Diff for /imach/src/imach.c between versions 1.266 and 1.295

version 1.266, 2017/05/13 07:26:12 version 1.295, 2019/05/18 09:52:50
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.295  2019/05/18 09:52:50  brouard
     Summary: doxygen tex bug
   
     Revision 1.294  2019/05/16 14:54:33  brouard
     Summary: There was some wrong lines added
   
     Revision 1.293  2019/05/09 15:17:34  brouard
     *** empty log message ***
   
     Revision 1.292  2019/05/09 14:17:20  brouard
     Summary: Some updates
   
     Revision 1.291  2019/05/09 13:44:18  brouard
     Summary: Before ncovmax
   
     Revision 1.290  2019/05/09 13:39:37  brouard
     Summary: 0.99r18 unlimited number of individuals
   
     The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.
   
     Revision 1.289  2018/12/13 09:16:26  brouard
     Summary: Bug for young ages (<-30) will be in r17
   
     Revision 1.288  2018/05/02 20:58:27  brouard
     Summary: Some bugs fixed
   
     Revision 1.287  2018/05/01 17:57:25  brouard
     Summary: Bug fixed by providing frequencies only for non missing covariates
   
     Revision 1.286  2018/04/27 14:27:04  brouard
     Summary: some minor bugs
   
     Revision 1.285  2018/04/21 21:02:16  brouard
     Summary: Some bugs fixed, valgrind tested
   
     Revision 1.284  2018/04/20 05:22:13  brouard
     Summary: Computing mean and stdeviation of fixed quantitative variables
   
     Revision 1.283  2018/04/19 14:49:16  brouard
     Summary: Some minor bugs fixed
   
     Revision 1.282  2018/02/27 22:50:02  brouard
     *** empty log message ***
   
     Revision 1.281  2018/02/27 19:25:23  brouard
     Summary: Adding second argument for quitting
   
     Revision 1.280  2018/02/21 07:58:13  brouard
     Summary: 0.99r15
   
     New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c
   
     Revision 1.279  2017/07/20 13:35:01  brouard
     Summary: temporary working
   
     Revision 1.278  2017/07/19 14:09:02  brouard
     Summary: Bug for mobil_average=0 and prevforecast fixed(?)
   
     Revision 1.277  2017/07/17 08:53:49  brouard
     Summary: BOM files can be read now
   
     Revision 1.276  2017/06/30 15:48:31  brouard
     Summary: Graphs improvements
   
     Revision 1.275  2017/06/30 13:39:33  brouard
     Summary: Saito's color
   
     Revision 1.274  2017/06/29 09:47:08  brouard
     Summary: Version 0.99r14
   
     Revision 1.273  2017/06/27 11:06:02  brouard
     Summary: More documentation on projections
   
     Revision 1.272  2017/06/27 10:22:40  brouard
     Summary: Color of backprojection changed from 6 to 5(yellow)
   
     Revision 1.271  2017/06/27 10:17:50  brouard
     Summary: Some bug with rint
   
     Revision 1.270  2017/05/24 05:45:29  brouard
     *** empty log message ***
   
     Revision 1.269  2017/05/23 08:39:25  brouard
     Summary: Code into subroutine, cleanings
   
     Revision 1.268  2017/05/18 20:09:32  brouard
     Summary: backprojection and confidence intervals of backprevalence
   
     Revision 1.267  2017/05/13 10:25:05  brouard
     Summary: temporary save for backprojection
   
   Revision 1.266  2017/05/13 07:26:12  brouard    Revision 1.266  2017/05/13 07:26:12  brouard
   Summary: Version 0.99r13 (improvements and bugs fixed)    Summary: Version 0.99r13 (improvements and bugs fixed)
   
Line 818  Back prevalence and projections: Line 909  Back prevalence and projections:
    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                         oldm=oldms;savm=savms;                          oldm=oldms;savm=savms;
   
    - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);     - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
      Computes the transition matrix starting at age 'age' over       Computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
Line 978  typedef struct { Line 1069  typedef struct {
 #define NINTERVMAX 8  #define NINTERVMAX 8
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20  /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/  /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
 #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1   #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1 
 #define MAXN 20000  /*#define MAXN 20000 */ /* Should by replaced by nobs, real number of observations and unlimited */
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 /* #define AGESUP 130 */  /* #define AGESUP 130 */
 #define AGESUP 150  /* #define AGESUP 150 */
   #define AGESUP 200
   #define AGEINF 0
 #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */  #define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
 #define AGEBASE 40  #define AGEBASE 40
 #define AGEOVERFLOW 1.e20  #define AGEOVERFLOW 1.e20
Line 1004  typedef struct { Line 1097  typedef struct {
 /* $State$ */  /* $State$ */
 #include "version.h"  #include "version.h"
 char version[]=__IMACH_VERSION__;  char version[]=__IMACH_VERSION__;
 char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";  char copyright[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1028  int nqfveff=0; /**< nqfveff Number of Qu Line 1121  int nqfveff=0; /**< nqfveff Number of Qu
 int ntveff=0; /**< ntveff number of effective time varying variables */  int ntveff=0; /**< ntveff number of effective time varying variables */
 int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */  int nqtveff=0; /**< ntqveff number of effective time varying quantitative variables */
 int cptcov=0; /* Working variable */  int cptcov=0; /* Working variable */
   int nobs=10;  /* Number of observations in the data lastobs-firstobs */
 int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */  int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
Line 1077  FILE *ficrescveij; Line 1171  FILE *ficrescveij;
 char filerescve[FILENAMELENGTH];  char filerescve[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
 char fileresv[FILENAMELENGTH];  char fileresv[FILENAMELENGTH];
 FILE  *ficresvpl;  
 char fileresvpl[FILENAMELENGTH];  
 char title[MAXLINE];  char title[MAXLINE];
 char model[MAXLINE]; /**< The model line */  char model[MAXLINE]; /**< The model line */
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
Line 1176  double *agedc; Line 1269  double *agedc;
 double  **covar; /**< covar[j,i], value of jth covariate for individual i,  double  **covar; /**< covar[j,i], value of jth covariate for individual i,
                   * 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 iqv */  double **coqvar; /* Fixed quantitative covariate nqv */
 double ***cotvar; /* Time varying covariate itv */  double ***cotvar; /* Time varying covariate 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 2480  void powell(double p[], double **xi, int Line 2573  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 
        (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 
   /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I */       * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1  = Wx-n Px-n ... Px-2 Px-1 I
   /* Wx is row vector: population in state 1, population in state 2, population dead */       * Wx is row vector: population in state 1, population in state 2, population dead
   /* or prevalence in state 1, prevalence in state 2, 0 */       * or prevalence in state 1, prevalence in state 2, 0
   /* newm is the matrix after multiplications, its rows are identical at a factor */       * newm is the matrix after multiplications, its rows are identical at a factor.
   /* Initial matrix pimij */       * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
        * Output is prlim.
        * Initial matrix pimij 
        */
   /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */    /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
   /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */    /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
   /*  0,                   0                  , 1} */    /*  0,                   0                  , 1} */
Line 2509  void powell(double p[], double **xi, int Line 2605  void powell(double p[], double **xi, int
   double **newm;    double **newm;
   double agefin, delaymax=200. ; /* 100 Max number of years to converge */    double agefin, delaymax=200. ; /* 100 Max number of years to converge */
   int ncvloop=0;    int ncvloop=0;
     int first=0;
       
   min=vector(1,nlstate);    min=vector(1,nlstate);
   max=vector(1,nlstate);    max=vector(1,nlstate);
Line 2605  void powell(double p[], double **xi, int Line 2702  void powell(double p[], double **xi, int
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return prlim;        return prlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\    if(!first){
 Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);      first=1;
       printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
     }
     fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM),  (int)(age-stepm/YEARM), (int)delaymax);
   
   /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */    /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
   free_vector(min,1,nlstate);    free_vector(min,1,nlstate);
   free_vector(max,1,nlstate);    free_vector(max,1,nlstate);
Line 2674  Earliest age to start was %d-%d=%d, ncvl Line 2775  Earliest age to start was %d-%d=%d, ncvl
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */    /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
   /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */    /* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
   for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */    /* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age *\/ */
     for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
     ncvloop++;      ncvloop++;
     newm=savm; /* oldm should be kept from previous iteration or unity at start */      newm=savm; /* oldm should be kept from previous iteration or unity at start */
                 /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */                  /* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
Line 2739  Earliest age to start was %d-%d=%d, ncvl Line 2841  Earliest age to start was %d-%d=%d, ncvl
     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
     /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */      /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind *\/ */
     out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */      out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
     /* if((int)age == 70){ */      /* if((int)age == 86 || (int)age == 87){ */
     /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */      /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
     /*   for(i=1; i<=nlstate+ndeath; i++) { */      /*   for(i=1; i<=nlstate+ndeath; i++) { */
     /*  printf("%d newm= ",i); */      /*  printf("%d newm= ",i); */
Line 2750  Earliest age to start was %d-%d=%d, ncvl Line 2852  Earliest age to start was %d-%d=%d, ncvl
     /*  for(j=1;j<=nlstate+ndeath;j++) { */      /*  for(j=1;j<=nlstate+ndeath;j++) { */
     /*    printf("%f ",oldm[i][j]); */      /*    printf("%f ",oldm[i][j]); */
     /*  } */      /*  } */
     /*  printf(" pmmij "); */      /*  printf(" bmmij "); */
     /*  for(j=1;j<=nlstate+ndeath;j++) { */      /*  for(j=1;j<=nlstate+ndeath;j++) { */
     /*    printf("%f ",pmmij[i][j]); */      /*    printf("%f ",pmmij[i][j]); */
     /*  } */      /*  } */
Line 2778  Earliest age to start was %d-%d=%d, ncvl Line 2880  Earliest age to start was %d-%d=%d, ncvl
       meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */        meandiff[i]=(max[i]-min[i])/(max[i]+min[i])*2.; /* mean difference for each column */
       maxmax=FMAX(maxmax,meandiff[i]);        maxmax=FMAX(maxmax,meandiff[i]);
       /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */        /* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
     } /* j loop */      } /* i loop */
     *ncvyear= -( (int)age- (int)agefin);      *ncvyear= -( (int)age- (int)agefin);
     /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear);*/      /* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */        /* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
       free_vector(min,1,nlstate);        free_vector(min,1,nlstate);
Line 2788  Earliest age to start was %d-%d=%d, ncvl Line 2890  Earliest age to start was %d-%d=%d, ncvl
       free_vector(meandiff,1,nlstate);        free_vector(meandiff,1,nlstate);
       return bprlim;        return bprlim;
     }      }
   } /* age loop */    } /* agefin loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   if(first){    if(!first){
     first=1;      first=1;
     printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\      printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
 Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);  Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
Line 2873  double **pmij(double **ps, double *cov, Line 2975  double **pmij(double **ps, double *cov,
       ps[ii][ii]=1;        ps[ii][ii]=1;
     }      }
   }    }
     
     
   /* for(ii=1; ii<= nlstate+ndeath; ii++){ */    /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
   /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */    /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
   /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */    /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
Line 2902  double **pmij(double **ps, double *cov, Line 3004  double **pmij(double **ps, double *cov,
   double **out, **pmij();    double **out, **pmij();
   double sumnew=0.;    double sumnew=0.;
   double agefin;    double agefin;
       double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
   double **dnewm, **dsavm, **doldm;    double **dnewm, **dsavm, **doldm;
   double **bbmij;    double **bbmij;
       
Line 2911  double **pmij(double **ps, double *cov, Line 3013  double **pmij(double **ps, double *cov,
   dsavm=ddsavms;    dsavm=ddsavms;
       
   agefin=cov[2];    agefin=cov[2];
     /* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
   /* bmij *//* age is cov[2], ij is included in cov, but we need for    /* bmij *//* age is cov[2], ij is included in cov, but we need for
      the observed prevalence (with this covariate ij) at beginning of transition */       the observed prevalence (with this covariate ij) at beginning of transition */
   /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */    /* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
   
     /* P_x */
   pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */    pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
   /* outputs pmmij which is a stochastic matrix */    /* outputs pmmij which is a stochastic matrix in row */
   /* We do have the matrix Px in savm  and we need pij */  
     /* Diag(w_x) */
     /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
     sumnew=0.;
     /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
     for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
       /* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]);  */
       sumnew+=prevacurrent[(int)agefin][ii][ij];
     }
     if(sumnew >0.01){  /* At least some value in the prevalence */
       for (ii=1;ii<=nlstate+ndeath;ii++){
         for (j=1;j<=nlstate+ndeath;j++)
           doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
       }
     }else{
       for (ii=1;ii<=nlstate+ndeath;ii++){
         for (j=1;j<=nlstate+ndeath;j++)
         doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
       }
       /* if(sumnew <0.9){ */
       /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
       /* } */
     }
     k3=0.0;  /* We put the last diagonal to 0 */
     for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
         doldm[ii][ii]= k3;
     }
     /* End doldm, At the end doldm is diag[(w_i)] */
     
     /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
     bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
   
