Diff for /imach/src/imach.c between versions 1.231 and 1.278

version 1.231, 2016/08/22 07:17:15 version 1.278, 2017/07/19 14:09:02
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     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
     Summary: Version 0.99r13 (improvements and bugs fixed)
   
     Revision 1.265  2017/04/26 16:22:11  brouard
     Summary: imach 0.99r13 Some bugs fixed
   
     Revision 1.264  2017/04/26 06:01:29  brouard
     Summary: Labels in graphs
   
     Revision 1.263  2017/04/24 15:23:15  brouard
     Summary: to save
   
     Revision 1.262  2017/04/18 16:48:12  brouard
     *** empty log message ***
   
     Revision 1.261  2017/04/05 10:14:09  brouard
     Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1
   
     Revision 1.260  2017/04/04 17:46:59  brouard
     Summary: Gnuplot indexations fixed (humm)
   
     Revision 1.259  2017/04/04 13:01:16  brouard
     Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3
   
     Revision 1.258  2017/04/03 10:17:47  brouard
     Summary: Version 0.99r12
   
     Some cleanings, conformed with updated documentation.
   
     Revision 1.257  2017/03/29 16:53:30  brouard
     Summary: Temp
   
     Revision 1.256  2017/03/27 05:50:23  brouard
     Summary: Temporary
   
     Revision 1.255  2017/03/08 16:02:28  brouard
     Summary: IMaCh version 0.99r10 bugs in gnuplot fixed
   
     Revision 1.254  2017/03/08 07:13:00  brouard
     Summary: Fixing data parameter line
   
     Revision 1.253  2016/12/15 11:59:41  brouard
     Summary: 0.99 in progress
   
     Revision 1.252  2016/09/15 21:15:37  brouard
     *** empty log message ***
   
     Revision 1.251  2016/09/15 15:01:13  brouard
     Summary: not working
   
     Revision 1.250  2016/09/08 16:07:27  brouard
     Summary: continue
   
     Revision 1.249  2016/09/07 17:14:18  brouard
     Summary: Starting values from frequencies
   
     Revision 1.248  2016/09/07 14:10:18  brouard
     *** empty log message ***
   
     Revision 1.247  2016/09/02 11:11:21  brouard
     *** empty log message ***
   
     Revision 1.246  2016/09/02 08:49:22  brouard
     *** empty log message ***
   
     Revision 1.245  2016/09/02 07:25:01  brouard
     *** empty log message ***
   
     Revision 1.244  2016/09/02 07:17:34  brouard
     *** empty log message ***
   
     Revision 1.243  2016/09/02 06:45:35  brouard
     *** empty log message ***
   
     Revision 1.242  2016/08/30 15:01:20  brouard
     Summary: Fixing a lots
   
     Revision 1.241  2016/08/29 17:17:25  brouard
     Summary: gnuplot problem in Back projection to fix
   
     Revision 1.240  2016/08/29 07:53:18  brouard
     Summary: Better
   
     Revision 1.239  2016/08/26 15:51:03  brouard
     Summary: Improvement in Powell output in order to copy and paste
   
     Author:
   
     Revision 1.238  2016/08/26 14:23:35  brouard
     Summary: Starting tests of 0.99
   
     Revision 1.237  2016/08/26 09:20:19  brouard
     Summary: to valgrind
   
     Revision 1.236  2016/08/25 10:50:18  brouard
     *** empty log message ***
   
     Revision 1.235  2016/08/25 06:59:23  brouard
     *** empty log message ***
   
     Revision 1.234  2016/08/23 16:51:20  brouard
     *** empty log message ***
   
     Revision 1.233  2016/08/23 07:40:50  brouard
     Summary: not working
   
     Revision 1.232  2016/08/22 14:20:21  brouard
     Summary: not working
   
   Revision 1.231  2016/08/22 07:17:15  brouard    Revision 1.231  2016/08/22 07:17:15  brouard
   Summary: not working    Summary: not working
   
Line 66 Line 211
   Author: Nicolas Brouard    Author: Nicolas Brouard
   
   Revision 1.210  2015/11/18 17:41:20  brouard    Revision 1.210  2015/11/18 17:41:20  brouard
   Summary: Start working on projected prevalences    Summary: Start working on projected prevalences  Revision 1.209  2015/11/17 22:12:03  brouard
   
   Revision 1.209  2015/11/17 22:12:03  brouard  
   Summary: Adding ftolpl parameter    Summary: Adding ftolpl parameter
   Author: N Brouard    Author: N Brouard
   
Line 711  Back prevalence and projections: Line 854  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 856  typedef struct { Line 999  typedef struct {
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
 #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */  #define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */
   
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
Line 879  typedef struct { Line 1022  typedef struct {
 #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 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 911  int cptcovsnq=0; /**< cptcovsnq number o Line 1055  int cptcovsnq=0; /**< cptcovsnq number o
 int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */  int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
 int cptcovprodnoage=0; /**< Number of covariate products without age */     int cptcovprodnoage=0; /**< Number of covariate products without age */   
 int cptcoveff=0; /* Total number of covariates to vary for printing results */  int cptcoveff=0; /* Total number of covariates to vary for printing results */
 int ncoveff=0; /* Total number of effective covariates in the model */  int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
   int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
   int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
   int nsd=0; /**< Total number of single dummy variables (output) */
   int nsq=0; /**< Total number of single quantitative variables (output) */
   int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
 int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */  int nqfveff=0; /**< nqfveff Number of Quantitative Fixed Variables Effective */
 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 */
Line 965  FILE *ficrescveij; Line 1114  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 optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH],  fileresplb[FILENAMELENGTH];
 char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH];   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
Line 1005  double dval; Line 1154  double dval;
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
   
 #define NRANSI   #define NRANSI 
 #define ITMAX 200   #define ITMAX 200
   #define ITPOWMAX 20 /* This is now multiplied by the number of parameters */ 
   
 #define TOL 2.0e-4   #define TOL 2.0e-4 
   
Line 1062  double *agedc; Line 1212  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 */
   /*           V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   /*k          1  2   3   4     5    6    7     8    9 */
   /*Tvar[k]=   5  4   3   6     5    2    7     1    1 */
   /* Tndvar[k]    1   2   3               4          5 */
   /*TDvar         4   3   6               7          1 */ /* For outputs only; combination of dummies fixed or varying */
   /* Tns[k]    1  2   2              4               5 */ /* Number of single cova */
   /* TvarsD[k]    1   2                              3 */ /* Number of single dummy cova */
   /* TvarsDind    2   3                              9 */ /* position K of single dummy cova */
   /* TvarsQ[k] 1                     2                 */ /* Number of single quantitative cova */
   /* TvarsQind 1                     6                 */ /* position K of single quantitative cova */
   /* Tprod[i]=k           4               7            */
   /* Tage[i]=k                  5               8      */
   /* */
   /* Type                    */
   /* V         1  2  3  4  5 */
   /*           F  F  V  V  V */
   /*           D  Q  D  D  Q */
   /*                         */
   int *TvarsD;
   int *TvarsDind;
   int *TvarsQ;
   int *TvarsQind;
   
   #define MAXRESULTLINES 10
   int nresult=0;
   int parameterline=0; /* # of the parameter (type) line */
   int TKresult[MAXRESULTLINES];
   int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
   int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
   double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
   int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */
   
   /* int *TDvar; /\**< TDvar[1]=4,  TDvarF[2]=3, TDvar[3]=6  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 *\/ */
   int *TvarF; /**< TvarF[1]=Tvar[6]=2,  TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarFind; /**< TvarFind[1]=6,  TvarFind[2]=7, Tvarind[3]=9  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarV; /**< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarVind; /**< TvarVind[1]=1, TvarVind[2]=2  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarA; /**< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
   int *TvarAind; /**< TvarindA[1]=5, TvarAind[2]=8  in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
 int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarFD; /**< TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
 int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */  int *TvarFDind; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
 int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */  int *TvarFQ; /* TvarFQ[1]=V2 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
Line 1081  double *Tvalsel; /**< Selected modality Line 1272  double *Tvalsel; /**< Selected modality
 int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
 int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
 int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
   int *DummyV; /** Dummy[v] 0=dummy (0 1), 1 quantitative */
   int *FixedV; /** FixedV[v] 0 fixed, 1 varying */
 int *Tage;  int *Tage;
 int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */   int anyvaryingduminmodel=0; /**< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq */ 
 int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/  int *Tmodelind; /** Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1*/
Line 1090  int *Ndum; /** Freq of modality (tricode Line 1283  int *Ndum; /** Freq of modality (tricode
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard;  int **Tvard;
 int *Tprod;/**< Gives the k position of the k1 product */  int *Tprod;/**< Gives the k position of the k1 product */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3  */
 int *Tposprod; /**< Gives the k1 product from the k position */  int *Tposprod; /**< Gives the k1 product from the k position */
 /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3     /* if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2) */
    if  V2+V1+V1*V4+age*V3+V3*V2   TProd[k1=2]=5 (V3*V2)     /* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3*V2)]=2 (2nd product without age) */
    Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2   
 */  
 int cptcovprod, *Tvaraff, *invalidvarcomb;  int cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
Line 1320  int nbocc(char *s, char occ) Line 1512  int nbocc(char *s, char occ)
   i=0;    i=0;
   lg=strlen(s);    lg=strlen(s);
   for(i=0; i<= lg; i++) {    for(i=0; i<= lg; i++) {
   if  (s[i] == occ ) j++;      if  (s[i] == occ ) j++;
   }    }
   return j;    return j;
 }  }
Line 1993  void powell(double p[], double **xi, int Line 2185  void powell(double p[], double **xi, int
  void linmin(double p[], double xi[], int n, double *fret,    void linmin(double p[], double xi[], int n, double *fret, 
               double (*func)(double []));                 double (*func)(double [])); 
 #else   #else 
  void linmin(double p[], double xi[], int n, double *fret,    void linmin(double p[], double xi[], int n, double *fret,
                                                  double (*func)(double []),int *flat);                double (*func)(double []),int *flat); 
 #endif  #endif
   int i,ibig,j;    int i,ibig,j,jk,k; 
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double directest;    double directest;
   double fp,fptt;    double fp,fptt;
Line 2028  void powell(double p[], double **xi, int Line 2220  void powell(double p[], double **xi, int
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
     for (i=1;i<=n;i++) {      for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);  
       fprintf(ficlog," %d %.12lf",i, p[i]);  
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
       fprintf(ficrespow,"\n");fflush(ficrespow);
       printf("\n#model=  1      +     age ");
       fprintf(ficlog,"\n#model=  1      +     age ");
       if(nagesqr==1){
           printf("  + age*age  ");
           fprintf(ficlog,"  + age*age  ");
       }
       for(j=1;j <=ncovmodel-2;j++){
         if(Typevar[j]==0) {
           printf("  +      V%d  ",Tvar[j]);
           fprintf(ficlog,"  +      V%d  ",Tvar[j]);
         }else if(Typevar[j]==1) {
           printf("  +    V%d*age ",Tvar[j]);
           fprintf(ficlog,"  +    V%d*age ",Tvar[j]);
         }else if(Typevar[j]==2) {
           printf("  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
           fprintf(ficlog,"  +    V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
         }
       }
     printf("\n");      printf("\n");
   /*     printf("12   47.0114589    0.0154322   33.2424412    0.3279905    2.3731903  */
   /* 13  -21.5392400    0.1118147    1.2680506    1.2973408   -1.0663662  */
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      for(i=1,jk=1; i <=nlstate; i++){
     if(*iter <=3){        for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%12.7f ",p[jk]);
               fprintf(ficlog,"%12.7f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
           }
         }
       }
       if(*iter <=3 && *iter >1){
       tml = *localtime(&rcurr_time);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tml));        strcpy(strcurr,asctime(&tml));
       rforecast_time=rcurr_time;         rforecast_time=rcurr_time; 
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
                                 strcurr[itmp-1]='\0';          strcurr[itmp-1]='\0';
       printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
                                 rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
                                 forecast_time = *localtime(&rforecast_time);          forecast_time = *localtime(&rforecast_time);
                                 strcpy(strfor,asctime(&forecast_time));          strcpy(strfor,asctime(&forecast_time));
                                 itmp = strlen(strfor);          itmp = strlen(strfor);
                                 if(strfor[itmp-1]=='\n')          if(strfor[itmp-1]=='\n')
                                         strfor[itmp-1]='\0';            strfor[itmp-1]='\0';
                                 printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
                                 fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) { /* For each direction i */      for (i=1;i<=n;i++) { /* For each direction i */
Line 2106  void powell(double p[], double **xi, int Line 2331  void powell(double p[], double **xi, int
                                 /* printf("\n"); */                                  /* printf("\n"); */
                                 /* fprintf(ficlog,"\n"); */                                  /* fprintf(ficlog,"\n"); */
                         }                          }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */      /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /\* Did we reach enough precision? *\/ */
       if (2.0*fabs(fp-(*fret)) <= ftol) { /* Did we reach enough precision? */
       /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */        /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
       /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */        /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
       /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */        /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
Line 2152  void powell(double p[], double **xi, int Line 2378  void powell(double p[], double **xi, int
       free_vector(pt,1,n);         free_vector(pt,1,n); 
       return;         return; 
     } /* enough precision */       } /* enough precision */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX*n) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */      for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
Line 2211  void powell(double p[], double **xi, int Line 2437  void powell(double p[], double **xi, int
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
 #endif  #endif
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
                                 printf("Before linmin in direction P%d-P0\n",n);          printf("Before linmin in direction P%d-P0\n",n);
                                 for (j=1;j<=n;j++) {          for (j=1;j<=n;j++) {
                                         printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         if(j % ncovmodel == 0){            if(j % ncovmodel == 0){
                                                 printf("\n");              printf("\n");
                                                 fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
                                         }            }
                                 }          }
 #endif  #endif
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
                                 linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
 #else  #else
                                 linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/          linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
                                 flatdir[i]=flat; /* Function is vanishing in that direction i */          flatdir[i]=flat; /* Function is vanishing in that direction i */
 #endif  #endif
           
 #ifdef DEBUGLINMIN  #ifdef DEBUGLINMIN
                                 for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
                                         printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);            fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
                                         if(j % ncovmodel == 0){            if(j % ncovmodel == 0){
                                                 printf("\n");              printf("\n");
                                                 fprintf(ficlog,"\n");              fprintf(ficlog,"\n");
                                         }            }
                                 }          }
 #endif  #endif
                                 for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
                                         xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */            xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
                                         xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */            xi[j][n]=xit[j];      /* and this nth direction by the by the average p_0 p_n */
                                 }          }
 #ifdef LINMINORIGINAL  #ifdef LINMINORIGINAL
 #else  #else
                                 for (j=1, flatd=0;j<=n;j++) {          for (j=1, flatd=0;j<=n;j++) {
                                         if(flatdir[j]>0)            if(flatdir[j]>0)
                                                 flatd++;              flatd++;
                                 }          }
                                 if(flatd >0){          if(flatd >0){
                                         printf("%d flat directions\n",flatd);            printf("%d flat directions: ",flatd);
                                         fprintf(ficlog,"%d flat directions\n",flatd);            fprintf(ficlog,"%d flat directions :",flatd);
                                         for (j=1;j<=n;j++) {             for (j=1;j<=n;j++) { 
                                                 if(flatdir[j]>0){              if(flatdir[j]>0){
                                                         printf("%d ",j);                printf("%d ",j);
                                                         fprintf(ficlog,"%d ",j);                fprintf(ficlog,"%d ",j);
                                                 }              }
                                         }            }
                                         printf("\n");            printf("\n");
                                         fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
                                 }          }
 #endif  #endif
                                 printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                 fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
                                           
 #ifdef DEBUG  #ifdef DEBUG
                                 printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                                 fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                                 for(j=1;j<=n;j++){          for(j=1;j<=n;j++){
                                         printf(" %lf",xit[j]);            printf(" %lf",xit[j]);
                                         fprintf(ficlog," %lf",xit[j]);            fprintf(ficlog," %lf",xit[j]);
                                 }          }
                                 printf("\n");          printf("\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       } /* end of t or directest negative */        } /* end of t or directest negative */
 #ifdef POWELLNOF3INFF1TEST  #ifdef POWELLNOF3INFF1TEST
 #else  #else
     } /* end if (fptt < fp)  */        } /* end if (fptt < fp)  */
 #endif  #endif
 #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */  #ifdef NODIRECTIONCHANGEDUNTILNITER  /* No change in drections until some iterations are done */
                 } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */      } /*NODIRECTIONCHANGEDUNTILNITER  No change in drections until some iterations are done */
 #else  #else
 #endif  #endif
   } /* loop iteration */                   } /* loop iteration */ 
 }   } 
     
 /**** Prevalence limit (stable or period prevalence)  ****************/  /**** Prevalence limit (stable or period prevalence)  ****************/
     
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)    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 ij by left multiplying the unit      /* Computes the prevalence limit in each live state at age x and for covariate combination ij 
      matrix by transitions matrix until convergence is reached with precision ftolpl */         (and selected quantitative values in nres)
          by left multiplying the unit
          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 */
Line 2309  double **prevalim(double **prlim, int nl Line 2537  double **prevalim(double **prlim, int nl
   /* {0.51571254859325999, 0.4842874514067399, */    /* {0.51571254859325999, 0.4842874514067399, */
   /*  0.51326036147820708, 0.48673963852179264} */    /*  0.51326036147820708, 0.48673963852179264} */
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
       
   int i, ii,j,k;    int i, ii,j,k;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
Line 2339  double **prevalim(double **prlim, int nl Line 2567  double **prevalim(double **prlim, int nl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
                         /* Here comes the value of the covariate 'ij' */        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        /* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */      }
     }      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */                          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */        cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];        /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
     for (k=1; k<=cptcovprod;k++) /* Useless */      }
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */      for (k=1; k<=cptcovage;k++){  /* For product with age */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];        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("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
       }
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/      /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
Line 2409  Earliest age to start was %d-%d=%d, ncvl Line 2658  Earliest age to start was %d-%d=%d, ncvl
   
  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
  /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */   /* double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double **oldm, double **savm, double **dnewm, double **doldm, double **dsavm, double ftolpl, int *ncvyear, int ij) */
  double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij)    double **bprevalim(double **bprlim, double ***prevacurrent, int nlstate, double x[], double age, double ftolpl, int *ncvyear, int ij, int nres)
 {  {
   /* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit    /* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) 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 */
Line 2432  Earliest age to start was %d-%d=%d, ncvl Line 2681  Earliest age to start was %d-%d=%d, ncvl
   /* If we start from prlim again, prlim tends to a constant matrix */    /* If we start from prlim again, prlim tends to a constant matrix */
   
   int i, ii,j,k;    int i, ii,j,k;
     int first=0;
   double *min, *max, *meandiff, maxmax,sumnew=0.;    double *min, *max, *meandiff, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **bmij();    double **out, cov[NCOVMAX+1], **bmij();
Line 2446  Earliest age to start was %d-%d=%d, ncvl Line 2696  Earliest age to start was %d-%d=%d, ncvl
   max=vector(1,nlstate);    max=vector(1,nlstate);
   meandiff=vector(1,nlstate);    meandiff=vector(1,nlstate);
   
         dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;    dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
         oldm=oldms; savm=savms;    oldm=oldms; savm=savms;
     
         /* Starting with matrix unity */    /* Starting with matrix unity */
         for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
                 for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
       
Line 2468  Earliest age to start was %d-%d=%d, ncvl Line 2718  Earliest age to start was %d-%d=%d, ncvl
     cov[2]=agefin;      cov[2]=agefin;
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */        /* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /* for (k=1; k<=cptcovn;k++) { */
     /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */      /*   /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];      /*   cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
     for (k=1; k<=cptcovprod;k++) /* Useless */      /*   /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); *\/ */
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */      /* } */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];      for (k=1; k<=nsq;k++) { /* For single varying covariates only */
                           /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
         cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
         /* printf("prevalim Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       }
       /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; */
       /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
       /*   /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; *\/ */
       /*   cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
       for (k=1; k<=cptcovage;k++){  /* For product with age */
         if(Dummy[Tvar[Tage[k]]]){
           cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
         } else{
           cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; 
         }
         /* printf("prevalim Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
       }
       for (k=1; k<=cptcovprod;k++){ /* For product without age */
         /* printf("prevalim Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
         if(Dummy[Tvard[k][1]==0]){
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
           }else{
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
           }
         }else{
           if(Dummy[Tvard[k][2]==0]){
             cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
           }else{
             cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]*  Tqinvresult[nres][Tvard[k][2]];
           }
         }
       }
           
     /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 2493  Earliest age to start was %d-%d=%d, ncvl Line 2775  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 == 86 || (int)age == 87){ */
       /*   printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
       /*   for(i=1; i<=nlstate+ndeath; i++) { */
       /*  printf("%d newm= ",i); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",newm[i][j]); */
       /*  } */
       /*  printf("oldm * "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",oldm[i][j]); */
       /*  } */
       /*  printf(" bmmij "); */
       /*  for(j=1;j<=nlstate+ndeath;j++) { */
       /*    printf("%f ",pmmij[i][j]); */
       /*  } */
       /*  printf("\n"); */
       /*   } */
       /* } */
     savm=oldm;      savm=oldm;
     oldm=newm;      oldm=newm;
   
     for(j=1; j<=nlstate; j++){      for(j=1; j<=nlstate; j++){
       max[j]=0.;        max[j]=0.;
       min[j]=1.;        min[j]=1.;
     }      }
     for(j=1; j<=nlstate; j++){       for(j=1; j<=nlstate; j++){ 
       for(i=1;i<=nlstate;i++){        for(i=1;i<=nlstate;i++){
                                 /* bprlim[i][j]= newm[i][j]/(1-sumnew); */          /* bprlim[i][j]= newm[i][j]/(1-sumnew); */
                                 bprlim[i][j]= newm[i][j];          bprlim[i][j]= newm[i][j];
                                 max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */          max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
                                 min[i]=FMIN(min[i],bprlim[i][j]);          min[i]=FMIN(min[i],bprlim[i][j]);
       }        }
     }      }
                                   
Line 2513  Earliest age to start was %d-%d=%d, ncvl Line 2814  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 2525  Earliest age to start was %d-%d=%d, ncvl Line 2826  Earliest age to start was %d-%d=%d, ncvl
     }      }
   } /* age loop */    } /* age loop */
     /* After some age loop it doesn't converge */      /* After some age loop it doesn't converge */
   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'. \n\    if(first){
       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\
   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);
     }
     fprintf(ficlog,"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'. \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);
   /* 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);
Line 2540  Oldest age to start was %d-%d=%d, ncvloo Line 2846  Oldest age to start was %d-%d=%d, ncvloo
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   /* According to parameters values stored in x and the covariate's values stored in cov,    /* According to parameters values stored in x and the covariate's values stored in cov,
      computes the probability to be observed in state j being in state i by appying the       computes the probability to be observed in state j (after stepm years) being in state i by appying the
      model to the ncovmodel covariates (including constant and age).       model to the ncovmodel covariates (including constant and age).
      lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]       lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
      and, according on how parameters are entered, the position of the coefficient xij(nc) of the       and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2549  double **pmij(double **ps, double *cov, Line 2855  double **pmij(double **ps, double *cov,
      j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel       j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
      Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,       Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
      sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.       sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
      Outputs ps[i][j] the probability to be observed in j being in j according to       Outputs ps[i][j] or probability to be observed in j being in i according to
      the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]       the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
        Sum on j ps[i][j] should equal to 1.
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
Line 2614  double **pmij(double **ps, double *cov, Line 2921  double **pmij(double **ps, double *cov,
   /*    /*
     for(i=1; i<= npar; i++) printf("%f ",x[i]);      for(i=1; i<= npar; i++) printf("%f ",x[i]);
                 goto end;*/                  goto end;*/
   return ps;    return ps; /* Pointer is unchanged since its call */
 }  }
   
