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version 1.226, 2016/07/12 18:42:34 version 1.227, 2016/07/21 08:43:33
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 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.227  2016/07/21 08:43:33  brouard
     Summary: 0.99 working (more or less) for Asian Workshop on multitate methods
   
   Revision 1.226  2016/07/12 18:42:34  brouard    Revision 1.226  2016/07/12 18:42:34  brouard
   Summary: temp    Summary: temp
   
Line 639 Line 642
   
   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
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   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  Important routines
   
Line 1037  double ***cotqvar; /* Time varying quant Line 1057  double ***cotqvar; /* Time varying quant
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
 int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */  int *Typevar; /**< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product */
 int *Fixed; /** Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */   int *Fixed; /** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */ 
 int *Dummy; /** Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */   int *Dummy; /** Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */ 
 int *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,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 2754  double ***hpxij(double ***po, int nhstep Line 2783  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 3867  void  freqsummary(char fileres[], int ia Line 3896  void  freqsummary(char fileres[], int ia
                   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;
Line 3928  Title=%s <br>Datafile=%s Firstpass=%d La Line 3957  Title=%s <br>Datafile=%s Firstpass=%d La
   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 *\/ */
     j=cptcoveff;  /* Only dummy covariates of the model */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   first=1;    first=1;
Line 3940  Title=%s <br>Datafile=%s Firstpass=%d La Line 3970  Title=%s <br>Datafile=%s Firstpass=%d La
      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);*/
Line 3955  Title=%s <br>Datafile=%s Firstpass=%d La Line 3985  Title=%s <br>Datafile=%s Firstpass=%d La
       posprop[i]=0;        posprop[i]=0;
       pospropt[i]=0;        pospropt[i]=0;
     }      }
     for (z1=1; z1<= nqfveff; z1++) {        /* for (z1=1; z1<= nqfveff; z1++) {   */
       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;      dateintsum=0;
     k2cpt=0;      k2cpt=0;
     /* For that comination of covariate j1, we count and print the frequencies */      /* For that combination of covariate j1, we count and print the frequencies in one pass */
     for (iind=1; iind<=imx; iind++) { /* For each individual iind */      for (iind=1; iind<=imx; iind++) { /* For each individual iind */
       bool=1;        bool=1;
       if (nqfveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */        if(anyvaryingduminmodel==0){ /* If All fixed covariates */
         for (z1=1; z1<= nqfveff; z1++) {            if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           meanq[z1]+=coqvar[Tvar[z1]][iind];            /* for (z1=1; z1<= nqfveff; z1++) {   */
         }            /*   meanq[z1]+=coqvar[Tvar[z1]][iind];  /\* Computes mean of quantitative with selected filter *\/ */
         for (z1=1; z1<=ncoveff; z1++) {              /* } */
           /* if(Tvaraff[z1] ==-20){ */            for (z1=1; z1<=cptcoveff; z1++) {  
           /*     /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */              /* if(Tvaraff[z1] ==-20){ */
           /* }else  if(Tvaraff[z1] ==-10){ */              /*   /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; *\/ */
           /*     /\* sumnew+=coqvar[z1][iind]; *\/ */              /* }else  if(Tvaraff[z1] ==-10){ */
           /* }else  */              /*   /\* sumnew+=coqvar[z1][iind]; *\/ */
           if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){              /* }else  */
             /* Tests if this individual i responded to j1 (V4=1 V3=0) */              if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
             bool=0;                /* Tests if this individual iind responded to j1 (V4=1 V3=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=0;
                bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),                /* 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", 
                j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/                   bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
             /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/                   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 */              } /* Onlyf fixed */
       } /* cptcovn > 0 */            } /* end z1 */
           } /* cptcovn > 0 */
       if (bool==1){ /* We selected an individual iin satisfying combination j1 */        } /* end any */
         if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */
         /* for(m=firstpass; m<=lastpass; m++){ */          /* for(m=firstpass; m<=lastpass; m++){ */
         for(mi=1; mi<wav[iind];mi++){          for(mi=1; mi<wav[iind];mi++){ /* For that wave */
           m=mw[mi][iind];            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]            if(anyvaryingduminmodel==1){ /* Some are varying covariates */
              and mw[mi+1][iind]. dh depends on stepm. */              for (z1=1; z1<=cptcoveff; z1++) {
           agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/                if( Fixed[Tmodelind[z1]]==1){
           ageend=agev[m][iind]+(dh[m][iind])*stepm/YEARM; /* Age at end of wave and transition */                  iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
           if(m >=firstpass && m <=lastpass){                  if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
             k2=anint[m][iind]+(mint[m][iind]/12.);                    bool=0;
             /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/                }else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
             if(agev[m][iind]==0) agev[m][iind]=iagemax+1;  /* All ages equal to 0 are in iagemax+1 */                  if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
             if(agev[m][iind]==1) agev[m][iind]=iagemax+2;  /* All ages equal to 1 are in iagemax+2 */                    bool=0;
             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 */  
             }              }
           }              }/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop  */
           if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {            /* bool =0 we keep that guy which corresponds to the combination of dummy values */
             dateintsum=dateintsum+k2;            if(bool==1){
             k2cpt++;              /* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
             /* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */                 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 */
                 }
               } /* end if between passes */  
               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 bool 2 */
         } /* end m */          } /* end m */
       } /* end bool */        } /* end bool */
     } /* end iind = 1 to imx */      } /* end iind = 1 to imx */
Line 4028  Title=%s <br>Datafile=%s Firstpass=%d La Line 4074  Title=%s <br>Datafile=%s Firstpass=%d La
   