     /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
     /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
   for (j=1;j<=nlstate+ndeath;j++){    for (j=1;j<=nlstate+ndeath;j++){
     sumnew=0.; /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */      sumnew=0.;
     for (ii=1;ii<=nlstate;ii++){      for (ii=1;ii<=nlstate;ii++){
       /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */        /* sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij]; */
       sumnew+=pmmij[ii][j]*prevacurrent[(int)agefin][ii][ij]; /* Yes prevalence at beginning of transition */        sumnew+=pmmij[ii][j]*doldm[ii][ii]; /* Yes prevalence at beginning of transition */
     } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */      } /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
     if(sumnew >= 1.e-10){      for (ii=1;ii<=nlstate+ndeath;ii++){
       for (ii=1;ii<=nlstate+ndeath;ii++){  
         /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */          /* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         /* }else if(agefin >= agemaxpar+stepm/YEARM){ */          /* }else if(agefin >= agemaxpar+stepm/YEARM){ */
         /*      doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */          /*      dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
         /* }else */          /* }else */
         doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);        dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
       } /*End ii */      } /*End ii */
     }else{ /* We put the identity matrix */    } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
       for (ii=1;ii<=nlstate+ndeath;ii++){  
         doldm[ii][j]=(ii==j ? 1. : 0.0);    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
       } /*End ii */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
       /* printf("Problem internal bmij A: sum_i w_i*p_ij=N.j/N.. <1.e-10 i=%d, j=%d, sumnew=%lf,agefin=%d\n",ii,j,sumnew, (int)agefin); */  
     }  
   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] or identity*/  
   /* left Product of this diag matrix by dsavm=Px (dnewm=dsavm*doldm) */  
   /* bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /\* Bug Valgrind *\/ */  
   bbmij=matprod2(dnewm, pmmij,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */  
   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */  
   /* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] *\/ */  
   /* left Product of this matrix by diag matrix of prevalences (savm) */  
   for (j=1;j<=nlstate+ndeath;j++){  
     sumnew=0.;  
     for (ii=1;ii<=nlstate+ndeath;ii++){  
       sumnew+=prevacurrent[(int)agefin][ii][ij];  
       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);  
     }  
     /* if(sumnew <0.9){ */  
     /*   printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */  
     /* } */  
   } /* End j, At the end dsavm is diag[(w_i)] */  
   /* What if dsavm doesn't sum ii to 1? */  
   /* ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /\* Bug Valgrind *\/ */  
   ps=matprod2(ps, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */  
   /* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */  
   /* end bmij */    /* end bmij */
   return ps; /*pointer is unchanged */    return ps; /*pointer is unchanged */
 }  }
Line 3174  double ***hpxij(double ***po, int nhstep Line 3287  double ***hpxij(double ***po, int nhstep
     }      }
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
                                 po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
                                 /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/          /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
       }        }
     /*printf("h=%d ",h);*/      /*printf("h=%d ",h);*/
   } /* end h */    } /* end h */
         /*     printf("\n H=%d \n",h); */    /*     printf("\n H=%d \n",h); */
   return po;    return po;
 }  }
   
 /************* Higher Back Matrix Product ***************/  /************* Higher Back Matrix Product ***************/
 /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */  /* double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, int ij ) */
 double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij )  double ***hbxij(double ***po, int nhstepm, double age, int hstepm, double *x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
 {  {
   /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over    /* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
      'nhstepm*hstepm*stepm' months (i.e. until       'nhstepm*hstepm*stepm' months (i.e. until
Line 3220  double ***hbxij(double ***po, int nhstep Line 3333  double ***hbxij(double ***po, int nhstep
       newm=savm;        newm=savm;
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       agexact=age-((h-1)*hstepm + (d))*stepm/YEARM; /* age just before transition, d or d-1? */        agexact=age-( (h-1)*hstepm + (d)  )*stepm/YEARM; /* age just before transition, d or d-1? */
       /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */        /* agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /\* age just before transition *\/ */
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
Line 3230  double ***hbxij(double ***po, int nhstep Line 3343  double ***hbxij(double ***po, int nhstep
       /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */        /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
         cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */          /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
   
       }        }
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        }
         for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
           if(Dummy[Tvar[Tage[k]]]){
             cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
           } else{
             cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
           }
           /* printf("hBxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        }                 
                           
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   
       /* Careful transposed matrix */        /* Careful transposed matrix */
       /* age is in cov[2], prevacurrent at beginning of transition. */        /* age is in cov[2], prevacurrent at beginning of transition. */
       /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */        /* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
Line 3268  double ***hbxij(double ***po, int nhstep Line 3389  double ***hbxij(double ***po, int nhstep
     for(i=1; i<=nlstate+ndeath; i++)      for(i=1; i<=nlstate+ndeath; i++)
       for(j=1;j<=nlstate+ndeath;j++) {        for(j=1;j<=nlstate+ndeath;j++) {
         po[i][j][h]=newm[i][j];          po[i][j][h]=newm[i][j];
         /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/          /* if(h==nhstepm) */
           /*   printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
       }        }
     /*printf("h=%d ",h);*/      /* printf("h=%d %.1f ",h, agexact); */
   } /* end h */    } /* end h */
   /*     printf("\n H=%d \n",h); */    /* printf("\n H=%d nhs=%d \n",h, nhstepm); */
   return po;    return po;
 }  }
   
Line 3727  double funcone( double *x) Line 3849  double funcone( double *x)
       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){ */
       /*        printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */        /*        printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
       /*        /\* exit(1); *\/ */        /*        /\* exit(1); *\/ */
       /* } */        /* } */
       bbh=(double)bh[mi][i]/(double)stepm;         bbh=(double)bh[mi][i]/(double)stepm; 
Line 3760  double funcone( double *x) Line 3882  double funcone( double *x)
         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,out[s1][s2],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);
Line 3781  return -l; Line 3903  return -l;
   
   
 /*************** function likelione ***********/  /*************** function likelione ***********/
 void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
 {  {
   /* This routine should help understanding what is done with     /* This routine should help understanding what is done with 
      the selection of individuals/waves and       the selection of individuals/waves and
Line 3805  void likelione(FILE *ficres,double p[], Line 3927  void likelione(FILE *ficres,double p[],
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }    }
   
   *fretone=(*funcone)(p);    *fretone=(*func)(p);
   if(*globpri !=0){    if(*globpri !=0){
     fclose(ficresilk);      fclose(ficresilk);
     if (mle ==0)      if (mle ==0)
Line 3813  void likelione(FILE *ficres,double p[], Line 3935  void likelione(FILE *ficres,double p[],
     else if(mle >=1)      else if(mle >=1)
       fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);        fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
     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); 
               
     for (k=1; k<= nlstate ; k++) {      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> \        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> \
Line 4280  void pstamp(FILE *fichier) Line 4402  void pstamp(FILE *fichier)
   fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {  
   
   /* y=a+bx regression */  
   double   sumx = 0.0;                        /* sum of x                      */  
   double   sumx2 = 0.0;                       /* sum of x**2                   */  
   double   sumxy = 0.0;                       /* sum of x * y                  */  
   double   sumy = 0.0;                        /* sum of y                      */  
   double   sumy2 = 0.0;                       /* sum of y**2                   */  
   double   sume2; /* sum of square or residuals */  
   double yhat;  
     
   double denom=0;  
   int i;  
   int ne=*no;  
     
   for ( i=ifi, ne=0;i<=ila;i++) {  
     if(!isfinite(x[i]) || !isfinite(y[i])){  
       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */  
       continue;  
     }  
     ne=ne+1;  
     sumx  += x[i];         
     sumx2 += x[i]*x[i];    
     sumxy += x[i] * y[i];  
     sumy  += y[i];        
     sumy2 += y[i]*y[i];   
     denom = (ne * sumx2 - sumx*sumx);  
     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */  
   }   
     
   denom = (ne * sumx2 - sumx*sumx);  
   if (denom == 0) {  
     // vertical, slope m is infinity  
     *b = INFINITY;  
     *a = 0;  
     if (r) *r = 0;  
     return 1;  
   }  
     
   *b = (ne * sumxy  -  sumx * sumy) / denom;  
   *a = (sumy * sumx2  -  sumx * sumxy) / denom;  
   if (r!=NULL) {  
     *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */  
       sqrt((sumx2 - sumx*sumx/ne) *  
            (sumy2 - sumy*sumy/ne));  
   }  
   *no=ne;  
   for ( i=ifi, ne=0;i<=ila;i++) {  
     if(!isfinite(x[i]) || !isfinite(y[i])){  
       /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */  
       continue;  
     }  
     ne=ne+1;  
     yhat = y[i] - *a -*b* x[i];  
     sume2  += yhat * yhat ;         
       
     denom = (ne * sumx2 - sumx*sumx);  
     /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */  
   }   
   *sb = sqrt(sume2/(ne-2)/(sumx2 - sumx * sumx /ne));  
   *sa= *sb * sqrt(sumx2/ne);  
     
   return 0;   
 }  
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
Line 4356  void  freqsummary(char fileres[], double Line 4415  void  freqsummary(char fileres[], double
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *x, *y, a,b,r, sa, sb; /* for regression, y=b+m*x and r is the correlation coefficient */    double *x, *y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+m*x and r is the correlation coefficient */
   int no;    int no=0, linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb);
   double *meanq;    double *meanq, *stdq, *idq;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
   double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
Line 4371  void  freqsummary(char fileres[], double Line 4430  void  freqsummary(char fileres[], double
   pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */     pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */ 
   /* prop=matrix(1,nlstate,iagemin,iagemax+3); */    /* prop=matrix(1,nlstate,iagemin,iagemax+3); */
   meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
     idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
   meanqt=matrix(1,lastpass,1,nqtveff);    meanqt=matrix(1,lastpass,1,nqtveff);
   strcpy(fileresp,"P_");    strcpy(fileresp,"P_");
   strcat(fileresp,fileresu);    strcat(fileresp,fileresu);
Line 4479  Title=%s <br>Datafile=%s Firstpass=%d La Line 4540  Title=%s <br>Datafile=%s Firstpass=%d La
         posprop[i]=0;          posprop[i]=0;
         pospropt[i]=0;          pospropt[i]=0;
       }        }
       /* for (z1=1; z1<= nqfveff; z1++) {   */        for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
       /*   meanq[z1]+=0.; */          idq[z1]=0.;
           meanq[z1]=0.;
           stdq[z1]=0.;
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
       /*   for(m=1;m<=lastpass;m++){ */        /*   for(m=1;m<=lastpass;m++){ */
       /*        meanqt[m][z1]=0.; */        /*          meanqt[m][z1]=0.; */
       /*   } */        /*        } */
       /* } */        /* }       */
         
       /* dateintsum=0; */        /* dateintsum=0; */
       /* k2cpt=0; */        /* k2cpt=0; */
               
Line 4495  Title=%s <br>Datafile=%s Firstpass=%d La Line 4559  Title=%s <br>Datafile=%s Firstpass=%d La
         if(j !=0){          if(j !=0){
           if(anyvaryingduminmodel==0){ /* If All fixed covariates */            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
             if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
               /* for (z1=1; z1<= nqfveff; z1++) {   */  
               /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */  
               /* } */  
               for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                 /* if(Tvaraff[z1] ==-20){ */                  /* if(Tvaraff[z1] ==-20){ */
                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
Line 4518  Title=%s <br>Datafile=%s Firstpass=%d La Line 4579  Title=%s <br>Datafile=%s Firstpass=%d La
         }/* end j==0 */          }/* end j==0 */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
           /* for(m=firstpass; m<=lastpass; m++){ */            /* for(m=firstpass; m<=lastpass; m++){ */
           for(mi=1; mi<wav[iind];mi++){ /* For that wave */            for(mi=1; mi<wav[iind];mi++){ /* For each wave */
             m=mw[mi][iind];              m=mw[mi][iind];
             if(j!=0){              if(j!=0){
               if(anyvaryingduminmodel==1){ /* Some are varying covariates */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
Line 4538  Title=%s <br>Datafile=%s Firstpass=%d La Line 4599  Title=%s <br>Datafile=%s Firstpass=%d La
               }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */                }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
             } /* end j==0 */              } /* end j==0 */
             /* bool =0 we keep that guy which corresponds to the combination of dummy values */              /* bool =0 we keep that guy which corresponds to the combination of dummy values */
             if(bool==1){              if(bool==1){ /*Selected */
               /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]                /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                  and mw[mi+1][iind]. dh depends on stepm. */                   and mw[mi+1][iind]. dh depends on stepm. */
               agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/                agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
Line 4556  Title=%s <br>Datafile=%s Firstpass=%d La Line 4617  Title=%s <br>Datafile=%s Firstpass=%d La
                   if(s[m][iind]==-1)                    if(s[m][iind]==-1)
                     printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));                      printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
                   freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                     for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
                       idq[z1]=idq[z1]+weight[iind];
                       meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /* Computes mean of quantitative with selected filter */
                       stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/  /* Computes mean of quantitative with selected filter */
                     }
                   /* if((int)agev[m][iind] == 55) */                    /* if((int)agev[m][iind] == 55) */
                   /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */                    /*   printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
                   /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */                    /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
Line 4571  Title=%s <br>Datafile=%s Firstpass=%d La Line 4637  Title=%s <br>Datafile=%s Firstpass=%d La
               bool=1;                bool=1;
             }/* end bool 2 */              }/* end bool 2 */
           } /* end m */            } /* end m */
             /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
             /*   idq[z1]=idq[z1]+weight[iind]; */
             /*   meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind];  /\* Computes mean of quantitative with selected filter *\/ */
             /*   stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/  /\* Computes mean of quantitative with selected filter *\/ */
             /* } */
         } /* end bool */          } /* end bool */
       } /* end iind = 1 to imx */        } /* end iind = 1 to imx */
       /* prop[s][age] is feeded for any initial and valid live state as well as        /* prop[s][age] is feeded for any initial and valid live state as well as
Line 4608  Title=%s <br>Datafile=%s Firstpass=%d La Line 4679  Title=%s <br>Datafile=%s Firstpass=%d La
         fprintf(ficresphtmfr, "**********</h3>\n");          fprintf(ficresphtmfr, "**********</h3>\n");
         fprintf(ficlog, "**********\n");          fprintf(ficlog, "**********\n");
       }        }
         /*
           Printing means of quantitative variables if any
         */
         for (z1=1; z1<= nqfveff; z1++) {
           fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
           fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
           if(weightopt==1){
             printf(" Weighted mean and standard deviation of");
             fprintf(ficlog," Weighted mean and standard deviation of");
             fprintf(ficresphtmfr," Weighted mean and standard deviation of");
           }
           printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
           fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
         }
         /* for (z1=1; z1<= nqtveff; z1++) { */
         /*        for(m=1;m<=lastpass;m++){ */
         /*          fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
         /*   } */
         /* } */
   
       fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");        fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
       if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
         fprintf(ficresp, " Age");          fprintf(ficresp, " Age");
Line 4795  Title=%s <br>Datafile=%s Firstpass=%d La Line 4887  Title=%s <br>Datafile=%s Firstpass=%d La
                     y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);                      y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
                     /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */                      /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
                   }                    }
                     /* Some are not finite, but linreg will ignore these ages */
                     no=0;
                   linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */                    linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
                   pstart[s1]=b;                    pstart[s1]=b;
                   pstart[s1-1]=a;                    pstart[s1-1]=a;
Line 4840  Title=%s <br>Datafile=%s Firstpass=%d La Line 4934  Title=%s <br>Datafile=%s Firstpass=%d La
             fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
           }            }
         }          }
       }        } /* end of state i */
       printf("#Freqsummary\n");        printf("#Freqsummary\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
       for(s1=-1; s1 <=nlstate+ndeath; s1++){        for(s1=-1; s1 <=nlstate+ndeath; s1++){
Line 4886  Title=%s <br>Datafile=%s Firstpass=%d La Line 4980  Title=%s <br>Datafile=%s Firstpass=%d La
   fclose(ficresp);    fclose(ficresp);
   fclose(ficresphtm);    fclose(ficresphtm);
   fclose(ficresphtmfr);    fclose(ficresphtmfr);
     free_vector(idq,1,nqfveff);
   free_vector(meanq,1,nqfveff);    free_vector(meanq,1,nqfveff);
     free_vector(stdq,1,nqfveff);
   free_matrix(meanqt,1,lastpass,1,nqtveff);    free_matrix(meanqt,1,lastpass,1,nqtveff);
   free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);    free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
   free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);    free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
Line 4898  Title=%s <br>Datafile=%s Firstpass=%d La Line 4994  Title=%s <br>Datafile=%s Firstpass=%d La
   /* End of freqsummary */    /* End of freqsummary */
 }  }
   
   /* Simple linear regression */
   int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
   
     /* y=a+bx regression */
     double   sumx = 0.0;                        /* sum of x                      */
     double   sumx2 = 0.0;                       /* sum of x**2                   */
     double   sumxy = 0.0;                       /* sum of x * y                  */
     double   sumy = 0.0;                        /* sum of y                      */
     double   sumy2 = 0.0;                       /* sum of y**2                   */
     double   sume2 = 0.0;                       /* sum of square or residuals */
     double yhat;
     
     double denom=0;
     int i;
     int ne=*no;
     
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       sumx  += x[i];       
       sumx2 += x[i]*x[i];  
       sumxy += x[i] * y[i];
       sumy  += y[i];      
       sumy2 += y[i]*y[i]; 
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     
     denom = (ne * sumx2 - sumx*sumx);
     if (denom == 0) {
       // vertical, slope m is infinity
       *b = INFINITY;
       *a = 0;
       if (r) *r = 0;
       return 1;
     }
     
     *b = (ne * sumxy  -  sumx * sumy) / denom;
     *a = (sumy * sumx2  -  sumx * sumxy) / denom;
     if (r!=NULL) {
       *r = (sumxy - sumx * sumy / ne) /          /* compute correlation coeff     */
         sqrt((sumx2 - sumx*sumx/ne) *
              (sumy2 - sumy*sumy/ne));
     }
     *no=ne;
     for ( i=ifi, ne=0;i<=ila;i++) {
       if(!isfinite(x[i]) || !isfinite(y[i])){
         /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
         continue;
       }
       ne=ne+1;
       yhat = y[i] - *a -*b* x[i];
       sume2  += yhat * yhat ;       
       
       denom = (ne * sumx2 - sumx*sumx);
       /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
     } 
     *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
     *sa= *sb * sqrt(sumx2/ne);
     
     return 0; 
   }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {    {  
Line 4927  void prevalence(double ***probs, double Line 5089  void prevalence(double ***probs, double
   /*j=cptcoveff;*/    /*j=cptcoveff;*/
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
   first=1;    first=0;
   for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */    for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
     for (i=1; i<=nlstate; i++)        for (i=1; i<=nlstate; i++)  
       for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
Line 4985  void prevalence(double ***probs, double Line 5147  void prevalence(double ***probs, double
           if(posprop>=1.e-5){             if(posprop>=1.e-5){ 
             probs[i][jk][j1]= prop[jk][i]/posprop;              probs[i][jk][j1]= prop[jk][i]/posprop;
           } else{            } else{
             if(first==1){              if(!first){
               first=0;                first=1;
               printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);  
             }else{              }else{
               fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);                fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
             }              }
           }            }
         }           } 
Line 5236  void  concatwav(int wav[], int **dh, int Line 5397  void  concatwav(int wav[], int **dh, int
    /* *cptcov=0; */     /* *cptcov=0; */
     
    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */     for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
      for (k=1; k <= maxncov; k++)
        for(j=1; j<=2; j++)
          nbcode[k][j]=0; /* Valgrind */
   
    /* Loop on covariates without age and products and no quantitative variable */     /* Loop on covariates without age and products and no quantitative variable */
    /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */  
    for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */     for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
      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 */        if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
Line 5256  void  concatwav(int wav[], int **dh, int Line 5419  void  concatwav(int wav[], int **dh, int
              modmaxcovj=ij;                modmaxcovj=ij; 
            else if (ij < modmincovj)              else if (ij < modmincovj) 
              modmincovj=ij;                modmincovj=ij; 
            if ((ij < -1) && (ij > NCOVMAX)){             if (ij <0 || ij >1 ){
                printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
                fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
              }
              if ((ij < -1) || (ij > NCOVMAX)){
              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );               printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
              exit(1);               exit(1);
            }else             }else
Line 5302  void  concatwav(int wav[], int **dh, int Line 5469  void  concatwav(int wav[], int **dh, int
          /* nbcode[Tvar[j]][3]=2; */           /* nbcode[Tvar[j]][3]=2; */
          /* To be continued (not working yet). */           /* To be continued (not working yet). */
          ij=0; /* ij is similar to i but can jump over null modalities */           ij=0; /* ij is similar to i but can jump over null modalities */
          for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/  
            /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
            /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
            /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
             * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
            /*, could be restored in the future */
            for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
            if (Ndum[i] == 0) { /* If nobody responded to this modality k */             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
              break;               break;
            }             }
            ij++;             ij++;
            nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/             nbcode[Tvar[k]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
            cptcode = ij; /* New max modality for covar j */             cptcode = ij; /* New max modality for covar j */
          } /* end of loop on modality i=-1 to 1 or more */           } /* end of loop on modality i=-1 to 1 or more */
          break;           break;
Line 5323  void  concatwav(int wav[], int **dh, int Line 5496  void  concatwav(int wav[], int **dh, int
          break;           break;
        } /* end switch */         } /* end switch */
      } /* end dummy test */       } /* end dummy test */
          } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/  
      /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */  
      /*         /\*recode from 0 *\/ */  
      /*                                      k is a modality. If we have model=V1+V1*sex  */  
      /*                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */  
      /*                                   But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */  
      /*         } */  
      /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */  
      /*         if (ij > ncodemax[j]) { */  
      /*           printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]);  */  
      /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */  
      /*           break; */  
      /*         } */  
      /*   }  /\* end of loop on modality k *\/ */  
    } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/    
       
    for (k=-1; k< maxncov; k++) Ndum[k]=0;      for (k=-1; k< maxncov; k++) Ndum[k]=0; 
    /* Look at fixed dummy (single or product) covariates to check empty modalities */     /* Look at fixed dummy (single or product) covariates to check empty modalities */
Line 5430  void  concatwav(int wav[], int **dh, int Line 5589  void  concatwav(int wav[], int **dh, int
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      nhstepm is the number of hstepm from age to agelim        nhstepm is the number of hstepm from age to agelim 
      nstepm is the number of stepm from age to agelin.        nstepm is the number of stepm from age to agelin. 
      Look at hpijx to understand the reason of that which relies in memory size       Look at hpijx to understand the reason which relies in memory size consideration
      and note for a fixed period like estepm months */       and note for a fixed period like estepm months */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      survival function given by stepm (the optimization length). Unfortunately it       survival function given by stepm (the optimization length). Unfortunately it
Line 5661  void  concatwav(int wav[], int **dh, int Line 5820  void  concatwav(int wav[], int **dh, int
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/            /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
                                                                                   
         }          }
                   
       /* Standard deviation of expectancies ij */         
     fprintf(ficresstdeij,"%3.0f",age );      fprintf(ficresstdeij,"%3.0f",age );
     for(i=1; i<=nlstate;i++){      for(i=1; i<=nlstate;i++){
       eip=0.;        eip=0.;
Line 5676  void  concatwav(int wav[], int **dh, int Line 5836  void  concatwav(int wav[], int **dh, int
     }      }
     fprintf(ficresstdeij,"\n");      fprintf(ficresstdeij,"\n");
                                   
       /* Variance of expectancies ij */           
     fprintf(ficrescveij,"%3.0f",age );      fprintf(ficrescveij,"%3.0f",age );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){        for(j=1; j<=nlstate;j++){
Line 5709  void  concatwav(int wav[], int **dh, int Line 5870  void  concatwav(int wav[], int **dh, int
 /************ Variance ******************/  /************ Variance ******************/
  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
  {   {
    /* Variance of health expectancies */     /** Variance of health expectancies 
    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      *  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
    /* double **newm;*/      * double **newm;
    /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/      * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav) 
       */
       
    /* int movingaverage(); */     /* int movingaverage(); */
    double **dnewm,**doldm;     double **dnewm,**doldm;
    double **dnewmp,**doldmp;     double **dnewmp,**doldmp;
    int i, j, nhstepm, hstepm, h, nstepm ;     int i, j, nhstepm, hstepm, h, nstepm ;
      int first=0;
    int k;     int k;
    double *xp;     double *xp;
    double **gp, **gm;  /* for var eij */     double **gp, **gm;  /**< for var eij */
    double ***gradg, ***trgradg; /*for var eij */     double ***gradg, ***trgradg; /**< for var eij */
    double **gradgp, **trgradgp; /* for var p point j */     double **gradgp, **trgradgp; /**< for var p point j */
    double *gpp, *gmp; /* for var p point j */     double *gpp, *gmp; /**< for var p point j */
    double **varppt; /* for var p point j nlstate to nlstate+ndeath */     double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
    double ***p3mat;     double ***p3mat;
    double age,agelim, hf;     double age,agelim, hf;
    /* double ***mobaverage; */     /* double ***mobaverage; */
Line 5785  void  concatwav(int wav[], int **dh, int Line 5948  void  concatwav(int wav[], int **dh, int
    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
    /*   } */  
    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    pstamp(ficresvij);     pstamp(ficresvij);
    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
Line 5840  void  concatwav(int wav[], int **dh, int Line 6003  void  concatwav(int wav[], int **dh, int
        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
          xp[i] = x[i] + (i==theta ?delti[theta]:0);           xp[i] = x[i] + (i==theta ?delti[theta]:0);
        }         }
                                  /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and 
           * returns into prlim .
           */
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                           
          /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
            for(i=1; i<=nlstate;i++)             for(i=1; i<=nlstate;i++)
Line 5852  void  concatwav(int wav[], int **dh, int Line 6018  void  concatwav(int wav[], int **dh, int
              prlim[i][i]=mobaverage[(int)age][i][ij];               prlim[i][i]=mobaverage[(int)age][i][ij];
          }           }
        }         }
                                  /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=1 to nhstepm */          */                      
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
          /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
           * at horizon h in state j including mortality.
           */
        for(j=1; j<= nlstate; j++){         for(j=1; j<= nlstate; j++){
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            for(i=1, gp[h][j]=0.;i<=nlstate;i++)             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
              gp[h][j] += prlim[i][i]*p3mat[i][j][h];               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
          }           }
        }         }
        /* Next for computing probability of death (h=1 means         /* Next for computing shifted+ probability of death (h=1 means
           computed over hstepm matrices product = hstepm*stepm months)             computed over hstepm matrices product = hstepm*stepm months) 
           as a weighted average of prlim.            as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
        */         */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){         for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gpp[j]=0.; i<= nlstate; i++)           for(i=1,gpp[j]=0.; i<= nlstate; i++)
            gpp[j] += prlim[i][i]*p3mat[i][j][1];             gpp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }
        /* end probability of death */         
                                  /* Again with minus shift */
                           
        for(i=1; i<=npar; i++) /* Computes gradient x - delta */         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
          xp[i] = x[i] - (i==theta ?delti[theta]:0);           xp[i] = x[i] - (i==theta ?delti[theta]:0);
                           