 /*************** backward transition probabilities ***************/   /*************** backward transition probabilities ***************/ 
Line 2623  double **pmij(double **ps, double *cov, Line 2930  double **pmij(double **ps, double *cov,
 /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */  /* double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, double ***dnewm, double **doldm, double **dsavm, int ij ) */
  double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )   double **bmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate,  double ***prevacurrent, int ij )
 {  {
   /* Computes the backward probability at age agefin and covariate ij    /* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
    * and returns in **ps as well as **bmij.     * Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in **ps as well as **bmij.
    */     */
   int i, ii, j,k;    int i, ii, j,k;
       
   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 matrixe (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 2640  double **pmij(double **ps, double *cov, Line 2947  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) */       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); */
   /* We do have the matrix Px in savm  and we need pij */  
     /* P_x */
     pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /*This is forward probability from agefin to agefin + stepm */
     /* outputs pmmij which is a stochastic matrix in row */
   
     /* Diag(w_x) */
     /* 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) */
     bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
   
     /* Diag(Sum_i w^i_x p^ij_x */
     /* 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 */      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]*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 */
     for (ii=1;ii<=nlstate+ndeath;ii++){      for (ii=1;ii<=nlstate+ndeath;ii++){
       if(sumnew >= 1.e-10){  
         /* 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);
       }else{  
         printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);  
       }  
     } /*End ii */      } /*End ii */
   } /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */    } /* 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 */
   /* left Product of this diag matrix by dsavm=Px (newm=dsavm*doldm) */  
   bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */    ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
   /* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten*\/ */    /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
   /* 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++){  
     for (ii=1;ii<=nlstate+ndeath;ii++){  
       dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);  
     }  
   } /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */  
   ps=matprod2(doldm, 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;     return ps; /*pointer is unchanged */
 }  }
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
   
Line 2699  double **bpmij(double **ps, double *cov, Line 3031  double **bpmij(double **ps, double *cov,
   /*double t34;*/    /*double t34;*/
   int i,j, nc, ii, jj;    int i,j, nc, ii, jj;
   
         for(i=1; i<= nlstate; i++){    for(i=1; i<= nlstate; i++){
                 for(j=1; j<i;j++){      for(j=1; j<i;j++){
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
                                 /*lnpijopii += param[i][j][nc]*cov[nc];*/          /*lnpijopii += param[i][j][nc]*cov[nc];*/
                                 lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];          lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
                                 /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */          /*       printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                         }        }
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
                         /*      printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */        /*        printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
                 }  
                 for(j=i+1; j<=nlstate+ndeath;j++){  
                         for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){  
                                 /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/  
                                 lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];  
                                 /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */  
                         }  
                         ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */  
                 }  
         }  
           
         for(i=1; i<= nlstate; i++){  
                 s1=0;  
                 for(j=1; j<i; j++){  
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */  
                         /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */  
                 }  
                 for(j=i+1; j<=nlstate+ndeath; j++){  
                         s1+=exp(ps[i][j]); /* In fact sums pij/pii */  
                         /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */  
                 }  
                 /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */  
                 ps[i][i]=1./(s1+1.);  
                 /* Computing other pijs */  
                 for(j=1; j<i; j++)  
                         ps[i][j]= exp(ps[i][j])*ps[i][i];  
                 for(j=i+1; j<=nlstate+ndeath; j++)  
                         ps[i][j]= exp(ps[i][j])*ps[i][i];  
                 /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  
         } /* end i */  
           
         for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
                 for(jj=1; jj<= nlstate+ndeath; jj++){  
                         ps[ii][jj]=0;  
                         ps[ii][ii]=1;  
                 }  
         }  
         /* Added for backcast */ /* Transposed matrix too */  
         for(jj=1; jj<= nlstate+ndeath; jj++){  
                 s1=0.;  
                 for(ii=1; ii<= nlstate+ndeath; ii++){  
                         s1+=ps[ii][jj];  
                 }  
                 for(ii=1; ii<= nlstate; ii++){  
                         ps[ii][jj]=ps[ii][jj]/s1;  
                 }  
         }  
         /* Transposition */  
         for(jj=1; jj<= nlstate+ndeath; jj++){  
                 for(ii=jj; ii<= nlstate+ndeath; ii++){  
                         s1=ps[ii][jj];  
                         ps[ii][jj]=ps[jj][ii];  
                         ps[jj][ii]=s1;  
                 }  
         }  
         /* for(ii=1; ii<= nlstate+ndeath; ii++){ */  
         /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */  
         /*      printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */  
         /*   } */  
         /*   printf("\n "); */  
         /* } */  
         /* printf("\n ");printf("%lf ",cov[2]);*/  
         /*  
                 for(i=1; i<= npar; i++) printf("%f ",x[i]);  
                 goto end;*/  
         return ps;  
 }  
   
   
 /**************** Product of 2 matrices ******************/  
   
 double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)  
 {  
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized   
      before: only the contents of out is modified. The function returns  
      a pointer to pointers identical to out */  
   int i, j, k;  
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++){  
       out[i][k]=0.;  
       for(j=ncl; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];  
     }      }
   return out;      for(j=i+1; j<=nlstate+ndeath;j++){
 }        for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
           /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
           lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
 /************* Higher Matrix Product ***************/          /*        printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
         }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
 {      }
   /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over     }
      'nhstepm*hstepm*stepm' months (i.e. until    
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying     for(i=1; i<= nlstate; i++){
      nhstepm*hstepm matrices.       s1=0;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step       for(j=1; j<i; j++){
      (typically every 2 years instead of every month which is too big         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      for the memory).        /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
      Model is determined by parameters x and covariates have to be       }
      included manually here.       for(j=i+1; j<=nlstate+ndeath; j++){
         s1+=exp(ps[i][j]); /* In fact sums pij/pii */
      */        /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
       }
   int i, j, d, h, k;      /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
   double **out, cov[NCOVMAX+1];      ps[i][i]=1./(s1+1.);
   double **newm;      /* Computing other pijs */
   double agexact;      for(j=1; j<i; j++)
   double agebegin, ageend;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
   /* Hstepm could be zero and should return the unit matrix */        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=nlstate+ndeath;i++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     for (j=1;j<=nlstate+ndeath;j++){    } /* end i */
     
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
         ps[ii][jj]=0;
         ps[ii][ii]=1;
       }
     }
     /* Added for backcast */ /* Transposed matrix too */
     for(jj=1; jj<= nlstate+ndeath; jj++){
       s1=0.;
       for(ii=1; ii<= nlstate+ndeath; ii++){
         s1+=ps[ii][jj];
       }
       for(ii=1; ii<= nlstate; ii++){
         ps[ii][jj]=ps[ii][jj]/s1;
       }
     }
     /* Transposition */
     for(jj=1; jj<= nlstate+ndeath; jj++){
       for(ii=jj; ii<= nlstate+ndeath; ii++){
         s1=ps[ii][jj];
         ps[ii][jj]=ps[jj][ii];
         ps[jj][ii]=s1;
       }
     }
     /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
     /*   for(jj=1; jj<= nlstate+ndeath; jj++){ */
     /*    printf(" pmij  ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
     /*   } */
     /*   printf("\n "); */
     /* } */
     /* printf("\n ");printf("%lf ",cov[2]);*/
     /*
       for(i=1; i<= npar; i++) printf("%f ",x[i]);
       goto end;*/
     return ps;
   }
   
   
   /**************** Product of 2 matrices ******************/
   
   double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
   {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
        before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
     int i, j, k;
     for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++){
         out[i][k]=0.;
         for(j=ncl; j<=nch; j++)
           out[i][k] +=in[i][j]*b[j][k];
       }
     return out;
   }
   
   
   /************* Higher Matrix Product ***************/
   
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij, int nres )
   {
     /* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over 
        'nhstepm*hstepm*stepm' months (i.e. until
        age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
        for the memory).
        Model is determined by parameters x and covariates have to be 
        included manually here. 
   
        */
   
     int i, j, d, h, k;
     double **out, cov[NCOVMAX+1];
     double **newm;
     double agexact;
     double agebegin, ageend;
   
     /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
       oldm[i][j]=(i==j ? 1.0 : 0.0);        oldm[i][j]=(i==j ? 1.0 : 0.0);
       po[i][j][0]=(i==j ? 1.0 : 0.0);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     }      }
Line 2835  double ***hpxij(double ***po, int nhstep Line 3167  double ***hpxij(double ***po, int nhstep
       cov[2]=agexact;        cov[2]=agexact;
       if(nagesqr==1)        if(nagesqr==1)
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)         for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];                          /* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */          /* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */        }
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
         cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];          /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
       /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */        }
         for (k=1; k<=cptcovage;k++){
           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("hPxij Age combi=%d k=%d  Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovprod;k++){ /*  */
           /* printf("hPxij Prod ij=%d k=%d  Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
         }
         /* for (k=1; k<=cptcovn;k++)  */
         /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
         /* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 *\/ */
         /*        cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; */
         /* 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)]; */
               
               
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
Line 2871  double ***hpxij(double ***po, int nhstep Line 3221  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 )
 {  {
   /* 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
      age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying
      nhstepm*hstepm matrices.       nhstepm*hstepm matrices.
Line 2892  double ***hbxij(double ***po, int nhstep Line 3242  double ***hbxij(double ***po, int nhstep
      (typically every 2 years instead of every month which is too big       (typically every 2 years instead of every month which is too big
      for the memory).       for the memory).
      Model is determined by parameters x and covariates have to be       Model is determined by parameters x and covariates have to be
      included manually here.       included manually here. Then we use a call to bmij(x and cov)
        The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
   */    */
   
   int i, j, d, h, k;    int i, j, d, h, k;
   double **out, cov[NCOVMAX+1];    double **out, cov[NCOVMAX+1], **bmij();
   double **newm;    double **newm, ***newmm;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
   double **oldm, **savm;    double **oldm, **savm;
   
   oldm=oldms;savm=savms;    newmm=po; /* To be saved */
     oldm=oldms;savm=savms; /* Global pointers */
   /* Hstepm could be zero and should return the unit matrix */    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=nlstate+ndeath;i++)    for (i=1;i<=nlstate+ndeath;i++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
Line 2916  double ***hbxij(double ***po, int nhstep Line 3267  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-1))*stepm/YEARM; /* age just before transition */        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)
         cov[3]= agexact*agexact;          cov[3]= agexact*agexact;
       for (k=1; k<=cptcovn;k++)        for (k=1; k<=cptcovn;k++){
         cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];        /*        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
       /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */        /* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; *\/ */
       for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */          cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
         /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
         cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];        }
       /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */        for (k=1; k<=nsq;k++) { /* For single varying covariates only */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */          /* Here comes the value of quantitative after renumbering k with single quantitative covariates */
           cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; 
           /* printf("hPxij Quantitative k=%d  TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
         }
         for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
           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] */        /* 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),\ */
       /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */        /*                                                 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
       out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\        out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
Line 2961  double ***hbxij(double ***po, int nhstep Line 3323  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 3023  double func( double *x) Line 3386  double func( double *x)
          Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
          to be observed in j being in i according to the model.           to be observed in j being in i according to the model.
       */        */
       ioffset=2+nagesqr+cptcovage;        ioffset=2+nagesqr ;
       /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */     /* Fixed */
       for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */        for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
         cov[++ioffset]=covar[Tvar[k]][i];          cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
       }  
       for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */  
         cov[++ioffset]=coqvar[Tvar[iqv]][i];  
       }        }
   
       /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]         /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4] 
          is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]            is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2] 
          has been calculated etc */           has been calculated etc */
Line 3045  double func( double *x) Line 3404  double func( double *x)
          meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
       */        */
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */          for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
                                         /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */            /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                                         cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];            cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                                 }          }
                                 for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */          for (ii=1;ii<=nlstate+ndeath;ii++)
                                         if(cotqvar[mw[mi][i]][iqtv][i] == -1){            for (j=1;j<=nlstate+ndeath;j++){
                                                 printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];            }
                                         /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */          for(d=0; d<dh[mi][i]; d++){
                                 }            newm=savm;
                                 /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                 for (ii=1;ii<=nlstate+ndeath;ii++)            cov[2]=agexact;
                                         for (j=1;j<=nlstate+ndeath;j++){            if(nagesqr==1)
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);              cov[3]= agexact*agexact;  /* Should be changed here */
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);            for (kk=1; kk<=cptcovage;kk++) {
                                         }            if(!FixedV[Tvar[Tage[kk]]])
                                 for(d=0; d<dh[mi][i]; d++){              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
                                         newm=savm;            else
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;              cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
                                         cov[2]=agexact;            }
                                         if(nagesqr==1)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                 cov[3]= agexact*agexact;  /* Should be changed here */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         for (kk=1; kk<=cptcovage;kk++) {            savm=oldm;
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */            oldm=newm;
                                         }          } /* end mult */
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                                         savm=oldm;          /* But now since version 0.9 we anticipate for bias at large stepm.
                                         oldm=newm;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                                 } /* end mult */           * (in months) between two waves is not a multiple of stepm, we rounded to 
                                            * the nearest (and in case of equal distance, to the lowest) interval but now
                                 /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
                                 /* But now since version 0.9 we anticipate for bias at large stepm.           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
                                  * If stepm is larger than one month (smallest stepm) and if the exact delay            * probability in order to take into account the bias as a fraction of the way
                                  * (in months) between two waves is not a multiple of stepm, we rounded to   
                                  * the nearest (and in case of equal distance, to the lowest) interval but now  
                                  * we keep into memory the bias bh[mi][i] and also the previous matrix product  
                                  * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the  
                                  * probability in order to take into account the bias as a fraction of the way  
                                  * from savm to out if bh is negative or even beyond if bh is positive. bh varies                                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
                                  * -stepm/2 to stepm/2 .                                   * -stepm/2 to stepm/2 .
                                  * For stepm=1 the results are the same as for previous versions of Imach.                                   * For stepm=1 the results are the same as for previous versions of Imach.
                                  * For stepm > 1 the results are less biased than in previous versions.                                    * For stepm > 1 the results are less biased than in previous versions. 
                                  */                                   */
                                 s1=s[mw[mi][i]][i];          s1=s[mw[mi][i]][i];
                                 s2=s[mw[mi+1][i]][i];          s2=s[mw[mi+1][i]][i];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 /* bias bh is positive if real duration          /* bias bh is positive if real duration
                                  * is higher than the multiple of stepm and negative otherwise.           * is higher than the multiple of stepm and negative otherwise.
                                  */           */
                                 /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
                                 if( s2 > nlstate){           if( s2 > nlstate){ 
                                         /* i.e. if s2 is a death state and if the date of death is known             /* i.e. if s2 is a death state and if the date of death is known 
                                                  then the contribution to the likelihood is the probability to                then the contribution to the likelihood is the probability to 
                                                  die between last step unit time and current  step unit time,                die between last step unit time and current  step unit time, 
                                                  which is also equal to probability to die before dh                which is also equal to probability to die before dh 
                                                  minus probability to die before dh-stepm .                minus probability to die before dh-stepm . 
                                                  In version up to 0.92 likelihood was computed               In version up to 0.92 likelihood was computed
                                                  as if date of death was unknown. Death was treated as any other               as if date of death was unknown. Death was treated as any other
                                                  health state: the date of the interview describes the actual state               health state: the date of the interview describes the actual state
                                                  and not the date of a change in health state. The former idea was               and not the date of a change in health state. The former idea was
                                                  to consider that at each interview the state was recorded               to consider that at each interview the state was recorded
                                                  (healthy, disable or death) and IMaCh was corrected; but when we               (healthy, disable or death) and IMaCh was corrected; but when we
                                                  introduced the exact date of death then we should have modified               introduced the exact date of death then we should have modified
                                                  the contribution of an exact death to the likelihood. This new               the contribution of an exact death to the likelihood. This new
                                                  contribution is smaller and very dependent of the step unit               contribution is smaller and very dependent of the step unit
                                                  stepm. It is no more the probability to die between last interview               stepm. It is no more the probability to die between last interview
                                                  and month of death but the probability to survive from last               and month of death but the probability to survive from last
                                                  interview up to one month before death multiplied by the               interview up to one month before death multiplied by the
                                                  probability to die within a month. Thanks to Chris               probability to die within a month. Thanks to Chris
                                                  Jackson for correcting this bug.  Former versions increased               Jackson for correcting this bug.  Former versions increased
                                                  mortality artificially. The bad side is that we add another loop               mortality artificially. The bad side is that we add another loop
                                                  which slows down the processing. The difference can be up to 10%               which slows down the processing. The difference can be up to 10%
                                                  lower mortality.               lower mortality.
                                         */            */
                                         /* If, at the beginning of the maximization mostly, the            /* If, at the beginning of the maximization mostly, the
                                                  cumulative probability or probability to be dead is               cumulative probability or probability to be dead is
                                                  constant (ie = 1) over time d, the difference is equal to               constant (ie = 1) over time d, the difference is equal to
                                                  0.  out[s1][3] = savm[s1][3]: probability, being at state               0.  out[s1][3] = savm[s1][3]: probability, being at state
                                                  s1 at precedent wave, to be dead a month before current               s1 at precedent wave, to be dead a month before current
                                                  wave is equal to probability, being at state s1 at               wave is equal to probability, being at state s1 at
                                                  precedent wave, to be dead at mont of the current               precedent wave, to be dead at mont of the current
                                                  wave. Then the observed probability (that this person died)               wave. Then the observed probability (that this person died)
                                                  is null according to current estimated parameter. In fact,               is null according to current estimated parameter. In fact,
                                                  it should be very low but not zero otherwise the log go to               it should be very low but not zero otherwise the log go to
                                                  infinity.               infinity.
                                         */            */
 /* #ifdef INFINITYORIGINAL */  /* #ifdef INFINITYORIGINAL */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #else */  /* #else */
Line 3351  double funcone( double *x) Line 3705  double funcone( double *x)
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;    ioffset=0;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     ioffset=2+nagesqr+cptcovage;      /* ioffset=2+nagesqr+cptcovage; */
       ioffset=2+nagesqr;
       /* Fixed */
     /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */      /* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
     for (k=1; k<=ncoveff;k++){ /* Simple and product fixed Dummy covariates without age* products */      /* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products *\/ */
       cov[++ioffset]=covar[TvarFD[k]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/      for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
     }        cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V1 is fixed (k=6)*/
     for (k=1; k<=nqfveff;k++){ /* Simple and product fixed Quantitative covariates without age* products */  /*    cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i];  */
       cov[++ioffset]=coqvar[TvarFQ[k]][i];/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*/  /*    cov[2+6]=covar[Tvar[6]][i];  */
   /*    cov[2+6]=covar[2][i]; V2  */
   /*    cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i];  */
   /*    cov[2+7]=covar[Tvar[7]][i];  */
   /*    cov[2+7]=covar[7][i]; V7=V1*V2  */
   /*    cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i];  */
   /*    cov[2+9]=covar[Tvar[9]][i];  */
   /*    cov[2+9]=covar[1][i]; V1  */
     }      }
       /* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products *\/ */
       /*   cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, only V2 and V1*V2 is fixed (k=6 and 7?)*\/ */
       /* } */
     /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */      /* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates *\/ */
     /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */      /*   cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1*V2 7 *\/ */
     /* } */      /* } */
           
   
     for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
       for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates (single??)*/      /* Wave varying (but not age varying) */
                                 /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */        for(k=1; k <= ncovv ; k++){ /* Varying  covariates (single and product but no age )*/
                                 /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */          /* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
                                 k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */          cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
                                 cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];        }
                                 /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */        /* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)*\/ */
       }        /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
       for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */        /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
                                 iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */        /* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model *\/ */
                                 /* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); */        /* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
                                 cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];        /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
       }        /* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates *\/ */
         /*        iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff *\/ */
         /*        /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); *\/ */
         /*        cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
         /* } */
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
                                 for (j=1;j<=nlstate+ndeath;j++){          for (j=1;j<=nlstate+ndeath;j++){
                                         oldm[ii][j]=(ii==j ? 1.0 : 0.0);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         savm[ii][j]=(ii==j ? 1.0 : 0.0);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                 }          }
               
       agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */        agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
       ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */        ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
       for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */        for(d=0; d<dh[mi][i]; d++){  /* Delay between two effective waves */
                                 /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]        /* for(d=0; d<=0; d++){  /\* Delay between two effective waves Only one matrix to speed up*\/ */
                                         and mw[mi+1][i]. dh depends on stepm.*/          /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
                                 newm=savm;            and mw[mi+1][i]. dh depends on stepm.*/
                                 agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          newm=savm;
                                 cov[2]=agexact;          agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;  /* Here d is needed */
                                 if(nagesqr==1)          cov[2]=agexact;
                                         cov[3]= agexact*agexact;          if(nagesqr==1)
                                 for (kk=1; kk<=cptcovage;kk++) {            cov[3]= agexact*agexact;
                                         cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;          for (kk=1; kk<=cptcovage;kk++) {
                                 }            if(!FixedV[Tvar[Tage[kk]]])
                                 /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                 /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */            else
                                 out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,              cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
                                                                                  1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          }
                                 /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */          /* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
                                 /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */          /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
                                 savm=oldm;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                 oldm=newm;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
           /*           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
           savm=oldm;
           oldm=newm;
       } /* end mult */        } /* end mult */
               
       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 3438  double funcone( double *x) Line 3813  double funcone( double *x)
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
       if(globpr){        if(globpr){
         fprintf(ficresilk,"%9ld %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);
         }          }
         fprintf(ficresilk," %10.6f\n", -llt);          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
     } /* end of wave */          } /* end of wave */
   } /* end of individual */  } /* end of individual */
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   if(globpr==0){ /* First time we count the contributions and weights */  if(globpr==0){ /* First time we count the contributions and weights */
     gipmx=ipmx;          gipmx=ipmx;
     gsw=sw;          gsw=sw;
   }  }
   return -l;  return -l;
 }  }
   
