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version 1.225, 2016/07/12 08:40:03 version 1.230, 2016/08/22 06:55:53
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 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.230  2016/08/22 06:55:53  brouard
     Summary: Not working
   
     Revision 1.229  2016/07/23 09:45:53  brouard
     Summary: Completing for func too
   
     Revision 1.228  2016/07/22 17:45:30  brouard
     Summary: Fixing some arrays, still debugging
   
     Revision 1.226  2016/07/12 18:42:34  brouard
     Summary: temp
   
   Revision 1.225  2016/07/12 08:40:03  brouard    Revision 1.225  2016/07/12 08:40:03  brouard
   Summary: saving but not running    Summary: saving but not running
   
Line 636 Line 648
   
   Short summary of the programme:    Short summary of the programme:
       
   This program computes Healthy Life Expectancies from    This program computes Healthy Life Expectancies or State-specific
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (if states aren't health statuses) Expectancies from
   first survey ("cross") where individuals from different ages are    cross-longitudinal data. Cross-longitudinal data consist in: 
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    -1- a first survey ("cross") where individuals from different ages
   second wave of interviews ("longitudinal") which measure each change    are interviewed on their health status or degree of disability (in
   (if any) in individual health status.  Health expectancies are    the case of a health survey which is our main interest)
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    -2- at least a second wave of interviews ("longitudinal") which
   Maximum Likelihood of the parameters involved in the model.  The    measure each change (if any) in individual health status.  Health
   simplest model is the multinomial logistic model where pij is the    expectancies are computed from the time spent in each health state
   probability to be observed in state j at the second wave    according to a model. More health states you consider, more time is
   conditional to be observed in state i at the first wave. Therefore    necessary to reach the Maximum Likelihood of the parameters involved
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    in the model.  The simplest model is the multinomial logistic model
   'age' is age and 'sex' is a covariate. If you want to have a more    where pij is the probability to be observed in state j at the second
   complex model than "constant and age", you should modify the program    wave conditional to be observed in state i at the first
   where the markup *Covariates have to be included here again* invites    wave. Therefore the model is: log(pij/pii)= aij + bij*age+ cij*sex +
   you to do it.  More covariates you add, slower the    etc , where 'age' is age and 'sex' is a covariate. If you want to
     have a more complex model than "constant and age", you should modify
     the program where the markup *Covariates have to be included here
     again* invites you to do it.  More covariates you add, slower the
   convergence.    convergence.
   
   The advantage of this computer programme, compared to a simple    The advantage of this computer programme, compared to a simple
Line 675 Line 690
   of the life expectancies. It also computes the period (stable) prevalence.    of the life expectancies. It also computes the period (stable) prevalence.
   
 Back prevalence and projections:  Back prevalence and projections:
  - back_prevalence_limit(double *p, double **bprlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj)  
     Computes the back prevalence limit  for any combination     of covariate values k   - back_prevalence_limit(double *p, double **bprlim, double ageminpar,
     at any age between ageminpar and agemaxpar and returns it in **bprlim. In the loops,     double agemaxpar, double ftolpl, int *ncvyearp, double
    - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm, **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);     dateprev1,double dateprev2, int firstpass, int lastpass, int
  - hBijx Back Probability to be in state i at age x-h being in j at x     mobilavproj)
   
       Computes the back prevalence limit for any combination of
       covariate values k at any age between ageminpar and agemaxpar and
       returns it in **bprlim. In the loops,
   
      - **bprevalim(**bprlim, ***mobaverage, nlstate, *p, age, **oldm,
          **savm, **dnewm, **doldm, **dsavm, ftolpl, ncvyearp, k);
   
      - hBijx Back Probability to be in state i at age x-h being in j at x
    Computes for any combination of covariates k and any age between bage and fage      Computes for any combination of covariates k and any age between bage and 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;
          - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      - hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
      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
      nhstepm*hstepm matrices. Returns p3mat[i][j][h] after calling        nhstepm*hstepm matrices. 
      p3mat[i][j][h]=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\  
                                                                          1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);       Returns p3mat[i][j][h] after calling
        p3mat[i][j][h]=matprod2(newm,
        bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm,
        dsavm,ij),\ 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
        oldm);
   
   Important routines
   
   - func (or funcone), computes logit (pij) distinguishing
     o fixed variables (single or product dummies or quantitative);
     o varying variables by:
      (1) wave (single, product dummies, quantitative), 
      (2) by age (can be month) age (done), age*age (done), age*Vn where Vn can be:
          % fixed dummy (treated) or quantitative (not done because time-consuming);
          % varying dummy (not done) or quantitative (not done);
   - Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
     and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
   - printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
     o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
       race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.
   
   
     
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
            Institut national d'études démographiques, Paris.             Institut national d'études démographiques, Paris.
   This software have been partly granted by Euro-REVES, a concerted action    This software have been partly granted by Euro-REVES, a concerted action
Line 761  Back prevalence and projections: Line 807  Back prevalence and projections:
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   #include <ctype.h>
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
Line 886  int **dh; /* dh[mi][i] is number of step Line 933  int **dh; /* dh[mi][i] is number of step
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 int countcallfunc=0;  /* Count the number of calls to func */  int countcallfunc=0;  /* Count the number of calls to func */
   int selected(int kvar); /* Is covariate kvar selected for printing results */
   
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
Line 1015  double ***cotvar; /* Time varying covari Line 1064  double ***cotvar; /* Time varying covari
 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 */
 int *Typevar; /**< 1 for qualitative fixed, 2 for quantitative fixed, 3 for qualitive varying, 4 for quanti varying*/  int *Tvarsel; /**< Selected covariates for output */
   double *Tvalsel; /**< Selected modality value of covariate for output */
   int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
   int *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 *Tage;  int *Tage;
   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 *TmodelInvind; /** 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 *TmodelInvQind; /** Tmodelqind[1]=1 for V5(quantitative varying) 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 *Ndum; /** Freq of modality (tricode */  int *Ndum; /** Freq of modality (tricode */
 /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */  /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
 int **Tvard, *Tprod, cptcovprod, *Tvaraff, *invalidvarcomb;  int **Tvard;
   int *Tprod;/**< Gives the k position of the k1 product */
   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)
      Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2 
   */
   int cptcovprod, *Tvaraff, *invalidvarcomb;
 double *lsurv, *lpop, *tpop;  double *lsurv, *lpop, *tpop;
   
 double ftol=FTOL; /**< Tolerance for computing Max Likelihood */  double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
Line 2731  double ***hpxij(double ***po, int nhstep Line 2795  double ***hpxij(double ***po, int nhstep
       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 */        for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
                                 /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
                                 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,k)]*cov[2];
                         /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */        /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
       for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */        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])]; */        /* 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]);*/
                         /* right multiplication of oldm by the current matrix */                          /* right multiplication of oldm by the current matrix */
Line 2890  double ***hbxij(double ***po, int nhstep Line 2954  double ***hbxij(double ***po, int nhstep
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
         int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
         int ioffset=0;    int ioffset=0;
         double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
         double **out;    double **out;
         double sw; /* Sum of weights */    double lli; /* Individual log likelihood */
         double lli; /* Individual log likelihood */    int s1, s2;
         int s1, s2;    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
         int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quatitative time varying covariate */    double bbh, survp;
         double bbh, survp;    long ipmx;
         long ipmx;    double agexact;
         double agexact;    /*extern weight */
         /*extern weight */    /* We are differentiating ll according to initial status */
         /* We are differentiating ll according to initial status */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*for(i=1;i<imx;i++) 
         /*for(i=1;i<imx;i++)       printf(" %d\n",s[4][i]);
                 printf(" %d\n",s[4][i]);    */
         */  
   
         ++countcallfunc;    ++countcallfunc;
   
         cov[1]=1.;    cov[1]=1.;
   
         for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ioffset=0;    ioffset=0;
         if(mle==1){    if(mle==1){
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         /* Computes the values of the ncovmodel covariates of the model        /* Computes the values of the ncovmodel covariates of the model
                                  depending if the covariates are fixed or varying (age dependent) and stores them in cov[]           depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
                                  Then computes with function pmij which return a matrix p[i][j] giving the elementary probability           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+cptcovage;
                         /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */        /* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products *\/ */
                         for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */        for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */
                                 cov[++ioffset]=covar[Tvar[k]][i];          cov[++ioffset]=covar[Tvar[k]][i];
                         }        }
                         for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */        for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
                                 cov[++ioffset]=coqvar[iqv][i];          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 */
                         /* For an individual i, wav[i] gives the number of effective waves */        /* For an individual i, wav[i] gives the number of effective waves */
                         /* We compute the contribution to Likelihood of each effective transition        /* We compute the contribution to Likelihood of each effective transition
                                  mw[mi][i] is real wave of the mi th effectve wave */           mw[mi][i] is real wave of the mi th effectve wave */
                         /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];        /* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
                                  s2=s[mw[mi+1][i]][i];           s2=s[mw[mi+1][i]][i];
                                  And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]           And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]
                                  But if the variable is not in the model TTvar[iv] is the real variable effective in the model:           But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
                                  meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]           meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
                         */        */
                         for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */          for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
                                         cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];            /* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? *\/ */
                                 }            cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
                                 for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */          }
                                         if(cotqvar[mw[mi][i]][iqtv][i] == -1){          for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
                                                 printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);            if(cotqvar[mw[mi][i]][iqtv][i] == -1){
                                         }              printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);
                                         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];            }
                                 }            cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];
                                 /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */            /* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */
                                 for (ii=1;ii<=nlstate+ndeath;ii++)          }
                                         for (j=1;j<=nlstate+ndeath;j++){          /* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */
                                                 oldm[ii][j]=(ii==j ? 1.0 : 0.0);          for (ii=1;ii<=nlstate+ndeath;ii++)
                                                 savm[ii][j]=(ii==j ? 1.0 : 0.0);            for (j=1;j<=nlstate+ndeath;j++){
                                         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                                 for(d=0; d<dh[mi][i]; d++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                                         newm=savm;            }
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;          for(d=0; d<dh[mi][i]; d++){
                                         cov[2]=agexact;            newm=savm;
                                         if(nagesqr==1)            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                                 cov[3]= agexact*agexact;  /* Should be changed here */            cov[2]=agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            if(nagesqr==1)
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */              cov[3]= agexact*agexact;  /* Should be changed here */
                                         }            for (kk=1; kk<=cptcovage;kk++) {
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
                                                                                          1,nlstate+ndeath,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));
                                 } /* end mult */            savm=oldm;
             oldm=newm;
           } /* end mult */
                                                                   
                                         /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
                                 /* But now since version 0.9 we anticipate for bias at large stepm.          /* But now since version 0.9 we anticipate for bias at large stepm.
                                  * If stepm is larger than one month (smallest stepm) and if the exact delay            * If stepm is larger than one month (smallest stepm) and if the exact delay 
                                  * (in months) between two waves is not a multiple of stepm, we rounded to            * (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           * 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           * 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           * (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           * 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 3037  double func( double *x) Line 3102  double func( double *x)
 /*        else */  /*        else */
 /*          lli=log(out[s1][s2] - savm[s1][s2]); */  /*          lli=log(out[s1][s2] - savm[s1][s2]); */
 /* #endif */  /* #endif */
                                         lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
                       
                                 } else if  ( s2==-1 ) { /* alive */          } else if  ( s2==-1 ) { /* alive */
                                         for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         /*survp += out[s1][j]; */            /*survp += out[s1][j]; */
                                         lli= log(survp);            lli= log(survp);
                                 }          }
                                 else if  (s2==-4) {           else if  (s2==-4) { 
                                         for (j=3,survp=0. ; j<=nlstate; j++)              for (j=3,survp=0. ; j<=nlstate; j++)  
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         lli= log(survp);             lli= log(survp); 
                                 }           } 
                                 else if  (s2==-5) {           else if  (s2==-5) { 
                                         for (j=1,survp=0. ; j<=2; j++)              for (j=1,survp=0. ; j<=2; j++)  
                                                 survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
                                         lli= log(survp);             lli= log(survp); 
                                 }           } 
                                 else{          else{
                                         lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                                         /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                                 }           } 
                                 /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                                 /*if(lli ==000.0)*/          /*if(lli ==000.0)*/
                                 /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                                 /* if (lli < log(mytinydouble)){ */          /* if (lli < log(mytinydouble)){ */
                                 /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */          /*   printf("Close to inf lli = %.10lf <  %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
                                 /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */          /*   fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
                                 /* } */          /* } */
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }  else if(mle==2){    }  else if(mle==2){
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         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(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 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);
                                         }            }
                                 for(d=0; d<=dh[mi][i]; d++){          for(d=0; d<=dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            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];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }  else if(mle==3){  /* exponential inter-extrapolation */    }  else if(mle==3){  /* exponential inter-extrapolation */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         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(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 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);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            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];
                                 bbh=(double)bh[mi][i]/(double)stepm;           bbh=(double)bh[mi][i]/(double)stepm; 
                                 lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }else if (mle==4){  /* ml=4 no inter-extrapolation */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         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(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 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);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                   
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            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 > nlstate){           if( s2 > nlstate){ 
                                         lli=log(out[s1][s2] - savm[s1][s2]);            lli=log(out[s1][s2] - savm[s1][s2]);
                                 } else if  ( s2==-1 ) { /* alive */          } else if  ( s2==-1 ) { /* alive */
                                         for (j=1,survp=0. ; j<=nlstate; j++)             for (j=1,survp=0. ; j<=nlstate; j++) 
                                                 survp += out[s1][j];              survp += out[s1][j];
                                         lli= log(survp);            lli= log(survp);
                                 }else{          }else{
                                         lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                                 }          }
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */  /*      printf("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]); */
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
                 for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                         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(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
                                 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);
                                         }            }
                                 for(d=0; d<dh[mi][i]; d++){          for(d=0; d<dh[mi][i]; d++){
                                         newm=savm;            newm=savm;
                                         agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;            agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
                                         cov[2]=agexact;            cov[2]=agexact;
                                         if(nagesqr==1)            if(nagesqr==1)
                                                 cov[3]= agexact*agexact;              cov[3]= agexact*agexact;
                                         for (kk=1; kk<=cptcovage;kk++) {            for (kk=1; kk<=cptcovage;kk++) {
                                                 cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;              cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
                                         }            }
                   