        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
Line 5901  void  concatwav(int wav[], int **dh, int Line 6072  void  concatwav(int wav[], int **dh, int
          for(i=1,gmp[j]=0.; i<= nlstate; i++)           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];             gmp[j] += prlim[i][i]*p3mat[i][j][1];
        }             }    
        /* end probability of death */         /* end shifting computations */
                           
          /**< Computing gradient matrix at horizon h 
           */
        for(j=1; j<= nlstate; j++) /* vareij */         for(j=1; j<= nlstate; j++) /* vareij */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
          }           }
                                  /**< Gradient of overall mortality p.3 (or p.j) 
        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */          */
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
        }         }
                                                   
      } /* End theta */       } /* End theta */
                        
        /* We got the gradient matrix for each theta and state j */                
      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
                                   
      for(h=0; h<=nhstepm; h++) /* veij */       for(h=0; h<=nhstepm; h++) /* veij */
Line 5924  void  concatwav(int wav[], int **dh, int Line 6099  void  concatwav(int wav[], int **dh, int
      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
        for(theta=1; theta <=npar; theta++)         for(theta=1; theta <=npar; theta++)
          trgradgp[j][theta]=gradgp[theta][j];           trgradgp[j][theta]=gradgp[theta][j];
                        /**< as well as its transposed matrix 
         */                
                                   
      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      for(i=1;i<=nlstate;i++)       for(i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate;j++)         for(j=1;j<=nlstate;j++)
          vareij[i][j][(int)age] =0.;           vareij[i][j][(int)age] =0.;
                   
        /* Computing trgradg by matcov by gradg at age and summing over h
         * and k (nhstepm) formula 15 of article
         * Lievre-Brouard-Heathcote
         */
        
      for(h=0;h<=nhstepm;h++){       for(h=0;h<=nhstepm;h++){
        for(k=0;k<=nhstepm;k++){         for(k=0;k<=nhstepm;k++){
          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 5941  void  concatwav(int wav[], int **dh, int Line 6122  void  concatwav(int wav[], int **dh, int
        }         }
      }       }
                                   
      /* pptj */       /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
         * p.j overall mortality formula 49 but computed directly because
         * we compute the grad (wix pijx) instead of grad (pijx),even if
         * wix is independent of theta.
         */
      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      for(j=nlstate+1;j<=nlstate+ndeath;j++)       for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 6029  void  concatwav(int wav[], int **dh, int Line 6214  void  concatwav(int wav[], int **dh, int
  }  /* end varevsij */   }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)   void varprevlim(char fileresvpl[], FILE *ficresvpl, double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, char strstart[], int nres)
 {  {
   /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/    /* Variance of prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
   double **dnewm,**doldm;    double **dnewmpar,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
Line 6044  void  concatwav(int wav[], int **dh, int Line 6229  void  concatwav(int wav[], int **dh, int
   int theta;    int theta;
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
   fprintf(ficresvpl,"# Age ");    fprintf(ficresvpl,"# Age ");
   if(nresult >=1)    if(nresult >=1)
     fprintf(ficresvpl," Result# ");      fprintf(ficresvpl," Result# ");
Line 6053  void  concatwav(int wav[], int **dh, int Line 6238  void  concatwav(int wav[], int **dh, int
   fprintf(ficresvpl,"\n");    fprintf(ficresvpl,"\n");
   
   xp=vector(1,npar);    xp=vector(1,npar);
   dnewm=matrix(1,nlstate,1,npar);    dnewmpar=matrix(1,nlstate,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,nlstate,1,nlstate);
       
   hstepm=1*YEARM; /* Every year of age */    hstepm=1*YEARM; /* Every year of age */
Line 6073  void  concatwav(int wav[], int **dh, int Line 6258  void  concatwav(int wav[], int **dh, int
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(i=1; i<=npar; i++){ /* Computes gradient */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }        }
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gp[i] = prlim[i][i];          gp[i] = prlim[i][i];
         mgp[theta][i] = prlim[i][i];          mgp[theta][i] = prlim[i][i];
       }        }
       for(i=1; i<=npar; i++) /* Computes gradient */        for(i=1; i<=npar; i++) /* Computes gradient */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       if((int)age==79 ||(int)age== 80 ||(int)age== 81 )        /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ) */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        /*        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
       else        /* else */
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
         gm[i] = prlim[i][i];          gm[i] = prlim[i][i];
         mgm[theta][i] = prlim[i][i];          mgm[theta][i] = prlim[i][i];
Line 6123  void  concatwav(int wav[], int **dh, int Line 6308  void  concatwav(int wav[], int **dh, int
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] =0.;        varpl[i][(int)age] =0.;
     if((int)age==79 ||(int)age== 80  ||(int)age== 81){      if((int)age==79 ||(int)age== 80  ||(int)age== 81){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
     }else{      }else{
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
     }      }
     for(i=1;i<=nlstate;i++)      for(i=1;i<=nlstate;i++)
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
Line 6135  void  concatwav(int wav[], int **dh, int Line 6320  void  concatwav(int wav[], int **dh, int
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
     if(nresult >=1)      if(nresult >=1)
       fprintf(ficresvpl,"%d ",nres );        fprintf(ficresvpl,"%d ",nres );
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         /* for(j=1;j<=nlstate;j++) */
         /*        fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
       }
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
     free_vector(gp,1,nlstate);      free_vector(gp,1,nlstate);
     free_vector(gm,1,nlstate);      free_vector(gm,1,nlstate);
Line 6148  void  concatwav(int wav[], int **dh, int Line 6336  void  concatwav(int wav[], int **dh, int
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
   }
   
   
   /************ Variance of backprevalence limit ******************/
    void varbrevlim(char fileresvbl[], FILE  *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
   {
     /* Variance of backward prevalence limit  for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   
     double **dnewmpar,**doldm;
     int i, j, nhstepm, hstepm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mgm, **mgp;
     double age,agelim;
     int theta;
     
     pstamp(ficresvbl);
     fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
     fprintf(ficresvbl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvbl," Result# ");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %1d-%1d",i,i);
     fprintf(ficresvbl,"\n");
   
     xp=vector(1,npar);
     dnewmpar=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGEINF;
     for (age=fage; age>=bage; age --){ /* If stepm=6 months */
       nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       mgp=matrix(1,npar,1,nlstate);
       mgm=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gp[i] = bprlim[i][i];
           mgp[theta][i] = bprlim[i][i];
         }
        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
          if(mobilavproj > 0 )
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
          else
           bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
         for(i=1;i<=nlstate;i++){
           gm[i] = bprlim[i][i];
           mgm[theta][i] = bprlim[i][i];
         }
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
         /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\nmgm mgp %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf(" %d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
       /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
       /*   printf("\n gradg %d ",(int)age); */
       /*   for(j=1; j<=nlstate;j++){ */
       /*  printf("%d ",j); */
       /*  for(theta=1; theta <=npar; theta++) */
       /*    printf("%d %lf ",theta,gradg[theta][j]); */
       /*  printf("\n "); */
       /*   } */
       /* } */
   
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] =0.;
       if((int)age==79 ||(int)age== 80  ||(int)age== 81){
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }else{
       matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
       }
       for(i=1;i<=nlstate;i++)
         varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvbl,"%.0f ",age );
       if(nresult >=1)
         fprintf(ficresvbl,"%d ",nres );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
       fprintf(ficresvbl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(mgm,1,npar,1,nlstate);
       free_matrix(mgp,1,npar,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewmpar,1,nlstate,1,nlstate);
   
 }  }
   
Line 6228  void varprob(char optionfilefiname[], do Line 6541  void varprob(char optionfilefiname[], do
    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
    fprintf(fichtm,"\n");     fprintf(fichtm,"\n");
   
    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);     fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 6425  To be simple, these graphs help to under Line 6738  To be simple, these graphs help to under
                  }                   }
                                                                                                                                   
                  /* Eigen vectors */                   /* Eigen vectors */
                  v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));                   if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
                      printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
                      v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
                    }else
                      v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                  /*v21=sqrt(1.-v11*v11); *//* error */                   /*v21=sqrt(1.-v11*v11); *//* error */
                  v21=(lc1-v1)/cv12*v11;                   v21=(lc1-v1)/cv12*v11;
                  v12=-v21;                   v12=-v21;
Line 6456  To be simple, these graphs help to under Line 6774  To be simple, these graphs help to under
                    fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                    fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                    fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",      \
                            mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \                             mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */                             mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
                  }else{                   }else{
                    first=0;                     first=0;
                    fprintf(fichtmcov," %d (%.3f),",(int) age, c12);                     fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
Line 6494  void printinghtml(char fileresu[], char Line 6812  void printinghtml(char fileresu[], char
                   int lastpass, int stepm, int weightopt, char model[],\                    int lastpass, int stepm, int weightopt, char model[],\
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                   int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \                    int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
                   double jprev1, double mprev1,double anprev1, double dateprev1, \                    double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
                   double jprev2, double mprev2,double anprev2, double dateprev2){                    double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
   int jj1, k1, i1, cpt, k4, nres;    int jj1, k1, i1, cpt, k4, nres;
   
    fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
Line 6516  void printinghtml(char fileresu[], char Line 6834  void printinghtml(char fileresu[], char
  - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",   - Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));             stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));             subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",   - Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));             subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \   - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
Line 6625  divided by h: <sub>h</sub>P<sub>ij</sub> Line 6943  divided by h: <sub>h</sub>P<sub>ij</sub>
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);   <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */       /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }       }
      /* State specific survival functions (period) */       /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\         fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   And probability to be observed in various states (up to %d) being in state %d at different ages.       \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);   <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }       }
      /* Period (stable) prevalence in each health state */       /* Period (forward stable) prevalence in each health state */
      for(cpt=1; cpt<=nlstate;cpt++){       for(cpt=1; cpt<=nlstate;cpt++){
        fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \         fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);  <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
      }       }
      if(backcast==1){       if(backcast==1){
        /* Period (stable) back 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> \
 <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);  <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);
        }         }
      }       }
      if(prevfcast==1){       if(prevfcast==1){
        /* Projection of prevalence up to period (stable) prevalence in each health state */         /* Projection of prevalence up to period (forward stable) prevalence in each health state */
          for(cpt=1; cpt<=nlstate;cpt++){
            fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
   <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
          }
        }
        if(backcast==1){
         /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \           fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
 <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);   from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
    account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
   with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
    <img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
        }         }
      }       }
                     
Line 6692  See page 'Matrix of variance-covariance Line 7020  See page 'Matrix of variance-covariance
    <a href=\"%s\">%s</a> <br>\n</li>",     <a href=\"%s\">%s</a> <br>\n</li>",
            estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));             estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",   - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));             estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",   - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
            estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));             estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
    fprintf(fichtm,"\     fprintf(fichtm,"\
  - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\   - Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));             subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
Line 6756  true period expectancies (those weighted Line 7084  true period expectancies (those weighted
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
     void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear){  void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   char gplotcondition[132], gplotlabel[132];    char gplotcondition[132], gplotlabel[132];
Line 6765  true period expectancies (those weighted Line 7093  true period expectancies (those weighted
   int ng=0;    int ng=0;
   int vpopbased;    int vpopbased;
   int ioffset; /* variable offset for columns */    int ioffset; /* variable offset for columns */
     int iyearc=1; /* variable column for year of projection  */
     int iagec=1; /* variable column for age of projection  */
   int nres=0; /* Index of resultline */    int nres=0; /* Index of resultline */
   int istart=1; /* For starting graphs in projections */    int istart=1; /* For starting graphs in projections */
   
Line 6778  true period expectancies (those weighted Line 7108  true period expectancies (those weighted
   /*#endif */    /*#endif */
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
   
     /* diagram of the model */
     fprintf(ficgp,"\n#Diagram of the model \n");
     fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
     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#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#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,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0.  font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
     fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
     fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
     fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
   
   /* Contribution to likelihood */    /* Contribution to likelihood */
   /* Plot the probability implied in the likelihood */    /* Plot the probability implied in the likelihood */
   fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");    fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
Line 6818  true period expectancies (those weighted Line 7162  true period expectancies (those weighted
           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: 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);
         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<=cptcoveff; 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 */            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
Line 6847  true period expectancies (those weighted Line 7191  true period expectancies (those weighted
               
         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\" font \"Helvetica,12\"\n",cpt,gplotlabel);
         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 6855  true period expectancies (those weighted Line 7200  true period expectancies (those weighted
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else        fprintf(ficgp," %%*lf (%%*lf)");            else        fprintf(ficgp," %%*lf (%%*lf)");
         }          }
         fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);          fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
         for (i=1; i<= nlstate ; i ++) {          for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
           else fprintf(ficgp," %%*lf (%%*lf)");            else fprintf(ficgp," %%*lf (%%*lf)");
Line 6869  true period expectancies (those weighted Line 7214  true period expectancies (those weighted
                   
         fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));          fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
         if(cptcoveff ==0){          if(cptcoveff ==0){
           fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+(cpt-1),  cpt );            fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3",      2+3*(cpt-1),  cpt );
         }else{          }else{
           kl=0;            kl=0;
           for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */            for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
Line 6920  true period expectancies (those weighted Line 7265  true period expectancies (those weighted
               }                }
             } /* end covariate */              } /* end covariate */
           } /* end if no covariate */            } /* end if no covariate */
             if(backcast == 1){
               fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               /* k1-1 error should be nres-1*/
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else        fprintf(ficgp," %%*lf (%%*lf)");
               }
               fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres); 
               for (i=1; i<= nlstate ; i ++) {
                 if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
                 else fprintf(ficgp," %%*lf (%%*lf)");
               } 
               fprintf(ficgp,"\" t\"\" w l lt 4");
             } /* end if backprojcast */
         } /* end if backcast */          } /* end if backcast */
         fprintf(ficgp,"\nset out ;unset label;\n");          /* fprintf(ficgp,"\nset out ;unset label;\n"); */
           fprintf(ficgp,"\nset out ;unset title;\n");
       } /* nres */        } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
Line 7164  set ter svg size 640, 480\nunset log y\n Line 7529  set ter svg size 640, 480\nunset log y\n
       continue;        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 (period): '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<=cptcoveff; k++){    /* For each covariate and each value */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
         /* 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 */
Line 7208  set ter svg size 640, 480\nunset log y\n Line 7573  set ter svg size 640, 480\nunset log y\n
       