   
Line 3494  void likelione(FILE *ficres,double p[], Line 3869  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 3796  double hessij( double x[], double **hess Line 4171  double hessij( double x[], double **hess
       kmax=kmax+10;        kmax=kmax+10;
     }      }
     if(kmax >=10 || firstime ==1){      if(kmax >=10 || firstime ==1){
       printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);        fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti*k=%.12e deltj*k=%.12e, xi-de*k=%.12e xj-de*k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     }      }
Line 3886  void ludcmp(double **a, int n, int *indx Line 4261  void ludcmp(double **a, int n, int *indx
     big=0.0;       big=0.0; 
     for (j=1;j<=n;j++)       for (j=1;j<=n;j++) 
       if ((temp=fabs(a[i][j])) > big) big=temp;         if ((temp=fabs(a[i][j])) > big) big=temp; 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");       if (big == 0.0){
         printf(" Singular Hessian matrix at row %d:\n",i);
         for (j=1;j<=n;j++) {
           printf(" a[%d][%d]=%f,",i,j,a[i][j]);
           fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
         }
         fflush(ficlog);
         fclose(ficlog);
         nrerror("Singular matrix in routine ludcmp"); 
       }
     vv[i]=1.0/big;       vv[i]=1.0/big; 
   }     } 
   for (j=1;j<=n;j++) {     for (j=1;j<=n;j++) { 
Line 3952  void pstamp(FILE *fichier) Line 4336  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);
 }  }
   
   
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 void  freqsummary(char fileres[], 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, \
                   int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \                    int *Tvaraff, int *invalidvarcomb, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[], \
                   int firstpass,  int lastpass, int stepm, int weightopt, char model[])                    int firstpass,  int lastpass, int stepm, int weightopt, char model[])
 {  /* Some frequencies */  {  /* Some frequencies as well as proposing some starting values */
       
   int i, m, jk, j1, bool, z1,j, k, iv;    int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
   int iind=0, iage=0;    int iind=0, iage=0;
   int mi; /* Effective wave */    int mi; /* Effective wave */
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
     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=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;
   double **meanqt;    double **meanqt;
   double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
Line 3971  void  freqsummary(char fileres[], int ia Line 4359  void  freqsummary(char fileres[], int ia
   double agebegin, ageend;    double agebegin, ageend;
           
   pp=vector(1,nlstate);    pp=vector(1,nlstate);
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
   posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */     posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */ 
   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); */
Line 3985  void  freqsummary(char fileres[], int ia Line 4373  void  freqsummary(char fileres[], int ia
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     exit(0);      exit(0);
   }    }
     
   strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));    strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
   if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {    if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
     printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));      printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
Line 3995  void  freqsummary(char fileres[], int ia Line 4383  void  freqsummary(char fileres[], int ia
   }    }
   else{    else{
     fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \      fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);              fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);    fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);
         
   strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));    strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
   if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {    if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
     printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));      printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
     fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));      fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
     fflush(ficlog);      fflush(ficlog);
     exit(70);       exit(70); 
   }    } else{
   else{  
     fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \      fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
 <hr size=\"2\" color=\"#EC5E5E\"> \n\  <hr size=\"2\" color=\"#EC5E5E\"> \n                                    \
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\  Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
             fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);              fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
   }    }
   fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);    fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
     
   freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);    y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
   j1=0;    j1=0;
       
   /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
   j=cptcoveff;  /* Only dummy covariates of the model */    j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   first=1;    
   
   /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:    /* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
      reference=low_education V1=0,V2=0       reference=low_education V1=0,V2=0
      med_educ                V1=1 V2=0,        med_educ                V1=1 V2=0, 
      high_educ               V1=0 V2=1       high_educ               V1=0 V2=1
      Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff        Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff 
   */    */
     dateintsum=0;
     k2cpt=0;
   
   for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */    if(cptcoveff == 0 )
     posproptt=0.;      nl=1;  /* Constant and age model only */
     /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    else
       scanf("%d", i);*/      nl=2;
     for (i=-5; i<=nlstate+ndeath; i++)    
       for (jk=-5; jk<=nlstate+ndeath; jk++)      /* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
                                 for(m=iagemin; m <= iagemax+3; m++)    /* Loop on nj=1 or 2 if dummy covariates j!=0
                                         freq[i][jk][m]=0;     *   Loop on j1(1 to 2**cptcoveff) covariate combination
                      *     freq[s1][s2][iage] =0.
     for (i=1; i<=nlstate; i++)  {     *     Loop on iind
       for(m=iagemin; m <= iagemax+3; m++)     *       ++freq[s1][s2][iage] weighted
                                 prop[i][m]=0;     *     end iind
       posprop[i]=0;     *     if covariate and j!0
       pospropt[i]=0;     *       headers Variable on one line
     }     *     endif cov j!=0
     /* for (z1=1; z1<= nqfveff; z1++) {   */     *     header of frequency table by age
     /*   meanq[z1]+=0.; */     *     Loop on age
     /*   for(m=1;m<=lastpass;m++){ */     *       pp[s1]+=freq[s1][s2][iage] weighted
     /*  meanqt[m][z1]=0.; */     *       pos+=freq[s1][s2][iage] weighted
     /*   } */     *       Loop on s1 initial state
     /* } */     *         fprintf(ficresp
                      *       end s1
     dateintsum=0;     *     end age
     k2cpt=0;     *     if j!=0 computes starting values
     /* For that combination of covariate j1, we count and print the frequencies in one pass */     *     end compute starting values
     for (iind=1; iind<=imx; iind++) { /* For each individual iind */     *   end j1
       bool=1;     * end nl 
       if(anyvaryingduminmodel==0){ /* If All fixed covariates */     */
                                 if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */    for (nj = 1; nj <= nl; nj++){   /* nj= 1 constant model, nl number of loops. */
           /* for (z1=1; z1<= nqfveff; z1++) {   */      if(nj==1)
           /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */        j=0;  /* First pass for the constant */
           /* } */      else{
                                         for (z1=1; z1<=cptcoveff; z1++) {          j=cptcoveff; /* Other passes for the covariate values */
                                                 /* if(Tvaraff[z1] ==-20){ */      }
                                                 /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */      first=1;
                                                 /* }else  if(Tvaraff[z1] ==-10){ */      for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
                                                 /*       /\* sumnew+=coqvar[z1][iind]; *\/ */        posproptt=0.;
                                                 /* }else  */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){          scanf("%d", i);*/
                                                         /* Tests if this individual iind responded to j1 (V4=1 V3=0) */        for (i=-5; i<=nlstate+ndeath; i++)  
                                                         bool=0;          for (s2=-5; s2<=nlstate+ndeath; s2++)  
                                                         /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",             for(m=iagemin; m <= iagemax+3; m++)
                                                                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),              freq[i][s2][m]=0;
                                                                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/        
                                                         /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/        for (i=1; i<=nlstate; i++)  {
                                                 } /* Onlyf fixed */          for(m=iagemin; m <= iagemax+3; m++)
                                         } /* end z1 */            prop[i][m]=0;
                                 } /* cptcovn > 0 */          posprop[i]=0;
       } /* end any */          pospropt[i]=0;
       if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */        }
                                 /* for(m=firstpass; m<=lastpass; m++){ */        /* for (z1=1; z1<= nqfveff; z1++) {   */
                                 for(mi=1; mi<wav[iind];mi++){ /* For that wave */        /*   meanq[z1]+=0.; */
                                         m=mw[mi][iind];        /*   for(m=1;m<=lastpass;m++){ */
                                         if(anyvaryingduminmodel==1){ /* Some are varying covariates */        /*        meanqt[m][z1]=0.; */
                                                 for (z1=1; z1<=cptcoveff; z1++) {        /*   } */
                                                         if( Fixed[Tmodelind[z1]]==1){        /* } */
                                                                 iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;        
                                                                 if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */        /* dateintsum=0; */
                                                                         bool=0;        /* k2cpt=0; */
                                                         }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */        
                                                                 if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {        /* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
                                                                         bool=0;        for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                                                                 }          bool=1;
                                                         }          if(j !=0){
                                                 }            if(anyvaryingduminmodel==0){ /* If All fixed covariates */
                                         }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */              if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                                         /* bool =0 we keep that guy which corresponds to the combination of dummy values */                /* for (z1=1; z1<= nqfveff; z1++) {   */
                                         if(bool==1){                /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
                                                 /* 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. */                for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
                                                 agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/                  /* if(Tvaraff[z1] ==-20){ */
                                                 ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */                  /*       /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                                                 if(m >=firstpass && m <=lastpass){                  /* }else  if(Tvaraff[z1] ==-10){ */
                                                         k2=anint[m][iind]+(mint[m][iind]/12.);                  /*       /\* sumnew+=coqvar[z1][iind]; *\/ */
                                                         /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/                  /* }else  */
                                                         if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
                                                         if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */                    /* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
                                                         if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */                    bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
                                                                 prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */                    /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                                                         if (m<lastpass) {                       bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                                                                 /* if(s[m][iind]==4 && s[m+1][iind]==4) */                       j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                                                                 /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */                    /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                                                                 if(s[m][iind]==-1)                  } /* Onlyf fixed */
                                                                         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.));                } /* end z1 */
                                                                 freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */              } /* cptcovn > 0 */
                                                                 /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */            } /* end any */
                                                                 freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */          }/* end j==0 */
                                                         }          if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
                                                 } /* end if between passes */              /* for(m=firstpass; m<=lastpass; m++){ */
                                                 if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {            for(mi=1; mi<wav[iind];mi++){ /* For that wave */
                                                         dateintsum=dateintsum+k2;              m=mw[mi][iind];
                                                         k2cpt++;              if(j!=0){
                                                         /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */                if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                                                 }                  for (z1=1; z1<=cptcoveff; z1++) {
                                         } /* end bool 2 */                    if( Fixed[Tmodelind[z1]]==1){
                                 } /* end m */                      iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
       } /* end bool */                      if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's 
     } /* end iind = 1 to imx */                                                                                        value is -1, we don't select. It differs from the 
     /* prop[s][age] is feeded for any initial and valid live state as well as                                                                                        constant and age model which counts them. */
        freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */                        bool=0; /* not selected */
                                     }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                                       if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/                        bool=0;
     pstamp(ficresp);                      }
     /* if  (ncoveff>0) { */                    }
     if  (cptcoveff>0) {                  }
       fprintf(ficresp, "\n#********** Variable ");                 }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");               } /* end j==0 */
       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");               /* bool =0 we keep that guy which corresponds to the combination of dummy values */
       for (z1=1; z1<=cptcoveff; z1++){              if(bool==1){
                                 fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                                 fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                   and mw[mi+1][iind]. dh depends on stepm. */
                                 fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
       }                ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
       fprintf(ficresp, "**********\n#");                if(m >=firstpass && m <=lastpass){
       fprintf(ficresphtm, "**********</h3>\n");                  k2=anint[m][iind]+(mint[m][iind]/12.);
       fprintf(ficresphtmfr, "**********</h3>\n");                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fprintf(ficlog, "\n#********** Variable ");                   if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
       fprintf(ficlog, "**********\n");                  if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
     }                    prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");                  if (m<lastpass) {
     for(i=1; i<=nlstate;i++) {                    /* if(s[m][iind]==4 && s[m+1][iind]==4) */
       fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);                    /*   printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
       fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);                    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.));
     fprintf(ficresp, "\n");                    freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
     fprintf(ficresphtm, "\n");                    /* 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); */
     /* Header of frequency table by age */                    /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
     fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");                    freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
     fprintf(ficresphtmfr,"<th>Age</th> ");                  }
     for(jk=-1; jk <=nlstate+ndeath; jk++){                } /* end if between passes */  
       for(m=-1; m <=nlstate+ndeath; m++){                if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
                                 if(jk!=0 && m!=0)                  dateintsum=dateintsum+k2; /* on all covariates ?*/
                                         fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);                  k2cpt++;
       }                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
     }                }
     fprintf(ficresphtmfr, "\n");              }else{
                                 bool=1;
     /* For each age */              }/* end bool 2 */
     for(iage=iagemin; iage <= iagemax+3; iage++){            } /* end m */
       fprintf(ficresphtm,"<tr>");          } /* end bool */
       if(iage==iagemax+1){        } /* end iind = 1 to imx */
                                 fprintf(ficlog,"1");        /* prop[s][age] is feeded for any initial and valid live state as well as
                                 fprintf(ficresphtmfr,"<tr><th>0</th> ");           freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
       }else if(iage==iagemax+2){        
                                 fprintf(ficlog,"0");        
                                 fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       }else if(iage==iagemax+3){        if(cptcoveff==0 && nj==1) /* no covariate and first pass */
                                 fprintf(ficlog,"Total");          pstamp(ficresp);
                                 fprintf(ficresphtmfr,"<tr><th>Total</th> ");        if  (cptcoveff>0 && j!=0){
       }else{          pstamp(ficresp);
                                 if(first==1){          printf( "\n#********** Variable "); 
                                         first=0;          fprintf(ficresp, "\n#********** Variable "); 
                                         printf("See log file for details...\n");          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                                 }          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                                 fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);          fprintf(ficlog, "\n#********** Variable "); 
                                 fprintf(ficlog,"Age %d", iage);          for (z1=1; z1<=cptcoveff; z1++){
       }            if(!FixedV[Tvaraff[z1]]){
       for(jk=1; jk <=nlstate ; jk++){              printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                 for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                         pp[jk] += freq[jk][m][iage];               fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       }              fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       for(jk=1; jk <=nlstate ; jk++){              fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                 for(m=-1, pos=0; m <=0 ; m++)            }else{
                                         pos += freq[jk][m][iage];              printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                 if(pp[jk]>=1.e-10){              fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                         if(first==1){              fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                                 printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);              fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                         }              fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                         fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
                                 }else{          }
                                         if(first==1)          printf( "**********\n#");
                                                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficresp, "**********\n#");
                                         fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          fprintf(ficresphtm, "**********</h3>\n");
                                 }          fprintf(ficresphtmfr, "**********</h3>\n");
       }          fprintf(ficlog, "**********\n");
                                 }
       for(jk=1; jk <=nlstate ; jk++){         fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
                                 /* posprop[jk]=0; */        if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
                                 for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */          fprintf(ficresp, " Age");
                                         pp[jk] += freq[jk][m][iage];        if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */        for(i=1; i<=nlstate;i++) {
                                   if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," Prev(%d)  N(%d)  N  ",i,i);
       for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
                                 pos += pp[jk]; /* pos is the total number of transitions until this age */        }
                                 posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state        if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp, "\n");
                                                                                                                                                                         from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */        fprintf(ficresphtm, "\n");
                                 pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state        
                                                                                                                                                                 from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */        /* Header of frequency table by age */
       }        fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
       for(jk=1; jk <=nlstate ; jk++){        fprintf(ficresphtmfr,"<th>Age</th> ");
                                 if(pos>=1.e-5){        for(s2=-1; s2 <=nlstate+ndeath; s2++){
                                         if(first==1)          for(m=-1; m <=nlstate+ndeath; m++){
                                                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            if(s2!=0 && m!=0)
                                         fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
                                 }else{          }
                                         if(first==1)        }
                                                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        fprintf(ficresphtmfr, "\n");
                                         fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      
                                 }        /* For each age */
                                 if( iage <= iagemax){        for(iage=iagemin; iage <= iagemax+3; iage++){
                                         if(pos>=1.e-5){          fprintf(ficresphtm,"<tr>");
                                                 fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);          if(iage==iagemax+1){
                                                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);            fprintf(ficlog,"1");
                                                 /*probs[iage][jk][j1]= pp[jk]/pos;*/            fprintf(ficresphtmfr,"<tr><th>0</th> ");
                                                 /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/          }else if(iage==iagemax+2){
                                         }            fprintf(ficlog,"0");
                                         else{            fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
                                                 fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);          }else if(iage==iagemax+3){
                                                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);            fprintf(ficlog,"Total");
                                         }            fprintf(ficresphtmfr,"<tr><th>Total</th> ");
                                 }          }else{
                                 pospropt[jk] +=posprop[jk];            if(first==1){
       } /* end loop jk */              first=0;
       /* pospropt=0.; */              printf("See log file for details...\n");
       for(jk=-1; jk <=nlstate+ndeath; jk++){            }
                                 for(m=-1; m <=nlstate+ndeath; m++){            fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
                                         if(freq[jk][m][iage] !=0 ) { /* minimizing output */            fprintf(ficlog,"Age %d", iage);
                                                 if(first==1){          }
                                                         printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);          for(s1=1; s1 <=nlstate ; s1++){
                                                 }            for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
                                                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);              pp[s1] += freq[s1][m][iage]; 
                                         }          }
                                         if(jk!=0 && m!=0)          for(s1=1; s1 <=nlstate ; s1++){
                                                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);            for(m=-1, pos=0; m <=0 ; m++)
                                 }              pos += freq[s1][m][iage];
       } /* end loop jk */            if(pp[s1]>=1.e-10){
       posproptt=0.;               if(first==1){
       for(jk=1; jk <=nlstate; jk++){                printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
                                 posproptt += pospropt[jk];              }
       }              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
       fprintf(ficresphtmfr,"</tr>\n ");            }else{
       if(iage <= iagemax){              if(first==1)
                                 fprintf(ficresp,"\n");                printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
                                 fprintf(ficresphtm,"</tr>\n");              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
             }
           }
         
           for(s1=1; s1 <=nlstate ; s1++){ 
             /* posprop[s1]=0; */
             for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
               pp[s1] += freq[s1][m][iage];
           }       /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */
         
           for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
             pos += pp[s1]; /* pos is the total number of transitions until this age */
             posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
                                               from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
             pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
                                             from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           }
           
           /* Writing ficresp */
           if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
             }
           }else if( nj==2){
             if( iage <= iagemax){
               fprintf(ficresp," %d",iage);
               for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
             }
           }
           for(s1=1; s1 <=nlstate ; s1++){
             if(pos>=1.e-5){
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
             }else{
               if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
             }
             if( iage <= iagemax){
               if(pos>=1.e-5){
                 if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
                   fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 }else if( nj==2){
                   fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 }
                 fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
                 /*probs[iage][s1][j1]= pp[s1]/pos;*/
                 /*printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);*/
               } else{
                 if((cptcoveff==0 && nj==1)|| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
                 fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
               }
             }
             pospropt[s1] +=posprop[s1];
           } /* end loop s1 */
           /* pospropt=0.; */
           for(s1=-1; s1 <=nlstate+ndeath; s1++){
             for(m=-1; m <=nlstate+ndeath; m++){
               if(freq[s1][m][iage] !=0 ) { /* minimizing output */
                 if(first==1){
                   printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
                 }
                 /* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
                 fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
               }
               if(s1!=0 && m!=0)
                 fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
             }
           } /* end loop s1 */
           posproptt=0.; 
           for(s1=1; s1 <=nlstate; s1++){
             posproptt += pospropt[s1];
           }
           fprintf(ficresphtmfr,"</tr>\n ");
           fprintf(ficresphtm,"</tr>\n");
           if((cptcoveff==0 && nj==1)|| nj==2 ) {
             if(iage <= iagemax)
               fprintf(ficresp,"\n");
           }
           if(first==1)
             printf("Others in log...\n");
           fprintf(ficlog,"\n");
         } /* end loop age iage */
         
         fprintf(ficresphtm,"<tr><th>Tot</th>");
         for(s1=1; s1 <=nlstate ; s1++){
           if(posproptt < 1.e-5){
             fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt); 
           }else{
             fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);  
           }
       }        }
       if(first==1)        fprintf(ficresphtm,"</tr>\n");
                                 printf("Others in log...\n");        fprintf(ficresphtm,"</table>\n");
       fprintf(ficlog,"\n");        fprintf(ficresphtmfr,"</table>\n");
     } /* end loop age iage */  
     fprintf(ficresphtm,"<tr><th>Tot</th>");  
     for(jk=1; jk <=nlstate ; jk++){  
       if(posproptt < 1.e-5){        if(posproptt < 1.e-5){
                                 fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);             fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
           fprintf(ficlog,"#  This combination (%d) is not valid and no result will be produced\n",j1);
           printf("#  This combination (%d) is not valid and no result will be produced\n",j1);
           invalidvarcomb[j1]=1;
       }else{        }else{
                                 fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);              fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
           invalidvarcomb[j1]=0;
       }        }
     }        fprintf(ficresphtmfr,"</table>\n");
     fprintf(ficresphtm,"</tr>\n");        fprintf(ficlog,"\n");
     fprintf(ficresphtm,"</table>\n");        if(j!=0){
     fprintf(ficresphtmfr,"</table>\n");          printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
     if(posproptt < 1.e-5){          for(i=1,s1=1; i <=nlstate; i++){
       fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);            for(k=1; k <=(nlstate+ndeath); k++){
       fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);              if (k != i) {
       fprintf(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);                for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
       invalidvarcomb[j1]=1;                  if(jj==1){  /* Constant case (in fact cste + age) */
     }else{                    if(j1==1){ /* All dummy covariates to zero */
       fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);                      freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
       invalidvarcomb[j1]=0;                      freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
     }                      printf("%d%d ",i,k);
     fprintf(ficresphtmfr,"</table>\n");                      fprintf(ficlog,"%d%d ",i,k);
   } /* end selected combination of covariate j1 */                      printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
   dateintmean=dateintsum/k2cpt;                       fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                               pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
   fclose(ficresp);                    }
   fclose(ficresphtm);                  }else if((j1==1) && (jj==2 || nagesqr==1)){ /* age or age*age parameter without covariate V4*age (to be done later) */
   fclose(ficresphtmfr);                    for(iage=iagemin; iage <= iagemax+3; iage++){
   free_vector(meanq,1,nqfveff);                      x[iage]= (double)iage;
   free_matrix(meanqt,1,lastpass,1,nqtveff);                      y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
   free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);                      /* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
   free_vector(pospropt,1,nlstate);                    }
   free_vector(posprop,1,nlstate);                    /* Some are not finite, but linreg will ignore these ages */
   free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);                    no=0;
   free_vector(pp,1,nlstate);                    linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
   /* End of freqsummary */                    pstart[s1]=b;
 }                    pstart[s1-1]=a;
                   }else if( j1!=1 && (j1==2 || (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj)  && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */ 
                     printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
                     pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
                     printf("%d%d ",i,k);
                     fprintf(ficlog,"%d%d ",i,k);
                     printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
                   }else{ /* Other cases, like quantitative fixed or varying covariates */
                     ;
                   }
                   /* printf("%12.7f )", param[i][jj][k]); */
                   /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                   s1++; 
                 } /* end jj */
               } /* end k!= i */
             } /* end k */
           } /* end i, s1 */
         } /* end j !=0 */
       } /* end selected combination of covariate j1 */
       if(j==0){ /* We can estimate starting values from the occurences in each case */
         printf("#Freqsummary: Starting values for the constants:\n");
         fprintf(ficlog,"\n");
         for(i=1,s1=1; i <=nlstate; i++){
           for(k=1; k <=(nlstate+ndeath); k++){
             if (k != i) {
               printf("%d%d ",i,k);
               fprintf(ficlog,"%d%d ",i,k);
               for(jj=1; jj <=ncovmodel; jj++){
                 pstart[s1]=p[s1]; /* Setting pstart to p values by default */
                 if(jj==1){ /* Age has to be done */
                   pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
                   printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                   fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
                 }
                 /* printf("%12.7f )", param[i][jj][k]); */
                 /* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
                 s1++; 
               }
               printf("\n");
               fprintf(ficlog,"\n");
             }
           }
         }
         printf("#Freqsummary\n");
         fprintf(ficlog,"\n");
         for(s1=-1; s1 <=nlstate+ndeath; s1++){
           for(s2=-1; s2 <=nlstate+ndeath; s2++){
             /* param[i]|j][k]= freq[s1][s2][iagemax+3] */
             printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
             /* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output *\/ */
             /*   printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /*   fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
             /* } */
           }
         } /* end loop s1 */
         
         printf("\n");
         fprintf(ficlog,"\n");
       } /* end j=0 */
     } /* end j */
   
     if(mle == -2){  /* We want to use these values as starting values */
       for(i=1, jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j!=i){
             /*ca[0]= k+'a'-1;ca[1]='\0';*/
             printf("%1d%1d",i,j);
             fprintf(ficparo,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               /*    printf(" %lf",param[i][j][k]); */
               /*    fprintf(ficparo," %lf",param[i][j][k]); */
               p[jk]=pstart[jk];
               printf(" %f ",pstart[jk]);
               fprintf(ficparo," %f ",pstart[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficparo,"\n");
           }
         }
       }
     } /* end mle=-2 */
     dateintmean=dateintsum/k2cpt; 
     
     fclose(ficresp);
     fclose(ficresphtm);
     fclose(ficresphtmfr);
     free_vector(meanq,1,nqfveff);
     free_matrix(meanqt,1,lastpass,1,nqtveff);
     free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(pospropt,1,nlstate);
     free_vector(posprop,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
     free_vector(pp,1,nlstate);
     /* 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 4333  void prevalence(double ***probs, double Line 4981  void prevalence(double ***probs, double
   iagemin= (int) agemin;    iagemin= (int) agemin;
   iagemax= (int) agemax;    iagemax= (int) agemax;
   /*pp=vector(1,nlstate);*/    /*pp=vector(1,nlstate);*/
   prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);     prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE); 
   /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   j1=0;    j1=0;
       
