);
     free_ivector(TvarVVind,1,NCOVMAX);
     
   free_ivector(Tvarsel,1,NCOVMAX);    free_ivector(Tvarsel,1,NCOVMAX);
   free_vector(Tvalsel,1,NCOVMAX);    free_vector(Tvalsel,1,NCOVMAX);
   free_ivector(Tposprod,1,NCOVMAX);    free_ivector(Tposprod,1,NCOVMAX);
   free_ivector(Tprod,1,NCOVMAX);    free_ivector(Tprod,1,NCOVMAX);
   free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(Tvaraff,1,NCOVMAX);
   free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(invalidvarcomb,0,ncovcombmax);
   free_ivector(Tage,1,NCOVMAX);    free_ivector(Tage,1,NCOVMAX);
   free_ivector(Tmodelind,1,NCOVMAX);    free_ivector(Tmodelind,1,NCOVMAX);
   free_ivector(TmodelInvind,1,NCOVMAX);    free_ivector(TmodelInvind,1,NCOVMAX);

Removed from v.1.335  
changed lines
  Added in v.1.358


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