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(backcast == 1){
     /* CV back preval stable (period) 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)        if(m != 1 && TKresult[nres]!= k1)
         continue;          continue;
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
         strcpy(gplotlabel,"(");                strcpy(gplotlabel,"(");      
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): '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<=cptcoveff; k++){    /* For each covariate and each value */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
           /* 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 */
Line 7237  set ter svg size 640, 480\nunset log y\n Line 7602  set ter svg size 640, 480\nunset log y\n
         }          }
                   
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
         fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);          fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
         k=3; /* Offset */          k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){ /* State of origin */          for (i=1; i<= nlstate ; i ++){ /* State of arrival */
           if(i==1)            if(i==1)
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
           else            else
Line 7254  set ter svg size 640, 480\nunset log y\n Line 7619  set ter svg size 640, 480\nunset log y\n
           /* for (j=2; j<= nlstate ; j ++) */            /* for (j=2; j<= nlstate ; j ++) */
           /*    fprintf(ficgp,"+$%d",k+l+j-1); */            /*    fprintf(ficgp,"+$%d",k+l+j-1); */
           /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */            /*    /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
           fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);            fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out; unset label;\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
Line 7263  set ter svg size 640, 480\nunset log y\n Line 7628  set ter svg size 640, 480\nunset log y\n
       
   /* 8eme */    /* 8eme */
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) 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 */
Line 7271  set ter svg size 640, 480\nunset log y\n Line 7636  set ter svg size 640, 480\nunset log y\n
         continue;          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 stable (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<=cptcoveff; k++){    /* For each correspondig covariate value  */
           lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
           /* 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 */
Line 7319  set ter svg size 640, 480\nunset log y\n Line 7684  set ter svg size 640, 480\nunset log y\n
             /*#  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 */
             fprintf(ficgp," u %d:(", ioffset);               fprintf(ficgp," u %d:(", ioffset); 
             if(i==nlstate+1){              if(i==nlstate+1){
               fprintf(ficgp," $%d/(1.-$%d)):5 t 'pw.%d' with line lc variable ",        \                fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ",        \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
               fprintf(ficgp,",\\\n '' ");                fprintf(ficgp,",\\\n '' ");
               fprintf(ficgp," u %d:(",ioffset);                 fprintf(ficgp," u %d:(",ioffset); 
               fprintf(ficgp," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", \                fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
                      offyear,                           \                       offyear,                           \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
             }else              }else
               fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \                fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ",      \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
           }else{ /* more than 2 covariates */            }else{ /* more than 2 covariates */
             if(cptcoveff ==1){              ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               ioffset=4; /* Age is in 4 */              /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             }else{              /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               ioffset=6; /* Age is in 6 */              iyearc=ioffset-1;
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/              iagec=ioffset;
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */  
             }     
             fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
             kl=0;              kl=0;
             strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
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             /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
             /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/              /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
             if(i==nlstate+1){              if(i==nlstate+1){
               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):5 t 'p.%d' with line lc variable", gplotcondition, \                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
               fprintf(ficgp,",\\\n '' ");                fprintf(ficgp,",\\\n '' ");
               fprintf(ficgp," u %d:(",ioffset);                 fprintf(ficgp," u %d:(",iagec); 
               fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \                fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                      offyear,                           \                        iyearc, iagec, offyear,                           \
                       ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );                        ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
 /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/  /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
             }else{              }else{
               fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \                fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
Line 7377  set ter svg size 640, 480\nunset log y\n Line 7740  set ter svg size 640, 480\nunset log y\n
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
       
     if(backcast==1){
       /* Back projection from cross-sectional to stable (mixed) for each covariate */
       
       for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           strcpy(gplotlabel,"(");      
           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  */
             lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
             /* 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];
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
           }
           for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
             fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
             sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           }       
           strcpy(gplotlabel+strlen(gplotlabel),")");
           fprintf(ficgp,"\n#\n");
           if(invalidvarcomb[k1]){
             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
             continue;
           }
           
           fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
           fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
   
           /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
           istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
           /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
           for (i=istart; i<= nlstate+1 ; i ++){  /* nlstate +1 p11 p21 p.1 */
             /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
             /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
             if(i==istart){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
             }else{
               fprintf(ficgp,",\\\n '' ");
             }
             if(cptcoveff ==0){ /* No covariate */
               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*/
               /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
               /*# V1  = 1 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 */
               fprintf(ficgp," u %d:(", ioffset); 
               if(i==nlstate+1){
                 fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
                        offbyear,                          \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
               }else
                 fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ",      \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
             }else{ /* more than 2 covariates */
               ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
               /*#  V1  = 1  V2 =  0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
               /*#   1    2   3    4    5      6  7   8   9   10   11 12  13   14  15 */
               iyearc=ioffset-1;
               iagec=ioffset;
               fprintf(ficgp," u %d:(",ioffset); 
               kl=0;
               strcpy(gplotcondition,"(");
               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 */
                 /* 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]; /* Value of the modality of Tvaraff[k] */
                 kl++;
                 sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                 kl++;
                 if(k <cptcoveff && cptcoveff>1)
                   sprintf(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 *\/ */
               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
               /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */ 
               /* ''  u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
               if(i==nlstate+1){
                 fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
                 fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",iagec); 
                 /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc,iagec,offbyear,                            \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
   /*  '' u 6:(($1==1 && $2==0  && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
               }else{
                 /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
                 fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
               }
             } /* end if covariate */
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/
       } /* end covariate */
     } /* End if backcast */
     
       
   /* 9eme writing MLE parameters */    /* 9eme writing MLE parameters */
   fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
Line 7422  set ter svg size 640, 480\nunset log y\n Line 7900  set ter svg size 640, 480\nunset log y\n
         continue;          continue;
       fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);        fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",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<=cptcoveff; k++){    /* For each correspondig covariate value  */
         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */          lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
         /* 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 */
Line 7439  set ter svg size 640, 480\nunset log y\n Line 7917  set ter svg size 640, 480\nunset log y\n
       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);
       fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);        fprintf(ficgp,"\nset key outside ");
         /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
         fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
       fprintf(ficgp,"\nset ter svg size 640, 480 ");        fprintf(ficgp,"\nset ter svg size 640, 480 ");
       if (ng==1){        if (ng==1){
         fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */          fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
Line 7483  set ter svg size 640, 480\nunset log y\n Line 7963  set ter svg size 640, 480\nunset log y\n
             /* for(j=3; j <=ncovmodel-nagesqr; j++) { */              /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
             for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */              for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
               /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */                /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
               if(j==Tage[ij]) { /* Product by age */                if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                 if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */                  if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
                   if(DummyV[j]==0){                    if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                     fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;                      if(DummyV[j]==0){
                   }else{ /* quantitative */                        fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                     fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */                      }else{ /* quantitative */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                        fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                   }                        /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   ij++;  
                 }  
               }else if(j==Tprod[ijp]) { /* */   
                 /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */  
                 if(ijp <=cptcovprod) { /* Product */  
                   if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */  
                     if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */  
                       /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */  
                       fprintf(ficgp,"+p%d*%d*%d",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",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);  
                     }                      }
                   }else{ /* Vn*Vm Vn is quanti */                      ij++;
                     if(DummyV[Tvard[ijp][2]]==0){                    }
                       fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);                  } 
                     }else{ /* Both quanti */                }else if(cptcovprod >0){
                       fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);                  if(j==Tprod[ijp]) { /* */ 
                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                     if(ijp <=cptcovprod) { /* Product */
                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                           fprintf(ficgp,"+p%d*%d*%d",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",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                       }else{ /* Vn*Vm Vn is quanti */
                         if(DummyV[Tvard[ijp][2]]==0){
                           fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
                         }else{ /* Both quanti */
                           fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
                         }
                     }                      }
                       ijp++;
                   }                    }
                   ijp++;                  } /* end Tprod */
                 }  
               } else{  /* simple covariate */                } else{  /* simple covariate */
                 /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */                  /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                 if(Dummy[j]==0){                  if(Dummy[j]==0){
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               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                 if((j-2)==Tage[ij]) { /* Bug valgrind */                   if(cptcovage >0){ 
                   if(ij <=cptcovage) { /* Bug valgrind */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);                       if(ij <=cptcovage) { /* Bug valgrind */
                     /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */                         fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
                     ij++;                         /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                   }                         ij++;
                 }                       }
                 else                     }
                   fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */                   }else
                      fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
               }                }
               fprintf(ficgp,")");                fprintf(ficgp,")");
             }              }
             fprintf(ficgp,")");              fprintf(ficgp,")");
             if(ng ==2)              if(ng ==2)
               fprintf(ficgp," t \"p%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
             else /* ng= 3 */              else /* ng= 3 */
               fprintf(ficgp," t \"i%d%d\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }else{ /* end ng <> 1 */            }else{ /* end ng <> 1 */
             if( k !=k2) /* logit p11 is hard to draw */              if( k !=k2) /* logit p11 is hard to draw */
               fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);                fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ",  nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
           }            }
           if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)            if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
             fprintf(ficgp,",");              fprintf(ficgp,",");
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           i=i+ncovmodel;            i=i+ncovmodel;
         } /* end k */          } /* end k */
       } /* end k2 */        } /* end k2 */
       fprintf(ficgp,"\n set out; unset label;\n");        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
         fprintf(ficgp,"\n set out; unset title;set key default;\n");
     } /* end k1 */      } /* end k1 */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
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    int modcovmax =1;     int modcovmax =1;
    int mobilavrange, mob;     int mobilavrange, mob;
    int iage=0;     int iage=0;
      int firstA1=0, firstA2=0;
   
    double sum=0., sumr=0.;     double sum=0., sumr=0.;
    double age;     double age;
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    double *agemingoodr, *agemaxgoodr;      double *agemingoodr, *agemaxgoodr; 
       
       
    /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose  */     /* modcovmax=2*cptcoveff;  Max number of modalities. We suppose  */
    /*              a covariate has 2 modalities, should be equal to ncovcombmax  *\/ */     /*              a covariate has 2 modalities, should be equal to ncovcombmax   */
   
    sumnewp = vector(1,ncovcombmax);     sumnewp = vector(1,ncovcombmax);
    sumnewm = vector(1,ncovcombmax);     sumnewm = vector(1,ncovcombmax);
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      } /* age */       } /* age */
      /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */       /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
      /* but they will change */       /* but they will change */
        firstA1=0;firstA2=0;
      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */       for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
        sumnewmr[cptcod]=0.;         sumnewmr[cptcod]=0.;
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          sumr+=probs[(int)age][i][cptcod];           sumr+=probs[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);           if(!firstA1){
              firstA1=1;
              printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         if(fabs(sumr - 1.) > 1.e-3) { /* bad */
          printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);           if(!firstA2){
              firstA2=1;
              printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
            }
            fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
   
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          sumr+=mobaverage[(int)age][i][cptcod];           sumr+=mobaverage[(int)age][i][cptcod];
        }         }
        if(fabs(sum - 1.) > 1.e-3) { /* bad */         if(fabs(sum - 1.) > 1.e-3) { /* bad */
          printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, fage);           printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
        } /* end bad */         } /* end bad */
        /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */         /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
        if(fabs(sumr - 1.) > 1.e-3) { /* bad */         if(fabs(sumr - 1.) > 1.e-3) { /* bad */
          printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, fage);           printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
   
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 /************** Forecasting ******************/  /************** Forecasting ******************/
  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){   void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
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   fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);    fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else{
       hstepm=estepm;   
     }
     if(estepm > stepm){ /* Yes every two year */
       stepsize=2;
     }
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=pow(2,cptcoveff);
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
     
   /*            if (h==(int)(YEARM*yearp)){ */
     for(nres=1; nres <= nresult; nres++) /* For each resultline */
     for(k=1; k<=i1;k++){
       if(i1 != 1 && TKresult[nres]!= k)
         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#");
       for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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(ficresf," yearproj age");
       for(j=1; j<=nlstate+ndeath;j++){ 
         for(i=1; i<=nlstate;i++)        
           fprintf(ficresf," p%d%d",i,j);
         fprintf(ficresf," wp.%d",j);
       }
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
         fprintf(ficresf,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
         /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
         for (agec=fage; agec>=(bage); agec--){ 
           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
           nhstepm = nhstepm/hstepm; 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           /* We compute pii at age agec over nhstepm);*/
           hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
           /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
           for (h=0; h<=nhstepm; h++){
             if (h*hstepm/YEARM*stepm ==yearp) {
               break;
             }
           }
           fprintf(ficresf,"\n");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           
           for(j=1; j<=nlstate+ndeath;j++) {
             ppij=0.;
             for(i=1; i<=nlstate;i++) {
               if (mobilav>=1)
                ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
               else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
                   ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
               }
               fprintf(ficresf," %.3f", p3mat[i][j][h]);
             } /* end i */
             fprintf(ficresf," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
         /* diffyear=(int) anproj1+yearp-ageminpar-1; */
         /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/
       } /* end yearp */
     } /* end  k */
           
     fclose(ficresf);
     printf("End of Computing forecasting \n");
     fprintf(ficlog,"End of Computing forecasting\n");
   