Line 4343  void prevalence(double ***probs, double Line 4991  void prevalence(double ***probs, double
   first=1;    first=1;
   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+3+AGEMARGE; iage++)        for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
         prop[i][iage]=0.0;          prop[i][iage]=0.0;
     printf("Prevalence combination of varying and fixed dummies %d\n",j1);      printf("Prevalence combination of varying and fixed dummies %d\n",j1);
     /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
Line 4374  void prevalence(double ***probs, double Line 5022  void prevalence(double ***probs, double
             if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               if(agev[m][i]==0) agev[m][i]=iagemax+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+4+AGEMARGE){
                 printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);                   printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d  m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m); 
                 exit(1);                  exit(1);
               }                }
Line 4400  void prevalence(double ***probs, double Line 5048  void prevalence(double ***probs, double
           } else{            } else{
             if(first==1){              if(first==1){
               first=0;                first=0;
               printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,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{
                 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]);
             }              }
           }            }
         }           } 
Line 4411  void prevalence(double ***probs, double Line 5062  void prevalence(double ***probs, double
       
   /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /*free_vector(pp,1,nlstate);*/    /*free_vector(pp,1,nlstate);*/
   free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
 }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
Line 4460  void  concatwav(int wav[], int **dh, int Line 5111  void  concatwav(int wav[], int **dh, int
 #else  #else
         if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){          if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
           if(firsthree == 0){            if(firsthree == 0){
             printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);              printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
             firsthree=1;              firsthree=1;
           }            }
           fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);            fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
           mw[++mi][i]=m;            mw[++mi][i]=m;
           mli=m;            mli=m;
         }          }
Line 4490  void  concatwav(int wav[], int **dh, int Line 5141  void  concatwav(int wav[], int **dh, int
       /* if(mi==0)  never been interviewed correctly before death */        /* if(mi==0)  never been interviewed correctly before death */
       /* Only death is a correct wave */        /* Only death is a correct wave */
       mw[mi][i]=m;        mw[mi][i]=m;
     }      } /* else not in a death state */
 #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE  #ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
     else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */      else if ((int) andc[i] != 9999) {  /* Date of death is known */
       /* m++; */  
       /* mi++; */  
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */  
       /* mw[mi][i]=m; */  
       if ((int)anint[m][i]!= 9999) { /* date of last interview is known */        if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
         if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */          if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
           nbwarn++;            nbwarn++;
Line 4509  void  concatwav(int wav[], int **dh, int Line 5156  void  concatwav(int wav[], int **dh, int
         }else{ /* Death occured afer last wave potential bias */          }else{ /* Death occured afer last wave potential bias */
           nberr++;            nberr++;
           if(firstwo==0){            if(firstwo==0){
             printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );              printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
             firstwo=1;              firstwo=1;
           }            }
           fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
         }          }
       }else{ /* end date of interview is known */        }else{ /* if date of interview is unknown */
         /* death is known but not confirmed by death status at any wave */          /* death is known but not confirmed by death status at any wave */
         if(firstfour==0){          if(firstfour==0){
           printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );            printf("Error! Death for individual %ld line=%d  occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
Line 4545  void  concatwav(int wav[], int **dh, int Line 5192  void  concatwav(int wav[], int **dh, int
       if (stepm <=0)        if (stepm <=0)
         dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
           if (agedc[i] < 2*AGESUP) {            if (agedc[i] < 2*AGESUP) {
             j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
Line 4632  void  concatwav(int wav[], int **dh, int Line 5279  void  concatwav(int wav[], int **dh, int
   
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
  void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)   void tricode(int *cptcov, int *Tvar, int **nbcode, int imx, int *Ndum)
 {   {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */     /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1      /*     Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
    * Boring subroutine which should only output nbcode[Tvar[j]][k]      * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable      * Tvar[5] in V2+V1+V3*age+V2*V4 is 4 (V4) even it is a time varying or quantitative variable
    * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);      * nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
   */      */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;     int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
   int modmaxcovj=0; /* Modality max of covariates j */     int modmaxcovj=0; /* Modality max of covariates j */
   int cptcode=0; /* Modality max of covariates j */     int cptcode=0; /* Modality max of covariates j */
   int modmincovj=0; /* Modality min of covariates j */     int modmincovj=0; /* Modality min of covariates j */
   
   
   /* cptcoveff=0;  */     /* cptcoveff=0;  */
         /* *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 */
   
   /* 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 (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 */ 
       switch(Fixed[k]) {         switch(Fixed[k]) {
       case 0: /* Testing on fixed dummy covariate, simple or product of fixed */         case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
                                 for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/           for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the  modality of this covariate Vj*/
                                         ij=(int)(covar[Tvar[k]][i]);             ij=(int)(covar[Tvar[k]][i]);
                                         /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i             /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                          * If product of Vn*Vm, still boolean *:              * If product of Vn*Vm, still boolean *:
                                          * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables              * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
                                          * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */              * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
                                         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the             /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
                                                  modality of the nth covariate of individual i. */                modality of the nth covariate of individual i. */
                                         if (ij > modmaxcovj)             if (ij > modmaxcovj)
                                                 modmaxcovj=ij;                modmaxcovj=ij; 
                                         else if (ij < modmincovj)              else if (ij < modmincovj) 
                                                 modmincovj=ij;                modmincovj=ij; 
                                         if ((ij < -1) && (ij > NCOVMAX)){             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
                                                 Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/               Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
                                         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */             /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
                                         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/             /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
                                         /* getting the maximum value of the modality of the covariate             /* getting the maximum value of the modality of the covariate
                                                  (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and                (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
                                                  female ies 1, then modmaxcovj=1.                female ies 1, then modmaxcovj=1.
                                         */             */
                                 } /* end for loop on individuals i */           } /* end for loop on individuals i */
                                 printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);           printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                                 fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);           fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
                                 cptcode=modmaxcovj;           cptcode=modmaxcovj;
                                 /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */           /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
                                 /*for (i=0; i<=cptcode; i++) {*/           /*for (i=0; i<=cptcode; i++) {*/
                                 for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */           for (j=modmincovj;  j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1*//* For each value j of the modality of model-cov k */
                                         printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);             printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                                         fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);             fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
                                         if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
                                                 if( j != -1){               if( j != -1){
                                                         ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th                 ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                                                                                                                                  covariate for which somebody answered excluding                                     covariate for which somebody answered excluding 
                                                                                                                                  undefined. Usually 2: 0 and 1. */                                    undefined. Usually 2: 0 and 1. */
                                                 }               }
                                                 ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th               ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                                                                                                                                                 covariate for which somebody answered including                                        covariate for which somebody answered including 
                                                                                                                                                 undefined. Usually 3: -1, 0 and 1. */                                       undefined. Usually 3: -1, 0 and 1. */
                                         }       /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for             }    /* In fact  ncodemax[k]=2 (dichotom. variables only) but it could be more for
                                                  * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */                   * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
                                 } /* Ndum[-1] number of undefined modalities */           } /* Ndum[-1] number of undefined modalities */
                                                   
                                 /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */           /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
                                 /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */           /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
                                 /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */           /* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
                                 /* modmincovj=3; modmaxcovj = 7; */           /* modmincovj=3; modmaxcovj = 7; */
                                 /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */           /* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
                                 /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */           /* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
                           /*             defining two dummy variables: variables V1_1 and V1_2.*/           /*              defining two dummy variables: variables V1_1 and V1_2.*/
               /* nbcode[Tvar[j]][ij]=k; */           /* nbcode[Tvar[j]][ij]=k; */
               /* nbcode[Tvar[j]][1]=0; */           /* nbcode[Tvar[j]][1]=0; */
               /* nbcode[Tvar[j]][2]=1; */           /* nbcode[Tvar[j]][2]=1; */
               /* 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*/
           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*/
                                         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;
       case 1: /* Testing on varying covariate, could be simple and         case 1: /* Testing on varying covariate, could be simple and
                * should look at waves or product of fixed *                  * should look at waves or product of fixed *
                * varying. No time to test -1, assuming 0 and 1 only */                  * varying. No time to test -1, assuming 0 and 1 only */
                                 ij=0;           ij=0;
                                 for(i=0; i<=1;i++){           for(i=0; i<=1;i++){
                                         nbcode[Tvar[k]][++ij]=i;             nbcode[Tvar[k]][++ij]=i;
                                 }           }
                                 break;           break;
       default:         default:
                                 break;           break;
       } /* end switch */         } /* end switch */
     } /* end dummy test */       } /* end dummy test */
           
     /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */       /*   for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
     /*  /\*recode from 0 *\/ */       /*         /\*recode from 0 *\/ */
     /*                               k is a modality. If we have model=V1+V1*sex  */       /*                                      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; */       /*                                      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 *\/ */       /*                                   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 *\/ */       /*         /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
     /*  if (ij > ncodemax[j]) { */       /*         if (ij > ncodemax[j]) { */
     /*    printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, 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]); */       /*           fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
     /*    break; */       /*           break; */
     /*  } */       /*         } */
     /*   }  /\* end of loop on modality k *\/ */       /*   }  /\* 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*/       } /* 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 */
   for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */      for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */ 
     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/        /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ 
     ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */        ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V4*age */ 
     Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */       Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
     /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */       /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1,  {2, 1, 1, 1, 2, 1, 1, 0, 0} */
   } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */     } /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */
       
   ij=0;     ij=0;
   /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */     /* for (i=0; i<=  maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) *\/ */
   for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */     for (k=1; k<=  cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/       /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */       /* if((Ndum[i]!=0) && (i<=ncovcol)){  /\* Tvar[i] <= ncovmodel ? *\/ */
     if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */       if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){  /* Only Dummy and non empty in the model */
       /* If product not in single variable we don't print results */         /* If product not in single variable we don't print results */
       /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/         /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
       ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */         ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
       Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/         Tvaraff[ij]=Tvar[k]; /* For printing combination *//* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
       Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */         Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
       TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */         TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
       if(Fixed[k]!=0)         if(Fixed[k]!=0)
         anyvaryingduminmodel=1;           anyvaryingduminmodel=1;
                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
                         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */         /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
                         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
                         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
                         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */         /*   Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet *\/ */
     }        } 
   } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */     } /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
   /* ij--; */     /* ij--; */
   /* cptcoveff=ij; /\*Number of total covariates*\/ */     /* cptcoveff=ij; /\*Number of total covariates*\/ */
   *cptcov=ij; /*Number of total real effective covariates: effective     *cptcov=ij; /*Number of total real effective covariates: effective
                                                          * because they can be excluded from the model and real                  * because they can be excluded from the model and real
                                                          * if in the model but excluded because missing values, but how to get k from ij?*/                  * if in the model but excluded because missing values, but how to get k from ij?*/
   for(j=ij+1; j<= cptcovt; j++){     for(j=ij+1; j<= cptcovt; j++){
     Tvaraff[j]=0;       Tvaraff[j]=0;
     Tmodelind[j]=0;       Tmodelind[j]=0;
   }     }
   for(j=ntveff+1; j<= cptcovt; j++){     for(j=ntveff+1; j<= cptcovt; j++){
     TmodelInvind[j]=0;       TmodelInvind[j]=0;
   }     }
   /* To be sorted */     /* To be sorted */
   ;     ;
 }   }
   
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
 void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )   void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[], int nres )
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
Line 4813  void evsij(double ***eij, double x[], in Line 5460  void evsij(double ***eij, double x[], in
   double ***p3mat;    double ***p3mat;
   double eip;    double eip;
   
   pstamp(ficreseij);    /* pstamp(ficreseij); */
   fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficreseij,"# Age");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++){    for(i=1; i<=nlstate;i++){
Line 4844  void evsij(double ***eij, double x[], in Line 5491  void evsij(double ***eij, double x[], in
   /* 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 4876  void evsij(double ***eij, double x[], in Line 5523  void evsij(double ***eij, double x[], in
     /* Computed by stepm unit matrices, product of hstepma matrices, stored      /* Computed by stepm unit matrices, product of hstepma matrices, stored
        in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */         in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
           
     hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);  
           
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           
Line 4911  void evsij(double ***eij, double x[], in Line 5558  void evsij(double ***eij, double x[], in
       
 }  }
   
 void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )   void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[], int nres )
   
 {  {
   /* Covariances of health expectancies eij and of total life expectancies according    /* Covariances of health expectancies eij and of total life expectancies according
Line 5024  void cvevsij(double ***eij, double x[], Line 5671  void cvevsij(double ***eij, double x[],
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         xm[i] = x[i] - (i==theta ?delti[theta]:0);          xm[i] = x[i] - (i==theta ?delti[theta]:0);
       }        }
       hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);          hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);  
       hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);          hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);  
                                                   
       for(j=1; j<= nlstate; j++){        for(j=1; j<= nlstate; j++){
         for(i=1; i<=nlstate; i++){          for(i=1; i<=nlstate; i++){
Line 5066  void cvevsij(double ***eij, double x[], Line 5713  void cvevsij(double ***eij, double x[],
     }      }
                                   
     /* Computing expectancies */      /* Computing expectancies */
     hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);        hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);  
     for(i=1; i<=nlstate;i++)      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)        for(j=1; j<=nlstate;j++)
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
Line 5075  void cvevsij(double ***eij, double x[], Line 5722  void cvevsij(double ***eij, double x[],
           /* 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 5090  void cvevsij(double ***eij, double x[], Line 5738  void cvevsij(double ***eij, double x[],
     }      }
     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 5121  void cvevsij(double ***eij, double x[], Line 5770  void cvevsij(double ***eij, double x[],
 }  }
     
 /************ 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[])   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);*/
Line 5178  void cvevsij(double ***eij, double x[], Line 5827  void cvevsij(double ***eij, double x[],
    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    pstamp(ficresprobmorprev);     pstamp(ficresprobmorprev);
    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);     fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
      fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
      for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
        fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
      }
      for(j=1;j<=cptcoveff;j++) 
        fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
      fprintf(ficresprobmorprev,"\n");
   
    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);     fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
    for(j=nlstate+1; j<=(nlstate+ndeath);j++){     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
      fprintf(ficresprobmorprev," p.%-d SE",j);       fprintf(ficresprobmorprev," p.%-d SE",j);
Line 5247  void cvevsij(double ***eij, double x[], Line 5904  void cvevsij(double ***eij, double x[],
          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);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
Line 5259  void cvevsij(double ***eij, double x[], Line 5916  void cvevsij(double ***eij, double x[],
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  /* 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=1 to nhstepm */
        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++)
Line 5279  void cvevsij(double ***eij, double x[], Line 5936  void cvevsij(double ***eij, double x[],
        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);         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);
                                                   
        if (popbased==1) {         if (popbased==1) {
          if(mobilav ==0){           if(mobilav ==0){
Line 5291  void cvevsij(double ***eij, double x[], Line 5948  void cvevsij(double ***eij, double x[],
          }           }
        }         }
                                                   
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);           hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  
                                                   
        for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */         for(j=1; j<= nlstate; j++){  /* Sum of wi * eij = e.j */
          for(h=0; h<=nhstepm; h++){           for(h=0; h<=nhstepm; h++){
Line 5356  void cvevsij(double ***eij, double x[], Line 6013  void cvevsij(double ***eij, double x[],
      /* end ppptj */       /* end ppptj */
      /*  x centered again */       /*  x centered again */
                                   
      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
                                   
      if (popbased==1) {       if (popbased==1) {
        if(mobilav ==0){         if(mobilav ==0){
Line 5372  void cvevsij(double ***eij, double x[], Line 6029  void cvevsij(double ***eij, double x[],
         computed over hstepm (estepm) matrices product = hstepm*stepm months)           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         as a weighted average of prlim.          as a weighted average of prlim.
      */       */
      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);         hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);  
      for(j=nlstate+1;j<=nlstate+ndeath;j++){       for(j=nlstate+1;j<=nlstate+ndeath;j++){
        for(i=1,gmp[j]=0.;i<= nlstate; i++)          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
          gmp[j] += prlim[i][i]*p3mat[i][j][1];            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
Line 5435  void cvevsij(double ***eij, double x[], Line 6092  void cvevsij(double ***eij, double x[],
  }  /* 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[])   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 5451  void cvevsij(double ***eij, double x[], Line 6108  void cvevsij(double ***eij, double x[],
       
   pstamp(ficresvpl);    pstamp(ficresvpl);
   fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
   fprintf(ficresvpl,"# Age");    fprintf(ficresvpl,"# Age ");
     if(nresult >=1)
       fprintf(ficresvpl," Result# ");
   for(i=1; i<=nlstate;i++)    for(i=1; i<=nlstate;i++)
       fprintf(ficresvpl," %1d-%1d",i,i);        fprintf(ficresvpl," %1d-%1d",i,i);
   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 5478  void cvevsij(double ***eij, double x[], Line 6137  void cvevsij(double ***eij, double x[],
         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);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       else        else
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);          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];
Line 5488  void cvevsij(double ***eij, double x[], Line 6147  void cvevsij(double ***eij, double x[],
       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);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
       else        else
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);          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 5527  void cvevsij(double ***eij, double x[], Line 6186  void cvevsij(double ***eij, double x[],
     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 */
   
     fprintf(ficresvpl,"%.0f ",age );      fprintf(ficresvpl,"%.0f ",age );
       if(nresult >=1)
         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]));
     fprintf(ficresvpl,"\n");      fprintf(ficresvpl,"\n");
Line 5550  void cvevsij(double ***eij, double x[], Line 6211  void cvevsij(double ***eij, double x[],
   
   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 5630  void varprob(char optionfilefiname[], do Line 6416  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.</li>\n",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. %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 5847  To be simple, these graphs help to under Line 6633  To be simple, these graphs help to under
                    fprintf(ficgp,"\nset parametric;unset label");                     fprintf(ficgp,"\nset parametric;unset label");
                    fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                    fprintf(ficgp,"\nset ter svg size 640, 480");                     fprintf(ficgp,"\nset ter svg size 640, 480");
                    fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\                     fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
  :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \   :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">                                                                                                                                           \
 %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\  %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
                            subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \                             subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,      \
Line 5858  To be simple, these graphs help to under Line 6644  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(lc2),                                                                         \                             mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(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);
                    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,"\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,"\nreplot %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,"\nreplot %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(lc2),                                 \                             mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)),   \
                            mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                             mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
                  }/* if first */                   }/* if first */
                } /* age mod 5 */                 } /* age mod 5 */
              } /* end loop age */               } /* end loop age */
Line 5895  To be simple, these graphs help to under Line 6681  To be simple, these graphs help to under
 void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \  void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
                   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 prevfcast, 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;    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 \
    <li><a href='#secondorder'>Result files (second order (variance)</a>\n \     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
 </ul>");  </ul>");
      fprintf(fichtm,"<ul><li> model=1+age+%s\n \
   </ul>", model);
    fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
    fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",     fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
            jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 5931  void printinghtml(char fileresu[], char Line 6719  void printinghtml(char fileresu[], char
    <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));     <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
    }     }
   
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  
   
    m=pow(2,cptcoveff);     m=pow(2,cptcoveff);
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    jj1=0;     jj1=0;
    for(k1=1; k1<=m;k1++){  
      fprintf(fichtm," \n<ul>");
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"\n<li><a  size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\">");
          
          /* if(nqfveff+nqtveff 0) */ /* Test to be done */
          fprintf(fichtm,"************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          if(invalidvarcomb[k1]){
            fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1); 
            continue;
          }
          fprintf(fichtm,"</a></li>");
        } /* cptcovn >0 */
      }
        fprintf(fichtm," \n</ul>");
   
      jj1=0;
   
      for(nres=1; nres <= nresult; nres++) /* For each resultline */
      for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
        if(m != 1 && TKresult[nres]!= k1)
          continue;
   
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
          fprintf(fichtm,"\n<p><a name=\"rescov");
          for (cpt=1; cpt<=cptcoveff;cpt++){ 
            fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
            fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
          }
          fprintf(fichtm,"\"</a>");
    
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
            /* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
        }         }
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
         }
          
        /* if(nqfveff+nqtveff 0) */ /* Test to be done */         /* if(nqfveff+nqtveff 0) */ /* Test to be done */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
Line 5956  void printinghtml(char fileresu[], char Line 6800  void printinghtml(char fileresu[], char
        }         }
      }       }
      /* aij, bij */       /* aij, bij */
      fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \       fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
 <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);  <img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \       fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
 <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);       <img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\       fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
  before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
  incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \   incidence (rates) are the limit when h tends to zero of the ratio of the probability  <sub>h</sub>P<sub>ij</sub> \
 divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \  divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
 <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);   <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.svg\">%s%d_%d.svg</a><br> \         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> \
 <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);  <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 from state %d in each live state and total.\
  Or probability to survive in various states (1 to %d) being in state %d at different ages.     \   Or probability to survive in various states (1 to %d) being in state %d at different ages.     \
  <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);   <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 (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 to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%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.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);  <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 */         /* Period (stable) back 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) back 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.svg\">%s_%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.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);  <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 (stable) 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) 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.svg\">%s%d_%d.svg</a><br> \           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) 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.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);  <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++){
            fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
    from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
    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);
        }         }
      }       }
                     
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
 <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);  <img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
      }       }
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
Line 6058  See page 'Matrix of variance-covariance Line 6912  See page 'Matrix of variance-covariance
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;     jj1=0;
   
      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
    for(k1=1; k1<=m;k1++){     for(k1=1; k1<=m;k1++){
        if(m != 1 && TKresult[nres]!= k1)
          continue;
      /* for(i1=1; i1<=ncodemax[k1];i1++){ */       /* for(i1=1; i1<=ncodemax[k1];i1++){ */
      jj1++;       jj1++;
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */         for (cpt=1; cpt<=cptcoveff;cpt++)  /**< cptcoveff number of variables */
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
            /* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
   