     /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/      /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     pstamp(ficresp);      pstamp(ficresp);
     if  (ncoveff>0) {      /* if  (ncoveff>0) { */
       if  (cptcoveff>0) {
       fprintf(ficresp, "\n#********** Variable ");         fprintf(ficresp, "\n#********** Variable "); 
       fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");         fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable "); 
       fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");         fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable "); 
       for (z1=1; z1<=ncoveff; z1++){        for (z1=1; z1<=cptcoveff; z1++){
         fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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(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(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
Line 4041  Title=%s <br>Datafile=%s Firstpass=%d La Line 4088  Title=%s <br>Datafile=%s Firstpass=%d La
       fprintf(ficresphtm, "**********</h3>\n");        fprintf(ficresphtm, "**********</h3>\n");
       fprintf(ficresphtmfr, "**********</h3>\n");        fprintf(ficresphtmfr, "**********</h3>\n");
       fprintf(ficlog, "\n#********** Variable ");         fprintf(ficlog, "\n#********** Variable "); 
       for (z1=1; z1<=ncoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);        for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
       fprintf(ficlog, "**********\n");        fprintf(ficlog, "**********\n");
     }      }
     fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");      fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
Line 4203  Title=%s <br>Datafile=%s Firstpass=%d La Line 4250  Title=%s <br>Datafile=%s Firstpass=%d La
 }  }
   
 /************ 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 4304  void  concatwav(int wav[], int **dh, int Line 4361  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 4323  void  concatwav(int wav[], int **dh, int Line 4380  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 4410  void  concatwav(int wav[], int **dh, int Line 4467  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 4424  void  concatwav(int wav[], int **dh, int Line 4481  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 4534  void  concatwav(int wav[], int **dh, int Line 4591  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 4627  void  concatwav(int wav[], int **dh, int Line 4694  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;
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){        Tvaraff[ij]=Tvar[k]; /*For printing */
       Tvaraff[++ij]=-10; /* Dont'n know how to treat quantitative variables yet */        Tmodelind[ij]=k;
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){        if(Fixed[k]!=0)
       Tvaraff[++ij]=i; /*For printing (unclear) */          anyvaryingduminmodel=1;
     }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){      /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
       Tvaraff[++ij]=-20; /* Dont'n know how to treat quantitative variables yet */      /*   Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet *\/ */
     }      /* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
       /*   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;
     }
     /* To be sorted */
     ;
 }  }
   