   }
   
   /************** Back Forecasting ******************/
    void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
     /* back1, year, month, day of starting backection
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anback2 year of end of backprojection (same day and month as back1).
        prevacurrent and prev are prevalences.
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
     double agec; /* generic age */
     double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     /* double ***mobaverage; */
     char fileresfb[FILENAMELENGTH];
    
     agelim=AGEINF;
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     */
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
     /*          firstpass, lastpass,  stepm,  weightopt, model); */
   
     /*Do we need to compute prevalence again?*/
   
     /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
     
     strcpy(fileresfb,"FB_");
     strcat(fileresfb,fileresu);
     if((ficresfb=fopen(fileresfb,"w"))==NULL) {
       printf("Problem with back forecast resultfile: %s\n", fileresfb);
       fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
     }
     printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
     
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
     
      
   stepsize=(int) (stepm+YEARM-1)/YEARM;    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if (stepm<=12) stepsize=1;    if (stepm<=12) stepsize=1;
   if(estepm < stepm){    if(estepm < stepm){
     printf ("Problem %d lower than %d\n",estepm, stepm);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
   else  hstepm=estepm;       else{
       hstepm=estepm;   
   hstepm=hstepm/stepm;     }
     if(estepm >= stepm){ /* Yes every two year */
       stepsize=2;
     }
     
     hstepm=hstepm/stepm;
   yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                fractional in yp1 */                                 fractional in yp1 */
   anprojmean=yp;    anprojmean=yp;
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   jprojmean=yp;    jprojmean=yp;
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
     
   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",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
     printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
       
 /*            if (h==(int)(YEARM*yearp)){ */  
   for(nres=1; nres <= nresult; nres++) /* For each resultline */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){
     if(i1 != 1 && TKresult[nres]!= k)      if(i1 != 1 && TKresult[nres]!= k)
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       printf("\nCombination (%d) projection ignored because no cases \n",k);         printf("\nCombination (%d) projection ignored because no cases \n",k); 
       continue;        continue;
     }      }
     fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
     for(j=1;j<=cptcoveff;j++) {      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     }      }
     for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
       fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
     }      }
     fprintf(ficresf," yearproj 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++)
         fprintf(ficresf," p%d%d",i,j);          fprintf(ficresfb," b%d%d",i,j);
       fprintf(ficresf," wp.%d",j);        fprintf(ficresfb," b.%d",j);
     }      }
     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {      for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
       fprintf(ficresf,"\n");        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresfb,"\n");
       for (agec=fage; agec>=(ageminpar-1); agec--){         fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);         /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
         nhstepm = nhstepm/hstepm;         /* for (agec=bage; agec<=agemax-1; agec++){  /\* testing *\/ */
         for (agec=bage; agec<=fage; agec++){  /* testing */
           /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
           nhstepm=(int) (agec-agelim) *YEARM/stepm;/*     nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
           nhstepm = nhstepm/hstepm;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);          /* computes hbxij at age agec over 1 to nhstepm */
                   /* printf("####prevbackforecast debug  agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
           hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
           /* hpxij(p3mat,nhstepm,agec,hstepm,p,             nlstate,stepm,oldm,savm, k,nres); */
           /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
           /* printf(" agec=%.2f\n",agec);fflush(stdout); */
         for (h=0; h<=nhstepm; h++){          for (h=0; h<=nhstepm; h++){
           if (h*hstepm/YEARM*stepm ==yearp) {            if (h*hstepm/YEARM*stepm ==-yearp) {
             fprintf(ficresf,"\n");              break;
             for(j=1;j<=cptcoveff;j++)             }
               fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          }
             fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);          fprintf(ficresfb,"\n");
           }           for(j=1;j<=cptcoveff;j++)
           for(j=1; j<=nlstate+ndeath;j++) {            fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             ppij=0.;          fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
             for(i=1; i<=nlstate;i++) {          for(i=1; i<=nlstate+ndeath;i++) {
               /* if (mobilav>=1)  */            ppij=0.;ppi=0.;
                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];            for(j=1; j<=nlstate;j++) {
                 /* else { */ /* even if mobilav==-1 we use mobaverage */              /* if (mobilav==1) */
               ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
               ppi=ppi+prevacurrent[(int)agec][j][k];
               /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
               /* ppi=ppi+mobaverage[(int)agec][j][k]; */
                 /* else { */
               /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */                /*        ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
               /* } */                /* } */
               if (h*hstepm/YEARM*stepm== yearp) {              fprintf(ficresfb," %.3f", p3mat[i][j][h]);
                 fprintf(ficresf," %.3f", p3mat[i][j][h]);            } /* end j */
               }            if(ppi <0.99){
             } /* end i */              printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
             if (h*hstepm/YEARM*stepm==yearp) {              fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
               fprintf(ficresf," %.3f", ppij);            }
             }            fprintf(ficresfb," %.3f", ppij);
           }/* end j */          }/* end j */
         } /* end h */  
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       } /* end agec */        } /* end agec */
       /* diffyear=(int) anproj1+yearp-ageminpar-1; */  
       /*printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);*/  
     } /* end yearp */      } /* end yearp */
   } /* end  k */    } /* end k */
           
   fclose(ficresf);  
   printf("End of Computing forecasting \n");  
   fprintf(ficlog,"End of Computing forecasting\n");  
   
 }  
   
 /* /\************** Back Forecasting ******************\/ */  
 /* void prevbackforecast(char fileres[], double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ */  
 /*   /\* back1, year, month, day of starting backection  */  
 /*      agemin, agemax range of age */  
 /*      dateprev1 dateprev2 range of dates during which prevalence is computed */  
 /*      anback2 year of en of backection (same day and month as back1). */  
 /*   *\/ */  
 /*   int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */  
 /*   double agec; /\* generic age *\/ */  
 /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */  
 /*   double *popeffectif,*popcount; */  
 /*   double ***p3mat; */  
 /*   /\* double ***mobaverage; *\/ */  
 /*   char fileresfb[FILENAMELENGTH]; */  
           
 /*   agelim=AGESUP; */  
 /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */  
 /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */  
 /*      We still use firstpass and lastpass as another selection. */  
 /*   *\/ */  
 /*   /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ *\/ */  
 /*   /\*              firstpass, lastpass,  stepm,  weightopt, model); *\/ */  
 /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */  
           
 /*   strcpy(fileresfb,"FB_");  */  
 /*   strcat(fileresfb,fileresu); */  
 /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */  
 /*     printf("Problem with back forecast resultfile: %s\n", fileresfb); */  
 /*     fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */  
 /*   } */  
 /*   printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  
 /*   fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */  
           
 /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */  
           
 /*   /\* if (mobilav!=0) { *\/ */  
 /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */  
 /*   /\*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ *\/ */  
 /*   /\*     fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); *\/ */  
 /*   /\*     printf(" Error in movingaverage mobilav=%d\n",mobilav); *\/ */  
 /*   /\*   } *\/ */  
 /*   /\* } *\/ */  
           
 /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */  
 /*   if (stepm<=12) stepsize=1; */  
 /*   if(estepm < stepm){ */  
 /*     printf ("Problem %d lower than %d\n",estepm, stepm); */  
 /*   } */  
 /*   else  hstepm=estepm;    */  
           
 /*   hstepm=hstepm/stepm;  */  
 /*   yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp  and */  
 /*                                fractional in yp1 *\/ */  
 /*   anprojmean=yp; */  
 /*   yp2=modf((yp1*12),&yp); */  
 /*   mprojmean=yp; */  
 /*   yp1=modf((yp2*30.5),&yp); */  
 /*   jprojmean=yp; */  
 /*   if(jprojmean==0) jprojmean=1; */  
 /*   if(mprojmean==0) jprojmean=1; */  
           
 /*   i1=cptcoveff; */  
 /*   if (cptcovn < 1){i1=1;} */  
       
 /*   fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);  */    /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
       
 /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */    fclose(ficresfb);
             printf("End of Computing Back forecasting \n");
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */    fprintf(ficlog,"End of Computing Back forecasting\n");
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */  
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */  
 /*       k=k+1; */  
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */  
 /*       for(j=1;j<=cptcoveff;j++) { */  
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */  
 /*       } */  
 /*       fprintf(ficresfb," yearbproj age"); */  
 /*       for(j=1; j<=nlstate+ndeath;j++){  */  
 /*                              for(i=1; i<=nlstate;i++)               */  
 /*           fprintf(ficresfb," p%d%d",i,j); */  
 /*                              fprintf(ficresfb," p.%d",j); */  
 /*       } */  
 /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */  
 /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */  
 /*                              fprintf(ficresfb,"\n"); */  
 /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */  
 /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */  
 /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */  
 /*                                      nhstepm = nhstepm/hstepm;  */  
 /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */  
 /*                                      oldm=oldms;savm=savms; */  
 /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */  
 /*                                      for (h=0; h<=nhstepm; h++){ */  
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */  
 /*               fprintf(ficresfb,"\n"); */  
 /*               for(j=1;j<=cptcoveff;j++)  */  
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */  
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */  
 /*                                              }  */  
 /*                                              for(j=1; j<=nlstate+ndeath;j++) { */  
 /*                                                      ppij=0.; */  
 /*                                                      for(i=1; i<=nlstate;i++) { */  
 /*                                                              if (mobilav==1)  */  
 /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */  
 /*                                                              else { */  
 /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */  
 /*                                                              } */  
 /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */  
 /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */  
 /*                                                              } */  
 /*                                                      } /\* end i *\/ */  
 /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */  
 /*                                                              fprintf(ficresfb," %.3f", ppij); */  
 /*                                                      } */  
 /*                                              }/\* end j *\/ */  
 /*                                      } /\* end h *\/ */  
 /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */  
 /*                              } /\* end agec *\/ */  
 /*       } /\* end yearp *\/ */  
 /*     } /\* end cptcod *\/ */  
 /*   } /\* end  cptcov *\/ */  
                   
 /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */  }
           
 /*   fclose(ficresfb); */  /* Variance of prevalence limit: varprlim */
 /*   printf("End of Computing Back forecasting \n"); */   void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
 /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */      /*------- Variance of forward period (stable) prevalence------*/   
            
 /* } */     char fileresvpl[FILENAMELENGTH];  
      FILE *ficresvpl;
      double **oldm, **savm;
      double **varpl; /* Variances of prevalence limits by age */   
      int i1, k, nres, j ;
      
       strcpy(fileresvpl,"VPL_");
       strcat(fileresvpl,fileresu);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of forward period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
       fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
       /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
       
       i1=pow(2,cptcoveff);
       if (cptcovn < 1){i1=1;}
   
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
         fprintf(ficresvpl,"\n#****** ");
         printf("\n#****** ");
         fprintf(ficlog,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
         fprintf(ficresvpl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         /*}*/
       }
       
       fclose(ficresvpl);
       printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);
   
    }
   /* Variance of back prevalence: varbprlim */
    void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
         /*------- Variance of back (stable) prevalence------*/
   
      char fileresvbl[FILENAMELENGTH];  
      FILE  *ficresvbl;
   
      double **oldm, **savm;
      double **varbpl; /* Variances of back prevalence limits by age */   
      int i1, k, nres, j ;
   
      strcpy(fileresvbl,"VBL_");
      strcat(fileresvbl,fileresu);
      if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
        printf("Problem with variance of back (stable) prevalence  resultfile: %s\n", fileresvbl);
        exit(0);
      }
      printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
      fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
      
      
      i1=pow(2,cptcoveff);
      if (cptcovn < 1){i1=1;}
      
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
        for(k=1; k<=i1;k++){
          if(i1 != 1 && TKresult[nres]!= k)
            continue;
          fprintf(ficresvbl,"\n#****** ");
          printf("\n#****** ");
          fprintf(ficlog,"\n#****** ");
          for(j=1;j<=cptcoveff;j++) {
            fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
            printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
          }
          for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
            printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
            fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
          }
          fprintf(ficresvbl,"******\n");
          printf("******\n");
          fprintf(ficlog,"******\n");
          
          varbpl=matrix(1,nlstate,(int) bage, (int) fage);
          oldm=oldms;savm=savms;
          
          varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
          free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
          /*}*/
        }
      
      fclose(ficresvbl);
      printf("done variance-covariance of back prevalence\n");fflush(stdout);
      fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
   
    } /* End of varbprlim */
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */  /* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
Line 9145  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9784  Dummy[k] 0=dummy (0 1), 1 quantitative (
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\
 Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\  Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
 Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
   for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}    for(k=-1;k<=cptcovt; 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, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
     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;
Line 9395  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 10034  Dummy[k] 0=dummy (0 1), 1 quantitative (
   /* 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++){
       if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){        /* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[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[Tvar[k1]],Dummy[Tvar[k1]]);              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]);
             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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);              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);
             return(1);              return(1);
           }            }
         }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
Line 9571  BOOL IsWow64() Line 10211  BOOL IsWow64()
 #endif  #endif
   
 void syscompilerinfo(int logged)  void syscompilerinfo(int logged)
  {  {
    /* #include "syscompilerinfo.h"*/  #include <stdint.h>
   