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   
        if(invalidvarcomb[k1]){         if(invalidvarcomb[k1]){
Line 6073  See page 'Matrix of variance-covariance Line 6936  See page 'Matrix of variance-covariance
        }         }
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \         fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
 prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\  prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
 <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);    <img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);  
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and \       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
 health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \  health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
 true period expectancies (those weighted with period prevalences are also\  true period expectancies (those weighted with period prevalences are also\
  drawn in addition to the population based expectancies computed using\   drawn in addition to the population based expectancies computed using\
  observed and cahotic prevalences:  <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\   observed and cahotic prevalences:  <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
 <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);  <img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
      /* } /\* end i1 *\/ */       /* } /\* end i1 *\/ */
    }/* End k1 */     }/* End k1 */
     }/* End nres */
    fprintf(fichtm,"</ul>");     fprintf(fichtm,"</ul>");
    fflush(fichtm);     fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){  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];    char gplotcondition[132], gplotlabel[132];
   int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
   int lv=0, vlv=0, kl=0;    int lv=0, vlv=0, kl=0;
   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 istart=1; /* For starting graphs in projections */
   
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 6110  void printinggnuplot(char fileresu[], ch Line 6978  void printinggnuplot(char fileresu[], ch
   /*#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 6142  void printinggnuplot(char fileresu[], ch Line 7024  void printinggnuplot(char fileresu[], ch
   strcpy(dirfileres,optionfilefiname);    strcpy(dirfileres,optionfilefiname);
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
     for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */      for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");          /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */          if(m != 1 && TKresult[nres]!= k1)
         lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */            continue;
         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* We are interested in selected combination by the resultline */
         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files  and live state =%d ", cpt);
         vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */          strcpy(gplotlabel,"(");
         /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */          for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
       }            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
       fprintf(ficgp,"\n#\n");            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       if(invalidvarcomb[k1]){            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
         continue;            /* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
       }            /* printf(" V%d=%d ",Tvaraff[k],vlv); */
             fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
       fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);          }
       fprintf(ficgp,"set xlabel \"Age\" \n\          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 set ylabel \"Probability\" \n   \            /* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
 set ter svg size 640, 480\n     \            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
                                   }
       for (i=1; i<= nlstate ; i ++) {          strcpy(gplotlabel+strlen(gplotlabel),")");
         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          /* printf("\n#\n"); */
         else        fprintf(ficgp," %%*lf (%%*lf)");          fprintf(ficgp,"\n#\n");
       }          if(invalidvarcomb[k1]){
       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);            /*k1=k1-1;*/ /* To be checked */
       for (i=1; i<= nlstate ; i ++) {            fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");            continue;
         else fprintf(ficgp," %%*lf (%%*lf)");          }
       }         
       fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
       for (i=1; i<= nlstate ; i ++) {          fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");          /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
         else fprintf(ficgp," %%*lf (%%*lf)");          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 ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));          /* 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 ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
       if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */        /* k1-1 error should be nres-1*/
         /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */          for (i=1; i<= nlstate ; i ++) {
         fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */            if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
         if(cptcoveff ==0){            else        fprintf(ficgp," %%*lf (%%*lf)");
           fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ",  2+(cpt-1),  cpt );          }
           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);
           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 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres); 
           for (i=1; i<= nlstate ; i ++) {
             if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
             else fprintf(ficgp," %%*lf (%%*lf)");
           }  
           /* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1)); */
           
           fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
           if(cptcoveff ==0){
             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 6202  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7099  plot [%.f:%.f] \"%s\" every :::%d::%d u
             /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/
             if(k==cptcoveff){              if(k==cptcoveff){
               fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                       4+(cpt-1),  cpt );  /* 4 or 6 ?*/                        2+cptcoveff*2+3*(cpt-1),  cpt );  /* 4 or 6 ?*/
             }else{              }else{
               fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);                fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
               kl++;                kl++;
             }              }
           } /* end covariate */            } /* end covariate */
         } /* end if no covariate */          } /* end if no covariate */
       } /* end if backcast */  
       fprintf(ficgp,"\nset out \n");          if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
             /* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
             fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
             if(cptcoveff ==0){
               fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3",    2+(cpt-1),  cpt );
             }else{
               kl=0;
               for (k=1; k<=cptcoveff; k++){    /* For each combination of covariate  */
                 lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
                 /* 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];
                 kl++;
                 /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                 /*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):($5==2000? 3:2) t 'p.1' with line lc variable*/
                 if(k==cptcoveff){
                   fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                           2+cptcoveff*2+(cpt-1),  cpt );  /* 4 or 6 ?*/
                 }else{
                   fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
                   kl++;
                 }
               } /* end 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 */
           /* fprintf(ficgp,"\nset out ;unset label;\n"); */
           fprintf(ficgp,"\nset out ;unset title;\n");
         } /* nres */
     } /* k1 */      } /* k1 */
   } /* cpt */    } /* cpt */
   /*2 eme*/  
   for (k1=1; k1<= m ; k1 ++) {   
   
     fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");    
     for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */    /*2 eme*/
       lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */    for (k1=1; k1<= m ; k1 ++){  
       /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
       /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */        if(m != 1 && TKresult[nres]!= k1)
       /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          continue;
       vlv= nbcode[Tvaraff[k]][lv];        fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
       fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);        strcpy(gplotlabel,"(");
     }  
     fprintf(ficgp,"\n#\n");  
     if(invalidvarcomb[k1]){  
       fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
       continue;  
     }  
                           
     fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);  
     for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/  
       if(vpopbased==0)  
         fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);  
       else  
         fprintf(ficgp,"\nreplot ");  
       for (i=1; i<= nlstate+1 ; i ++) {  
         k=2*i;  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);  
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         fprintf(ficgp,"\" t\"\" w l lt 0,");  
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);  
         for (j=1; j<= nlstate+1 ; j ++) {  
           if (j==i) fprintf(ficgp," %%lf (%%lf)");  
           else fprintf(ficgp," %%*lf (%%*lf)");  
         }     
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");  
         else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");  
       } /* state */  
     } /* vpopbased */  
     fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */  
   } /* k1 */  
           
           
   /*3eme*/  
   for (k1=1; k1<= m ; k1 ++) {   
   
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files:  cov=%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 6278  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 7176  plot [%.f:%.f] \"%s\" every :::%d::%d u
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
       }        }
         /* for(k=1; k <= ncovds; k++){ */
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         strcpy(gplotlabel+strlen(gplotlabel),")");
       fprintf(ficgp,"\n#\n");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         continue;          continue;
       }        }
                                                   
       /*       k=2+nlstate*(2*cpt-2); */        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
       k=2+(nlstate+1)*(cpt-1);        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
       fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);          fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
       fprintf(ficgp,"set ter svg size 640, 480\n\          if(vpopbased==0){
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);            fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);          }else
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            fprintf(ficgp,"\nreplot ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          for (i=1; i<= nlstate+1 ; i ++) {
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);            k=2*i;
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");            fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);            for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
             else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             fprintf(ficgp,"\" t\"\" w l lt 0,");
             fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
             for (j=1; j<= nlstate+1 ; j ++) {
               if (j==i) fprintf(ficgp," %%lf (%%lf)");
               else fprintf(ficgp," %%*lf (%%*lf)");
             }   
             if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
             else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
           } /* state */
         } /* vpopbased */
         fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
       } /* end nres */
     } /* k1 end 2 eme*/
           
           
     /*3eme*/
     for (k1=1; k1<= m ; k1 ++){
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
   
         for (cpt=1; cpt<= nlstate ; cpt ++) {
           fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files:  combination=%d state=%d",k1, cpt);
           strcpy(gplotlabel,"(");
           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 */
             /* 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;
           }
                           
           /*       k=2+nlstate*(2*cpt-2); */
           k=2+(nlstate+1)*(cpt-1);
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
           fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
           fprintf(ficgp,"set ter svg size 640, 480\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
           /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
             fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                                                                   
       */          */
       for (i=1; i< nlstate ; i ++) {          for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);            fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
         /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/            /*    fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
                                                                   
       }           } 
       fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
     }        }
   }        fprintf(ficgp,"\nunset label;\n");
       } /* end nres */
     } /* end kl 3eme */
       
   /* 4eme */    /* 4eme */
   /* Survival functions (period) from state i in state j by initial state i */    /* Survival functions (period) from state i in state j by initial state i */
   for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */    for (k1=1; k1<=m; k1++){    /* For each covariate and each value */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        if(m != 1 && TKresult[nres]!= k1)
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);  
       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 */  
         /* 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);  
       }  
       fprintf(ficgp,"\n#\n");  
       if(invalidvarcomb[k1]){  
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
         continue;          continue;
       }        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
                                   strcpy(gplotlabel,"(");
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);          fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\          for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */
 set ter svg size 640, 480\n                                                                                                                                                                                     \            lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
 unset log y\n                                                                                                                                                                                                                                           \            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
 plot [%.f:%.f]  ", ageminpar, agemaxpar);            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
       k=3;            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
       for (i=1; i<= nlstate ; i ++){            vlv= nbcode[Tvaraff[k]][lv];
         if(i==1){            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
         }else{  
           fprintf(ficgp,", '' ");  
         }          }
         l=(nlstate+ndeath)*(i-1)+1;          for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);            fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         for (j=2; j<= nlstate+ndeath ; j ++)            sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficgp,"+$%d",k+l+j-1);          }       
         fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);          strcpy(gplotlabel+strlen(gplotlabel),")");
       } /* nlstate */          fprintf(ficgp,"\n#\n");
       fprintf(ficgp,"\nset out\n");          if(invalidvarcomb[k1]){
     } /* end cpt state*/             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
   } /* end covariate */              continue;
                   }
         
           fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),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 xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
   set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
           k=3;
           for (i=1; i<= nlstate ; i ++){
             if(i==1){
               fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
             }else{
               fprintf(ficgp,", '' ");
             }
             l=(nlstate+ndeath)*(i-1)+1;
             fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
             for (j=2; j<= nlstate+ndeath ; j ++)
               fprintf(ficgp,"+$%d",k+l+j-1);
             fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
           } /* nlstate */
           fprintf(ficgp,"\nset out; unset label;\n");
         } /* end cpt state*/ 
       } /* end nres */
     } /* end covariate k1 */  
   
 /* 5eme */  /* 5eme */
   /* Survival functions (period) from state i in state j by final state j */    /* Survival functions (period) from state i in state j by final state j */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */    for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
                                 if(m != 1 && TKresult[nres]!= k1)
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);  
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */  
         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(1,2,4) = 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);  
       }  
       fprintf(ficgp,"\n#\n");  
       if(invalidvarcomb[k1]){  
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);   
         continue;          continue;
       }        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state  */
           strcpy(gplotlabel,"(");
           fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
           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 */
             /* 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,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\          fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
 set ter svg size 640, 480\n                                             \          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 unset log y\n                                                           \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 plot [%.f:%.f]  ", ageminpar, agemaxpar);          k=3;
       k=3;          for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */            if(j==1)
         if(j==1)              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            else
         else              fprintf(ficgp,", '' ");
           fprintf(ficgp,", '' ");            l=(nlstate+ndeath)*(cpt-1) +j;
         l=(nlstate+ndeath)*(cpt-1) +j;            fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
         fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);            /* for (i=2; i<= nlstate+ndeath ; i ++) */
         /* for (i=2; i<= nlstate+ndeath ; i ++) */            /*   fprintf(ficgp,"+$%d",k+l+i-1); */
         /*   fprintf(ficgp,"+$%d",k+l+i-1); */            fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
         fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);          } /* nlstate */
       } /* nlstate */          fprintf(ficgp,", '' ");
       fprintf(ficgp,", '' ");          fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
       fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);          for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
       for (j=1; j<= nlstate ; j ++){ /* Lived in state j */            l=(nlstate+ndeath)*(cpt-1) +j;
         l=(nlstate+ndeath)*(cpt-1) +j;            if(j < nlstate)
         if(j < nlstate)              fprintf(ficgp,"$%d +",k+l);
           fprintf(ficgp,"$%d +",k+l);            else
         else              fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
           fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);          }
       }          fprintf(ficgp,"\nset out; unset label;\n");
       fprintf(ficgp,"\nset out\n");        } /* end cpt state*/ 
     } /* end cpt state*/       } /* end covariate */  
   } /* end covariate */      } /* end nres */
       
 /* 6eme */  /* 6eme */
   /* CV preval stable (period) for each covariate */    /* CV preval stable (period) for each covariate */
   for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */    for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */    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 of arrival */
         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 (period): '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 */
Line 6412  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7407  plot [%.f:%.f]  ", ageminpar, agemaxpar)
         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
         vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          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");        fprintf(ficgp,"\n#\n");
       if(invalidvarcomb[k1]){        if(invalidvarcomb[k1]){
         fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
         continue;          continue;
       }        }
               
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),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 xlabel \"Age\" \nset ylabel \"Probability\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n                                             \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n                                                           \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){ /* State of origin */
         if(i==1)          if(i==1)
           fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));            fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
         else          else
           fprintf(ficgp,", '' ");            fprintf(ficgp,", '' ");
         l=(nlstate+ndeath)*(i-1)+1;          l=(nlstate+ndeath)*(i-1)+1; /* 1, 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
         fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);          fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
         for (j=2; j<= nlstate ; j ++)          for (j=2; j<= nlstate ; j ++)
           fprintf(ficgp,"+$%d",k+l+j-1);            fprintf(ficgp,"+$%d",k+l+j-1);
         fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);          fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
       } /* nlstate */        } /* nlstate */
       fprintf(ficgp,"\nset out\n");        fprintf(ficgp,"\nset out; unset label;\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
       
Line 6444  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7444  plot [%.f:%.f]  ", ageminpar, agemaxpar)
 /* 7eme */  /* 7eme */
   if(backcast == 1){    if(backcast == 1){
     /* CV back preval stable (period) for each covariate */      /* CV back preval stable (period) for each covariate */
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);        if(m != 1 && TKresult[nres]!= k1)
           continue;
         for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
           strcpy(gplotlabel,"(");      
           fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): '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 6454  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7458  plot [%.f:%.f]  ", ageminpar, agemaxpar)
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            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");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
           continue;            continue;
         }          }
                   
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),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 \"Probability\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
 set ter svg size 640, 480\n                                             \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n                                                           \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  
         k=3; /* Offset */          k=3; /* Offset */
         for (i=1; i<= nlstate ; i ++){          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
             fprintf(ficgp,", '' ");              fprintf(ficgp,", '' ");
           /* l=(nlstate+ndeath)*(i-1)+1; */            /* l=(nlstate+ndeath)*(i-1)+1; */
           l=(nlstate+ndeath)*(cpt-1)+1;            l=(nlstate+ndeath)*(cpt-1)+1; /* fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2*(nlstate+ndeath) */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier *\/ */
           /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */            /* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier *\/ */
           fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */            fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
           /* 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\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
Line 6491  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7500  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   if(prevfcast==1){    if(prevfcast==1){
     /* Projection from cross-sectional to stable (period) for each covariate */      /* Projection from cross-sectional to stable (period) for each covariate */
           
     for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */      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 */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
           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 stable (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 */
Line 6501  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7514  plot [%.f:%.f]  ", ageminpar, agemaxpar)
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
           vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
           fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            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");          fprintf(ficgp,"\n#\n");
         if(invalidvarcomb[k1]){          if(invalidvarcomb[k1]){
           fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);             fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1); 
Line 6509  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7528  plot [%.f:%.f]  ", ageminpar, agemaxpar)
         }          }
                   
         fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");          fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
         fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);          fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),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 xlabel \"Age\" \nset ylabel \"Prevalence\" \n\          fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
 set ter svg size 640, 480\n                                             \  set ter svg size 640, 480\nunset log y\nplot [%.f:%.f]  ", ageminpar, agemaxpar);
 unset log y\n                                                           \  
 plot [%.f:%.f]  ", ageminpar, agemaxpar);          /* for (i=1; i<= nlstate+1 ; i ++){  /\* nlstate +1 p11 p21 p.1 *\/ */
         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*/            /*#  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 */               /*#   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*/            /*# 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 */               /*#   1       2   3    4    5      6  7   8   9   10   11 12  13   14  15 */   
           if(i==1){            if(i==istart){
             fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
           }else{            }else{
             fprintf(ficgp,",\\\n '' ");              fprintf(ficgp,",\\\n '' ");
Line 6531  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7553  plot [%.f:%.f]  ", ageminpar, agemaxpar)
             /*# V1  = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*# 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 */              /*#  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)) t 'pw.%d' with line ",      \                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 );
             else                fprintf(ficgp,",\\\n '' ");
                 fprintf(ficgp," u %d:(",ioffset); 
                 fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
                        offyear,                           \
                         ioffset+(cpt-1)*(nlstate+1)+1+(i-1),  ioffset+1+(i-1)+(nlstate+1)*nlstate );
               }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,"(");
Line 6566  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7591  plot [%.f:%.f]  ", ageminpar, agemaxpar)
             /*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) t 'p.%d' with line ", 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," u %d:(",iagec); 
                 fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
                         iyearc, iagec, offyear,                           \
                         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*/
             }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, \
                       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 );
             }              }
           } /* end if covariate */            } /* end if covariate */
         } /* nlstate */          } /* nlstate */
         fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out; unset label;\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* 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 */
     
       
   /* proba elementaires */    /* 9eme writing MLE parameters */
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficgp,"# initial state %d\n",i);      fprintf(ficgp,"# initial state %d\n",i);
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
Line 6598  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7744  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
       
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");    /* 10eme Graphics of probabilities or incidences using written MLE parameters */
     fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
   fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
   fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");    fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
   fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");    fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
Line 6613  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7760  plot [%.f:%.f]  ", ageminpar, agemaxpar)
   fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");    fprintf(ficgp,"#       +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
   fprintf(ficgp,"#\n");    fprintf(ficgp,"#\n");
   for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/    for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
     fprintf(ficgp,"# ng=%d\n",ng);      fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
     fprintf(ficgp,"#   jk=1 to 2^%d=%d\n",cptcoveff,m);      fprintf(ficgp,"#model=%s \n",model);
     for(jk=1; jk <=m; jk++) {      fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
       fprintf(ficgp,"#    jk=%d\n",jk);      fprintf(ficgp,"#   k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
       fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);      for(k1=1; k1 <=m; k1++)  /* For each combination of covariate */
       for(nres=1; nres <= nresult; nres++){ /* For each resultline */
         if(m != 1 && TKresult[nres]!= k1)
           continue;
         fprintf(ficgp,"\n\n# Combination of dummy  k1=%d which is ",k1);
         strcpy(gplotlabel,"(");
         /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
         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");
         fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
         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 6657  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7829  plot [%.f:%.f]  ", ageminpar, agemaxpar)
               break;                break;
             }              }
             ij=1;/* To be checked else nbcode[0][0] wrong */              ij=1;/* To be checked else nbcode[0][0] wrong */
             for(j=3; j <=ncovmodel-nagesqr; j++) {              ijp=1; /* product no age */
               /* for(j=3; j <=ncovmodel-nagesqr; j++) { */
               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(ij <=cptcovage) { /* Bug valgrind */                if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
                 if((j-2)==Tage[ij]) { /* Bug valgrind */                  if(j==Tage[ij]) { /* Product by age  To be looked at!!*/
                   fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                    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+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */                      if(DummyV[j]==0){
                   ij++;                        fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
                       }else{ /* quantitative */
                         fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
                         /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                       }
                       ij++;
                     }
                   } 
                 }else if(cptcovprod >0){
                   if(j==Tprod[ijp]) { /* */ 
                     /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
                     if(ijp <=cptcovprod) { /* Product */
                       if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
                         if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
                           /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
                           fprintf(ficgp,"+p%d*%d*%d",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++;
                     }
                   } /* end Tprod */
                 } else{  /* simple covariate */
                   /* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
                   if(Dummy[j]==0){
                     fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /*  */
                   }else{ /* quantitative */
                     fprintf(ficgp,"+p%d*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* */
                     /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
                 }                  }
               }                } /* end simple */
               else              } /* end j */
                 fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */  
             }  
           }else{            }else{
             i=i-ncovmodel;              i=i-ncovmodel;
             if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */              if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
Line 6678  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7886  plot [%.f:%.f]  ", ageminpar, agemaxpar)
           if(ng != 1){            if(ng != 1){
             fprintf(ficgp,")/(1");              fprintf(ficgp,")/(1");
                           
             for(k1=1; k1 <=nlstate; k1++){               for(cpt=1; cpt <=nlstate; cpt++){ 
               if(nagesqr==0)                if(nagesqr==0)
                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1);
               else /* nagesqr =1 */                else /* nagesqr =1 */
                 fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);                  fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(cpt-1)*ncovmodel,k3+(cpt-1)*ncovmodel+1,k3+(cpt-1)*ncovmodel+1+nagesqr);
                                 
               ij=1;                ij=1;
               for(j=3; j <=ncovmodel-nagesqr; j++){                for(j=3; j <=ncovmodel-nagesqr; j++){
                 if(ij <=cptcovage) { /* Bug valgrind */                   if(cptcovage >0){ 
                   if((j-2)==Tage[ij]) { /* Bug valgrind */                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);                       if(ij <=cptcovage) { /* Bug valgrind */
                     /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,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+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,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,",");
Line 6714  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7923  plot [%.f:%.f]  ", ageminpar, agemaxpar)
           i=i+ncovmodel;            i=i+ncovmodel;
         } /* end k */          } /* end k */
       } /* end k2 */        } /* end k2 */
       fprintf(ficgp,"\n set out\n");        /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
     } /* end jk */        fprintf(ficgp,"\n set out; unset title;set key default;\n");
       } /* end k1 */
   } /* end ng */    } /* end ng */
   /* avoid: */    /* avoid: */
   fflush(ficgp);     fflush(ficgp); 
Line 6731  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7941  plot [%.f:%.f]  ", ageminpar, agemaxpar)
    int mobilavrange, mob;     int mobilavrange, mob;
    int iage=0;     int iage=0;
   
    double sum=0.;     double sum=0., sumr=0.;
    double age;     double age;
    double *sumnewp, *sumnewm;     double *sumnewp, *sumnewm, *sumnewmr;
    double *agemingood, *agemaxgood; /* Currently identical for all covariates */     double *agemingood, *agemaxgood; 
      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);
      sumnewmr = vector(1,ncovcombmax);
    agemingood = vector(1,ncovcombmax);       agemingood = vector(1,ncovcombmax);  
      agemingoodr = vector(1,ncovcombmax); 
    agemaxgood = vector(1,ncovcombmax);     agemaxgood = vector(1,ncovcombmax);
      agemaxgoodr = vector(1,ncovcombmax);
   
    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
      sumnewm[cptcod]=0.;       sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
      sumnewp[cptcod]=0.;       sumnewp[cptcod]=0.;
      agemingood[cptcod]=0;       agemingood[cptcod]=0, agemingoodr[cptcod]=0;
      agemaxgood[cptcod]=0;       agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
    }     }
    if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */     if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */
       