                                         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                                                                                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                                         savm=oldm;            savm=oldm;
                                         oldm=newm;            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];
                                 lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                                 ipmx +=1;          ipmx +=1;
                                 sw += weight[i];          sw += weight[i];
                                 ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                                 /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/          /*printf("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]);*/
                         } /* end of wave */        } /* end of wave */
                 } /* end of individual */      } /* end of individual */
         } /* End of if */    } /* End of if */
         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 */
         return -l;    return -l;
 }  }
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double funcone( double *x)  double funcone( double *x)
 {  {
   /* Same as likeli but slower because of a lot of printf and if */    /* Same as func but slower because of a lot of printf and if */
   int i, ii, j, k, mi, d, kk;    int i, ii, j, k, mi, d, kk;
         int ioffset=0;    int ioffset=0;
   double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];    double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
   double **out;    double **out;
   double lli; /* Individual log likelihood */    double lli; /* Individual log likelihood */
   double llt;    double llt;
   int s1, s2;    int s1, s2;
         int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate */    int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */
   
   double bbh, survp;    double bbh, survp;
   double agexact;    double agexact;
   double agebegin, ageend;    double agebegin, ageend;
Line 3248  double funcone( double *x) Line 3314  double funcone( double *x)
   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;
     /* 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 covariates without age* products */      for (k=1; k<=ncoveff+nqfveff;k++){ /* Simple and product fixed Dummy covariates without age* products */
       cov[++ioffset]=covar[Tvar[k]][i];        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(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives Fixed covariates */      for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitative fixed covariates */
       cov[++ioffset]=coqvar[iqv][i];        cov[++ioffset]=coqvar[Tvar[iqv]][i]; /* Only V1 k=9 */
     }      }
           
     for(mi=1; mi<= wav[i]-1; mi++){      for(mi=1; mi<= wav[i]-1; mi++){  /* Varying with waves */
       for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */        for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */
         cov[ioffset+itv]=cotvar[mw[mi][i]][itv][i];          /* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff *\/ */
           /* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
           k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */
           cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];
           /* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
       }        }
       for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */        for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */
         cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i];          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++){
Line 3839  void pstamp(FILE *fichier) Line 3911  void pstamp(FILE *fichier)
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \  void  freqsummary(char fileres[], 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 */
       
          int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, k, iv;
          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 *meanq;    double *meanq;
          double **meanqt;    double **meanqt;
          double *pp, **prop, *posprop, *pospropt;    double *pp, **prop, *posprop, *pospropt;
          double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;    double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
          char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];    char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
          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+3+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); */
          meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */    meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
          meanqt=matrix(1,lastpass,1,nqtveff);    meanqt=matrix(1,lastpass,1,nqtveff);
          strcpy(fileresp,"P_");    strcpy(fileresp,"P_");
          strcat(fileresp,fileresu);    strcat(fileresp,fileresu);
          /*strcat(fileresphtm,fileresu);*/    /*strcat(fileresphtm,fileresu);*/
          if((ficresp=fopen(fileresp,"w"))==NULL) {    if((ficresp=fopen(fileresp,"w"))==NULL) {
                  printf("Problem with prevalence resultfile: %s\n", fileresp);      printf("Problem with prevalence resultfile: %s\n", fileresp);
                  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));
                  fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));      fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
                  fflush(ficlog);      fflush(ficlog);
                  exit(70);       exit(70); 
          }    }
          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</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 by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
   
          freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
          j1=0;    j1=0;
       
          j=ncoveff;    /* j=ncoveff;  /\* Only fixed dummy covariates *\/ */
          if (cptcovn<1) {j=1;ncodemax[1]=1;}    j=cptcoveff;  /* Only dummy covariates of the model */
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
          first=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 
          */    */
   
          for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination excluding varying and quantitatives */    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 */
                  posproptt=0.;      posproptt=0.;
                  /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
                          scanf("%d", i);*/        scanf("%d", i);*/
                  for (i=-5; i<=nlstate+ndeath; i++)        for (i=-5; i<=nlstate+ndeath; i++)  
                          for (jk=-5; jk<=nlstate+ndeath; jk++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
                                  for(m=iagemin; m <= iagemax+3; m++)          for(m=iagemin; m <= iagemax+3; m++)
                                          freq[i][jk][m]=0;            freq[i][jk][m]=0;
               
                  for (i=1; i<=nlstate; i++)  {      for (i=1; i<=nlstate; i++)  {
                          for(m=iagemin; m <= iagemax+3; m++)        for(m=iagemin; m <= iagemax+3; m++)
                                  prop[i][m]=0;          prop[i][m]=0;
                          posprop[i]=0;        posprop[i]=0;
                          pospropt[i]=0;        pospropt[i]=0;
                  }      }
                  for (z1=1; z1<= nqfveff; z1++) {        /* for (z1=1; z1<= nqfveff; z1++) {   */
                          meanq[z1]+=0.;      /*   meanq[z1]+=0.; */
                          for(m=1;m<=lastpass;m++){      /*   for(m=1;m<=lastpass;m++){ */
                                  meanqt[m][z1]=0.;      /*  meanqt[m][z1]=0.; */
                          }      /*   } */
                  }      /* } */
         
                  dateintsum=0;  
                  k2cpt=0;  
      /* For that comination of covariate j1, we count and print the frequencies */  
                  for (iind=1; iind<=imx; iind++) { /* For each individual iind */  
                          bool=1;  
                          if (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */  
                                  for (z1=1; z1<= nqfveff; z1++) {    
                                          meanq[z1]+=coqvar[Tvar[z1]][iind];  
                                  }  
                                  for (z1=1; z1<=ncoveff; z1++) {    
                                          /* if(Tvaraff[z1] ==-20){ */  
                                          /*      /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */  
                                          /* }else  if(Tvaraff[z1] ==-10){ */  
                                          /*      /\* sumnew+=coqvar[z1][iind]; *\/ */  
                                          /* }else  */  
                                          if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){  
                                                  /* Tests if this individual i responded to j1 (V4=1 V3=0) */  
                                                  bool=0;  
                                                  /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",   
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),  
                 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*/  
                                          }   
                                  } /* end z1 */  
                          } /* cptcovn > 0 */  
   
                          if (bool==1){ /* We selected an individual iin satisfying combination j1 */  
                                  /* for(m=firstpass; m<=lastpass; m++){ */  
                                  for(mi=1; mi<wav[iind];mi++){  
                                          m=mw[mi][iind];  
                                          /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]  
                                                         and mw[mi+1][iind]. dh depends on stepm. */  
                                          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 */  
                                          if(m >=firstpass && m <=lastpass){  
                                                  k2=anint[m][iind]+(mint[m][iind]/12.);  
                                                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/  
                                                  if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */  
                                                  if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */  
                                                  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 */  
                                                  if (m<lastpass) {  
                                                          /* if(s[m][iind]==4 && s[m+1][iind]==4) */  
                                                          /*   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]); */  
                                                          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.));  
                                                          freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */  
                                                          /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */  
                                                          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 */  
                                                  }  
                                          }    
                                          if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {  
                                                  dateintsum=dateintsum+k2;  
                                                  k2cpt++;  
                                                  /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */  
                                          }  
                                          /*}*/  
                                  } /* end m */  
                          } /* end bool */  
                  } /* end iind = 1 to imx */  
        /* prop[s][age] is feeded for any initial and valid live state as well as  
                                         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */  
   
   
                  /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/  
                  pstamp(ficresp);  
                  if  (ncoveff>0) {  
                          fprintf(ficresp, "\n#********** Variable ");   
                          fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");   
                          fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");   
                          for (z1=1; z1<=ncoveff; z1++){  
                                  fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
                                  fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
                                  fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
                          }  
                          fprintf(ficresp, "**********\n#");  
                          fprintf(ficresphtm, "**********</h3>\n");  
                          fprintf(ficresphtmfr, "**********</h3>\n");  
                          fprintf(ficlog, "\n#********** Variable ");   
                          for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);  
                          fprintf(ficlog, "**********\n");  
                  }  
                  fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");  
                  for(i=1; i<=nlstate;i++) {  
                          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  
                          fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);  
                  }  
                  fprintf(ficresp, "\n");  
                  fprintf(ficresphtm, "\n");  
         
                  /* Header of frequency table by age */  
                  fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");  
                  fprintf(ficresphtmfr,"<th>Age</th> ");  
                  for(jk=-1; jk <=nlstate+ndeath; jk++){  
                          for(m=-1; m <=nlstate+ndeath; m++){  
                                  if(jk!=0 && m!=0)  
                                          fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);  
                          }  
                  }  
                  fprintf(ficresphtmfr, "\n");  
               