     /* #include "syscompilerinfo.h"*/
    /* command line Intel compiler 32bit windows, XP compatible:*/     /* command line Intel compiler 32bit windows, XP compatible:*/
    /* /GS /W3 /Gy     /* /GS /W3 /Gy
       /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D        /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 9607  void syscompilerinfo(int logged) Line 10249  void syscompilerinfo(int logged)
       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF        /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
       /NOLOGO /TLBID:1        /NOLOGO /TLBID:1
    */     */
   
   
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 9623  void syscompilerinfo(int logged) Line 10267  void syscompilerinfo(int logged)
    }     }
 #endif  #endif
   
 #include <stdint.h>  
   
    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");     printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)  #if defined(__clang__)
    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */     printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");       /* Clang/LLVM. ---------------------------------------------- */
Line 9710  void syscompilerinfo(int logged) Line 10352  void syscompilerinfo(int logged)
 #endif  #endif
 #endif  #endif
   
    //   void main()     //   void main ()
    //   {     //   {
 #if defined(_MSC_VER)  #if defined(_MSC_VER)
    if (IsWow64()){     if (IsWow64()){
Line 9731  void syscompilerinfo(int logged) Line 10373  void syscompilerinfo(int logged)
 }  }
   
 int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){  int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
   /*--------------- Prevalence limit  (period or stable prevalence) --------------*/    /*--------------- Prevalence limit  (forward period or forward stable prevalence) --------------*/
   int i, j, k, i1, k4=0, nres=0 ;    int i, j, k, i1, k4=0, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
Line 9740  int prevalence_limit(double *p, double * Line 10382  int prevalence_limit(double *p, double *
   strcpy(filerespl,"PL_");    strcpy(filerespl,"PL_");
   strcat(filerespl,fileresu);    strcat(filerespl,fileresu);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
   pstamp(ficrespl);    pstamp(ficrespl);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
   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,"\n");    fprintf(ficrespl,"\n");
Line 9821  int prevalence_limit(double *p, double * Line 10463  int prevalence_limit(double *p, double *
 }  }
   
 int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){  int back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
         /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/          /*--------------- Back Prevalence limit  (backward stable prevalence) --------------*/
                   
         /* Computes the back prevalence limit  for any combination      of covariate values           /* Computes the back prevalence limit  for any combination      of covariate values 
    * at any age between ageminpar and agemaxpar     * at any age between ageminpar and agemaxpar
Line 9836  int back_prevalence_limit(double *p, dou Line 10478  int back_prevalence_limit(double *p, dou
   strcpy(fileresplb,"PLB_");    strcpy(fileresplb,"PLB_");
   strcat(fileresplb,fileresu);    strcat(fileresplb,fileresu);
   if((ficresplb=fopen(fileresplb,"w"))==NULL) {    if((ficresplb=fopen(fileresplb,"w"))==NULL) {
     printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
     fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;      fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
   }    }
   printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
   fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);    fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
   pstamp(ficresplb);    pstamp(ficresplb);
   fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficresplb,"#Age ");    fprintf(ficresplb,"#Age ");
   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,"\n");    fprintf(ficresplb,"\n");
Line 10031  int hPijx(double *p, int bage, int fage) Line 10673  int hPijx(double *p, int bage, int fage)
   /*if (stepm<=24) stepsize=2;*/    /*if (stepm<=24) stepsize=2;*/
       
   /* agelim=AGESUP; */    /* agelim=AGESUP; */
   ageminl=30;    ageminl=AGEINF; /* was 30 */
   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 */
       
Line 10071  int hPijx(double *p, int bage, int fage) Line 10713  int hPijx(double *p, int bage, int fage)
   
         /* oldm=oldms;savm=savms; */          /* oldm=oldms;savm=savms; */
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
         /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /* 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=");          fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
Line 10110  int main(int argc, char *argv[]) Line 10752  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;    int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
     /* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
   int ncvyear=0; /* Number of years needed for the period prevalence to converge */    int ncvyear=0; /* Number of years needed for the period prevalence to converge */
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
Line 10120  int main(int argc, char *argv[]) Line 10763  int main(int argc, char *argv[])
   int vpopbased=0;    int vpopbased=0;
   int nres=0;    int nres=0;
   int endishere=0;    int endishere=0;
     int noffset=0;
     int ncurrv=0; /* Temporary variable */
     
   char ca[32], cb[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
Line 10143  int main(int argc, char *argv[]) Line 10788  int main(int argc, char *argv[])
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
   int c,  h , cpt, c2;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
Line 10151  int main(int argc, char *argv[]) Line 10796  int main(int argc, char *argv[])
   
   int *tab;     int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int backcast=0;    int backcast=0; /* defined as global for mlikeli and mle*/
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;    int hstepm=0, nhstepm=0;
   int agemortsup;    int agemortsup;
Line 10172  int main(int argc, char *argv[]) Line 10817  int main(int argc, char *argv[])
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   
   double *epj, vepp;    double *epj, vepp;
   
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2;
   double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;    double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
     double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;
   
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 10253  int main(int argc, char *argv[]) Line 10900  int main(int argc, char *argv[])
       if(pathr[0] == '\0') break; /* Dirty */        if(pathr[0] == '\0') break; /* Dirty */
     }      }
   }    }
     else if (argc<=2){
       strcpy(pathtot,argv[1]);
     }
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
       strcpy(z,argv[2]);
       printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
   }    }
   /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
Line 10332  int main(int argc, char *argv[]) Line 10984  int main(int argc, char *argv[])
     exit(70);       exit(70); 
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileresu);    strcat(filereso,fileresu);
   if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
Line 10342  int main(int argc, char *argv[]) Line 10992  int main(int argc, char *argv[])
     fflush(ficlog);      fflush(ficlog);
     goto end;      goto end;
   }    }
         /*-------- Rewriting parameter file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name */
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
       fflush(ficlog);
       goto end;
     }
     fprintf(ficres,"#IMaCh %s\n",version);
   
                                         
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
     /* Is it a BOM UTF-8 Windows file? */
     /* First parameter line */    /* First parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
       noffset=0;
       if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
       {
         noffset=noffset+3;
         printf("# File is an UTF8 Bom.\n"); // 0xBF
       }
       else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
       {
         noffset=noffset+2;
         printf("# File is an UTF16BE BOM file\n");
       }
       else if( line[0] == 0 && line[1] == 0)
       {
         if( line[2] == (char)0xFE && line[3] == (char)0xFF){
           noffset=noffset+4;
           printf("# File is an UTF16BE BOM file\n");
         }
       } else{
         ;/*printf(" Not a BOM file\n");*/
       }
     
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[noffset] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        fputs(line,stdout);
       fputs(line,ficparo);        fputs(line,ficparo);
         fputs(line,ficres);
       fputs(line,ficlog);        fputs(line,ficlog);
       continue;        continue;
     }else      }else
Line 10362  int main(int argc, char *argv[]) Line 11047  int main(int argc, char *argv[])
                         title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){                          title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
     if (num_filled != 5) {      if (num_filled != 5) {
       printf("Should be 5 parameters\n");        printf("Should be 5 parameters\n");
         fprintf(ficlog,"Should be 5 parameters\n");
     }      }
     numlinepar++;      numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
       fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
   }    }
   /* Second parameter line */    /* Second parameter line */
   while(fgets(line, MAXLINE, ficpar)) {    while(fgets(line, MAXLINE, ficpar)) {
     /* If line starts with a # it is a comment */      /* while(fscanf(ficpar,"%[^\n]", line)) { */
       /* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
Line 10383  int main(int argc, char *argv[]) Line 11074  int main(int argc, char *argv[])
     if (num_filled != 11) {      if (num_filled != 11) {
       printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");        printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
       printf("but line=%s\n",line);        printf("but line=%s\n",line);
         fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1  nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
         fprintf(ficlog,"but line=%s\n",line);
       }
       if( lastpass > maxwav){
         printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
         fflush(ficlog);
         goto end;
     }      }
     printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);        printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
       fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
       fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
       fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
   }    }
   /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */    /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
   /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */    /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 10393  int main(int argc, char *argv[]) Line 11095  int main(int argc, char *argv[])
     /* If line starts with a # it is a comment */      /* If line starts with a # it is a comment */
     if (line[0] == '#') {      if (line[0] == '#') {
       numlinepar++;        numlinepar++;
       fputs(line,stdout);        printf("%s",line);
       fputs(line,ficparo);        fprintf(ficres,"%s",line);
       fputs(line,ficlog);        fprintf(ficparo,"%s",line);
         fprintf(ficlog,"%s",line);
       continue;        continue;
     }else      }else
       break;        break;
   }    }
   if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){    if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
     if (num_filled == 0){      if (num_filled != 1){
       printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);        printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
       model[0]='\0';  
       goto end;  
     } else if (num_filled != 1){  
       printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);  
       model[0]='\0';        model[0]='\0';
       goto end;        goto end;
     }      }
Line 10421  int main(int argc, char *argv[]) Line 11119  int main(int argc, char *argv[])
     }      }
     /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */      /* printf(" model=1+age%s modeltemp= %s, model=%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(ficres,"model=1+age+%s\n",model);fflush(stdout);
       fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
   }    }
   /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */    /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
   /* numlinepar=numlinepar+3; /\* In general *\/ */    /* numlinepar=numlinepar+3; /\* In general *\/ */
   /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */    /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);    /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);    /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
     printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \      printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
  'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \   'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
  'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n");          \   'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n");            \
     if(mle != -1){      if(mle != -1){
       printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");        printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
       exit(1);        exit(1);
     }      }
   }    }
Line 10454  int main(int argc, char *argv[]) Line 11155  int main(int argc, char *argv[])
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,firstobs,lastobs);  /**< used in readdata */
   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs);  /**< Fixed quantitative covariate */
   cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n);  /**< Time varying covariate (dummy and quantitative)*/    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs);  /**< Time varying quantitative covariate */
   cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< Time varying quantitative covariate */    if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs);  /**< Time varying covariate (dummy and quantitative)*/
   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 10520  int main(int argc, char *argv[]) Line 11221  int main(int argc, char *argv[])
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;          if(jj==i) continue;
         j++;          j++;
           while((c=getc(ficpar))=='#' && c!= EOF){
             ungetc(c,ficpar);
             fgets(line, MAXLINE, ficpar);
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
           }
           ungetc(c,ficpar);
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) || (j1 != jj)){          if ((i1 != i) || (j1 != jj)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
Line 10656  Please run with mle=-1 to get a correct Line 11366  Please run with mle=-1 to get a correct
           
     fflush(ficlog);      fflush(ficlog);
           
     /*-------- Rewriting parameter file ----------*/  
     strcpy(rfileres,"r");    /* "Rparameterfile */  
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
     strcat(rfileres,".");    /* */  
     strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {  
       printf("Problem writing new parameter file: %s\n", rfileres);goto end;  
       fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;  
     }  
     fprintf(ficres,"#%s\n",version);  
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
       
   /*  Main data    /*  Main data
    */     */
   n= lastobs;    nobs=lastobs-firstobs+1; /* was = lastobs;*/
   num=lvector(1,n);    /* num=lvector(1,n); */
   moisnais=vector(1,n);    /* moisnais=vector(1,n); */
   annais=vector(1,n);    /* annais=vector(1,n); */
   moisdc=vector(1,n);    /* moisdc=vector(1,n); */
   andc=vector(1,n);    /* andc=vector(1,n); */
   weight=vector(1,n);    /* weight=vector(1,n); */
   agedc=vector(1,n);    /* agedc=vector(1,n); */
   cod=ivector(1,n);    /* cod=ivector(1,n); */
   for(i=1;i<=n;i++){    /* for(i=1;i<=n;i++){ */
     num=lvector(firstobs,lastobs);
     moisnais=vector(firstobs,lastobs);
     annais=vector(firstobs,lastobs);
     moisdc=vector(firstobs,lastobs);
     andc=vector(firstobs,lastobs);
     weight=vector(firstobs,lastobs);
     agedc=vector(firstobs,lastobs);
     cod=ivector(firstobs,lastobs);
     for(i=firstobs;i<=lastobs;i++){
     num[i]=0;      num[i]=0;
     moisnais[i]=0;      moisnais[i]=0;
     annais[i]=0;      annais[i]=0;
Line 10689  Please run with mle=-1 to get a correct Line 11398  Please run with mle=-1 to get a correct
     cod[i]=0;      cod[i]=0;
     weight[i]=1.0; /* Equal weights, 1 by default */      weight[i]=1.0; /* Equal weights, 1 by default */
   }    }
   mint=matrix(1,maxwav,1,n);    mint=matrix(1,maxwav,firstobs,lastobs);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,firstobs,lastobs);
   s=imatrix(1,maxwav+1,1,n); /* 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 */ 
   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 10793  Please run with mle=-1 to get a correct Line 11502  Please run with mle=-1 to get a correct
   
   
   agegomp=(int)agemin;    agegomp=(int)agemin;
   free_vector(moisnais,1,n);    free_vector(moisnais,firstobs,lastobs);
   free_vector(annais,1,n);    free_vector(annais,firstobs,lastobs);
   /* free_matrix(mint,1,maxwav,1,n);    /* free_matrix(mint,1,maxwav,1,n);
      free_matrix(anint,1,maxwav,1,n);*/       free_matrix(anint,1,maxwav,1,n);*/
   /* free_vector(moisdc,1,n); */    /* free_vector(moisdc,1,n); */
Line 10820  Please run with mle=-1 to get a correct Line 11529  Please run with mle=-1 to get a correct
   concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   /* Concatenates waves */    /* Concatenates waves */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,firstobs,lastobs);
   free_vector(andc,1,n);    free_vector(andc,firstobs,lastobs);
   