    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){     if(mobilav==-1 || mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
      if(mobilav==1) mobilavrange=5; /* default */       if(mobilav==1 || mobilav==-1) mobilavrange=5; /* default */
      else mobilavrange=mobilav;       else mobilavrange=mobilav;
      for (age=bage; age<=fage; age++)       for (age=bage; age<=fage; age++)
        for (i=1; i<=nlstate;i++)         for (i=1; i<=nlstate;i++)
Line 6766  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 7980  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      */        */ 
      for (mob=3;mob <=mobilavrange;mob=mob+2){       for (mob=3;mob <=mobilavrange;mob=mob+2){
        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
          for (i=1; i<=nlstate;i++){           for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
            for (cptcod=1;cptcod<=ncovcombmax;cptcod++){             sumnewm[cptcod]=0.;
              for (i=1; i<=nlstate;i++){
              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
              for (cpt=1;cpt<=(mob-1)/2;cpt++){               for (cpt=1;cpt<=(mob-1)/2;cpt++){
                mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];                 mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
              }               }
              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
            }               sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
          }             } /* end i */
              if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
            } /* end cptcod */
        }/* end age */         }/* end age */
      }/* end mob */       }/* end mob */
    }else     }else{
        printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
      return -1;       return -1;
    for (cptcod=1;cptcod<=ncovcombmax;cptcod++){     }
   
      for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
      /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */       /* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
      if(invalidvarcomb[cptcod]){       if(invalidvarcomb[cptcod]){
        printf("\nCombination (%d) ignored because no cases \n",cptcod);          printf("\nCombination (%d) ignored because no cases \n",cptcod); 
        continue;         continue;
      }       }
   
      agemingood[cptcod]=fage-(mob-1)/2;       for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /*looking for the youngest and oldest good age */
      for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */  
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemingoodr[cptcod]=age;
        }         }
        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
          agemingood[cptcod]=age;             agemingood[cptcod]=age;
        }else{ /* bad */         }
          for (i=1; i<=nlstate;i++){       } /* age */
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /*looking for the youngest and oldest good age */
          } /* i */  
        } /* end bad */  
      }/* age */  
      sum=0.;  
      for (i=1; i<=nlstate;i++){  
        sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];  
      }  
      if(fabs(sum - 1.) > 1.e-3) { /* bad */  
        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);  
        /* for (i=1; i<=nlstate;i++){ */  
        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */  
        /* } /\* i *\/ */  
      } /* end bad */  
      /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */  
      /* From youngest, finding the oldest wrong */  
      agemaxgood[cptcod]=bage+(mob-1)/2;  
      for (age=bage+(mob-1)/2; age<=fage; age++){  
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
          sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
            agemaxgoodr[cptcod]=age;
        }         }
        if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */         if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
          agemaxgood[cptcod]=age;           agemaxgood[cptcod]=age;
        }else{ /* bad */         }
          for (i=1; i<=nlstate;i++){       } /* age */
            mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];       /* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
          } /* i */       /* but they will change */
        for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
          sumnewm[cptcod]=0.;
          sumnewmr[cptcod]=0.;
          for (i=1; i<=nlstate;i++){
            sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
            sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
          }
          if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
            if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
              agemaxgoodr[cptcod]=age;  /* age min */
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemaxgood[cptcod]=age;
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=probs[(int)age][i][cptcod];
          }
          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, (int)bage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          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, (int)bage);
        } /* end bad */         } /* end bad */
      }/* age */       }/* age */
      sum=0.;  
      for (i=1; i<=nlstate;i++){       for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
        sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];         sumnewm[cptcod]=0.;
      }         sumnewmr[cptcod]=0.;
      if(fabs(sum - 1.) > 1.e-3) { /* bad */         for (i=1; i<=nlstate;i++){
        printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);           sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
        /* for (i=1; i<=nlstate;i++){ */           sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
        /*   mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */         } 
        /* } /\* i *\/ */         if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
      } /* end bad */           if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingoodr[cptcod]=age;
              for (i=1; i<=nlstate;i++)
                mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
            }else{ /* bad we change the value with the values of good ages */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }else{
            if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
              agemingood[cptcod]=age;
            }else{ /* bad */
              for (i=1; i<=nlstate;i++){
                mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
              } /* i */
            } /* end bad */
          }/* end else */
          sum=0.;sumr=0.;
          for (i=1; i<=nlstate;i++){
            sum+=mobaverage[(int)age][i][cptcod];
            sumr+=mobaverage[(int)age][i][cptcod];
          }
          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, (int)fage);
          } /* end bad */
          /* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
          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, (int)fage);
          } /* end bad */
        }/* age */
   
                                   
      for (age=bage; age<=fage; age++){       for (age=bage; age<=fage; age++){
        printf("%d %d ", cptcod, (int)age);         /* printf("%d %d ", cptcod, (int)age); */
        sumnewp[cptcod]=0.;         sumnewp[cptcod]=0.;
        sumnewm[cptcod]=0.;         sumnewm[cptcod]=0.;
        for (i=1; i<=nlstate;i++){         for (i=1; i<=nlstate;i++){
Line 6851  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 8131  plot [%.f:%.f]  ", ageminpar, agemaxpar)
      }       }
      /* printf("\n"); */       /* printf("\n"); */
      /* } */       /* } */
   
      /* brutal averaging */       /* brutal averaging */
      for (i=1; i<=nlstate;i++){       /* for (i=1; i<=nlstate;i++){ */
        for (age=1; age<=bage; age++){       /*   for (age=1; age<=bage; age++){ */
          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];       /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        }               /*   }      */
        for (age=fage; age<=AGESUP; age++){       /*   for (age=fage; age<=AGESUP; age++){ */
          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];       /*          mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
          /* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */       /*          /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); *\/ */
        }       /*   } */
      } /* end i status */       /* } /\* end i status *\/ */
      for (i=nlstate+1; i<=nlstate+ndeath;i++){       /* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
        for (age=1; age<=AGESUP; age++){       /*   for (age=1; age<=AGESUP; age++){ */
          /*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*/       /*          /\*printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);*\/ */
          mobaverage[(int)age][i][cptcod]=0.;       /*          mobaverage[(int)age][i][cptcod]=0.; */
        }       /*   } */
      }       /* } */
    }/* end cptcod */     }/* end cptcod */
    free_vector(sumnewm,1, ncovcombmax);     free_vector(agemaxgoodr,1, ncovcombmax);
    free_vector(sumnewp,1, ncovcombmax);  
    free_vector(agemaxgood,1, ncovcombmax);     free_vector(agemaxgood,1, ncovcombmax);
    free_vector(agemingood,1, ncovcombmax);     free_vector(agemingood,1, ncovcombmax);
      free_vector(agemingoodr,1, ncovcombmax);
      free_vector(sumnewmr,1, ncovcombmax);
      free_vector(sumnewm,1, ncovcombmax);
      free_vector(sumnewp,1, ncovcombmax);
    return 0;     return 0;
  }/* End movingaverage */   }/* End movingaverage */
     
   
 /************** 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;    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;
Line 6906  void prevforecast(char fileres[], double Line 8190  void prevforecast(char fileres[], double
     printf("Problem with forecast resultfile: %s\n", fileresf);      printf("Problem with forecast resultfile: %s\n", fileresf);
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   }    }
   printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);    printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
   fprintf(ficlog,"Computing 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;
   
Line 6917  void prevforecast(char fileres[], double Line 8201  void prevforecast(char fileres[], double
   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;   
     }
     if(estepm > stepm){ /* Yes every two year */
       stepsize=2;
     }
   
   hstepm=hstepm/stepm;     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
Line 6938  void prevforecast(char fileres[], double Line 8227  void prevforecast(char fileres[], double
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
       
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(k=1;k<=i1;k++){    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]){      if(invalidvarcomb[k]){
       printf("\nCombination (%d) projection ignored because no cases \n",k);         printf("\nCombination (%d) projection ignored because no cases \n",k); 
       continue;        continue;
Line 6947  void prevforecast(char fileres[], double Line 8239  void prevforecast(char fileres[], double
     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(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");      fprintf(ficresf," yearproj age");
     for(j=1; j<=nlstate+ndeath;j++){       for(j=1; j<=nlstate+ndeath;j++){ 
       for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)        
Line 6956  void prevforecast(char fileres[], double Line 8251  void prevforecast(char fileres[], double
     for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {      for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
       fprintf(ficresf,"\n");        fprintf(ficresf,"\n");
       fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
       for (agec=fage; agec>=(ageminpar-1); agec--){         /* for (agec=fage; agec>=(ageminpar-1); agec--){  */
         for (agec=fage; agec>=(bage); agec--){ 
         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);           nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         nhstepm = nhstepm/hstepm;           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);          /* 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++){          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(ficresf,"\n");
           }           for(j=1;j<=cptcoveff;j++) 
           for(j=1; j<=nlstate+ndeath;j++) {            fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
             ppij=0.;          fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             for(i=1; i<=nlstate;i++) {          
               if (mobilav==1)           for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];            ppij=0.;
               else {            for(i=1; i<=nlstate;i++) {
                 ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];              if (mobilav>=1)
               }               ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
               if (h*hstepm/YEARM*stepm== yearp) {              else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
                 fprintf(ficresf," %.3f", p3mat[i][j][h]);                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
               }  
             } /* end i */  
             if (h*hstepm/YEARM*stepm==yearp) {  
               fprintf(ficresf," %.3f", ppij);  
             }              }
           }/* end j */              fprintf(ficresf," %.3f", p3mat[i][j][h]);
         } /* end h */            } /* end i */
             fprintf(ficresf," %.3f", ppij);
           }/* end j */
         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 */
                   
Line 6998  void prevforecast(char fileres[], double Line 8295  void prevforecast(char fileres[], double
   
 }  }
   
 /* /\************** Back Forecasting ******************\/ */  /************** 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){ */   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  */    /* back1, year, month, day of starting backection
 /*      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
 /*      anback2 year of en of backection (same day and month as back1). */       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; */    */
 /*   double agec; /\* generic age *\/ */    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
 /*   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */    double agec; /* generic age */
 /*   double *popeffectif,*popcount; */    double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
 /*   double ***p3mat; */    double *popeffectif,*popcount;
 /*   /\* double ***mobaverage; *\/ */    double ***p3mat;
 /*   char fileresfb[FILENAMELENGTH]; */    /* double ***mobaverage; */
             char fileresfb[FILENAMELENGTH];
 /*   agelim=AGESUP; */   
 /*   /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */    agelim=AGEINF;
 /*      in each health status at the date of interview (if between dateprev1 and dateprev2). */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
 /*      We still use firstpass and lastpass as another selection. */       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); *\/ */    /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
 /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */    /*          firstpass, lastpass,  stepm,  weightopt, model); */
           
 /*   strcpy(fileresfb,"FB_");  */    /*Do we need to compute prevalence again?*/
 /*   strcat(fileresfb,fileresu); */  
 /*   if((ficresfb=fopen(fileresfb,"w"))==NULL) { */    /* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
 /*     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);  */    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);
       
 /*   fprintf(ficresfb,"#****** Routine prevbackforecast **\n"); */    if (cptcoveff==0) ncodemax[cptcoveff]=1;
             
 /*      /\*           if (h==(int)(YEARM*yearp)){ *\/ */     
 /*   for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */    stepsize=(int) (stepm+YEARM-1)/YEARM;
 /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */    if (stepm<=12) stepsize=1;
 /*       k=k+1; */    if(estepm < stepm){
 /*       fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */      printf ("Problem %d lower than %d\n",estepm, stepm);
 /*       for(j=1;j<=cptcoveff;j++) { */    }
 /*                              fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    else{
 /*       } */      hstepm=estepm;   
 /*       fprintf(ficresfb," yearbproj age"); */    }
 /*       for(j=1; j<=nlstate+ndeath;j++){  */    if(estepm >= stepm){ /* Yes every two year */
 /*                              for(i=1; i<=nlstate;i++)               */      stepsize=2;
 /*           fprintf(ficresfb," p%d%d",i,j); */    }
 /*                              fprintf(ficresfb," p.%d",j); */    
 /*       } */    hstepm=hstepm/stepm;
 /*       for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {  */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
 /*                              /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  *\/ */                                 fractional in yp1 */
 /*                              fprintf(ficresfb,"\n"); */    anprojmean=yp;
 /*                              fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);    */    yp2=modf((yp1*12),&yp);
 /*                              for (agec=fage; agec>=(ageminpar-1); agec--){  */    mprojmean=yp;
 /*                                      nhstepm=(int) rint((agelim-agec)*YEARM/stepm);  */    yp1=modf((yp2*30.5),&yp);
 /*                                      nhstepm = nhstepm/hstepm;  */    jprojmean=yp;
 /*                                      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */    if(jprojmean==0) jprojmean=1;
 /*                                      oldm=oldms;savm=savms; */    if(mprojmean==0) jprojmean=1;
 /*                                      hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k);       */    
 /*                                      for (h=0; h<=nhstepm; h++){ */    i1=pow(2,cptcoveff);
 /*                                              if (h*hstepm/YEARM*stepm ==yearp) { */    if (cptcovn < 1){i1=1;}
 /*               fprintf(ficresfb,"\n"); */    
 /*               for(j=1;j<=cptcoveff;j++)  */    fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
 /*                 fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */    printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
 /*                                                      fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm); */    
 /*                                              }  */    fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
 /*                                              for(j=1; j<=nlstate+ndeath;j++) { */    
 /*                                                      ppij=0.; */    for(nres=1; nres <= nresult; nres++) /* For each resultline */
 /*                                                      for(i=1; i<=nlstate;i++) { */    for(k=1; k<=i1;k++){
 /*                                                              if (mobilav==1)  */      if(i1 != 1 && TKresult[nres]!= k)
 /*                                                                      ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; */        continue;
 /*                                                              else { */      if(invalidvarcomb[k]){
 /*                                                                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; */        printf("\nCombination (%d) projection ignored because no cases \n",k); 
 /*                                                              } */        continue;
 /*                                                              if (h*hstepm/YEARM*stepm== yearp) { */      }
 /*                                                                      fprintf(ficresfb," %.3f", p3mat[i][j][h]); */      fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
 /*                                                              } */      for(j=1;j<=cptcoveff;j++) {
 /*                                                      } /\* end i *\/ */        fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
 /*                                                      if (h*hstepm/YEARM*stepm==yearp) { */      }
 /*                                                              fprintf(ficresfb," %.3f", ppij); */      for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
 /*                                                      } */        fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
 /*                                              }/\* end j *\/ */      }
 /*                                      } /\* end h *\/ */      fprintf(ficresfb," yearbproj age");
 /*                                      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */      for(j=1; j<=nlstate+ndeath;j++){
 /*                              } /\* end agec *\/ */        for(i=1; i<=nlstate;i++)
 /*       } /\* end yearp *\/ */          fprintf(ficresfb," b%d%d",i,j);
 /*     } /\* end cptcod *\/ */        fprintf(ficresfb," b.%d",j);
 /*   } /\* end  cptcov *\/ */      }
               for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
 /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */        /* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {  */
                 fprintf(ficresfb,"\n");
 /*   fclose(ficresfb); */        fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
 /*   printf("End of Computing Back forecasting \n"); */        /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
 /*   fprintf(ficlog,"End of Computing Back forecasting\n"); */        /* 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);
           oldm=oldms;savm=savms;
           /* 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++){
             if (h*hstepm/YEARM*stepm ==-yearp) {
               break;
             }
           }
           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(i=1; i<=nlstate+ndeath;i++) {
             ppij=0.;ppi=0.;
             for(j=1; j<=nlstate;j++) {
               /* 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]; */
                 /* } */
               fprintf(ficresfb," %.3f", p3mat[i][j][h]);
             } /* end j */
             if(ppi <0.99){
               printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
               fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
             }
             fprintf(ficresfb," %.3f", ppij);
           }/* end j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         } /* end agec */
       } /* end yearp */
     } /* end k */
     
     /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
     
     fclose(ficresfb);
     printf("End of Computing Back forecasting \n");
     fprintf(ficlog,"End of Computing Back forecasting\n");
                   
 /* } */  }
   
   /* Variance of prevalence limit: varprlim */
    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){
       /*------- Variance of 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 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(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 period prevalence\n");fflush(stdout);
       fprintf(ficlog,"done variance-covariance of 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 7554  int readdata(char datafile[], int firsto Line 8989  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i=0, j=0, n=0, iv=0;    int i=0, j=0, n=0, iv=0, v;
   int lstra;    int lstra;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[MAXLINE], strb[MAXLINE];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   
     DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
     FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
   
     for(v=1; v <=ncovcol;v++){
       DummyV[v]=0;
       FixedV[v]=0;
     }
     for(v=ncovcol+1; v <=ncovcol+nqv;v++){
       DummyV[v]=1;
       FixedV[v]=0;
     }
     for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
       DummyV[v]=0;
       FixedV[v]=1;
     }
     for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
       DummyV[v]=1;
       FixedV[v]=1;
     }
     for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
       printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
       fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
     }
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);      printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
Line 7595  int readdata(char datafile[], int firsto Line 9052  int readdata(char datafile[], int firsto
         if(strb[0]=='.') { /* Missing value */          if(strb[0]=='.') { /* Missing value */
           lval=-1;            lval=-1;
           cotqvar[j][iv][i]=-1; /* 0.0/0.0 */            cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
             cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
           if(isalpha(strb[1])) { /* .m or .d Really Missing value */            if(isalpha(strb[1])) { /* .m or .d Really Missing value */
             printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);              printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);
             fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);              fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value.  Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
Line 7614  int readdata(char datafile[], int firsto Line 9072  int readdata(char datafile[], int firsto
             return 1;              return 1;
           }            }
           cotqvar[j][iv][i]=dval;             cotqvar[j][iv][i]=dval; 
             cotvar[j][ntv+iv][i]=dval; 
         }          }
         strcpy(line,stra);          strcpy(line,stra);
       }/* end loop ntqv */        }/* end loop ntqv */
Line 7827  int readdata(char datafile[], int firsto Line 9286  int readdata(char datafile[], int firsto
   return (1);    return (1);
 }  }
   
 void removespace(char **stri){/*, char stro[]) {*/  void removefirstspace(char **stri){/*, char stro[]) {*/
   char *p1 = *stri, *p2 = *stri;    char *p1 = *stri, *p2 = *stri;
   do    while (*p2 == ' ')
     while (*p2 == ' ')      p2++; 
       p2++;    /* while ((*p1++ = *p2++) !=0) */
   while (*p1++ == *p2++);    /*   ; */
   *stri=p1;     /* do */
     /*   while (*p2 == ' ') */
     /*     p2++; */
     /* while (*p1++ == *p2++); */
     *stri=p2; 
 }  }
   
 int decoderesult ( char resultline[])  int decoderesult ( char resultline[], int nres)
 /**< This routine decode one result line and returns the combination # of dummy covariates only **/  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
 {  {
   int j=0, k=0;    int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
   char resultsav[MAXLINE];    char resultsav[MAXLINE];
     int resultmodel[MAXLINE];
     int modelresult[MAXLINE];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
   removespace(&resultline);    removefirstspace(&resultline);
   printf("decoderesult=%s\n",resultline);    printf("decoderesult:%s\n",resultline);
   
   if (strstr(resultline,"v") !=0){    if (strstr(resultline,"v") !=0){
     printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);      printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 7855  int decoderesult ( char resultline[]) Line 9320  int decoderesult ( char resultline[])
   if (strlen(resultsav) >1){    if (strlen(resultsav) >1){
     j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */      j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
   }    }
     if(j == 0){ /* Resultline but no = */
   for(k=1; k<=j;k++){ /* Loop on total covariates of the model */      TKresult[nres]=0; /* Combination for the nresult and the model */
     cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '       return (0);
                                      resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */    }
     cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */      
     if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
       printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
       fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
     }
     for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
       if(nbocc(resultsav,'=') >1){
          cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' 
                                         resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
          cutl(strc,strd,strb,'=');  /* strb:V4=1 strc=1 strd=V4 */
       }else
         cutl(strc,strd,resultsav,'=');
     Tvalsel[k]=atof(strc); /* 1 */      Tvalsel[k]=atof(strc); /* 1 */
       
     cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;      cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
     Tvarsel[k]=atoi(strc);      Tvarsel[k]=atoi(strc);
     /* Typevarsel[k]=1;  /\* 1 for age product *\/ */      /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
Line 7869  int decoderesult ( char resultline[]) Line 9345  int decoderesult ( char resultline[])
     if (nbocc(stra,'=') >0)      if (nbocc(stra,'=') >0)
       strcpy(resultsav,stra); /* and analyzes it */        strcpy(resultsav,stra); /* and analyzes it */
   }    }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       if(Typevar[k1]==0){ /* Single covariate in model */
         match=0;
         for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
           if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5   */
             modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2  modelresult[3]=3  modelresult[6]=4 modelresult[9]=5 */
             match=1;
             break;
           }
         }
         if(match == 0){
           printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
         }
       }
     }
     /* Checking for missing or useless values in comparison of current model needs */
     for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
       match=0;
       for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         if(Typevar[k1]==0){ /* Single */
           if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4   */
             resultmodel[k1]=k2;  /* resultmodel[2]=1 resultmodel[1]=2  resultmodel[3]=3  resultmodel[6]=4 resultmodel[9]=5 */
             ++match;
           }
         }
       }
       if(match == 0){
         printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
       }else if(match > 1){
         printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
       }
     }
         
     /* We need to deduce which combination number is chosen and save quantitative values */
     /* model line V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     /* result line V4=1 V5=25.1 V3=0  V2=8 V1=1 */
     /* should give a combination of dummy V4=1, V3=0, V1=1 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 5 + (1offset) = 6*/
     /* result line V4=1 V5=24.1 V3=1  V2=8 V1=0 */
     /* should give a combination of dummy V4=1, V3=1, V1=0 => V4*2**(0) + V3*2**(1) + V1*2**(2) = 3 + (1offset) = 4*/
     /*    1 0 0 0 */
     /*    2 1 0 0 */
     /*    3 0 1 0 */ 
     /*    4 1 1 0 */ /* V4=1, V3=1, V1=0 */
     /*    5 0 0 1 */
     /*    6 1 0 1 */ /* V4=1, V3=0, V1=1 */
     /*    7 0 1 1 */
     /*    8 1 1 1 */
     /* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
     /* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
     /* V5*age V5 known which value for nres?  */
     /* Tqinvresult[2]=8 Tqinvresult[1]=25.1  */
     for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
       if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
         k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
         k2=(int)Tvarsel[k3]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         k+=Tvalsel[k3]*pow(2,k4);  /*  Tvalsel[1]=1  */
         Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1)  Tresult[nres][2]=0(V3=0) */
         Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
         Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
         printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
         k4++;;
       }  else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
         k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
         k2q=(int)Tvarsel[k3q]; /*  Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
         Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
         Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
         Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
         printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
         k4q++;;
       }
     }
     