                  /* For each age */      dateintsum=0;
                  for(iage=iagemin; iage <= iagemax+3; iage++){      k2cpt=0;
                          fprintf(ficresphtm,"<tr>");      /* For that combination of covariate j1, we count and print the frequencies in one pass */
                          if(iage==iagemax+1){      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
                                  fprintf(ficlog,"1");        bool=1;
                                  fprintf(ficresphtmfr,"<tr><th>0</th> ");        if(anyvaryingduminmodel==0){ /* If All fixed covariates */
                          }else if(iage==iagemax+2){          if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
                                  fprintf(ficlog,"0");            /* for (z1=1; z1<= nqfveff; z1++) {   */
                                  fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");            /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
                          }else if(iage==iagemax+3){            /* } */
                                  fprintf(ficlog,"Total");            for (z1=1; z1<=cptcoveff; z1++) {  
                                  fprintf(ficresphtmfr,"<tr><th>Total</th> ");              /* if(Tvaraff[z1] ==-20){ */
                          }else{              /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
                                  if(first==1){              /* }else  if(Tvaraff[z1] ==-10){ */
                                          first=0;              /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
                                          printf("See log file for details...\n");              /* }else  */
                                  }              if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                                  fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);                /* Tests if this individual iind responded to j1 (V4=1 V3=0) */
                                  fprintf(ficlog,"Age %d", iage);                bool=0;
                          }                /* 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(jk=1; jk <=nlstate ; jk++){                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                                  for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                   j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
                                          pp[jk] += freq[jk][m][iage];                 /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
                          }              } /* Onlyf fixed */
                          for(jk=1; jk <=nlstate ; jk++){            } /* end z1 */
                                  for(m=-1, pos=0; m <=0 ; m++)          } /* cptcovn > 0 */
                                          pos += freq[jk][m][iage];        } /* end any */
                                  if(pp[jk]>=1.e-10){        if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
                                          if(first==1){          /* for(m=firstpass; m<=lastpass; m++){ */
                                                  printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for(mi=1; mi<wav[iind];mi++){ /* For that wave */
                                          }            m=mw[mi][iind];
                                          fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            if(anyvaryingduminmodel==1){ /* Some are varying covariates */
                                  }else{              for (z1=1; z1<=cptcoveff; z1++) {
                                          if(first==1)                if( Fixed[Tmodelind[z1]]==1){
                                                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                  iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
                                          fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                  if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
                                  }                    bool=0;
                          }                }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
                   if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                          for(jk=1; jk <=nlstate ; jk++){                     bool=0;
                                  /* posprop[jk]=0; */                  }
                                  for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */                }
                                          pp[jk] += freq[jk][m][iage];              }
                          }      /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */            }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
             /* bool =0 we keep that guy which corresponds to the combination of dummy values */
                          for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){            if(bool==1){
                                  pos += pp[jk]; /* pos is the total number of transitions until this age */              /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
                                  posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state                 and mw[mi+1][iind]. dh depends on stepm. */
                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */              agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
                                  pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state              ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */
                                                                                                                                                                          from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */              if(m >=firstpass && m <=lastpass){
                          }                k2=anint[m][iind]+(mint[m][iind]/12.);
                          for(jk=1; jk <=nlstate ; jk++){                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                                  if(pos>=1.e-5){                if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */
                                          if(first==1)                if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */
                                                  printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                if (s[m][iind]>0 && s[m][iind]<=nlstate)  /* If status at wave m is known and a live state */
                                          fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                  prop[s[m][iind]][(int)agev[m][iind]] += weight[iind];  /* At age of beginning of transition, where status is known */
                                  }else{                if (m<lastpass) {
                                          if(first==1)                  /* if(s[m][iind]==4 && s[m+1][iind]==4) */
                                                  printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                  /*   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(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);                  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.));
                                  if( iage <= iagemax){                  freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
                                          if(pos>=1.e-5){                  /* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
                                                  fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);                  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(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);                }
                                                  /*probs[iage][jk][j1]= pp[jk]/pos;*/              } /* end if between passes */  
                                                  /*printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);*/              if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
                                          }                dateintsum=dateintsum+k2;
                                          else{                k2cpt++;
                                                  fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);                /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
                                                  fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);              }
                                          }            } /* end bool 2 */
                                  }          } /* end m */
                                  pospropt[jk] +=posprop[jk];        } /* end bool */
                          } /* end loop jk */      } /* end iind = 1 to imx */
                          /* pospropt=0.; */      /* prop[s][age] is feeded for any initial and valid live state as well as
                          for(jk=-1; jk <=nlstate+ndeath; jk++){         freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
                                  for(m=-1; m <=nlstate+ndeath; m++){  
                                          if(freq[jk][m][iage] !=0 ) { /* minimizing output */  
                                                  if(first==1){      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
                                                          printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);      pstamp(ficresp);
                                                  }      /* if  (ncoveff>0) { */
                                                  fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);      if  (cptcoveff>0) {
                                          }        fprintf(ficresp, "\n#********** Variable "); 
                                          if(jk!=0 && m!=0)        fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
                                                  fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);        fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
                                  }        for (z1=1; z1<=cptcoveff; z1++){
                          } /* end loop jk */          fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                          posproptt=0.;           fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                          for(jk=1; jk <=nlstate; jk++){          fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                                  posproptt += pospropt[jk];        }
                          }        fprintf(ficresp, "**********\n#");
                          fprintf(ficresphtmfr,"</tr>\n ");        fprintf(ficresphtm, "**********</h3>\n");
                          if(iage <= iagemax){        fprintf(ficresphtmfr, "**********</h3>\n");
                                  fprintf(ficresp,"\n");        fprintf(ficlog, "\n#********** Variable "); 
                                  fprintf(ficresphtm,"</tr>\n");        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
                          }        fprintf(ficlog, "**********\n");
                          if(first==1)      }
                                  printf("Others in log...\n");      fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
                          fprintf(ficlog,"\n");      for(i=1; i<=nlstate;i++) {
                  } /* end loop age iage */        fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
                  fprintf(ficresphtm,"<tr><th>Tot</th>");        fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
                  for(jk=1; jk <=nlstate ; jk++){      }
                          if(posproptt < 1.e-5){      fprintf(ficresp, "\n");
                                  fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);        fprintf(ficresphtm, "\n");
                          }else{        
                                  fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);         /* Header of frequency table by age */
                          }      fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
                  }      fprintf(ficresphtmfr,"<th>Age</th> ");
                  fprintf(ficresphtm,"</tr>\n");      for(jk=-1; jk <=nlstate+ndeath; jk++){
                  fprintf(ficresphtm,"</table>\n");        for(m=-1; m <=nlstate+ndeath; m++){
                  fprintf(ficresphtmfr,"</table>\n");          if(jk!=0 && m!=0)
                  if(posproptt < 1.e-5){            fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
                          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(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);      fprintf(ficresphtmfr, "\n");
                          invalidvarcomb[j1]=1;        
                  }else{      /* For each age */
                          fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);      for(iage=iagemin; iage <= iagemax+3; iage++){
                          invalidvarcomb[j1]=0;        fprintf(ficresphtm,"<tr>");
                  }        if(iage==iagemax+1){
                  fprintf(ficresphtmfr,"</table>\n");          fprintf(ficlog,"1");
          } /* end selected combination of covariate j1 */          fprintf(ficresphtmfr,"<tr><th>0</th> ");
          dateintmean=dateintsum/k2cpt;         }else if(iage==iagemax+2){
           fprintf(ficlog,"0");
           fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
         }else if(iage==iagemax+3){
           fprintf(ficlog,"Total");
           fprintf(ficresphtmfr,"<tr><th>Total</th> ");
         }else{
           if(first==1){
             first=0;
             printf("See log file for details...\n");
           }
           fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
           fprintf(ficlog,"Age %d", iage);
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
             pp[jk] += freq[jk][m][iage]; 
         }
         for(jk=1; jk <=nlstate ; jk++){
           for(m=-1, pos=0; m <=0 ; m++)
             pos += freq[jk][m][iage];
           if(pp[jk]>=1.e-10){
             if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
           }else{
             if(first==1)
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           }
         }
   
         for(jk=1; jk <=nlstate ; jk++){ 
           /* posprop[jk]=0; */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
             pp[jk] += freq[jk][m][iage];
         } /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */
   
         for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
           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
                                             from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
           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] */
         }
         for(jk=1; jk <=nlstate ; jk++){
           if(pos>=1.e-5){
             if(first==1)
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           }else{
             if(first==1)
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           }
           if( iage <= iagemax){
             if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
               /*probs[iage][jk][j1]= pp[jk]/pos;*/
               /*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{
               fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
               fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
             }
           }
           pospropt[jk] +=posprop[jk];
         } /* end loop jk */
         /* pospropt=0.; */
         for(jk=-1; jk <=nlstate+ndeath; jk++){
           for(m=-1; m <=nlstate+ndeath; m++){
             if(freq[jk][m][iage] !=0 ) { /* minimizing output */
               if(first==1){
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
               }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
             }
             if(jk!=0 && m!=0)
               fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
           }
         } /* end loop jk */
         posproptt=0.; 
         for(jk=1; jk <=nlstate; jk++){
           posproptt += pospropt[jk];
         }
         fprintf(ficresphtmfr,"</tr>\n ");
         if(iage <= iagemax){
           fprintf(ficresp,"\n");
           fprintf(ficresphtm,"</tr>\n");
         }
         if(first==1)
           printf("Others in log...\n");
         fprintf(ficlog,"\n");
       } /* end loop age iage */
       fprintf(ficresphtm,"<tr><th>Tot</th>");
       for(jk=1; jk <=nlstate ; jk++){
         if(posproptt < 1.e-5){
           fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);   
         }else{
           fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);    
         }
       }
       fprintf(ficresphtm,"</tr>\n");
       fprintf(ficresphtm,"</table>\n");
       fprintf(ficresphtmfr,"</table>\n");
       if(posproptt < 1.e-5){
         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(ficres,"\n  This combination (%d) is not valid and no result will be produced\n\n",j1);
         invalidvarcomb[j1]=1;
       }else{
         fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
         invalidvarcomb[j1]=0;
       }
       fprintf(ficresphtmfr,"</table>\n");
     } /* end selected combination of covariate j1 */
     dateintmean=dateintsum/k2cpt; 
                                     
          fclose(ficresp);    fclose(ficresp);
          fclose(ficresphtm);    fclose(ficresphtm);
          fclose(ficresphtmfr);    fclose(ficresphtmfr);
          free_vector(meanq,1,nqfveff);    free_vector(meanq,1,nqfveff);
          free_matrix(meanqt,1,lastpass,1,nqtveff);    free_matrix(meanqt,1,lastpass,1,nqtveff);
          free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);
          free_vector(pospropt,1,nlstate);    free_vector(pospropt,1,nlstate);
          free_vector(posprop,1,nlstate);    free_vector(posprop,1,nlstate);
          free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);    free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);
          free_vector(pp,1,nlstate);    free_vector(pp,1,nlstate);
          /* End of freqsummary */    /* End of freqsummary */
  }  }
   
 /************ 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)
  {    {  
    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       in each health status at the date of interview (if between dateprev1 and dateprev2).       in each health status at the date of interview (if between dateprev1 and dateprev2).
       We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
    */    */
     
    int i, m, jk, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j, iv;
    int mi; /* Effective wave */    int mi; /* Effective wave */
    int iage;    int iage;
    double agebegin, ageend;    double agebegin, ageend;
   
    double **prop;    double **prop;
    double posprop;     double posprop; 
    double  y2; /* in fractional years */    double  y2; /* in fractional years */
    int iagemin, iagemax;    int iagemin, iagemax;
    int first; /** to stop verbosity which is redirected to log file */    int first; /** to stop verbosity which is redirected to log file */
   
    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+3+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;
       
    /*j=cptcoveff;*/    /*j=cptcoveff;*/
    if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       
    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+3+AGEMARGE; iage++)
          prop[i][iage]=0.0;          prop[i][iage]=0.0;
           printf("Prevalence combination of varying and fixed dummies %d\n",j1);
      for (i=1; i<=imx; i++) { /* Each individual */      /* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
        bool=1;      fprintf(ficlog,"Prevalence combination of varying and fixed dummies %d\n",j1);
        if  (cptcovn>0) {  /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */      
          for (z1=1; z1<=cptcoveff; z1++) /* For each covariate, look at the value for individual i and checks if it is equal to the corresponding value of this covariate according to current combination j1*/      for (i=1; i<=imx; i++) { /* Each individual */
            if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])         bool=1;
              bool=0;        /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
        }         for(mi=1; mi<wav[i];mi++){ /* For this wave too look where individual can be counted V4=0 V3=0 */
        if (bool==1) { /* For this combination of covariates values, this individual fits */          m=mw[mi][i];
          /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */          /* Tmodelind[z1]=k is the position of the varying covariate in the model, but which # within 1 to ntv? */
          for(mi=1; mi<wav[i];mi++){          /* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
            m=mw[mi][i];          for (z1=1; z1<=cptcoveff; z1++){
            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/            if( Fixed[Tmodelind[z1]]==1){
            /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */              iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
            if(m >=firstpass && m <=lastpass){              if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */                bool=0;
              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */            }else if( Fixed[Tmodelind[z1]]== 0)  /* fixed */
                if(agev[m][i]==0) agev[m][i]=iagemax+1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
                if(agev[m][i]==1) agev[m][i]=iagemax+2;                bool=0;
                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+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);           }
                  exit(1);          if(bool==1){ /* Otherwise we skip that wave/person */
                }            agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
                if (s[m][i]>0 && s[m][i]<=nlstate) {             /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/            if(m >=firstpass && m <=lastpass){
                  prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  prop[s[m][i]][iagemax+3] += weight[i];               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                } /* end valid statuses */                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
              } /* end selection of dates */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
            } /* end selection of waves */                if((int)agev[m][i] <iagemin-AGEMARGE || (int)agev[m][i] >iagemax+3+AGEMARGE){
          } /* end effective waves */                  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); 
        } /* end bool */                  exit(1);
      }                }
      for(i=iagemin; i <= iagemax+3; i++){                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
        for(jk=1,posprop=0; jk <=nlstate ; jk++) {                   /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
          posprop += prop[jk][i];                   prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
        }                   prop[s[m][i]][iagemax+3] += weight[i]; 
                       } /* end valid statuses */ 
        for(jk=1; jk <=nlstate ; jk++){                    } /* end selection of dates */
          if( i <=  iagemax){             } /* end selection of waves */
            if(posprop>=1.e-5){           } /* end bool */
              probs[i][jk][j1]= prop[jk][i]/posprop;        } /* end wave */
            } else{      } /* end individual */
              if(first==1){      for(i=iagemin; i <= iagemax+3; i++){  
                first=0;        for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
                printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);          posprop += prop[jk][i]; 
              }        } 
            }        
          }         for(jk=1; jk <=nlstate ; jk++){       
        }/* end jk */           if( i <=  iagemax){ 
      }/* end i */             if(posprop>=1.e-5){ 
               probs[i][jk][j1]= prop[jk][i]/posprop;
             } else{
               if(first==1){
                 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]);
               }
             }
           } 
         }/* end jk */ 
       }/* end i */ 
      /*} *//* end i1 */       /*} *//* end i1 */
    } /* end j1 */    } /* end j1 */
       
    /*  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+3+AGEMARGE);
  }  /* End of prevalence */  }  /* End of prevalence */
   
 /************* Waves Concatenation ***************/  /************* Waves Concatenation ***************/
   
Line 4281  void  concatwav(int wav[], int **dh, int Line 4381  void  concatwav(int wav[], int **dh, int
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
      dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      and mw[mi+1][i]. dh depends on stepm.       and mw[mi+1][i]. dh depends on stepm.
      */    */
   
   int i=0, mi=0, m=0, mli=0;    int i=0, mi=0, m=0, mli=0;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
Line 4300  void  concatwav(int wav[], int **dh, int Line 4400  void  concatwav(int wav[], int **dh, int
 /* Treating live states */  /* Treating live states */
   for(i=1; i<=imx; i++){  /* For simple cases and if state is death */    for(i=1; i<=imx; i++){  /* For simple cases and if state is death */
     mi=0;  /* First valid wave */      mi=0;  /* First valid wave */
                 mli=0; /* Last valid wave */      mli=0; /* Last valid wave */
     m=firstpass;      m=firstpass;
     while(s[m][i] <= nlstate){  /* a live state */      while(s[m][i] <= nlstate){  /* a live state */
                         if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */        if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
                                 mli=m-1;/* mw[++mi][i]=m-1; */          mli=m-1;/* mw[++mi][i]=m-1; */
                         }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */        }else if(s[m][i]>=1 || s[m][i]==-4 || s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
                                 mw[++mi][i]=m;          mw[++mi][i]=m;
                                 mli=m;          mli=m;
       } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */        } /* else might be a useless wave  -1 and mi is not incremented and mw[mi] not updated */
       if(m < lastpass){ /* m < lastpass, standard case */        if(m < lastpass){ /* m < lastpass, standard case */
                                 m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */          m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
       }        }
                         else{ /* m >= lastpass, eventual special issue with warning */        else{ /* m >= lastpass, eventual special issue with warning */
 #ifdef UNKNOWNSTATUSNOTCONTRIBUTING  #ifdef UNKNOWNSTATUSNOTCONTRIBUTING
                                 break;          break;
 #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 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);
                                                 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 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);
                                         mw[++mi][i]=m;            mw[++mi][i]=m;
                                         mli=m;            mli=m;
                                 }          }
                                 if(s[m][i]==-2){ /* Vital status is really unknown */          if(s[m][i]==-2){ /* Vital status is really unknown */
                                         nbwarn++;            nbwarn++;
                                         if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */            if((int)anint[m][i] == 9999){  /*  Has the vital status really been verified? */
                                                 printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                                 fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);              fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
                                         }            }
                                         break;            break;
                                 }          }
                                 break;          break;
 #endif  #endif
                         }/* End m >= lastpass */        }/* End m >= lastpass */
     }/* end while */      }/* end while */
   