   
Line 6056  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 6137  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 6210  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6291  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 6347  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6428  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 6521  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 6602  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 6784  void prevforecast(char fileres[], double Line 6865  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 6982  void prevforecast(char fileres[], double Line 7064  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 7705  int decodemodel ( char model[], int last Line 7787  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 7806  int decodemodel ( char model[], int last Line 7888  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 7846  int decodemodel ( char model[], int last Line 7929  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 7864  int decodemodel ( char model[], int last Line 7948  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 7892  int decodemodel ( char model[], int last Line 7976  int decodemodel ( char model[], int last
    k =           1    2   3     4       5       6      7      8        9     k =           1    2   3     4       5       6      7      8        9
    Tvar[k]=      5    4   3 1+1+2+1+1=6 5       2      7      1        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      2      1        1     Typevar[k]=   0    0   0     2       1       0      2      1        1
    Fixed[Tvar[k]]1    1   1     1       2       0      1      2        3     Fixed[k]      1    1   1     1       3       0    0 or 2   2        3
    Dummy[Tvar[k]]1    0   0     0       2       1      1      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 */    /* 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 */          /* 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 && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */      if (Tvar[k] <=ncovcol && (Typevar[k]==0 || Typevar[k]==2)){ /* Simple or product fixed dummy covariatee */
       Fixed[Tvar[k]]= 0;        Fixed[k]= 0;
       Dummy[Tvar[k]]= 0;        Dummy[k]= 0;
       ncoveff++;        ncoveff++;
     }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*/
       Fixed[Tvar[k]]= 0;        Fixed[k]= 0;
       Dummy[Tvar[k]]= 1;        Dummy[k]= 1;
       nqfveff++;  /* Only simple fixed quantitative variable */        nqfveff++;  /* 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[Tvar[k]]= 1;        Fixed[k]= 1;
       Dummy[Tvar[k]]= 0;        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){      }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv  && Typevar[k]==0){
       if( Typevar[k]==0){          Fixed[k]= 1;
         Fixed[Tvar[k]]= 1;          Dummy[k]= 1;
         Dummy[Tvar[k]]= 1;  
         nqtveff++;/* Only simple time varying quantitative variable */          nqtveff++;/* Only simple time varying quantitative variable */
       }      }else if (Typevar[k] == 1) {  /* product with age */
     }else if (Typevar[k] == 2) {        if (Tvar[k] <=ncovcol ){ /* Simple or product fixed dummy covariatee */
       for(k1=1; k1 <= cptcovprodnoage; k1++){          Fixed[k]= 2;
         if(Tvard[k1][1] <=ncovcol){          Dummy[k]= 2;
           if(Tvard[k1][2] <=ncovcol){          /* ncoveff++; */
             Fixed[Tvar[k]]= 1;        }else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product Vn*Vm are added in k*/
             Dummy[Tvar[k]]= 0;          Fixed[k]= 2;
           }else if(Tvard[k1][2] <=ncovcol+nqv){          Dummy[k]= 3;
             Fixed[Tvar[k]]= 0;          /* nqfveff++;  /\* Only simple fixed quantitative variable *\/ */
             Dummy[Tvar[k]]= 1;        }else if( Tvar[k] <=ncovcol+nqv+ntv ){
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          Fixed[k]= 3;
             Fixed[Tvar[k]]= 1;          Dummy[k]= 2;
             Dummy[Tvar[k]]= 0;          /* ntveff++; /\* Only simple time varying dummy variable *\/ */
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){        }else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
             Fixed[Tvar[k]]= 1;          Fixed[k]= 3;
             Dummy[Tvar[k]]= 1;          Dummy[k]= 3;
           }           /* nqtveff++;/\* Only simple time varying quantitative variable *\/ */
         }else if(Tvard[k1][1] <=ncovcol+nqv){        }
           if(Tvard[k1][2] <=ncovcol){      }else if (Typevar[k] == 2) {  /* product without age */
             Fixed[Tvar[k]]= 0;        k1=Tposprod[k];
             Dummy[Tvar[k]]= 1;        if(Tvard[k1][1] <=ncovcol){
           }else if(Tvard[k1][2] <=ncovcol+nqv){          if(Tvard[k1][2] <=ncovcol){
             Fixed[Tvar[k]]= 0;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 0;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 0;  /* or 2 ?*/
             Dummy[Tvar[k]]= 1;            Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 0;
           }           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){            Fixed[k]= 1;
           if(Tvard[k1][2] <=ncovcol){            Dummy[k]= 1;
             Fixed[Tvar[k]]= 1;          } 
             Dummy[Tvar[k]]= 1;        }else if(Tvard[k1][1] <=ncovcol+nqv){
           }else if(Tvard[k1][2] <=ncovcol+nqv){          if(Tvard[k1][2] <=ncovcol){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 0;  /* or 2 ?*/
             Dummy[Tvar[k]]= 1;            Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 0; /* or 2 ?*/
             Dummy[Tvar[k]]= 0;            Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 1;
           }           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
         }else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){            Fixed[k]= 1;
           if(Tvard[k1][2] <=ncovcol){            Dummy[k]= 1;
             Fixed[Tvar[k]]= 1;          } 
             Dummy[Tvar[k]]= 1;        }else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
           }else if(Tvard[k1][2] <=ncovcol+nqv){          if(Tvard[k1][2] <=ncovcol){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){          }else if(Tvard[k1][2] <=ncovcol+nqv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 1;
           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){          }else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
             Fixed[Tvar[k]]= 1;            Fixed[k]= 1;
             Dummy[Tvar[k]]= 1;            Dummy[k]= 0;
           }           }else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
         }else{            Fixed[k]= 1;
           printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);            Dummy[k]= 1;
           fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);          } 
         }        }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 */        } /* end k1 */
     }else{      }else{
       printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
       fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);        fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
     }      }
     printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[Tvar[k]],Dummy[Tvar[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[Tvar[k]],Dummy[Tvar[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("Model=%s\n\  
 Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for  product \n\  
 Fixed[Tvar[k]] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product \n\  
 Dummy[Tvar[k]] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);  
   