     TKresult[nres]=++k; /* Combination for the nresult and the model */
   return (0);    return (0);
 }  }
 int selected( int kvar){ /* Selected combination of covariates */  
   if(Tvarsel[kvar])  
     return (0);  
   else  
     return(1);  
 }  
 int decodemodel( char model[], int lastobs)  int decodemodel( char model[], int lastobs)
  /**< This routine decodes the model and returns:   /**< This routine decodes the model and returns:
         * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age          * Model  V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
Line 7893  int decodemodel( char model[], int lasto Line 9438  int decodemodel( char model[], int lasto
         * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .          * - Tvard[k]  p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
         */          */
 {  {
   int i, j, k, ks;    int i, j, k, ks, v;
   int  j1, k1, k2, k3, k4;    int  j1, k1, k2, k3, k4;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
Line 7916  int decodemodel( char model[], int lasto Line 9461  int decodemodel( char model[], int lasto
     if ((strpt=strstr(model,"age*age")) !=0){      if ((strpt=strstr(model,"age*age")) !=0){
       printf(" strpt=%s, model=%s\n",strpt, model);        printf(" strpt=%s, model=%s\n",strpt, model);
       if(strpt != model){        if(strpt != model){
                                 printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model);   corresponding column of parameters.\n",model);
                                 fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \          fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
  'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \   'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
  corresponding column of parameters.\n",model); fflush(ficlog);   corresponding column of parameters.\n",model); fflush(ficlog);
                                 return 1;          return 1;
       }        }
       nagesqr=1;        nagesqr=1;
       if (strstr(model,"+age*age") !=0)        if (strstr(model,"+age*age") !=0)
                                 substrchaine(modelsav, model, "+age*age");          substrchaine(modelsav, model, "+age*age");
       else if (strstr(model,"age*age+") !=0)        else if (strstr(model,"age*age+") !=0)
                                 substrchaine(modelsav, model, "age*age+");          substrchaine(modelsav, model, "age*age+");
       else         else 
                                 substrchaine(modelsav, model, "age*age");          substrchaine(modelsav, model, "age*age");
     }else      }else
       nagesqr=0;        nagesqr=0;
     if (strlen(modelsav) >1){      if (strlen(modelsav) >1){
Line 8029  int decodemodel( char model[], int lasto Line 9574  int decodemodel( char model[], int lasto
             cptcovprodnoage++;k1++;              cptcovprodnoage++;k1++;
             cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/              cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
             Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but              Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
                                    because this model-covariate is a construction we invent a new column                                                  because this model-covariate is a construction we invent a new column
                                    which is after existing variables ncovcol+nqv+ntv+nqtv + k1                                                  which is after existing variables ncovcol+nqv+ntv+nqtv + k1
                                    If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2                                                  If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
                                    Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */                                                  Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
             Typevar[k]=2;  /* 2 for double fixed dummy covariates */              Typevar[k]=2;  /* 2 for double fixed dummy covariates */
             cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */              cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */              Tprod[k1]=k;  /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2  */
Line 8099  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9644  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, 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 || Typevar[k]==2)){ /* Simple or product fixed dummy (<=ncovcol) covariates */      if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
         Fixed[k]= 0;
         Dummy[k]= 0;
         ncoveff++;
         ncovf++;
         nsd++;
         modell[k].maintype= FTYPE;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       }else if( Tvar[k] <=ncovcol &&  Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 0;        Dummy[k]= 0;
       ncoveff++;        ncoveff++;
                         modell[k].maintype= FTYPE;        ncovf++;
         modell[k].maintype= FTYPE;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
       TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
       TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */        TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
     }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/ /* Only simple fixed quantitative variable */      }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product Vn*Vm are added in k Only simple fixed quantitative variable */
       Fixed[k]= 0;        Fixed[k]= 0;
       Dummy[k]= 1;        Dummy[k]= 1;
       nqfveff++;        nqfveff++;
                         modell[k].maintype= FTYPE;        modell[k].maintype= FTYPE;
                         modell[k].subtype= FQ;        modell[k].subtype= FQ;
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         ncovf++;
         TvarF[ncovf]=Tvar[k];
         TvarFind[ncovf]=k;
       TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */        TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */        TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
     }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){      }else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
       Fixed[k]= 1;        Fixed[k]= 1;
       Dummy[k]= 0;        Dummy[k]= 0;
       ntveff++; /* Only simple time varying dummy variable */        ntveff++; /* Only simple time varying dummy variable */
                         modell[k].maintype= VTYPE;        modell[k].maintype= VTYPE;
                         modell[k].subtype= VD;        modell[k].subtype= VD;
         nsd++;
         TvarsD[nsd]=Tvar[k];
         TvarsDind[nsd]=k;
         ncovv++; /* Only simple time varying variables */
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[2]=2  TvarVind[3]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
       TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */        TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4  TvarVD[2]=V3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
       TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */        TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying dummy variable */
       printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);        printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
       printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);        printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/      }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
                         Fixed[k]= 1;        Fixed[k]= 1;
                         Dummy[k]= 1;        Dummy[k]= 1;
                         nqtveff++;        nqtveff++;
                         modell[k].maintype= VTYPE;        modell[k].maintype= VTYPE;
                         modell[k].subtype= VQ;        modell[k].subtype= VQ;
         ncovv++; /* Only simple time varying variables */
         nsq++;
         TvarsQ[nsq]=Tvar[k];
         TvarsQind[nsq]=k;
         TvarV[ncovv]=Tvar[k];
         TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Any time varying singele */
       TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */        TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
       TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */        TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple time varying quantitative variable */
                         TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */        TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
                         /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */        /* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable *\/ */
                         printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);        printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
       printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);        printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
     }else if (Typevar[k] == 1) {  /* product with age */      }else if (Typevar[k] == 1) {  /* product with age */
         ncova++;
         TvarA[ncova]=Tvar[k];
         TvarAind[ncova]=k;
       if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */        if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
                                 Fixed[k]= 2;          Fixed[k]= 2;
                                 Dummy[k]= 2;          Dummy[k]= 2;
                                 modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
                                 modell[k].subtype= APFD;          modell[k].subtype= APFD;
                                 /* ncoveff++; */          /* ncoveff++; */
       }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
                                 Fixed[k]= 2;          Fixed[k]= 2;
                                 Dummy[k]= 3;          Dummy[k]= 3;
                                 modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
                                 modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */          modell[k].subtype= APFQ;                /*      Product age * fixed quantitative */
                                 /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv ){        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
                                 Fixed[k]= 3;          Fixed[k]= 3;
                                 Dummy[k]= 2;          Dummy[k]= 2;
                                 modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
                                 modell[k].subtype= APVD;                /*      Product age * varying dummy */          modell[k].subtype= APVD;                /*      Product age * varying dummy */
                                 /* ntveff++; /\* Only simple time varying dummy variable *\/ */          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
                                 Fixed[k]= 3;          Fixed[k]= 3;
                                 Dummy[k]= 3;          Dummy[k]= 3;
                                 modell[k].maintype= ATYPE;          modell[k].maintype= ATYPE;
                                 modell[k].subtype= APVQ;                /*      Product age * varying quantitative */          modell[k].subtype= APVQ;                /*      Product age * varying quantitative */
                                 /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */          /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
       }        }
     }else if (Typevar[k] == 2) {  /* product without age */      }else if (Typevar[k] == 2) {  /* product without age */
       k1=Tposprod[k];        k1=Tposprod[k];
       if(Tvard[k1][1] <=ncovcol){        if(Tvard[k1][1] <=ncovcol){
                                 if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
                                         Fixed[k]= 1;            Fixed[k]= 1;
                                         Dummy[k]= 0;            Dummy[k]= 0;
                                         modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
                                         modell[k].subtype= FPDD;                /*      Product fixed dummy * fixed dummy */            modell[k].subtype= FPDD;              /*      Product fixed dummy * fixed dummy */
                                 }else if(Tvard[k1][2] <=ncovcol+nqv){            ncovf++; /* Fixed variables without age */
                                         Fixed[k]= 0;  /* or 2 ?*/            TvarF[ncovf]=Tvar[k];
                                         Dummy[k]= 1;            TvarFind[ncovf]=k;
                                         modell[k].maintype= FTYPE;          }else if(Tvard[k1][2] <=ncovcol+nqv){
                                         modell[k].subtype= FPDQ;                /*      Product fixed dummy * fixed quantitative */            Fixed[k]= 0;  /* or 2 ?*/
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            Dummy[k]= 1;
                                         Fixed[k]= 1;            modell[k].maintype= FTYPE;
                                         Dummy[k]= 0;            modell[k].subtype= FPDQ;              /*      Product fixed dummy * fixed quantitative */
                                         modell[k].maintype= VTYPE;            ncovf++; /* Varying variables without age */
                                         modell[k].subtype= VPDD;                /*      Product fixed dummy * varying dummy */            TvarF[ncovf]=Tvar[k];
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            TvarFind[ncovf]=k;
                                         Fixed[k]= 1;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                                         Dummy[k]= 1;            Fixed[k]= 1;
                                         modell[k].maintype= VTYPE;            Dummy[k]= 0;
                                         modell[k].subtype= VPDQ;                /*      Product fixed dummy * varying quantitative */            modell[k].maintype= VTYPE;
                                 }             modell[k].subtype= VPDD;              /*      Product fixed dummy * varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product fixed dummy * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
       }else if(Tvard[k1][1] <=ncovcol+nqv){        }else if(Tvard[k1][1] <=ncovcol+nqv){
                                 if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
                                         Fixed[k]= 0;  /* or 2 ?*/            Fixed[k]= 0;  /* or 2 ?*/
                                         Dummy[k]= 1;            Dummy[k]= 1;
                                         modell[k].maintype= FTYPE;            modell[k].maintype= FTYPE;
                                         modell[k].subtype= FPDQ;                /*      Product fixed quantitative * fixed dummy */            modell[k].subtype= FPDQ;              /*      Product fixed quantitative * fixed dummy */
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            ncovf++; /* Fixed variables without age */
                                         Fixed[k]= 1;            TvarF[ncovf]=Tvar[k];
                                         Dummy[k]= 1;            TvarFind[ncovf]=k;
                                         modell[k].maintype= VTYPE;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                                         modell[k].subtype= VPDQ;                /*      Product fixed quantitative * varying dummy */            Fixed[k]= 1;
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            Dummy[k]= 1;
                                         Fixed[k]= 1;            modell[k].maintype= VTYPE;
                                         Dummy[k]= 1;            modell[k].subtype= VPDQ;              /*      Product fixed quantitative * varying dummy */
                                         modell[k].maintype= VTYPE;            ncovv++; /* Varying variables without age */
                                         modell[k].subtype= VPQQ;                /*      Product fixed quantitative * varying quantitative */            TvarV[ncovv]=Tvar[k];
                                 }             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product fixed quantitative * varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
                                 if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
                                         Fixed[k]= 1;            Fixed[k]= 1;
                                         Dummy[k]= 1;            Dummy[k]= 1;
                                         modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
                                         modell[k].subtype= VPDD;                /*      Product time varying dummy * fixed dummy */            modell[k].subtype= VPDD;              /*      Product time varying dummy * fixed dummy */
                                 }else if(Tvard[k1][2] <=ncovcol+nqv){            ncovv++; /* Varying variables without age */
                                         Fixed[k]= 1;            TvarV[ncovv]=Tvar[k];
                                         Dummy[k]= 1;            TvarVind[ncovv]=k;
                                         modell[k].maintype= VTYPE;          }else if(Tvard[k1][2] <=ncovcol+nqv){
                                         modell[k].subtype= VPDQ;                /*      Product time varying dummy * fixed quantitative */            Fixed[k]= 1;
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            Dummy[k]= 1;
                                         Fixed[k]= 1;            modell[k].maintype= VTYPE;
                                         Dummy[k]= 0;            modell[k].subtype= VPDQ;              /*      Product time varying dummy * fixed quantitative */
                                         modell[k].maintype= VTYPE;            ncovv++; /* Varying variables without age */
                                         modell[k].subtype= VPDD;                /*      Product time varying dummy * time varying dummy */            TvarV[ncovv]=Tvar[k];
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            TvarVind[ncovv]=k;
                                         Fixed[k]= 1;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                                         Dummy[k]= 1;            Fixed[k]= 1;
                                         modell[k].maintype= VTYPE;            Dummy[k]= 0;
                                         modell[k].subtype= VPDQ;                /*      Product time varying dummy * time varying quantitative */            modell[k].maintype= VTYPE;
                                 }             modell[k].subtype= VPDD;              /*      Product time varying dummy * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPDQ;              /*      Product time varying dummy * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
       }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
                                 if(Tvard[k1][2] <=ncovcol){          if(Tvard[k1][2] <=ncovcol){
                                         Fixed[k]= 1;            Fixed[k]= 1;
                                         Dummy[k]= 1;            Dummy[k]= 1;
                                         modell[k].maintype= VTYPE;            modell[k].maintype= VTYPE;
                                         modell[k].subtype= VPDQ;                /*      Product time varying quantitative * fixed dummy */            modell[k].subtype= VPDQ;              /*      Product time varying quantitative * fixed dummy */
                                 }else if(Tvard[k1][2] <=ncovcol+nqv){            ncovv++; /* Varying variables without age */
                                         Fixed[k]= 1;            TvarV[ncovv]=Tvar[k];
                                         Dummy[k]= 1;            TvarVind[ncovv]=k;
                                         modell[k].maintype= VTYPE;          }else if(Tvard[k1][2] <=ncovcol+nqv){
                                         modell[k].subtype= VPQQ;                /*      Product time varying quantitative * fixed quantitative */            Fixed[k]= 1;
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){            Dummy[k]= 1;
                                         Fixed[k]= 1;            modell[k].maintype= VTYPE;
                                         Dummy[k]= 1;            modell[k].subtype= VPQQ;              /*      Product time varying quantitative * fixed quantitative */
                                         modell[k].maintype= VTYPE;            ncovv++; /* Varying variables without age */
                                         modell[k].subtype= VPDQ;                /*      Product time varying quantitative * time varying dummy */            TvarV[ncovv]=Tvar[k];
                                 }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){            TvarVind[ncovv]=k;
                                         Fixed[k]= 1;          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
                                         Dummy[k]= 1;            Fixed[k]= 1;
                                         modell[k].maintype= VTYPE;            Dummy[k]= 1;
                                         modell[k].subtype= VPQQ;                /*      Product time varying quantitative * time varying quantitative */            modell[k].maintype= VTYPE;
                                 }             modell[k].subtype= VPDQ;              /*      Product time varying quantitative * time varying dummy */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
             modell[k].maintype= VTYPE;
             modell[k].subtype= VPQQ;              /*      Product time varying quantitative * time varying quantitative */
             ncovv++; /* Varying variables without age */
             TvarV[ncovv]=Tvar[k];
             TvarVind[ncovv]=k;
           }
       }else{        }else{
                                 printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
                                 fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
       } /* end k1 */        } /*end k1*/
     }else{      }else{
       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
Line 8265  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9895  Dummy[k] 0=dummy (0 1), 1 quantitative (
   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] == 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[Tvar[k1]],Dummy[Tvar[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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
                                                 return(1);              return(1);
                                         }            }
                                 }else if (Typevar[k1] ==2){          }else if (Typevar[k1] ==2){
                                         k3=Tposprod[k1];            k3=Tposprod[k1];
                                         k4=Tposprod[k2];            k4=Tposprod[k2];
                                         if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){            if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) || ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
                                                 printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);              printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
                                                 fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);              fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
                                                 return(1);              return(1);
                                         }            }
                                 }          }
       }        }
     }      }
   }    }
   printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
   fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);    fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
     printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
     fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   /*endread:*/    /*endread:*/
   printf("Exiting decodemodel: ");    printf("Exiting decodemodel: ");
Line 8292  Dummy[k] 0=dummy (0 1), 1 quantitative ( Line 9924  Dummy[k] 0=dummy (0 1), 1 quantitative (
 }  }
   
 int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {/* Check ages at death */
   int i, m;    int i, m;
   int firstone=0;    int firstone=0;
       
Line 8307  int calandcheckages(int imx, int maxwav, Line 9939  int calandcheckages(int imx, int maxwav,
         *nberr = *nberr + 1;          *nberr = *nberr + 1;
         if(firstone == 0){          if(firstone == 0){
           firstone=1;            firstone=1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);          printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
         }          }
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);          fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
         s[m][i]=-1;          s[m][i]=-1;  /* Droping the death status */
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         (*nberr)++;          (*nberr)++;
         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);           printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }        }
     }      }
   }    }
Line 8599  void syscompilerinfo(int logged) Line 10231  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  (period or stable prevalence) --------------*/
   int i, j, k, i1 ;    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;
   double tot;    double tot;
Line 8624  int prevalence_limit(double *p, double * Line 10256  int prevalence_limit(double *p, double *
   agelim=agemaxpar;    agelim=agemaxpar;
   
   /* i1=pow(2,ncoveff); */    /* i1=pow(2,ncoveff); */
   i1=pow(2,cptcoveff); /* Number of dummy covariates */    i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(k=1; k<=i1;k++){    for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */      for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */        if(i1 != 1 && TKresult[nres]!= k)
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          continue;
     /* k=k+1; */  
     /* to clean */  
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));  
     fprintf(ficrespl,"#******");  
     printf("#******");  
     fprintf(ficlog,"#******");  
     for(j=1;j<=cptcoveff ;j++) {/* all covariates */  
       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/  
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  
     }  
     fprintf(ficrespl,"******\n");  
     printf("******\n");  
     fprintf(ficlog,"******\n");  
     if(invalidvarcomb[k]){  
       printf("\nCombination (%d) ignored because no case \n",k);   
       fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);   
       fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);   
                                                 continue;  
     }  
   
     fprintf(ficrespl,"#Age ");        /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
     for(j=1;j<=cptcoveff;j++) {        /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
     }        /* k=k+1; */
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);        /* to clean */
     fprintf(ficrespl,"Total Years_to_converge\n");        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"#******");
         printf("#******");
         fprintf(ficlog,"#******");
         for(j=1;j<=cptcoveff ;j++) {/* all covariates */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no case \n",k); 
           fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
           continue;
         }
   
         fprintf(ficrespl,"#Age ");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         }
         for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
         fprintf(ficrespl,"Total Years_to_converge\n");
           
     for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
       /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);          prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
       fprintf(ficrespl,"%.0f ",age );          fprintf(ficrespl,"%.0f ",age );
       for(j=1;j<=cptcoveff;j++)          for(j=1;j<=cptcoveff;j++)
         fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);            fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       tot=0.;          tot=0.;
       for(i=1; i<=nlstate;i++){          for(i=1; i<=nlstate;i++){
         tot +=  prlim[i][i];            tot +=  prlim[i][i];
         fprintf(ficrespl," %.5f", prlim[i][i]);            fprintf(ficrespl," %.5f", prlim[i][i]);
       }          }
       fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);          fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
     } /* Age */        } /* Age */
     /* was end of cptcod */        /* was end of cptcod */
   } /* cptcov */      } /* cptcov */
     } /* nres */
   return 0;    return 0;
 }  }
   
Line 8683  int back_prevalence_limit(double *p, dou Line 10325  int back_prevalence_limit(double *p, dou
         /* 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
          */           */
   int i, j, k, i1 ;    int i, j, k, i1, nres=0 ;
   /* double ftolpl = 1.e-10; */    /* double ftolpl = 1.e-10; */
   double age, agebase, agelim;    double age, agebase, agelim;
   double tot;    double tot;
Line 8714  int back_prevalence_limit(double *p, dou Line 10356  int back_prevalence_limit(double *p, dou
   i1=pow(2,cptcoveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   for(k=1; k<=i1;k++){     for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     fprintf(ficresplb,"#******");       if(i1 != 1 && TKresult[nres]!= k)
     printf("#******");          continue;
     fprintf(ficlog,"#******");        //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
     for(j=1;j<=cptcoveff ;j++) {/* all covariates */        fprintf(ficresplb,"#******");
       fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf("#******");
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficlog,"#******");
       fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        for(j=1;j<=cptcoveff ;j++) {/* all covariates */
     }          fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     fprintf(ficresplb,"******\n");          printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     printf("******\n");          fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     fprintf(ficlog,"******\n");        }
     if(invalidvarcomb[k]){        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
       printf("\nCombination (%d) ignored because no cases \n",k);           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);           fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       continue;        }
     }        fprintf(ficresplb,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
         if(invalidvarcomb[k]){
           printf("\nCombination (%d) ignored because no cases \n",k); 
           fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k); 
           fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
           continue;
         }
           
     fprintf(ficresplb,"#Age ");        fprintf(ficresplb,"#Age ");
     for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     }        }
     for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);        for(i=1; i<=nlstate;i++) fprintf(ficresplb,"  %d-%d   ",i,i);
     fprintf(ficresplb,"Total Years_to_converge\n");        fprintf(ficresplb,"Total Years_to_converge\n");
           
           
     for (age=agebase; age<=agelim; age++){        for (age=agebase; age<=agelim; age++){
       /* for (age=agebase; age<=agebase; age++){ */          /* for (age=agebase; age<=agebase; age++){ */
       if(mobilavproj > 0){          if(mobilavproj > 0){
         /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
         /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
         bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);            bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
       }else if (mobilavproj == 0){          }else if (mobilavproj == 0){
         printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);            printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
         fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);            fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
         exit(1);            exit(1);
       }else{          }else{
         /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */            /* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
         bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);            bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
       }            /* printf("TOTOT\n"); */
       fprintf(ficresplb,"%.0f ",age );            /* exit(1); */
       for(j=1;j<=cptcoveff;j++)          }
         fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"%.0f ",age );
       tot=0.;          for(j=1;j<=cptcoveff;j++)
       for(i=1; i<=nlstate;i++){            fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         tot +=  bprlim[i][i];          tot=0.;
         fprintf(ficresplb," %.5f", bprlim[i][i]);          for(i=1; i<=nlstate;i++){
       }            tot +=  bprlim[i][i];
       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);            fprintf(ficresplb," %.5f", bprlim[i][i]);
     } /* Age */          }
     /* was end of cptcod */          fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
   } /* cptcov */        } /* Age */
           /* was end of cptcod */
         /*fprintf(ficresplb,"\n");*/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
       } /* end of any combination */
     } /* end of nres */  
   /* hBijx(p, bage, fage); */    /* hBijx(p, bage, fage); */
   /* fclose(ficrespijb); */    /* fclose(ficrespijb); */
       
Line 8782  int hPijx(double *p, int bage, int fage) Line 10435  int hPijx(double *p, int bage, int fage)
   int agelim;    int agelim;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, k4, nres=0;
   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 8809  int hPijx(double *p, int bage, int fage) Line 10462  int hPijx(double *p, int bage, int fage)
                 /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */                  /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
                 /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */                  /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
                 /*      k=k+1;  */                  /*      k=k+1;  */
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
           fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
         }
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 8823  int hPijx(double *p, int bage, int fage) Line 10483  int hPijx(double *p, int bage, int fage)
                   
         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,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");          fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
Line 8853  int hPijx(double *p, int bage, int fage) Line 10513  int hPijx(double *p, int bage, int fage)
         int ageminl;          int ageminl;
   int hstepm;    int hstepm;
   int nhstepm;    int nhstepm;
   int h, i, i1, j, k;    int h, i, i1, j, k, nres;
                   
   double agedeb;    double agedeb;
   double ***p3mat;    double ***p3mat;
Line 8876  int hPijx(double *p, int bage, int fage) Line 10536  int hPijx(double *p, int bage, int fage)
       