   /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */    /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
Line 11003  Title=%s <br>Datafile=%s Firstpass=%d La Line 11712  Title=%s <br>Datafile=%s Firstpass=%d La
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   fprintf(fichtm,"<br>Total number of observations=%d <br>\n\    fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
             ftol, stepm);
     fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
     ncurrv=1;
     for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv); 
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Number of time varying  quantitative covariates: nqtv=%d ", nqtv);
     ncurrv=i;
     for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
     fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
              nlstate, ndeath, maxwav, mle, weightopt);
   
     fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
   <img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
   
     
     fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\  Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\  Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);    imx,agemin,agemax,jmin,jmax,jmean);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
         oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
   
   /* For Powell, parameters are in a vector p[] starting at p[1]    /* For Powell, parameters are in a vector p[] starting at p[1]
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
Line 11025  Interval (in months) between two waves: Line 11755  Interval (in months) between two waves:
       for(j=1;j<=NDIM;j++)        for(j=1;j<=NDIM;j++)
         ximort[i][j]=0.;          ximort[i][j]=0.;
     /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(firstobs,lastobs);
     ageexmed=vector(1,n);      ageexmed=vector(firstobs,lastobs);
     agecens=vector(1,n);      agecens=vector(firstobs,lastobs);
     dcwave=ivector(1,n);      dcwave=ivector(firstobs,lastobs);
                                   
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
Line 11242  Please run with mle=-1 to get a correct Line 11972  Please run with mle=-1 to get a correct
     free_vector(lpop,1,AGESUP);      free_vector(lpop,1,AGESUP);
     free_vector(tpop,1,AGESUP);      free_vector(tpop,1,AGESUP);
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
     free_ivector(cens,1,n);      free_ivector(dcwave,firstobs,lastobs);
     free_vector(agecens,1,n);      free_vector(agecens,firstobs,lastobs);
     free_ivector(dcwave,1,n);      free_vector(ageexmed,firstobs,lastobs);
       free_ivector(cens,firstobs,lastobs);
 #ifdef GSL  #ifdef GSL
 #endif  #endif
   } /* Endof if mle==-3 mortality only */    } /* Endof if mle==-3 mortality only */
Line 11278  Please run with mle=-1 to get a correct Line 12009  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
           
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);      /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
           
           
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 11566  Please run with mle=-1 to get a correct Line 12297  Please run with mle=-1 to get a correct
           fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);            fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
           /* day and month of proj2 are not used but only year anproj2.*/            /* day and month of proj2 are not used but only year anproj2.*/
             dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
             dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
   
         }          }
         break;          break;
       case 12:        case 12:
Line 11581  Please run with mle=-1 to get a correct Line 12315  Please run with mle=-1 to get a correct
           fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);            fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
           fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);            fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
           /* day and month of proj2 are not used but only year anproj2.*/            /* day and month of proj2 are not used but only year anproj2.*/
             dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
             dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
         }          }
         break;          break;
       case 13:        case 13:
Line 11631  Please run with mle=-1 to get a correct Line 12367  Please run with mle=-1 to get a correct
 This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\  This is probably because your parameter file doesn't \n  contain the exact number of lines (or columns) corresponding to your model line.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);  Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
     }else{      }else{
       printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)ageminpar);        /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
         printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
     }      }
     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,backcast, estepm, \                   model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
                  jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);                   jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
                                   
     /*------------ free_vector  -------------*/      /*------------ free_vector  -------------*/
     /*  chdir(path); */      /*  chdir(path); */
Line 11644  Please run with mle=-1 to get a correct Line 12381  Please run with mle=-1 to get a correct
     /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */      /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
     /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */      /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx);    */
     free_lvector(num,1,n);      free_lvector(num,firstobs,lastobs);
     free_vector(agedc,1,n);      free_vector(agedc,firstobs,lastobs);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
Line 11671  Please run with mle=-1 to get a correct Line 12408  Please run with mle=-1 to get a correct
     k=1;      k=1;
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
           
     /* Prevalence for each covariates in probs[age][status][cov] */      /* Prevalence for each covariate combination in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=AGEINF;i<=AGESUP;i++)
       for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */        for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
         for(k=1;k<=ncovcombmax;k++)          for(k=1;k<=ncovcombmax;k++)
           probs[i][j][k]=0.;            probs[i][j][k]=0.;
     prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, 
                  ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     if (mobilav!=0 ||mobilavproj !=0 ) {      if (mobilav!=0 ||mobilavproj !=0 ) {
       mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);        mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
       for(i=1;i<=AGESUP;i++)        for(i=AGEINF;i<=AGESUP;i++)
         for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate+ndeath;j++)
           for(k=1;k<=ncovcombmax;k++)            for(k=1;k<=ncovcombmax;k++)
             mobaverages[i][j][k]=0.;              mobaverages[i][j][k]=0.;
       mobaverage=mobaverages;        mobaverage=mobaverages;
Line 11692  Please run with mle=-1 to get a correct Line 12430  Please run with mle=-1 to get a correct
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);            fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);            printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }          }
       }        } else if (mobilavproj !=0) {
       /* else if(mobilavproj==-1){ /\* Forcing raw observed prevalences *\/ */  
       /*        for(i=1;i<=AGESUP;i++) */  
       /*          for(j=1;j<=nlstate;j++) */  
       /*            for(k=1;k<=ncovcombmax;k++) */  
       /*              mobaverages[i][j][k]=probs[i][j][k]; */  
       /*        /\* /\\* Prevalence for each covariates in probs[age][status][cov] *\\/ *\/ */  
       /*        /\* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); *\/ */  
       /* } */  
       else if (mobilavproj !=0) {  
         printf("Movingaveraging projected observed prevalence\n");          printf("Movingaveraging projected observed prevalence\n");
         fprintf(ficlog,"Movingaveraging projected observed prevalence\n");          fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
           fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);            fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
           printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);            printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
         }          }
         }else{
           printf("Internal error moving average\n");
           fflush(stdout);
           exit(1);
       }        }
     }/* end if moving average */      }/* end if moving average */
           
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/  
     if(prevfcast==1){      if(prevfcast==1){
       /*    if(stepm ==1){*/        /*    if(stepm ==1){*/
       prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
     }      }
   
       /* Backcasting */
     if(backcast==1){      if(backcast==1){
       ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
       ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);                ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);        
Line 11725  Please run with mle=-1 to get a correct Line 12459  Please run with mle=-1 to get a correct
       /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/        /*--------------- Back Prevalence limit  (period or stable prevalence) --------------*/
   
       bprlim=matrix(1,nlstate,1,nlstate);        bprlim=matrix(1,nlstate,1,nlstate);
   
       back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);        back_prevalence_limit(p, bprlim,  ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
       fclose(ficresplb);        fclose(ficresplb);
   
       hBijx(p, bage, fage, mobaverage);        hBijx(p, bage, fage, mobaverage);
       fclose(ficrespijb);        fclose(ficrespijb);
       free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */  
   
       /* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,        prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
          bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */                         mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
         varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
   
         
         free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
       free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
       free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);        free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
     }      }    /* end  Backcasting */
        
     
     /* ------ Other prevalence ratios------------ */      /* ------ Other prevalence ratios------------ */
   
Line 11790  Please run with mle=-1 to get a correct Line 12528  Please run with mle=-1 to get a correct
     fclose(ficreseij);      fclose(ficreseij);
     printf("done evsij\n");fflush(stdout);      printf("done evsij\n");fflush(stdout);
     fprintf(ficlog,"done evsij\n");fflush(ficlog);      fprintf(ficlog,"done evsij\n");fflush(ficlog);
   
                                   
     /*---------- State-specific expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                                   
                   
     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 11802  Please run with mle=-1 to get a correct Line 12540  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);      printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
     fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);      fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
                   
   
     strcpy(fileresstde,"STDE_");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileresu);      strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
Line 11831  Please run with mle=-1 to get a correct Line 12567  Please run with mle=-1 to get a correct
     printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
             
     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;}
           
Line 11895  Please run with mle=-1 to get a correct Line 12628  Please run with mle=-1 to get a correct
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       pstamp(ficrest);        pstamp(ficrest);
               
               epj=vector(1,nlstate+1);
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
         oldm=oldms;savm=savms; /* ZZ Segmentation fault */          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
         cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
Line 11906  Please run with mle=-1 to get a correct Line 12639  Please run with mle=-1 to get a correct
         if(vpopbased==1)          if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
         else          else
           fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
         /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
         epj=vector(1,nlstate+1);          printf("Computing age specific forward period (stable) prevalences in each health state \n");
         printf("Computing age specific period (stable) prevalences in each health state \n");          fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
         fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");  
         for(age=bage; age <=fage ;age++){          for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */            prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /*ZZ Is it the correct prevalim */
           if (vpopbased==1) {            if (vpopbased==1) {
Line 11949  Please run with mle=-1 to get a correct Line 12681  Please run with mle=-1 to get a correct
           fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
         }          }
       } /* End vpopbased */        } /* End vpopbased */
         free_vector(epj,1,nlstate+1);
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_vector(epj,1,nlstate+1);  
       printf("done selection\n");fflush(stdout);        printf("done selection\n");fflush(stdout);
       fprintf(ficlog,"done selection\n");fflush(ficlog);        fprintf(ficlog,"done selection\n");fflush(ficlog);
               
       /*}*/  
     } /* End k selection */      } /* End k selection */
   
     printf("done State-specific expectancies\n");fflush(stdout);      printf("done State-specific expectancies\n");fflush(stdout);
     fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);      fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
     /*------- Variance of period (stable) prevalence------*/         /* variance-covariance of forward period prevalence*/
           varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
     strcpy(fileresvpl,"VPL_");  
     strcat(fileresvpl,fileresu);  
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  
       printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);  
       exit(0);  
     }  
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);  
     fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);  
       
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){  
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/  
       
     i1=pow(2,cptcoveff);  
     if (cptcovn < 1){i1=1;}  
   
     for(nres=1; nres <= nresult; nres++) /* For each resultline */  
     for(k=1; k<=i1;k++){  
       if(i1 != 1 && TKresult[nres]!= k)  
         continue;  
       fprintf(ficresvpl,"\n#****** ");  
       printf("\n#****** ");  
       fprintf(ficlog,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
       }  
       for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */  
         printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
         fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
         fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);  
       }   
       fprintf(ficresvpl,"******\n");  
       printf("******\n");  
       fprintf(ficlog,"******\n");  
         
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;  
       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);  
       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
       /*}*/  
     }  
           
     fclose(ficresvpl);      free_vector(weight,firstobs,lastobs);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);  
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);  
       
     free_vector(weight,1,n);  
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
     free_imatrix(s,1,maxwav+1,1,n);      free_imatrix(s,1,maxwav+1,firstobs,lastobs);
     free_matrix(anint,1,maxwav,1,n);       free_matrix(anint,1,maxwav,firstobs,lastobs); 
     free_matrix(mint,1,maxwav,1,n);      free_matrix(mint,1,maxwav,firstobs,lastobs);
     free_ivector(cod,1,n);      free_ivector(cod,firstobs,lastobs);
     free_ivector(tab,1,NCOVMAX);      free_ivector(tab,1,NCOVMAX);
     fclose(ficresstdeij);      fclose(ficresstdeij);
     fclose(ficrescveij);      fclose(ficrescveij);
Line 12026  Please run with mle=-1 to get a correct Line 12712  Please run with mle=-1 to get a correct
           
     /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
     if (mobilav!=0 ||mobilavproj !=0)      if (mobilav!=0 ||mobilavproj !=0)
       free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */        free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
     free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
Line 12035  Please run with mle=-1 to get a correct Line 12721  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);
   free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);    if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
   free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
   free_matrix(coqvar,1,maxwav,1,n);    if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
   free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
   free_matrix(matcov,1,npar,1,npar);    free_matrix(matcov,1,npar,1,npar);
   free_matrix(hess,1,npar,1,npar);    free_matrix(hess,1,npar,1,npar);
   /*free_vector(delti,1,npar);*/    /*free_vector(delti,1,npar);*/
   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
   free_matrix(agev,1,maxwav,1,imx);    free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
       
   free_ivector(ncodemax,1,NCOVMAX);    free_ivector(ncodemax,1,NCOVMAX);
Line 12120  Please run with mle=-1 to get a correct Line 12807  Please run with mle=-1 to get a correct
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
       
   
   /* Executes gnuplot */
       
   printf("Before Current directory %s!\n",pathcd);    printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
Line 12155  Please run with mle=-1 to get a correct Line 12844  Please run with mle=-1 to get a correct
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     strcpy(pplotcmd,plotcmd);
       
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
     if((outcmd=system(plotcmd)) != 0)      if((outcmd=system(plotcmd)) != 0){
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
         strcpy(plotcmd,pplotcmd);
       }
   }    }
   printf(" Successful, please wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {
Line 12188  end: Line 12880  end:
     printf("\nType  q for exiting: "); fflush(stdout);      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
     printf("End\n");
     exit(0);
 }  }

Removed from v.1.266  
changed lines
  Added in v.1.295


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