         /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */      /* mi is the last effective wave, m is lastpass, mw[j][i] gives the # of j-th effective wave for individual i */
     /* After last pass */      /* After last pass */
 /* Treating death states */  /* Treating death states */
     if (s[m][i] > nlstate){  /* In a death state */      if (s[m][i] > nlstate){  /* In a death state */
                         /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */        /* if( mint[m][i]==mdc[m][i] && anint[m][i]==andc[m][i]){ /\* same date of death and date of interview *\/ */
                         /* } */        /* } */
       mi++;     /* Death is another wave */        mi++;     /* Death is another wave */
       /* 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;
     }      }
 #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) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */
       /* m++; */        /* m++; */
       /* mi++; */        /* mi++; */
       /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */        /* s[m][i]=nlstate+1;  /\* We are setting the status to the last of non live state *\/ */
       /* mw[mi][i]=m; */        /* 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++;
                                         if(firstfiv==0){            if(firstfiv==0){
                                                 printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing 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], s[m][i], i,m );              printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing 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], s[m][i], i,m );
                                                 firstfiv=1;              firstfiv=1;
                                         }else{            }else{
                                                 fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );              fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
                                         }            }
                                 }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.\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.\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{ /* end date of interview is known */
                                 /* 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 );
                                         firstfour=1;            firstfour=1;
                                 }          }
                                 fprintf(ficlog,"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.\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 %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.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
       }        }
     } /* end if date of death is known */      } /* end if date of death is known */
 #endif  #endif
Line 4387  void  concatwav(int wav[], int **dh, int Line 4487  void  concatwav(int wav[], int **dh, int
     if(mi==0){      if(mi==0){
       nbwarn++;        nbwarn++;
       if(first==0){        if(first==0){
                                 printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
                                 first=1;          first=1;
       }        }
       if(first==1){        if(first==1){
                                 fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
Line 4401  void  concatwav(int wav[], int **dh, int Line 4501  void  concatwav(int wav[], int **dh, int
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     for(mi=1; mi<wav[i];mi++){      for(mi=1; mi<wav[i];mi++){
       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 */
                                         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 */
                                                 else if(j<0){              else if(j<0){
                                                         nberr++;                nberr++;
                                                         printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                         j=1; /* Temporary Dangerous patch */                j=1; /* Temporary Dangerous patch */
                                                         printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                                                         fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                         fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
                                                 }              }
                                                 k=k+1;              k=k+1;
                                                 if (j >= jmax){              if (j >= jmax){
                                                         jmax=j;                jmax=j;
                                                         ijmax=i;                ijmax=i;
                                                 }              }
                                                 if (j <= jmin){              if (j <= jmin){
                                                         jmin=j;                jmin=j;
                                                         ijmin=i;                ijmin=i;
                                                 }              }
                                                 sum=sum+j;              sum=sum+j;
                                                 /*if (j<0) printf("j=%d num=%d \n",j,i);*/              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
                                                 /*        printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                                         }            }
                                 }          }
                                 else{          else{
                                         j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
                                                                                   
                                         k=k+1;            k=k+1;
                                         if (j >= jmax) {            if (j >= jmax) {
                                                 jmax=j;              jmax=j;
                                                 ijmax=i;              ijmax=i;
                                         }            }
                                         else if (j <= jmin){            else if (j <= jmin){
                                                 jmin=j;              jmin=j;
                                                 ijmin=i;              ijmin=i;
                                         }            }
                                         /*          if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
                                         /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                                         if(j<0){            if(j<0){
                                                 nberr++;              nberr++;
                                                 printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                                 fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                                         }            }
                                         sum=sum+j;            sum=sum+j;
                                 }          }
                                 jk= j/stepm;          jk= j/stepm;
                                 jl= j -jk*stepm;          jl= j -jk*stepm;
                                 ju= j -(jk+1)*stepm;          ju= j -(jk+1)*stepm;
                                 if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
                                         if(jl==0){            if(jl==0){
                                                 dh[mi][i]=jk;              dh[mi][i]=jk;
                                                 bh[mi][i]=0;              bh[mi][i]=0;
                                         }else{ /* We want a negative bias in order to only have interpolation ie            }else{ /* We want a negative bias in order to only have interpolation ie
                                                                         * to avoid the price of an extra matrix product in likelihood */                    * to avoid the price of an extra matrix product in likelihood */
                                                 dh[mi][i]=jk+1;              dh[mi][i]=jk+1;
                                                 bh[mi][i]=ju;              bh[mi][i]=ju;
                                         }            }
                                 }else{          }else{
                                         if(jl <= -ju){            if(jl <= -ju){
                                                 dh[mi][i]=jk;              dh[mi][i]=jk;
                                                 bh[mi][i]=jl;   /* bias is positive if real duration              bh[mi][i]=jl;       /* bias 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.
                                                                                                          */                                   */
                                         }            }
                                         else{            else{
                                                 dh[mi][i]=jk+1;              dh[mi][i]=jk+1;
                                                 bh[mi][i]=ju;              bh[mi][i]=ju;
                                         }            }
                                         if(dh[mi][i]==0){            if(dh[mi][i]==0){
                                                 dh[mi][i]=1; /* At least one step */              dh[mi][i]=1; /* At least one step */
                                                 bh[mi][i]=ju; /* At least one step */              bh[mi][i]=ju; /* At least one step */
                                                 /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                                         }            }
                                 } /* end if mle */          } /* end if mle */
       }        }
     } /* end wave */      } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
   printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
  }  }
   
 /*********** 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)
Line 4511  void  concatwav(int wav[], int **dh, int Line 4611  void  concatwav(int wav[], int **dh, int
   
   /* Loop on covariates without age and products and no quantitative variable */    /* Loop on covariates without age and products and no quantitative variable */
   /* for (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 (j=1; j<=cptcovsnq; 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 < maxncov; k++) Ndum[k]=0;      for (j=-1; (j < maxncov); j++) Ndum[j]=0;
     for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the       if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */ 
                                 modality of this covariate Vj*/        switch(Fixed[k]) {
       switch(Typevar[j]) {        case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
       case 1: /* A real fixed dummy covariate */          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[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i            ij=(int)(covar[Tvar[k]][i]);
                                       * If product of Vn*Vm, still boolean *:            /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                       * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables             * If product of Vn*Vm, still boolean *:
                                       * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */             * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
         /* Finds for covariate j, n=Tvar[j] of Vn . ij is the             * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0   */
            modality of the nth covariate of individual i. */            /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
         if (ij > modmaxcovj)               modality of the nth covariate of individual i. */
           modmaxcovj=ij;             if (ij > modmaxcovj)
         else if (ij < modmincovj)               modmaxcovj=ij; 
           modmincovj=ij;             else if (ij < modmincovj) 
         if ((ij < -1) && (ij > NCOVMAX)){              modmincovj=ij; 
           printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );            if ((ij < -1) && (ij > NCOVMAX)){
           exit(1);              printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
         }else              exit(1);
           Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/            }else
         /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */              Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/            /*  If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
         /* getting the maximum value of the modality of the covariate            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and            /* getting the maximum value of the modality of the covariate
            female ies 1, then modmaxcovj=1.*/               (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
         break;               female ies 1, then modmaxcovj=1.
       case 2:            */
           } /* 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);
           fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
           cptcode=modmaxcovj;
           /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
           /*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 */
             printf("Frequencies of covariates %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]);
             if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
               if( j != -1){
                 ncodemax[k]++;  /* ncodemax[k]= Number of modalities of the k th
                                    covariate for which somebody answered excluding 
                                    undefined. Usually 2: 0 and 1. */
               }
               ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
                                       covariate for which somebody answered including 
                                       undefined. Usually 3: -1, 0 and 1. */
             }
             /* 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 */
           } /* Ndum[-1] number of undefined modalities */
           
           /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
           /* 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;
              modmincovj=3; modmaxcovj = 7;
              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;
              defining two dummy variables: variables V1_1 and V1_2.
              nbcode[Tvar[j]][ij]=k;
              nbcode[Tvar[j]][1]=0;
              nbcode[Tvar[j]][2]=1;
              nbcode[Tvar[j]][3]=2;
              To be continued (not working yet).
           */
           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*/
             if (Ndum[i] == 0) { /* If nobody responded to this modality k */
               break;
             }
             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*/
             cptcode = ij; /* New max modality for covar j */
           } /* end of loop on modality i=-1 to 1 or more */
           break;
         case 1: /* Testing on varying covariate, could be simple and
                  * should look at waves or product of fixed *
                  * varying. No time to test -1, assuming 0 and 1 only */
           ij=0;
           for(i=0; i<=1;i++){
             nbcode[Tvar[k]][++ij]=i;
           }
         break;          break;
         default:
       }  
     } /* end for loop on individuals i */  
     printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);  
     fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);  
     cptcode=modmaxcovj;  
     /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */  
     /*for (i=0; i<=cptcode; i++) {*/  
     for (k=modmincovj;  k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */  
       printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);  
       fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);  
       if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */  
         if( k != -1){  
           ncodemax[j]++;  /* ncodemax[j]= Number of modalities of the j th  
                              covariate for which somebody answered excluding   
                              undefined. Usually 2: 0 and 1. */  
         }  
         ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th  
                                 covariate for which somebody answered including   
                                 undefined. Usually 3: -1, 0 and 1. */  
       }  
       /* In fact  ncodemax[j]=2 (dichotom. variables only) but it could be more for  
        * historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */  
     } /* Ndum[-1] number of undefined modalities */  
       
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */  
     /* 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;  
        modmincovj=3; modmaxcovj = 7;  
        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;  
        defining two dummy variables: variables V1_1 and V1_2.  
        nbcode[Tvar[j]][ij]=k;  
        nbcode[Tvar[j]][1]=0;  
        nbcode[Tvar[j]][2]=1;  
        nbcode[Tvar[j]][3]=2;  
        To be continued (not working yet).  
     */  
     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*/  
       if (Ndum[i] == 0) { /* If nobody responded to this modality k */  
         break;          break;
       }        } /* end switch */
       ij++;      } /* end dummy test */
       nbcode[Tvar[j]][ij]=i;  /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/  
       cptcode = ij; /* New max modality for covar j */  
     } /* end of loop on modality i=-1 to 1 or more */  
           
     /*   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 *\/ */
Line 4604  void  concatwav(int wav[], int **dh, int Line 4714  void  concatwav(int wav[], int **dh, int
   } /* 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 */
   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 might be -1 if status was unknown */       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]++; /* Might be supersed V1 + V1*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 */
       /* 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) */
     /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/      /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
     if((Ndum[i]!=0) && (i<=ncovcol)){      /* 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 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]);*/
       Tvaraff[++ij]=i; /*For printing (unclear) */        ++ij;/* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, */
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){        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]=-10; /* Dont'n know how to treat quantitative variables yet */        Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){        TmodelInvind[k]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
       Tvaraff[++ij]=i; /*For printing (unclear) */        if(Fixed[k]!=0)
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){          anyvaryingduminmodel=1;
       Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */        /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
     }        /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
         /*   Tvaraff[++ij]=i; /\*For printing (unclear) *\/ */
         /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
         /*   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*/                 * if in the model but excluded because missing values, but how to get k from ij?*/
     for(j=ij+1; j<= cptcovt; j++){
       Tvaraff[j]=0;
       Tmodelind[j]=0;
     }
     for(j=ntveff+1; j<= cptcovt; j++){
       TmodelInvind[j]=0;
     }
     /* To be sorted */
     ;
 }  }
   