   /* hstepm=1;   aff par mois*/    /* hstepm=1;   aff par mois*/
   pstamp(ficrespijb);    pstamp(ficrespijb);
   fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");    fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
   i1= pow(2,cptcoveff);    i1= pow(2,cptcoveff);
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */    /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
   /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */    /*    /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
   /*    k=k+1;  */    /*    k=k+1;  */
   for (k=1; k <= (int) pow(2,cptcoveff); k++){    for(nres=1; nres <= nresult; nres++){ /* For each resultline */
     fprintf(ficrespijb,"\n#****** ");      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
     for(j=1;j<=cptcoveff;j++)        if(i1 != 1 && TKresult[nres]!= k)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          continue;
     fprintf(ficrespijb,"******\n");        fprintf(ficrespijb,"\n#****** ");
     if(invalidvarcomb[k]){        for(j=1;j<=cptcoveff;j++)
       fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);           fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       continue;        for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
     }          fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
             }
     /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */        fprintf(ficrespijb,"******\n");
     for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */        if(invalidvarcomb[k]){  /* Is it necessary here? */
       /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */          fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k); 
       nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          continue;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */        }
               
       /*          nhstepm=nhstepm*YEARM; aff par mois*/        /* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months *\/ */
               for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          /* nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /\* Typically 20 years = 20*12/6=40 *\/ */
       /* oldm=oldms;savm=savms; */          nhstepm=(int) rint((agedeb-ageminl)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */          nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
       hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);          
       /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */          /*        nhstepm=nhstepm*YEARM; aff par mois*/
       fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");          
       for(i=1; i<=nlstate;i++)          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
         for(j=1; j<=nlstate+ndeath;j++)          /* and memory limitations if stepm is small */
           fprintf(ficrespijb," %1d-%1d",i,j);  
       fprintf(ficrespijb,"\n");          /* oldm=oldms;savm=savms; */
       for (h=0; h<=nhstepm; h++){          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
         /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/          hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
         fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );          /* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
         /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */          fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
         for(i=1; i<=nlstate;i++)          for(i=1; i<=nlstate;i++)
           for(j=1; j<=nlstate+ndeath;j++)            for(j=1; j<=nlstate+ndeath;j++)
             fprintf(ficrespijb," %.5f", p3mat[i][j][h]);              fprintf(ficrespijb," %1d-%1d",i,j);
         fprintf(ficrespijb,"\n");          fprintf(ficrespijb,"\n");
       }          for (h=0; h<=nhstepm; h++){
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
       fprintf(ficrespijb,"\n");            fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - h*hstepm/YEARM*stepm );
     }            /* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm ); */
     /*}*/            for(i=1; i<=nlstate;i++)
   }              for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
             fprintf(ficrespijb,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespijb,"\n");
         } /* end age deb */
       } /* end combination */
     } /* end nres */
   return 0;    return 0;
  } /*  hBijx */   } /*  hBijx */
   
Line 8949  int main(int argc, char *argv[]) Line 10617  int main(int argc, char *argv[])
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
     int nres=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 8967  int main(int argc, char *argv[]) Line 10639  int main(int argc, char *argv[])
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char model[MAXLINE], modeltemp[MAXLINE];    char  modeltemp[MAXLINE];
   char resultline[MAXLINE];    char resultline[MAXLINE];
       
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
Line 8993  int main(int argc, char *argv[]) Line 10665  int main(int argc, char *argv[])
   double **prlim;    double **prlim;
   double **bprlim;    double **bprlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
   double  *p;    double ***paramstart; /* Matrix of starting parameter values */
     double  *p, *pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
   double **matcov; /* Matrix of covariance */    double **matcov; /* Matrix of covariance */
   double **hess; /* Hessian matrix */    double **hess; /* Hessian matrix */
   double ***delti3; /* Scale */    double ***delti3; /* Scale */
   double *delti; /* Scale */    double *delti; /* Scale */
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   
   double *epj, vepp;    double *epj, vepp;
   
   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 9170  int main(int argc, char *argv[]) Line 10845  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 9201  int main(int argc, char *argv[]) Line 10911  int main(int argc, char *argv[])
       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 9223  int main(int argc, char *argv[]) Line 10934  int main(int argc, char *argv[])
       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
       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 == 0){
             model[0]='\0';        printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
     else if (num_filled != 1){        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%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);        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);        fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
       model[0]='\0';        model[0]='\0';
Line 9280  int main(int argc, char *argv[]) Line 10995  int main(int argc, char *argv[])
   
         
   covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */    covar=matrix(0,NCOVMAX,1,n);  /**< used in readdata */
   coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */    if(nqv>=1)coqvar=matrix(1,nqv,1,n);  /**< Fixed quantitative covariate */
   cotvar=ma3x(1,maxwav,1,ntv,1,n);  /**< Time varying covariate */    if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n);  /**< 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,1,n);  /**< 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 9304  int main(int argc, char *argv[]) Line 11019  int main(int argc, char *argv[])
   delti=delti3[1][1];    delti=delti3[1][1];
   /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
   if(mle==-1){ /* Print a wizard for help writing covariance matrix */    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
   /* We could also provide initial parameters values giving by simple logistic regression 
    * only one way, that is without matrix product. We will have nlstate maximizations */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 9333  int main(int argc, char *argv[]) Line 11054  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
           
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
                         j=0;        j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){        for(jj=1; jj <=nlstate+ndeath; jj++){
                                 if(jj==i) continue;          if(jj==i) continue;
                                 j++;          j++;
                                 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 \
 It might be a problem of design; if ncovcol and the model are correct\n \  It might be a problem of design; if ncovcol and the model are correct\n \
 run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);  run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
                                         exit(1);            exit(1);
                                 }          }
                                 fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
                                 if(mle==1)          if(mle==1)
                                         printf("%1d%1d",i,jj);            printf("%1d%1d",i,jj);
                                 fprintf(ficlog,"%1d%1d",i,jj);          fprintf(ficlog,"%1d%1d",i,jj);
                                 for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
                                         fscanf(ficpar," %lf",&param[i][j][k]);            fscanf(ficpar," %lf",&param[i][j][k]);
                                         if(mle==1){            if(mle==1){
                                                 printf(" %lf",param[i][j][k]);              printf(" %lf",param[i][j][k]);
                                                 fprintf(ficlog," %lf",param[i][j][k]);              fprintf(ficlog," %lf",param[i][j][k]);
                                         }            }
                                         else            else
                                                 fprintf(ficlog," %lf",param[i][j][k]);              fprintf(ficlog," %lf",param[i][j][k]);
                                         fprintf(ficparo," %lf",param[i][j][k]);            fprintf(ficparo," %lf",param[i][j][k]);
                                 }          }
                                 fscanf(ficpar,"\n");          fscanf(ficpar,"\n");
                                 numlinepar++;          numlinepar++;
                                 if(mle==1)          if(mle==1)
                                         printf("\n");            printf("\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
                                 fprintf(ficparo,"\n");          fprintf(ficparo,"\n");
       }        }
     }        }  
     fflush(ficlog);      fflush(ficlog);
       
     /* Reads scales values */      /* Reads parameters values */
     p=param[1][1];      p=param[1][1];
       pstart=paramstart[1][1];
           
     /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
Line 9385  run imach with mle=-1 to get a correct t Line 11108  run imach with mle=-1 to get a correct t
   
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
                                 fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
                                 if ( (i1-i) * (j1-j) != 0){          if ( (i1-i) * (j1-j) != 0){
                                         printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
                                         exit(1);            exit(1);
                                 }          }
                                 printf("%1d%1d",i,j);          printf("%1d%1d",i,j);
                                 fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(ficparo,"%1d%1d",i1,j1);
                                 fprintf(ficlog,"%1d%1d",i1,j1);          fprintf(ficlog,"%1d%1d",i1,j1);
                                 for(k=1; k<=ncovmodel;k++){          for(k=1; k<=ncovmodel;k++){
                                         fscanf(ficpar,"%le",&delti3[i][j][k]);            fscanf(ficpar,"%le",&delti3[i][j][k]);
                                         printf(" %le",delti3[i][j][k]);            printf(" %le",delti3[i][j][k]);
                                         fprintf(ficparo," %le",delti3[i][j][k]);            fprintf(ficparo," %le",delti3[i][j][k]);
                                         fprintf(ficlog," %le",delti3[i][j][k]);            fprintf(ficlog," %le",delti3[i][j][k]);
                                 }          }
                                 fscanf(ficpar,"\n");          fscanf(ficpar,"\n");
                                 numlinepar++;          numlinepar++;
                                 printf("\n");          printf("\n");
                                 fprintf(ficparo,"\n");          fprintf(ficparo,"\n");
                                 fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
       }        }
     }      }
     fflush(ficlog);      fflush(ficlog);
                       
     /* Reads covariance matrix */      /* Reads covariance matrix */
     delti=delti3[1][1];      delti=delti3[1][1];
                                   
Line 9473  Please run with mle=-1 to get a correct Line 11196  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
Line 9497  Please run with mle=-1 to get a correct Line 11210  Please run with mle=-1 to get a correct
   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[i]=0;      num[i]=0;
                 moisnais[i]=0;      moisnais[i]=0;
                 annais[i]=0;      annais[i]=0;
                 moisdc[i]=0;      moisdc[i]=0;
                 andc[i]=0;      andc[i]=0;
                 agedc[i]=0;      agedc[i]=0;
                 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,1,n);
   anint=matrix(1,maxwav,1,n);    anint=matrix(1,maxwav,1,n);
   s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */     s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */ 
Line 9518  Please run with mle=-1 to get a correct Line 11231  Please run with mle=-1 to get a correct
     goto end;      goto end;
   
   /* Calculation of the number of parameters from char model */    /* Calculation of the number of parameters from char model */
     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4     /*    modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 
         k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4          k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
         k=3 V4 Tvar[k=3]= 4 (from V4)          k=3 V4 Tvar[k=3]= 4 (from V4)
         k=2 V1 Tvar[k=2]= 1 (from V1)          k=2 V1 Tvar[k=2]= 1 (from V1)
         k=1 Tvar[1]=2 (from V2)          k=1 Tvar[1]=2 (from V2)
     */    */
     
         Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */    Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
     TvarsDind=ivector(1,NCOVMAX); /*  */
     TvarsD=ivector(1,NCOVMAX); /*  */
     TvarsQind=ivector(1,NCOVMAX); /*  */
     TvarsQ=ivector(1,NCOVMAX); /*  */
     TvarF=ivector(1,NCOVMAX); /*  */
     TvarFind=ivector(1,NCOVMAX); /*  */
     TvarV=ivector(1,NCOVMAX); /*  */
     TvarVind=ivector(1,NCOVMAX); /*  */
     TvarA=ivector(1,NCOVMAX); /*  */
     TvarAind=ivector(1,NCOVMAX); /*  */
   TvarFD=ivector(1,NCOVMAX); /*  */    TvarFD=ivector(1,NCOVMAX); /*  */
   TvarFDind=ivector(1,NCOVMAX); /*  */    TvarFDind=ivector(1,NCOVMAX); /*  */
   TvarFQ=ivector(1,NCOVMAX); /*  */    TvarFQ=ivector(1,NCOVMAX); /*  */
Line 9536  Please run with mle=-1 to get a correct Line 11259  Please run with mle=-1 to get a correct
   TvarVQind=ivector(1,NCOVMAX); /*  */    TvarVQind=ivector(1,NCOVMAX); /*  */
   
   Tvalsel=vector(1,NCOVMAX); /*  */    Tvalsel=vector(1,NCOVMAX); /*  */
     Tvarsel=ivector(1,NCOVMAX); /*  */
   Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */    Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
   Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */    Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
   Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */    Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
Line 9624  Please run with mle=-1 to get a correct Line 11348  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 */
     
   free_vector(moisdc,1,n);    free_vector(moisdc,1,n);
   free_vector(andc,1,n);    free_vector(andc,1,n);
Line 9805  Title=%s <br>Datafile=%s Firstpass=%d La Line 11529  Title=%s <br>Datafile=%s Firstpass=%d La
   /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age 
                  and for any valid combination of covariates                   and for any valid combination of covariates
      and prints on file fileres'p'. */       and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \    freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
               firstpass, lastpass,  stepm,  weightopt, model);                firstpass, lastpass,  stepm,  weightopt, model);
   
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   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=%f \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) 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 quantitative time varying 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 9827  Interval (in months) between two waves: Line 11572  Interval (in months) between two waves:
   /* For mortality only */    /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
                 for(i=1;i<=NDIM;i++)      for(i=1;i<=NDIM;i++)
                         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(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
Line 10065  Please run with mle=-1 to get a correct Line 11810  Please run with mle=-1 to get a correct
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2, Real Maximization */      if(mle>=1){ /* Could be 1 or 2, Real Maximization */
       /* mlikeli uses func not funcone */        /* mlikeli uses func not funcone */
         /* for(i=1;i<nlstate;i++){ */
         /*        /\*reducing xi for 1 to npar to 1 to ncovmodel; *\/ */
         /*    mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
         /* } */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
     if(mle==0) {/* No optimization, will print the likelihoods for the datafile */      if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Line 10280  Please run with mle=-1 to get a correct Line 12029  Please run with mle=-1 to get a correct
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
                                   
     /* Other stuffs, more or less useful */          /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while(fgets(line, MAXLINE, ficpar)) {
       ungetc(c,ficpar);        /* If line starts with a # it is a comment */
       fgets(line, MAXLINE, ficpar);        if (line[0] == '#') {
       fputs(line,stdout);          numlinepar++;
       fputs(line,ficparo);          fputs(line,stdout);
     }          fputs(line,ficparo);
     ungetc(c,ficpar);          fputs(line,ficlog);
               continue;
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        }else
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          break;
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
       
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       fputs(line,stdout);  
       fputs(line,ficparo);  
     }  
     ungetc(c,ficpar);  
       
       
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;  
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;  
       
     fscanf(ficpar,"pop_based=%d\n",&popbased);  
     fprintf(ficlog,"pop_based=%d\n",popbased);  
     fprintf(ficparo,"pop_based=%d\n",popbased);     
     fprintf(ficres,"pop_based=%d\n",popbased);     
       
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);  
       fputs(line,stdout);  
       fputs(line,ficparo);  
     }      }
     ungetc(c,ficpar);  
           if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
     fscanf(ficpar,"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(ficparo,"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);        if (num_filled != 7) {
     printf("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);          printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     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,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004  mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
     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);          goto end;
     /* day and month of proj2 are not used but only year anproj2.*/        }
             printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       ungetc(c,ficpar);        fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fputs(line,stdout);  
       fputs(line,ficparo);  
     }      }
     ungetc(c,ficpar);  
       
     fscanf(ficpar,"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(ficparo,"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);  
     /* day and month of proj2 are not used but only year anproj2.*/  
       
     /* Results */  
     while(fgets(line, MAXLINE, ficpar)) {      while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */        /* If line starts with a # it is a comment */
       if (line[0] == '#') {        if (line[0] == '#') {
Line 10352  Please run with mle=-1 to get a correct Line 12065  Please run with mle=-1 to get a correct
       }else        }else
         break;          break;
     }      }
     while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){      
       if (num_filled == 0)      
         resultline[0]='\0';      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       else if (num_filled != 1){      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
         printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);      
       }      if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
       printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);        if (num_filled != 1) {
       decoderesult(resultline);          printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
       while(fgets(line, MAXLINE, ficpar)) {          fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
         /* If line starts with a # it is a comment */          goto end;
         if (line[0] == '#') {  
           numlinepar++;  
           fputs(line,stdout);  
           fputs(line,ficparo);  
           fputs(line,ficlog);  
           continue;  
         }else  
           break;  
       }        }
       if (feof(ficpar))        printf("pop_based=%d\n",popbased);
         break;        fprintf(ficlog,"pop_based=%d\n",popbased);
       else{ /* Processess output results for this combination of covariate values */        fprintf(ficparo,"pop_based=%d\n",popbased);   
       }                                    fprintf(ficres,"pop_based=%d\n",popbased);   
     }      }
        
       /* Results */
       nresult=0;
       do{
         if(!fgets(line, MAXLINE, ficpar)){
           endishere=1;
           parameterline=14;
         }else if (line[0] == '#') {
           /* If line starts with a # it is a comment */
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
           parameterline=11;
         else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
           parameterline=12;
         else if(sscanf(line,"result:%[^\n]\n",modeltemp))
           parameterline=13;
         else{
           parameterline=14;
         }
         switch (parameterline){ 
         case 11:
           if((num_filled=sscanf(line,"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)) !=EOF){
             if (num_filled != 8) {
               printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             fprintf(ficparo,"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);
             printf("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);
             /* 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;
         case 12:
           /*fscanf(ficpar,"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);*/
           if((num_filled=sscanf(line,"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)) !=EOF){
             if (num_filled != 8) {
               printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
               goto end;
             }
             printf("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(ficparo,"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);
             /* 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;
         case 13:
           if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
             if (num_filled == 0){
               resultline[0]='\0';
               printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
               break;
             } else if (num_filled != 1){
               printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
               fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
             }
             nresult++; /* Sum of resultlines */
             printf("Result %d: result=%s\n",nresult, resultline);
             if(nresult > MAXRESULTLINES){
               printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
               goto end;
             }
             decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
             fprintf(ficparo,"result: %s\n",resultline);
             fprintf(ficres,"result: %s\n",resultline);
             fprintf(ficlog,"result: %s\n",resultline);
             break;
           case 14: 
             if(ncovmodel >2 && nresult==0 ){
               printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
               goto end;
             }
             break;
           default:
             nresult=1;
             decoderesult(".",nresult ); /* No covariate */
           }
         } /* End switch parameterline */
       }while(endishere==0); /* End do */
           
     /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */      /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
     /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */      /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
Line 10391  Please run with mle=-1 to get a correct Line 12187  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);        /* 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,prevfcast,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 10431  Please run with mle=-1 to get a correct Line 12228  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;
       if (mobilav!=0) {        if (mobilav!=0) {
           printf("Movingaveraging observed prevalence\n");
           fprintf(ficlog,"Movingaveraging observed prevalence\n");
         if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){          if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
           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) {
       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */          printf("Movingaveraging projected observed prevalence\n");
       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */          fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
       else if (mobilavproj !=0) {  
         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 10475  Please run with mle=-1 to get a correct Line 12279  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 10508  Please run with mle=-1 to get a correct Line 12316  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);      printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
   
       pstamp(ficreseij);
                                   
     for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       if (cptcovn < 1){i1=1;}
       
       for(nres=1; nres <= nresult; nres++) /* For each resultline */
       for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
         if(i1 != 1 && TKresult[nres]!= k)
           continue;
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
         printf("\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficreseij,"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(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
         printf("******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);          evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);  
               
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     }      }
     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 10537  Please run with mle=-1 to get a correct Line 12360  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 10566  Please run with mle=-1 to get a correct Line 12387  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++){      i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/      if (cptcovn < 1){i1=1;}
                 
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for(nres=1; nres <= nresult; nres++) /* For each resultline */
       printf("\n#****** ");      for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
       fprintf(ficrest,"\n#****** ");        if(i1 != 1 && TKresult[nres]!= k)
       fprintf(ficlog,"\n#****** ");          continue;
         printf("\n#****** Result for:");
         fprintf(ficrest,"\n#****** Result for:");
         fprintf(ficlog,"\n#****** Result for:");
       for(j=1;j<=cptcoveff;j++){         for(j=1;j<=cptcoveff;j++){ 
         printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
       fprintf(ficlog,"******\n");        fprintf(ficlog,"******\n");
       printf("******\n");        printf("******\n");
Line 10588  Please run with mle=-1 to get a correct Line 12417  Please run with mle=-1 to get a correct
         fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
           fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
               
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
         /* pstamp(ficresvij); */
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
         for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
           fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
         } 
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
               
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;        oldm=oldms;savm=savms;
       printf(" cvevsij combination#=%d, ",k);        printf(" cvevsij ");
       fprintf(ficlog, " cvevsij combination#=%d, ",k);        fprintf(ficlog, " cvevsij ");
       cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);        cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
       printf(" end cvevsij \n ");        printf(" end cvevsij \n ");
       fprintf(ficlog, " end cvevsij \n ");        fprintf(ficlog, " end cvevsij \n ");
               
Line 10611  Please run with mle=-1 to get a correct Line 12448  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 */
         printf("varevsij vpopbased=%d \n",vpopbased);          printf("varevsij vpopbased=%d \n",vpopbased);
         fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);          fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
         fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");          fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
         if(vpopbased==1)          if(vpopbased==1)
           fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);            fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
Line 10627  Please run with mle=-1 to get a correct Line 12464  Please run with mle=-1 to get a correct
         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 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 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); /*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) {
             if(mobilav ==0){              if(mobilav ==0){
               for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
Line 10665  Please run with mle=-1 to get a correct Line 12501  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 \n");fflush(stdout);        fprintf(ficlog,"done selection\n");fflush(ficlog);
       fprintf(ficlog,"done\n");fflush(ficlog);  
               
       /*}*/      } /* End k selection */
     } /* End k */  
   
     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 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++){*/  
       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){  
       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)]);  
       }  
       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);  
       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
       /*}*/  
     }  
       
     fclose(ficresvpl);  
     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_vector(weight,1,n);
     free_imatrix(Tvard,1,NCOVMAX,1,2);      free_imatrix(Tvard,1,NCOVMAX,1,2);
Line 10731  Please run with mle=-1 to get a correct Line 12532  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 10740  Please run with mle=-1 to get a correct Line 12541  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,1,n);
   free_ma3x(cotvar,1,maxwav,1,ntv,1,n);    if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
   free_matrix(coqvar,1,maxwav,1,n);    if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
   free_matrix(covar,0,NCOVMAX,1,n);    free_matrix(covar,0,NCOVMAX,1,n);
   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);
   free_ivector(ncodemaxwundef,1,NCOVMAX);    free_ivector(ncodemaxwundef,1,NCOVMAX);
   free_ivector(Dummy,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
   free_ivector(Fixed,-1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(DummyV,1,NCOVMAX);
     free_ivector(FixedV,1,NCOVMAX);
   free_ivector(Typevar,-1,NCOVMAX);    free_ivector(Typevar,-1,NCOVMAX);
   free_ivector(Tvar,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
     free_ivector(TvarsQ,1,NCOVMAX);
     free_ivector(TvarsQind,1,NCOVMAX);
     free_ivector(TvarsD,1,NCOVMAX);
     free_ivector(TvarsDind,1,NCOVMAX);
   free_ivector(TvarFD,1,NCOVMAX);    free_ivector(TvarFD,1,NCOVMAX);
   free_ivector(TvarFDind,1,NCOVMAX);    free_ivector(TvarFDind,1,NCOVMAX);
     free_ivector(TvarF,1,NCOVMAX);
     free_ivector(TvarFind,1,NCOVMAX);
     free_ivector(TvarV,1,NCOVMAX);
     free_ivector(TvarVind,1,NCOVMAX);
     free_ivector(TvarA,1,NCOVMAX);
     free_ivector(TvarAind,1,NCOVMAX);
   free_ivector(TvarFQ,1,NCOVMAX);    free_ivector(TvarFQ,1,NCOVMAX);
   free_ivector(TvarFQind,1,NCOVMAX);    free_ivector(TvarFQind,1,NCOVMAX);
   free_ivector(TvarVD,1,NCOVMAX);    free_ivector(TvarVD,1,NCOVMAX);

Removed from v.1.231  
changed lines
  Added in v.1.278


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