   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 8320  int prevalence_limit(double *p, double * Line 8446  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 8333  int prevalence_limit(double *p, double * Line 8459  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 8346  int prevalence_limit(double *p, double * Line 8473  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 8420  int back_prevalence_limit(double *p, dou Line 8547  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 8441  int back_prevalence_limit(double *p, dou Line 8563  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 8461  int back_prevalence_limit(double *p, dou Line 8583  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 8519  int hPijx(double *p, int bage, int fage) Line 8641  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 8591  int hPijx(double *p, int bage, int fage) Line 8713  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 9249  Please run with mle=-1 to get a correct Line 9371  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 9261  Please run with mle=-1 to get a correct Line 9385  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);/** five 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*/
 /* Main decodemodel */  /* Main decodemodel */
   
   
Line 9323  Please run with mle=-1 to get a correct Line 9451  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 9492  Title=%s <br>Datafile=%s Firstpass=%d La Line 9620  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 10074  Please run with mle=-1 to get a correct Line 10202  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 10089  Please run with mle=-1 to get a correct Line 10217  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 10158  Please run with mle=-1 to get a correct Line 10286  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 10175  Please run with mle=-1 to get a correct Line 10303  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 10191  Please run with mle=-1 to get a correct Line 10319  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 10212  Please run with mle=-1 to get a correct Line 10340  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 10255  Please run with mle=-1 to get a correct Line 10390  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 10315  Please run with mle=-1 to get a correct Line 10450  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 10340  Please run with mle=-1 to get a correct Line 10464  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 10368  Please run with mle=-1 to get a correct Line 10513  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(Dummy,-1,NCOVMAX);    free_ivector(Dummy,-1,NCOVMAX);
     free_ivector(Fixed,-1,NCOVMAX);    free_ivector(Fixed,-1,NCOVMAX);
     free_ivector(Typevar,-1,NCOVMAX);    free_ivector(Typevar,-1,NCOVMAX);
     free_ivector(Tvar,1,NCOVMAX);    free_ivector(Tvar,1,NCOVMAX);
     free_ivector(Tprod,1,NCOVMAX);    free_ivector(Tposprod,1,NCOVMAX);
     free_ivector(Tvaraff,1,NCOVMAX);    free_ivector(Tprod,1,NCOVMAX);
     free_ivector(invalidvarcomb,1,ncovcombmax);    free_ivector(Tvaraff,1,NCOVMAX);
     free_ivector(Tage,1,NCOVMAX);    free_ivector(invalidvarcomb,1,ncovcombmax);
     free_ivector(Tage,1,NCOVMAX);
     free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);    free_ivector(Tmodelind,1,NCOVMAX);
     /* free_imatrix(codtab,1,100,1,10); */    
     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 10417  Please run with mle=-1 to get a correct Line 10564  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 10430  Please run with mle=-1 to get a correct Line 10577  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 10466  Please run with mle=-1 to get a correct Line 10613  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 10494  Please run with mle=-1 to get a correct Line 10641  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.1.226  
changed lines
  Added in v.1.227

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