   
Line 5779  void printinghtml(char fileresu[], char Line 5907  void printinghtml(char fileresu[], char
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
        }         }
          /* 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]){
          fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);            fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1); 
Line 5974  void printinggnuplot(char fileresu[], ch Line 6103  void printinggnuplot(char fileresu[], ch
   strcpy(optfileres,"vpl");    strcpy(optfileres,"vpl");
   /* 1eme*/    /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */    for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
     for (k1=1; k1<= m ; k1 ++) { /* For each valid combination of covariate */      for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */
       /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */        /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
       fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");        fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
       for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */        for (k=1; k<=cptcoveff; k++){    /* For each covariate k get corresponding value lv for combination k1 */
Line 6033  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6162  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)? $%d : 1/0) t 'Backward prevalence in state %d' with line ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \                fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
                       6+(cpt-1),  cpt );                        4+(cpt-1),  cpt );  /* 4 or 6 ?*/
             }else{              }else{
               fprintf(ficgp,"$%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++;
Line 6187  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6316  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                                                   
       fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);        fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
       for (k=1; k<=cptcoveff; k++){    /* For each covariate and each value */        for (k=1; k<=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 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       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,"LIJT_"),cpt,k1);        fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
 set ter svg size 640, 480\n                                                                                                                                                                                     \  set ter svg size 640, 480\n                                             \
 unset log y\n                                                                                                                                                                                                                                           \  unset log y\n                                                           \
 plot [%.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\n");        fprintf(ficgp,"\nset out\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
             
 /* 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 (1 to m=2**k), if any covariate is present */
     for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */      for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 
       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 */
                                 /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */          /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                 /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */          /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                 /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */          /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                 vlv= nbcode[Tvaraff[k]][lv];          vlv= nbcode[Tvaraff[k]][lv];
                                 fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);          fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
       }        }
       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.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
       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\n                                             \
 unset log y\n                                                                                                                                                                                                                                    \  unset log y\n                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
       k=3; /* Offset */        k=3; /* Offset */
       for (i=1; i<= nlstate ; i ++){        for (i=1; i<= nlstate ; i ++){
                                 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;
                                 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\n");
     } /* end cpt state*/       } /* end cpt state*/ 
   } /* end covariate */      } /* end covariate */  
             
             
 /* 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 (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);          fprintf(ficgp,"\n#\n#\n#CV Back 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 */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
           /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }          }
                                 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.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);
                                 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\n                                             \
 unset log y\n                                                                                                                                                                                                                                           \  unset log y\n                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  plot [%.f:%.f]  ", ageminpar, agemaxpar);
                                 k=3; /* Offset */          k=3; /* Offset */
                                 for (i=1; i<= nlstate ; i ++){          for (i=1; i<= nlstate ; i ++){
                                         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;
                                         /* 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+(cpt-1)+i-1); /* a vérifier */
                                         /* 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",i,cpt);
                                 } /* nlstate */          } /* nlstate */
                                 fprintf(ficgp,"\nset out\n");          fprintf(ficgp,"\nset out\n");
       } /* end cpt state*/         } /* end cpt state*/ 
     } /* end covariate */        } /* end covariate */  
   } /* End if backcast */    } /* End if backcast */
Line 6324  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6453  plot [%.f:%.f]  ", ageminpar, agemaxpar)
           
     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 (1 to m=2**k), if any covariate is present */
       for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */        for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
                                 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 */
                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */            /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */            /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */            /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                         vlv= nbcode[Tvaraff[k]][lv];            vlv= nbcode[Tvaraff[k]][lv];
                                         fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);            fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
                                 }          }
                                 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,"# 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.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
                                 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\n                                             \
 unset log y\n                                                                                                                                                                                                                                           \  unset log y\n                                                           \
 plot [%.f:%.f]  ", ageminpar, agemaxpar);  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 */
                                         /*#  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==1){
                                                 fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));              fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
                                         }else{            }else{
                                                 fprintf(ficgp,",\\\n '' ");              fprintf(ficgp,",\\\n '' ");
                                         }            }
                                         if(cptcoveff ==0){ /* No covariate */            if(cptcoveff ==0){ /* No covariate */
                                                 ioffset=2; /* Age is in 2 */              ioffset=2; /* Age is in 2 */
                                                 /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/              /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
                                                 /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */              /*#   1       2   3   4   5  6    7  8   9   10  11  12  13  14  15  16  17  18 */
                                                 /*# 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)) t 'pw.%d' with line ",      \
                                                                                         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              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){              if(cptcoveff ==1){
                                                         ioffset=4; /* Age is in 4 */                ioffset=4; /* Age is in 4 */
                                                 }else{              }else{
                                                         ioffset=6; /* Age is in 6 */                ioffset=6; /* Age is in 6 */
                                                         /*#  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 */
                                                 }                 }   
                                                 fprintf(ficgp," u %d:(",ioffset);               fprintf(ficgp," u %d:(",ioffset); 
                                                 kl=0;              kl=0;
                                                 strcpy(gplotcondition,"(");              strcpy(gplotcondition,"(");
                                                 for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */              for (k=1; k<=cptcoveff; k++){    /* For each covariate writing the chain of conditions */
                                                         lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */                lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
                                                         /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */                /* decodtabm(1,1,4) = 1 because h=1  k= (1) 1  1  1 */
                                                         /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */                /* decodtabm(1,2,4) = 1 because h=1  k=  1 (1) 1  1 */
                                                         /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */                /* decodtabm(13,3,4)= 2 because h=13 k=  1  1 (2) 2 */
                                                         vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */                vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
                                                         kl++;                kl++;
                                                         sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);                sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
                                                         kl++;                kl++;
                                                         if(k <cptcoveff && cptcoveff>1)                if(k <cptcoveff && cptcoveff>1)
                                                                 sprintf(gplotcondition+strlen(gplotcondition)," && ");                  sprintf(gplotcondition+strlen(gplotcondition)," && ");
                                                 }              }
                                                 strcpy(gplotcondition+strlen(gplotcondition),")");              strcpy(gplotcondition+strlen(gplotcondition),")");
                                                 /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */              /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
                                                 /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */               /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */ 
                                                 /*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) t 'p.%d' with line ", 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,cpt );
                                                 }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\n");
       } /* end cpt state*/        } /* end cpt state*/
     } /* end covariate */      } /* end covariate */
   } /* End if prevfcast */    } /* End if prevfcast */
             
             
   /* proba elementaires */    /* proba elementaires */
   fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");    fprintf(ficgp,"\n##############\n#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++){
       if (k != i) {        if (k != i) {
                                 fprintf(ficgp,"#   current state %d\n",k);          fprintf(ficgp,"#   current state %d\n",k);
                                 for(j=1; j <=ncovmodel; j++){          for(j=1; j <=ncovmodel; j++){
                                         fprintf(ficgp,"p%d=%f; ",jk,p[jk]);            fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
                                         jk++;             jk++; 
                                 }          }
                                 fprintf(ficgp,"\n");          fprintf(ficgp,"\n");
       }        }
     }      }
   }    }
   fprintf(ficgp,"##############\n#\n");    fprintf(ficgp,"##############\n#\n");
             
   /*goto avoid;*/    /*goto avoid;*/
   fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");    fprintf(ficgp,"\n##############\n#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");
Line 6498  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6627  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                 }                  }
               }                }
               else                else
                                         fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); /* Valgrind bug nbcode */                  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 */
               fprintf(ficgp," (1.");                fprintf(ficgp," (1.");
           }            }
                        
           if(ng != 1){            if(ng != 1){
             fprintf(ficgp,")/(1");              fprintf(ficgp,")/(1");
                            
             for(k1=1; k1 <=nlstate; k1++){               for(k1=1; k1 <=nlstate; k1++){ 
               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+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
Line 6761  void prevforecast(char fileres[], double Line 6890  void prevforecast(char fileres[], double
   if(jprojmean==0) jprojmean=1;    if(jprojmean==0) jprojmean=1;
   if(mprojmean==0) jprojmean=1;    if(mprojmean==0) jprojmean=1;
   
   i1=cptcoveff;    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
       
   fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
       
   fprintf(ficresf,"#****** Routine prevforecast **\n");    fprintf(ficresf,"#****** Routine prevforecast **\n");
     
 /*            if (h==(int)(YEARM*yearp)){ */  /*            if (h==(int)(YEARM*yearp)){ */
   for(cptcov=1, k=0;cptcov<=i1;cptcov++){    for(k=1;k<=i1;k++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if(invalidvarcomb[k]){
       k=k+1;        printf("\nCombination (%d) projection ignored because no cases \n",k); 
       fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");        continue;
       for(j=1;j<=cptcoveff;j++) {      }
                                 fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);      fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
       }      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficresf," yearproj age");        fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       for(j=1; j<=nlstate+ndeath;j++){       }
                                 for(i=1; i<=nlstate;i++)                    fprintf(ficresf," yearproj age");
           fprintf(ficresf," p%d%d",i,j);      for(j=1; j<=nlstate+ndeath;j++){ 
                                 fprintf(ficresf," wp.%d",j);        for(i=1; i<=nlstate;i++)        
       }          fprintf(ficresf," p%d%d",i,j);
       for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {        fprintf(ficresf," wp.%d",j);
                                 fprintf(ficresf,"\n");      }
                                 fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
                                 for (agec=fage; agec>=(ageminpar-1); agec--){         fprintf(ficresf,"\n");
                                         nhstepm=(int) rint((agelim-agec)*YEARM/stepm);         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
                                         nhstepm = nhstepm/hstepm;         for (agec=fage; agec>=(ageminpar-1); agec--){ 
                                         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                                         oldm=oldms;savm=savms;          nhstepm = nhstepm/hstepm; 
                                         hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                                                   oldm=oldms;savm=savms;
                                         for (h=0; h<=nhstepm; h++){          hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
                                                 if (h*hstepm/YEARM*stepm ==yearp) {          
               fprintf(ficresf,"\n");          for (h=0; h<=nhstepm; h++){
               for(j=1;j<=cptcoveff;j++)             if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);              fprintf(ficresf,"\n");
                                                         fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);              for(j=1;j<=cptcoveff;j++) 
                                                 }                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                                                 for(j=1; j<=nlstate+ndeath;j++) {              fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
                                                         ppij=0.;            } 
                                                         for(i=1; i<=nlstate;i++) {            for(j=1; j<=nlstate+ndeath;j++) {
                                                                 if (mobilav==1)               ppij=0.;
                                                                         ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];              for(i=1; i<=nlstate;i++) {
                                                                 else {                if (mobilav==1) 
                                                                         ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];                  ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
                                                                 }                else {
                                                                 if (h*hstepm/YEARM*stepm== yearp) {                  ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
                                                                         fprintf(ficresf," %.3f", p3mat[i][j][h]);                }
                                                                 }                if (h*hstepm/YEARM*stepm== yearp) {
                                                         } /* end i */                  fprintf(ficresf," %.3f", p3mat[i][j][h]);
                                                         if (h*hstepm/YEARM*stepm==yearp) {                }
                                                                 fprintf(ficresf," %.3f", ppij);              } /* end i */
                                                         }              if (h*hstepm/YEARM*stepm==yearp) {
                                                 }/* end j */                fprintf(ficresf," %.3f", ppij);
                                         } /* end h */              }
                                         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }/* end j */
                                 } /* end agec */          } /* end h */
       } /* end yearp */          free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* end cptcod */        } /* end agec */
   } /* end  cptcov */      } /* end yearp */
     } /* end  k */
                   
   fclose(ficresf);    fclose(ficresf);
   printf("End of Computing forecasting \n");    printf("End of Computing forecasting \n");
Line 6959  void prevforecast(char fileres[], double Line 7089  void prevforecast(char fileres[], double
 /* } */  /* } */
   
 /************** 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 dateprev2, 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){ */
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  /*   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; */
   int *popage;  /*   int *popage; */
   double calagedatem, agelim, kk1, kk2;  /*   double calagedatem, agelim, kk1, kk2; */
   double *popeffectif,*popcount;  /*   double *popeffectif,*popcount; */
   double ***p3mat,***tabpop,***tabpopprev;  /*   double ***p3mat,***tabpop,***tabpopprev; */
   /* double ***mobaverage; */  /*   /\* double ***mobaverage; *\/ */
   char filerespop[FILENAMELENGTH];  /*   char filerespop[FILENAMELENGTH]; */
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   agelim=AGESUP;  /*   agelim=AGESUP; */
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;  /*   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; */
       
   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);  /*   prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
       
       
   strcpy(filerespop,"POP_");   /*   strcpy(filerespop,"POP_");  */
   strcat(filerespop,fileresu);  /*   strcat(filerespop,fileresu); */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {  /*   if((ficrespop=fopen(filerespop,"w"))==NULL) { */
     printf("Problem with forecast resultfile: %s\n", filerespop);  /*     printf("Problem with forecast resultfile: %s\n", filerespop); */
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);  /*     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop); */
   }  /*   } */
   printf("Computing forecasting: result on file '%s' \n", filerespop);  /*   printf("Computing forecasting: result on file '%s' \n", filerespop); */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);  /*   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop); */
   
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  /*   if (cptcoveff==0) ncodemax[cptcoveff]=1; */
   
   /* if (mobilav!=0) { */  /*   /\* if (mobilav!=0) { *\/ */
   /*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */  /*   /\*   mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
   /*   if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ */  /*   /\*   if (movingaverage(probs, ageminpar, fage, 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); *\/ */
   /*   } */  /*   /\*   } *\/ */
   /* } */  /*   /\* } *\/ */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*   stepsize=(int) (stepm+YEARM-1)/YEARM; */
   if (stepm<=12) stepsize=1;  /*   if (stepm<=12) stepsize=1; */
       
   agelim=AGESUP;  /*   agelim=AGESUP; */
       
   hstepm=1;  /*   hstepm=1; */
   hstepm=hstepm/stepm;   /*   hstepm=hstepm/stepm;  */
                   
   if (popforecast==1) {  /*   if (popforecast==1) { */
     if((ficpop=fopen(popfile,"r"))==NULL) {  /*     if((ficpop=fopen(popfile,"r"))==NULL) { */
       printf("Problem with population file : %s\n",popfile);exit(0);  /*       printf("Problem with population file : %s\n",popfile);exit(0); */
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);  /*       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0); */
     }   /*     }  */
     popage=ivector(0,AGESUP);  /*     popage=ivector(0,AGESUP); */
     popeffectif=vector(0,AGESUP);  /*     popeffectif=vector(0,AGESUP); */
     popcount=vector(0,AGESUP);  /*     popcount=vector(0,AGESUP); */
           
     i=1;     /*     i=1;    */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  /*     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1; */
           
     imx=i;  /*     imx=i; */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  /*     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i]; */
   }  /*   } */
       
   for(cptcov=1,k=0;cptcov<=i2;cptcov++){  /*   for(cptcov=1,k=0;cptcov<=i2;cptcov++){ */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  /*     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
       k=k+1;  /*       k=k+1; */
       fprintf(ficrespop,"\n#******");  /*       fprintf(ficrespop,"\n#******"); */
       for(j=1;j<=cptcoveff;j++) {  /*       for(j=1;j<=cptcoveff;j++) { */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);  /*      fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
       }  /*       } */
       fprintf(ficrespop,"******\n");  /*       fprintf(ficrespop,"******\n"); */
       fprintf(ficrespop,"# Age");  /*       fprintf(ficrespop,"# Age"); */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);  /*       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j); */
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /*       if (popforecast==1)  fprintf(ficrespop," [Population]"); */
               
       for (cpt=0; cpt<=0;cpt++) {   /*       for (cpt=0; cpt<=0;cpt++) {  */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
                   
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*        nhstepm=(int) rint((agelim-agedeb)*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,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
                       
           for (h=0; h<=nhstepm; h++){  /*        for (h=0; h<=nhstepm; h++){ */
             if (h==(int) (calagedatem+YEARM*cpt)) {  /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*            fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 if (mobilav==1)   /*              if (mobilav==1)  */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; */
                 else {  /*              else { */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  /*                kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; */
                 }  /*              } */
               }  /*            } */
               if (h==(int)(calagedatem+12*cpt)){  /*            if (h==(int)(calagedatem+12*cpt)){ */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  /*              tabpop[(int)(agedeb)][j][cptcod]=kk1; */
                 /*fprintf(ficrespop," %.3f", kk1);  /*              /\*fprintf(ficrespop," %.3f", kk1); */
                   if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  /*                if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*\/ */
               }  /*            } */
             }  /*          } */
             for(i=1; i<=nlstate;i++){  /*          for(i=1; i<=nlstate;i++){ */
               kk1=0.;  /*            kk1=0.; */
               for(j=1; j<=nlstate;j++){  /*            for(j=1; j<=nlstate;j++){ */
                 kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];   /*              kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  */
               }  /*            } */
               tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];  /*            tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; */
             }  /*          } */
                           
             if (h==(int)(calagedatem+12*cpt))  /*          if (h==(int)(calagedatem+12*cpt)) */
               for(j=1; j<=nlstate;j++)   /*            for(j=1; j<=nlstate;j++)  */
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);  /*              fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); */
           }  /*        } */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
         }  /*      } */
       }  /*       } */
               
       /******/  /*       /\******\/ */
               
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {   /*       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {  */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     /*      fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    */
         for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){   /*      for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){  */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);   /*        nhstepm=(int) rint((agelim-agedeb)*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,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /*        hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);   */
           for (h=0; h<=nhstepm; h++){  /*        for (h=0; h<=nhstepm; h++){ */
             if (h==(int) (calagedatem+YEARM*cpt)) {  /*          if (h==(int) (calagedatem+YEARM*cpt)) { */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  /*            fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); */
             }   /*          }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*          for(j=1; j<=nlstate+ndeath;j++) { */
               kk1=0.;kk2=0;  /*            kk1=0.;kk2=0; */
               for(i=1; i<=nlstate;i++) {                /*            for(i=1; i<=nlstate;i++) {               */
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      /*              kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];     */
               }  /*            } */
               if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);          /*            if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);         */
             }  /*          } */
           }  /*        } */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*        free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
         }  /*      } */
       }  /*       } */
     }   /*     }  */
   }  /*   } */
       
   /* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */  /*   /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); *\/ */
       
   if (popforecast==1) {  /*   if (popforecast==1) { */
     free_ivector(popage,0,AGESUP);  /*     free_ivector(popage,0,AGESUP); */
     free_vector(popeffectif,0,AGESUP);  /*     free_vector(popeffectif,0,AGESUP); */
     free_vector(popcount,0,AGESUP);  /*     free_vector(popcount,0,AGESUP); */
   }  /*   } */
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */
   fclose(ficrespop);  /*   fclose(ficrespop); */
 } /* End of popforecast */  /* } /\* End of popforecast *\/ */
     
 int fileappend(FILE *fichier, char *optionfich)  int fileappend(FILE *fichier, char *optionfich)
 {  {
Line 7590  int readdata(char datafile[], int firsto Line 7720  int readdata(char datafile[], int firsto
           return 1;            return 1;
         }          }
         coqvar[iv][i]=dval;           coqvar[iv][i]=dval; 
           covar[ncovcol+iv][i]=dval; /* including qvar in standard covar for performance reasons */ 
       }        }
       strcpy(line,stra);        strcpy(line,stra);
     }/* end loop nqv */      }/* end loop nqv */
Line 7656  int readdata(char datafile[], int firsto Line 7787  int readdata(char datafile[], int firsto
   return (1);    return (1);
 }  }
   
 void removespace(char *str) {  void removespace(char **stri){/*, char stro[]) {*/
   char *p1 = str, *p2 = str;    char *p1 = *stri, *p2 = *stri;
   do    do
     while (*p2 == ' ')      while (*p2 == ' ')
       p2++;        p2++;
   while (*p1++ == *p2++);    while (*p1++ == *p2++);
     *stri=p1; 
 }  }
   
 int decodemodel ( char model[], int lastobs)  int decoderesult ( char resultline[])
  /**< This routine decode the model and returns:  /**< This routine decode one result line and returns the combination # of dummy covariates only **/
   {
     int j=0, k=0;
     char resultsav[MAXLINE];
     char stra[80], strb[80], strc[80], strd[80],stre[80];
   
     removespace(&resultline);
     printf("decoderesult=%s\n",resultline);
   
     if (strstr(resultline,"v") !=0){
       printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
       fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
       return 1;
     }
     trimbb(resultsav, resultline);
     if (strlen(resultsav) >1){
       j=nbocc(resultsav,'='); /**< j=Number of covariate values'=' */
     }
   
     for(k=1; k<=j;k++){ /* Loop on total covariates of the model */
       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 */
       Tvalsel[k]=atof(strc); /* 1 */
   
       cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
       Tvarsel[k]=atoi(strc);
       /* Typevarsel[k]=1;  /\* 1 for age product *\/ */
       /* cptcovsel++;     */
       if (nbocc(stra,'=') >0)
         strcpy(resultsav,stra); /* and analyzes it */
     }
     return (0);
   }
   int selected( int kvar){ /* Selected combination of covariates */
     if(Tvarsel[kvar])
       return (0);
     else
       return(1);
   }
   int decodemodel( char model[], int lastobs)
    /**< 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
         * - nagesqr = 1 if age*age in the model, otherwise 0.          * - nagesqr = 1 if age*age in the model, otherwise 0.
         * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age          * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
Line 7681  int decodemodel ( char model[], int last Line 7854  int decodemodel ( char model[], int last
         */          */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int  j1, k1, k2;    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];
   char *strpt;    char *strpt;
Line 7782  int decodemodel ( char model[], int last Line 7955  int decodemodel ( char model[], int last
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */        /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
       /*        /*
        * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */         * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
       for(k=cptcovt; k>=1;k--) /**< Number of covariates not including constant and age, neither age*age*/        for(k=cptcovt; k>=1;k--){ /**< Number of covariates not including constant and age, neither age*age*/
         Tvar[k]=0;          Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
         }
       cptcovage=0;        cptcovage=0;
       for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */        for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
         cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'           cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' 
Line 7798  int decodemodel ( char model[], int last Line 7972  int decodemodel ( char model[], int last
             cptcovprod--;              cptcovprod--;
             cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */              cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
             Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */              Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
             Typevar[k]=1;  /* 2 for age product */              Typevar[k]=1;  /* 1 for age product */
             cptcovage++; /* Sums the number of covariates which include age as a product */              cptcovage++; /* Sums the number of covariates which include age as a product */
             Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */              Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
             /*printf("stre=%s ", stre);*/              /*printf("stre=%s ", stre);*/
Line 7822  int decodemodel ( char model[], int last Line 7996  int decodemodel ( char model[], int last
             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  */
               Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
             Tvard[k1][1] =atoi(strc); /* m 1 for V1*/              Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
             Tvard[k1][2] =atoi(stre); /* n 4 for V4*/              Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
             k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */              k2=k2+2;  /* k2 is initialize to -1, We want to store the n and m in Vn*Vm at the end of Tvar */
Line 7840  int decodemodel ( char model[], int last Line 8015  int decodemodel ( char model[], int last
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/            /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
           /*  scanf("%d",i);*/            /*  scanf("%d",i);*/
           cutl(strd,strc,strb,'V');            cutl(strd,strc,strb,'V');
           ks++; /**< Number of simple covariates*/            ks++; /**< Number of simple covariates dummy or quantitative, fixe or varying */
           cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */            cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
           Tvar[k]=atoi(strd);            Tvar[k]=atoi(strd);
           Typevar[k]=0;  /* 0 for simple covariates */            Typevar[k]=0;  /* 0 for simple covariates */
Line 7861  int decodemodel ( char model[], int last Line 8036  int decodemodel ( char model[], int last
      scanf("%d ",i);*/       scanf("%d ",i);*/
   
   
 /* Decodemodel knows only the grammar (simple, product, age*) of the model but not what kind  /* Until here, decodemodel knows only the grammar (simple, product, age*) of the model but not what kind
    of variable (dummy vs quantitative, fixed vs time varying) is behind */     of variable (dummy vs quantitative, fixed vs time varying) is behind. But we know the # of each. */
 /* ncovcol= 1, nqv=1, ntv=2, nqtv= 1  = 5 possible variables data  /* ncovcol= 1, nqv=1 | ntv=2, nqtv= 1  = 5 possible variables data: 2 fixed 3, varying
    model=  V2 + V4 +V3 + V4*V3 + V5*age + V5 , V1 is not used saving its place     model=        V5 + V4 +V3 + V4*V3 + V5*age + V2 + V1*V2 + V1*age + V5*age, V1 is not used saving its place
    k =      1    2   3     4       5       6     k =           1    2   3     4       5       6      7      8        9
    Tvar[k]= 2    4   3 1+1+2+1+1=6 5       5     Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        5
    Typevar[k]=0  0   0     2       1       0     Typevar[k]=   0    0   0     2       1       0      2      1        1
      Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
      Dummy[k]      1    0   0     0       3       1      1      2        3
             Tmodelind[combination of covar]=k;
 */    */  
 /* Dispatching between quantitative and time varying covariates */  /* Dispatching between quantitative and time varying covariates */
     /* If Tvar[k] >ncovcol it is a product */
   /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */    /* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p  Vp=Vn*Vm for product */
           /* Computing effective variables, ie used by the model, that is from the cptcovt variables */
     printf("Model=%s\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\
   Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
     fprintf(ficlog,"Model=%s\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\
   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, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */    for(k=1, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
     if (Tvar[k] <=ncovcol){ /* Simple fixed dummy covariatee */      if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
         Fixed[k]= 0;
         Dummy[k]= 0;
       ncoveff++;        ncoveff++;
         TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */
         TvarFDind[ncoveff]=Tvar[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*/      }else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product Vn*Vm are added in k*/
       nqfveff++;  /* Only simple fixed quantitative variable */        Fixed[k]= 0;
         Dummy[k]= 1;
         nqfveff++;
         TvarFQ[nqfveff]=Tvar[k]; /* TvarFQ[1]=V2 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){
         Fixed[k]= 1;
         Dummy[k]= 0;
       ntveff++; /* Only simple time varying dummy variable */        ntveff++; /* Only simple time varying dummy variable */
     }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){        TvarVD[ntvveff]=Tvar[k]; /* TvarVD[1]=V5 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative variable */
       nqtveff++;/* Only simple time varying quantitative variable */        TvarVDind[ntveff++]=k; /* TvarVDind[1]=1 in V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1 */ /* Only simple fixed quantitative 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 TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
       }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
           Fixed[k]= 1;
           Dummy[k]= 1;
           TmodelInvQind[++nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* 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 TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
       }else if (Typevar[k] == 1) {  /* product with age */
         if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
           Fixed[k]= 2;
           Dummy[k]= 2;
           /* ncoveff++; */
         }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
           Fixed[k]= 2;
           Dummy[k]= 3;
           /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           Fixed[k]= 3;
           Dummy[k]= 2;
           /* ntveff++; /\* Only simple time varying dummy variable *\/ */
         }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
           Fixed[k]= 3;
           Dummy[k]= 3;
           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }
       }else if (Typevar[k] == 2) {  /* product without age */
         k1=Tposprod[k];
         if(Tvard[k1][1] <=ncovcol){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 0;  /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 0; /* or 2 ?*/
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
           if(Tvard[k1][2] <=ncovcol){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
             Fixed[k]= 1;
             Dummy[k]= 1;
           } 
         }else{
           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
         } /* end k1 */
     }else{      }else{
       printf("Other types in effective covariates \n");        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]);
       }
       printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
       fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
     }
     /* Searching for doublons in the model */
     for(k1=1; k1<= cptcovt;k1++){
       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] == 0 || Typevar[k1] == 1)){ /* Simple or age product */
             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]]);
               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);
             }
           }else if (Typevar[k1] ==2){
             k3=Tposprod[k1];
             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])) ){
               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);
               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);
   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 */ 
Line 8212  int prevalence_limit(double *p, double * Line 8524  int prevalence_limit(double *p, double *
     printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
     fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;      fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
   }    }
   printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);    printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);    fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);
   pstamp(ficrespl);    pstamp(ficrespl);
   fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);    fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
   fprintf(ficrespl,"#Age ");    fprintf(ficrespl,"#Age ");
Line 8225  int prevalence_limit(double *p, double * Line 8537  int prevalence_limit(double *p, double *
   agebase=ageminpar;    agebase=ageminpar;
   agelim=agemaxpar;    agelim=agemaxpar;
   
   i1=pow(2,ncoveff);    /* i1=pow(2,ncoveff); */
     i1=pow(2,cptcoveff); /* Number 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++){
Line 8238  int prevalence_limit(double *p, double * Line 8551  int prevalence_limit(double *p, double *
     fprintf(ficrespl,"#******");      fprintf(ficrespl,"#******");
     printf("#******");      printf("#******");
     fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
     for(j=1;j<=nqfveff;j++) {      for(j=1;j<=cptcoveff ;j++) {/* all covariates */
       fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
       printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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)]);
     }      }
     fprintf(ficrespl,"******\n");      fprintf(ficrespl,"******\n");
     printf("******\n");      printf("******\n");
     fprintf(ficlog,"******\n");      fprintf(ficlog,"******\n");
                 if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
                                                 printf("\nCombination (%d) ignored because no cases \n",k);         printf("\nCombination (%d) ignored because no case \n",k); 
                                                 fprintf(ficrespl,"#Combination (%d) ignored because no cases \n",k);         fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k); 
                                                 fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);         fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k); 
                                                 continue;                                                  continue;
                 }      }
   
     fprintf(ficrespl,"#Age ");      fprintf(ficrespl,"#Age ");
     for(j=1;j<=nqfveff;j++) {      for(j=1;j<=cptcoveff;j++) {
       fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     }      }
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"  %d-%d   ",i,i);
     fprintf(ficrespl,"Total Years_to_converge\n");      fprintf(ficrespl,"Total Years_to_converge\n");
               
     for (age=agebase; age<=agelim; age++){      for (age=agebase; age<=agelim; age++){
       /* for (age=agebase; age<=agebase; age++){ */        /* for (age=agebase; age<=agebase; age++){ */
       prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);        prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
       fprintf(ficrespl,"%.0f ",age );        fprintf(ficrespl,"%.0f ",age );
       for(j=1;j<=nqfveff;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 */
Line 8312  int back_prevalence_limit(double *p, dou Line 8625  int back_prevalence_limit(double *p, dou
   agelim=agemaxpar;    agelim=agemaxpar;
       
       
   i1=pow(2,nqfveff);    i1=pow(2,cptcoveff);
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
     
         for(k=1; k<=i1;k++){     for(k=1; k<=i1;k++){ 
   /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */  
     /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */  
     //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
     /* k=k+1; */  
     /* to clean */  
     //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));      //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
     fprintf(ficresplb,"#******");      fprintf(ficresplb,"#******");
     printf("#******");      printf("#******");
     fprintf(ficlog,"#******");      fprintf(ficlog,"#******");
     for(j=1;j<=nqfveff;j++) {      for(j=1;j<=cptcoveff ;j++) {/* all covariates */
       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)]);
       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(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)]);
Line 8333  int back_prevalence_limit(double *p, dou Line 8641  int back_prevalence_limit(double *p, dou
     fprintf(ficresplb,"******\n");      fprintf(ficresplb,"******\n");
     printf("******\n");      printf("******\n");
     fprintf(ficlog,"******\n");      fprintf(ficlog,"******\n");
                 if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
                                                 printf("\nCombination (%d) ignored because no cases \n",k);         printf("\nCombination (%d) ignored because no cases \n",k); 
                                                 fprintf(ficresplb,"#Combination (%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);         fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k); 
                                                 continue;        continue;
                 }      }
           
     fprintf(ficresplb,"#Age ");      fprintf(ficresplb,"#Age ");
     for(j=1;j<=nqfveff;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);
Line 8353  int back_prevalence_limit(double *p, dou Line 8661  int back_prevalence_limit(double *p, dou
       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);
       }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);
       }        }
       fprintf(ficresplb,"%.0f ",age );        fprintf(ficresplb,"%.0f ",age );
       for(j=1;j<=nqfveff;j++)        for(j=1;j<=cptcoveff;j++)
                                 fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresplb,"%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 +=  bprlim[i][i];          tot +=  bprlim[i][i];
                                 fprintf(ficresplb," %.5f", bprlim[i][i]);          fprintf(ficresplb," %.5f", bprlim[i][i]);
       }        }
       fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);        fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
     } /* Age */      } /* Age */
Line 8411  int hPijx(double *p, int bage, int fage) Line 8719  int hPijx(double *p, int bage, int fage)
     /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
     pstamp(ficrespij);      pstamp(ficrespij);
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     i1= pow(2,nqfveff);      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,nqfveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=nqfveff;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)]);
       fprintf(ficrespij,"******\n");        fprintf(ficrespij,"******\n");
               
Line 8483  int hPijx(double *p, int bage, int fage) Line 8791  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 Pij x Back Probability to be in state i at age x-h being in j at x ");
   i1= pow(2,nqfveff);    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,nqfveff); k++){    for (k=1; k <= (int) pow(2,cptcoveff); k++){
     fprintf(ficrespijb,"\n#****** ");      fprintf(ficrespijb,"\n#****** ");
     for(j=1;j<=nqfveff;j++)      for(j=1;j<=cptcoveff;j++)
       fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
     fprintf(ficrespijb,"******\n");      fprintf(ficrespijb,"******\n");
     if(invalidvarcomb[k]){      if(invalidvarcomb[k]){
Line 8574  int main(int argc, char *argv[]) Line 8882  int main(int argc, char *argv[])
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
   char model[MAXLINE], modeltemp[MAXLINE];    char model[MAXLINE], modeltemp[MAXLINE];
     char resultline[MAXLINE];
     
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
Line 9036  run imach with mle=-1 to get a correct t Line 9346  run imach with mle=-1 to get a correct t
                                   
     /* Scans npar lines */      /* Scans npar lines */
     for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
       count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);        count=fscanf(ficpar,"%1d%1d%d",&i1,&j1,&jk);
       if(count != 3){        if(count != 3){
                                 printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\          printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
                                 fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\          fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
 This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\  This is probably because your covariance matrix doesn't \n  contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
 Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);  Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
                                 exit(1);          exit(1);
       }else{        }else{
                                 if(mle==1)          if(mle==1)
                                         printf("%1d%1d%1d",i1,j1,jk);            printf("%1d%1d%d",i1,j1,jk);
                         }        }
       fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);        fprintf(ficlog,"%1d%1d%d",i1,j1,jk);
       fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);        fprintf(ficparo,"%1d%1d%d",i1,j1,jk);
       for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
                                 fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
                                 if(mle==1){          if(mle==1){
                                         printf(" %.5le",matcov[i][j]);            printf(" %.5le",matcov[i][j]);
                                 }          }
                                 fprintf(ficlog," %.5le",matcov[i][j]);          fprintf(ficlog," %.5le",matcov[i][j]);
                                 fprintf(ficparo," %.5le",matcov[i][j]);          fprintf(ficparo," %.5le",matcov[i][j]);
       }        }
       fscanf(ficpar,"\n");        fscanf(ficpar,"\n");
       numlinepar++;        numlinepar++;
Line 9069  Please run with mle=-1 to get a correct Line 9379  Please run with mle=-1 to get a correct
     /* End of read covariance matrix npar lines */      /* End of read covariance matrix npar lines */
     for(i=1; i <=npar; i++)      for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)        for(j=i+1;j<=npar;j++)
                                 matcov[i][j]=matcov[j][i];          matcov[i][j]=matcov[j][i];
           
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
Line 9129  Please run with mle=-1 to get a correct Line 9439  Please run with mle=-1 to get a correct
         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. */
   Typevar=ivector(1,NCOVMAX); /* -1 to 4 */    Tvarsel=ivector(1,NCOVMAX); /*  */
     Tvalsel=vector(1,NCOVMAX); /*  */
     Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
     Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
     Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
   /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).     /*  V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs). 
       For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,         For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4, 
       Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.        Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 9139  Please run with mle=-1 to get a correct Line 9453  Please run with mle=-1 to get a correct
     ncovcol + k1      ncovcol + k1
     If already ncovcol=4 and model=V2+V1+V1*V4+age*V3      If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
     Tvar[3=V1*V4]=4+1 etc */      Tvar[3=V1*V4]=4+1 etc */
   Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */    Tprod=ivector(1,NCOVMAX); /* Gives the k position of the k1 product */
     Tposprod=ivector(1,NCOVMAX); /* Gives the k1 product from the k position */
   /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3    /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
      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]=2 
   */    */
   Tvaraff=ivector(1,NCOVMAX); /* Unclear */    Tvaraff=ivector(1,NCOVMAX); /* Unclear */
   Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm    Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1]  and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
Line 9151  Please run with mle=-1 to get a correct Line 9467  Please run with mle=-1 to get a correct
                          4 covariates (3 plus signs)                           4 covariates (3 plus signs)
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
     Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual dummy, fixed or varying:
                                   * Tmodelind[Tvaraff[3]]=9,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 , 
                                   * V1 df, V2 qf, V3 & V4 dv, V5 qv
                                   * Tmodelind[1]@9={9,0,3,2,}*/
     TmodelInvind=ivector(1,NCOVMAX); /* TmodelInvind=Tvar[k]- ncovcol-nqv={5-2-1=2,*/
     TmodelInvQind=ivector(1,NCOVMAX);/** gives the k model position of an
                                   * individual quantitative, fixed or varying:
                                   * Tmodelqind[1]=1,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*/
 /* Main decodemodel */  /* Main decodemodel */
   
   
Line 9213  Please run with mle=-1 to get a correct Line 9541  Please run with mle=-1 to get a correct
   cptcoveff=0;    cptcoveff=0;
   if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */    if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and age*age */
     tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */      tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
         }    }
             
         ncovcombmax=pow(2,cptcoveff);    ncovcombmax=pow(2,cptcoveff);
         invalidvarcomb=ivector(1, ncovcombmax);     invalidvarcomb=ivector(1, ncovcombmax); 
         for(i=1;i<ncovcombmax;i++)    for(i=1;i<ncovcombmax;i++)
                 invalidvarcomb[i]=0;      invalidvarcomb[i]=0;
     
   /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in    /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
      V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/       V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
   /* 1 to ncodemax[j] which is the maximum value of this jth covariate */    /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
     
   /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */    /*  codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
   /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/    /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
   /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/    /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
Line 9382  Title=%s <br>Datafile=%s Firstpass=%d La Line 9710  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, 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,"<br>Total number of observations=%d <br>\n\
Line 9416  Interval (in months) between two waves: Line 9744  Interval (in months) between two waves:
     for (i=1; i<=imx; i++){      for (i=1; i<=imx; i++){
       dcwave[i]=-1;        dcwave[i]=-1;
       for (m=firstpass; m<=lastpass; m++)        for (m=firstpass; m<=lastpass; m++)
                                 if (s[m][i]>nlstate) {          if (s[m][i]>nlstate) {
                                         dcwave[i]=m;            dcwave[i]=m;
                                         /*      printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/            /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
                                         break;            break;
                                 }          }
     }      }
                       
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       if (wav[i]>0){        if (wav[i]>0){
                                 ageexmed[i]=agev[mw[1][i]][i];          ageexmed[i]=agev[mw[1][i]][i];
                                 j=wav[i];          j=wav[i];
                                 agecens[i]=1.;           agecens[i]=1.; 
                                           
                                 if (ageexmed[i]> 1 && wav[i] > 0){          if (ageexmed[i]> 1 && wav[i] > 0){
                                         agecens[i]=agev[mw[j][i]][i];            agecens[i]=agev[mw[j][i]][i];
                                         cens[i]= 1;            cens[i]= 1;
                                 }else if (ageexmed[i]< 1)           }else if (ageexmed[i]< 1) 
                                         cens[i]= -1;            cens[i]= -1;
                                 if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)          if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
                                         cens[i]=0 ;            cens[i]=0 ;
       }        }
       else cens[i]=-1;        else cens[i]=-1;
     }      }
           
     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]=(i == j ? 1.0 : 0.0);          ximort[i][j]=(i == j ? 1.0 : 0.0);
     }      }
           
     /*p[1]=0.0268; p[NDIM]=0.083;*/      /*p[1]=0.0268; p[NDIM]=0.083;*/
Line 9917  Please run with mle=-1 to get a correct Line 10245  Please run with mle=-1 to get a correct
     fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);      fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/      /* day and month of proj2 are not used but only year anproj2.*/
           
       /* Results */
       while(fgets(line, MAXLINE, ficpar)) {
         /* If line starts with a # it is a comment */
         if (line[0] == '#') {
           numlinepar++;
           fputs(line,stdout);
           fputs(line,ficparo);
           fputs(line,ficlog);
           continue;
         }else
           break;
       }
       while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
         if (num_filled == 0)
           resultline[0]='\0';
         else if (num_filled != 1){
           printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
         }
         printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);
         decoderesult(resultline);
         while(fgets(line, MAXLINE, ficpar)) {
           /* If line starts with a # it is a comment */
           if (line[0] == '#') {
             numlinepar++;
             fputs(line,stdout);
             fputs(line,ficparo);
             fputs(line,ficlog);
             continue;
           }else
             break;
         }
         if (feof(ficpar))
           break;
         else{ /* Processess output results for this combination of covariate values */
         }                            
       }
   
   
           
                 /* 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); */
           
     replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */      replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
     if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){      if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
                         printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\        printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\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\  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);
                         fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\        fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\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\  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{
Line 9964  Please run with mle=-1 to get a correct Line 10330  Please run with mle=-1 to get a correct
     /*#include "hpijx.h"*/      /*#include "hpijx.h"*/
     hPijx(p, bage, fage);      hPijx(p, bage, fage);
     fclose(ficrespij);      fclose(ficrespij);
       
     /* ncovcombmax=  pow(2,cptcoveff); */      /* ncovcombmax=  pow(2,cptcoveff); */
     /*-------------- Variance of one-step probabilities---*/      /*-------------- Variance of one-step probabilities---*/
     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 covariates in probs[age][status][cov] */
     probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);      probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
     for(i=1;i<=AGESUP;i++)      for(i=1;i<=AGESUP;i++)
Line 9979  Please run with mle=-1 to get a correct Line 10345  Please run with mle=-1 to get a correct
     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(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
                         for(i=1;i<=AGESUP;i++)        for(i=1;i<=AGESUP;i++)
                                 for(j=1;j<=nlstate;j++)          for(j=1;j<=nlstate;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) {
                                 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);
                                 }          }
       }        }
       /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */        /* /\* Prevalence for each covariates in probs[age][status][cov] *\/ */
       /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */        /* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
       else if (mobilavproj !=0) {        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);
                                 }          }
       }        }
     }/* end if moving average */      }/* end if moving average */
                       
     /*---------- Forecasting ------------------*/      /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/      /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){      if(prevfcast==1){
Line 10048  Please run with mle=-1 to get a correct Line 10414  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);
                                   
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\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)]);
       }        }
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
               
Line 10065  Please run with mle=-1 to get a correct Line 10431  Please run with mle=-1 to get a correct
     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);
                                   
     /*---------- Health expectancies and variances ------------*/      /*---------- State-specific expectancies and variances ------------*/
                                   
                                   
     strcpy(filerest,"T_");      strcpy(filerest,"T_");
Line 10081  Please run with mle=-1 to get a correct Line 10447  Please run with mle=-1 to get a correct
     strcpy(fileresstde,"STDE_");      strcpy(fileresstde,"STDE_");
     strcat(fileresstde,fileresu);      strcat(fileresstde,fileresu);
     if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {      if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
       printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        printf("Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);        fprintf(ficlog,"Problem with State specific Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
     }      }
     printf("  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      printf("  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
     fprintf(ficlog,"  Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);      fprintf(ficlog,"  Computing State-specific Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
     strcpy(filerescve,"CVE_");      strcpy(filerescve,"CVE_");
     strcat(filerescve,fileresu);      strcat(filerescve,fileresu);
     if((ficrescveij=fopen(filerescve,"w"))==NULL) {      if((ficrescveij=fopen(filerescve,"w"))==NULL) {
       printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        printf("Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
       fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);        fprintf(ficlog,"Problem with Covar. State-specific Exp. resultfile: %s\n", filerescve); exit(0);
     }      }
     printf("    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      printf("    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
     fprintf(ficlog,"    Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);      fprintf(ficlog,"    Computing Covar. of State-specific Expectancies: result on file '%s' \n", filerescve);
   
     strcpy(fileresv,"V_");      strcpy(fileresv,"V_");
     strcat(fileresv,fileresu);      strcat(fileresv,fileresu);
Line 10102  Please run with mle=-1 to get a correct Line 10468  Please run with mle=-1 to get a correct
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }      }
     printf("      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);      printf("      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
     fprintf(ficlog,"      Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);      fprintf(ficlog,"      Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
   
     /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){      /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
                       
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         printf("\n#****** ");
       fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         fprintf(ficlog,"\n#****** ");
                                 fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        for(j=1;j<=cptcoveff;j++){ 
           printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(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(ficrest,"******\n");        fprintf(ficrest,"******\n");
         fprintf(ficlog,"******\n");
         printf("******\n");
               
       fprintf(ficresstdeij,"\n#****** ");        fprintf(ficresstdeij,"\n#****** ");
       fprintf(ficrescveij,"\n#****** ");        fprintf(ficrescveij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
                                 fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);          fprintf(ficresstdeij,"V%d=%d ",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)]);
       }        }
       fprintf(ficresstdeij,"******\n");        fprintf(ficresstdeij,"******\n");
       fprintf(ficrescveij,"******\n");        fprintf(ficrescveij,"******\n");
               
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       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)]);
       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 %d, ",k);        printf(" cvevsij combination#=%d, ",k);
       fprintf(ficlog, " cvevsij %d, ",k);        fprintf(ficlog, " cvevsij combination#=%d, ",k);
       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);
       printf(" end cvevsij \n ");        printf(" end cvevsij \n ");
       fprintf(ficlog, " end cvevsij \n ");        fprintf(ficlog, " end cvevsij \n ");
Line 10145  Please run with mle=-1 to get a correct Line 10518  Please run with mle=-1 to get a correct
               
               
       for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/        for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
                                 oldm=oldms;savm=savms; /* ZZ Segmentation fault */          oldm=oldms;savm=savms; /* ZZ Segmentation fault */
                                 cptcod= 0; /* To be deleted */          cptcod= 0; /* To be deleted */
                                 printf("varevsij %d \n",vpopbased);          printf("varevsij vpopbased=%d \n",vpopbased);
                                 fprintf(ficlog, "varevsij %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); /* 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);
                                 else          else
                                         fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");            fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
                                 fprintf(ficrest,"# Age popbased mobilav e.. (std) ");          fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
                                 for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
                                 fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
                                 /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */          /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
                                 epj=vector(1,nlstate+1);          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); /*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++)
                                                                 prlim[i][i]=probs[(int)age][i][k];                  prlim[i][i]=probs[(int)age][i][k];
                                                 }else{ /* mobilav */               }else{ /* mobilav */ 
                                                         for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
                                                                 prlim[i][i]=mobaverage[(int)age][i][k];                  prlim[i][i]=mobaverage[(int)age][i][k];
                                                 }              }
                                         }            }
                       
                                         fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);            fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
                                         /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */            /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
                                         /* printf(" age %4.0f ",age); */            /* printf(" age %4.0f ",age); */
                                         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
                                                 for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(i=1, epj[j]=0.;i <=nlstate;i++) {
                                                         epj[j] += prlim[i][i]*eij[i][j][(int)age];                epj[j] += prlim[i][i]*eij[i][j][(int)age];
                                                         /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                /*ZZZ  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
                                                         /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */                /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
                                                 }              }
                                                 epj[nlstate+1] +=epj[j];              epj[nlstate+1] +=epj[j];
                                         }            }
                                         /* printf(" age %4.0f \n",age); */            /* printf(" age %4.0f \n",age); */
                       
                                         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1, vepp=0.;i <=nlstate;i++)
                                                 for(j=1;j <=nlstate;j++)              for(j=1;j <=nlstate;j++)
                                                         vepp += vareij[i][j][(int)age];                vepp += vareij[i][j][(int)age];
                                         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
                                         for(j=1;j <=nlstate;j++){            for(j=1;j <=nlstate;j++){
                                                 fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
                                         }            }
                                         fprintf(ficrest,"\n");            fprintf(ficrest,"\n");
                                 }          }
       } /* End vpopbased */        } /* End vpopbased */
       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);
Line 10205  Please run with mle=-1 to get a correct Line 10578  Please run with mle=-1 to get a correct
               
       /*}*/        /*}*/
     } /* End k */      } /* End k */
     free_vector(weight,1,n);  
     free_imatrix(Tvard,1,NCOVMAX,1,2);  
     free_imatrix(s,1,maxwav+1,1,n);  
     free_matrix(anint,1,maxwav,1,n);   
     free_matrix(mint,1,maxwav,1,n);  
     free_ivector(cod,1,n);  
     free_ivector(tab,1,NCOVMAX);  
     fclose(ficresstdeij);  
     fclose(ficrescveij);  
     fclose(ficresvij);  
     fclose(ficrest);  
     printf("done Health expectancies\n");fflush(stdout);  
     fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);  
     fclose(ficpar);  
     
     /*------- Variance of period (stable) prevalence------*/     
   
       printf("done State-specific expectancies\n");fflush(stdout);
       fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
   
       /*------- Variance of period (stable) prevalence------*/   
       
     strcpy(fileresvpl,"VPL_");      strcpy(fileresvpl,"VPL_");
     strcat(fileresvpl,fileresu);      strcat(fileresvpl,fileresu);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
Line 10230  Please run with mle=-1 to get a correct Line 10592  Please run with mle=-1 to get a correct
     }      }
     printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);      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);      fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
       
     /*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++){*/
                 
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
         fprintf(ficresvpl,"\n#****** ");        fprintf(ficresvpl,"\n#****** ");
                         for(j=1;j<=cptcoveff;j++)         printf("\n#****** ");
                                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);        fprintf(ficlog,"\n#****** ");
                         fprintf(ficresvpl,"******\n");        for(j=1;j<=cptcoveff;j++) {
                 fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                         varpl=matrix(1,nlstate,(int) bage, (int) fage);          fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                         oldm=oldms;savm=savms;          printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
                         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);        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);      fclose(ficresvpl);
     printf("done variance-covariance of period prevalence\n");fflush(stdout);      printf("done variance-covariance of period prevalence\n");fflush(stdout);
     fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);      fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
       
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,NCOVMAX,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
       
       
     /*---------- 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,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
Line 10258  Please run with mle=-1 to get a correct Line 10641  Please run with mle=-1 to get a correct
     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 */
  /* endfree:*/    /* endfree:*/
     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);    free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
     free_ma3x(cotvar,1,maxwav,1,ntv,1,n);    free_ma3x(cotvar,1,maxwav,1,ntv,1,n);
     free_matrix(coqvar,1,maxwav,1,n);    free_matrix(coqvar,1,maxwav,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(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(Typevar,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);    free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(Tvarsel,1,NCOVMAX);
     free_ivector(Tage,1,NCOVMAX);    free_vector(Tvalsel,1,NCOVMAX);
     free_ivector(Tposprod,1,NCOVMAX);
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_ivector(Tprod,1,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */    free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_ivector(Tmodelind,1,NCOVMAX);
     free_ivector(TmodelInvind,1,NCOVMAX);
     free_ivector(TmodelInvQind,1,NCOVMAX);
     
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */
   fflush(fichtm);    fflush(fichtm);
   fflush(ficgp);    fflush(ficgp);
       
     
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);      printf("End of Imach with %d errors and/or %d warnings. Please look at the log file for details.\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d. Please look at the log file for details.\n",nberr,nbwarn);
Line 10305  Please run with mle=-1 to get a correct Line 10696  Please run with mle=-1 to get a correct
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend);     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
   printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
     
   printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
Line 10318  Please run with mle=-1 to get a correct Line 10709  Please run with mle=-1 to get a correct
   fclose(ficgp);    fclose(ficgp);
   fclose(ficlog);    fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
     
     
    printf("Before Current directory %s!\n",pathcd);    printf("Before Current directory %s!\n",pathcd);
 #ifdef WIN32  #ifdef WIN32
    if (_chdir(pathcd) != 0)    if (_chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n",path);      printf("Can't move to directory %s!\n",path);
    if(_getcwd(pathcd,MAXLINE) > 0)    if(_getcwd(pathcd,MAXLINE) > 0)
 #else  #else
    if(chdir(pathcd) != 0)      if(chdir(pathcd) != 0)
            printf("Can't move to directory %s!\n", path);        printf("Can't move to directory %s!\n", path);
    if (getcwd(pathcd, MAXLINE) > 0)    if (getcwd(pathcd, MAXLINE) > 0)
 #endif   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
Line 10354  Please run with mle=-1 to get a correct Line 10745  Please run with mle=-1 to get a correct
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
     
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
Line 10382  Please run with mle=-1 to get a correct Line 10773  Please run with mle=-1 to get a correct
     else if (z[0] == 'g') system(plotcmd);      else if (z[0] == 'g') system(plotcmd);
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
   end:  end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: "); fflush(stdout);      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
Removed from v.1.225  
changed lines
  Added in v.1.230

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