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Diff for /imach/src/imach.c between versions 1.3 and 1.11

version 1.3, 2001/05/02 17:21:42 version 1.11, 2001/05/17 16:07:14
Line 8 Line 8
   Health expectancies are computed from the transistions observed between    Health expectancies are computed from the transistions observed between
   waves and are computed for each degree of severity of disability (number    waves and are computed for each degree of severity of disability (number
   of life states). More degrees you consider, more time is necessary to    of life states). More degrees you consider, more time is necessary to
   reach the Maximum Likelihood of the parameters involved in the model.    reach the Maximum Likelihood of the parameters involved in the model.
   The simplest model is the multinomial logistic model where pij is    The simplest model is the multinomial logistic model where pij is
   the probabibility to be observed in state j at the second wave conditional    the probabibility to be observed in state j at the second wave conditional
   to be observed in state i at the first wave. Therefore the model is:    to be observed in state i at the first wave. Therefore the model is:
Line 51 Line 51
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 80
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  #define windows
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
Line 66 Line 68
   
   
 int nvar;  int nvar;
 static int cptcov;  int cptcovn, cptcovage=0, cptcoveff=0,cptcov;
 int cptcovn;  
 int npar=NPARMAX;  int npar=NPARMAX;
 int nlstate=2; /* Number of live states */  int nlstate=2; /* Number of live states */
 int ndeath=1; /* Number of dead states */  int ndeath=1; /* Number of dead states */
Line 75  int ncovmodel, ncov;     /* Total number Line 76  int ncovmodel, ncov;     /* Total number
   
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int mle, weightopt;  int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   double jmean; /* Mean space between 2 waves */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;
Line 89  FILE *ficreseij; Line 92  FILE *ficreseij;
  FILE  *ficresvpl;   FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];    char fileresvpl[FILENAMELENGTH];
   
   
   
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
 #define FTOL 1.0e-10  #define FTOL 1.0e-10
Line 125  int stepm; Line 125  int stepm;
 /* Stepm, step in month: minimum step interpolation*/  /* Stepm, step in month: minimum step interpolation*/
   
 int m,nb;  int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij;  double **pmmij;
   
 double *weight;  double *weight;
 int **s; /* Status */  int **s; /* Status */
 double *agedc, **covar, idx;  double *agedc, **covar, idx;
 int **nbcode, *Tcode, *Tvar, **codtab;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double ftolhess; /* Tolerance for computing hessian */  double ftolhess; /* Tolerance for computing hessian */
   
   /**************** split *************************/
   static  int split( char *path, char *dirc, char *name )
   {
      char *s;                             /* pointer */
      int  l1, l2;                         /* length counters */
   
      l1 = strlen( path );                 /* length of path */
      if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      s = strrchr( path, '\\' );           /* find last / */
      if ( s == NULL ) {                   /* no directory, so use current */
   #if     defined(__bsd__)                /* get current working directory */
         extern char       *getwd( );
   
         if ( getwd( dirc ) == NULL ) {
   #else
         extern char       *getcwd( );
   
         if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   #endif
            return( GLOCK_ERROR_GETCWD );
         }
         strcpy( name, path );             /* we've got it */
      } else {                             /* strip direcotry from path */
         s++;                              /* after this, the filename */
         l2 = strlen( s );                 /* length of filename */
         if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         strcpy( name, s );                /* save file name */
         strncpy( dirc, path, l1 - l2 );   /* now the directory */
         dirc[l1-l2] = 0;                  /* add zero */
      }
      l1 = strlen( dirc );                 /* length of directory */
      if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
      return( 0 );                         /* we're done */
   }
   
   
 /******************************************/  /******************************************/
   
Line 166  int nbocc(char *s, char occ) Line 201  int nbocc(char *s, char occ)
   
 void cutv(char *u,char *v, char*t, char occ)  void cutv(char *u,char *v, char*t, char occ)
 {  {
   int i,lg,j,p;    int i,lg,j,p=0;
   i=0;    i=0;
   for(j=0; j<=strlen(t)-1; j++) {    for(j=0; j<=strlen(t)-1; j++) {
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
Line 175  void cutv(char *u,char *v, char*t, char Line 210  void cutv(char *u,char *v, char*t, char
   lg=strlen(t);    lg=strlen(t);
   for(j=0; j<p; j++) {    for(j=0; j<p; j++) {
     (u[j] = t[j]);      (u[j] = t[j]);
     u[p]='\0';  
   }    }
        u[p]='\0';
   
    for(j=0; j<= lg; j++) {     for(j=0; j<= lg; j++) {
     if (j>=(p+1))(v[j-p-1] = t[j]);      if (j>=(p+1))(v[j-p-1] = t[j]);
Line 613  double **prevalim(double **prlim, int nl Line 648  double **prevalim(double **prlim, int nl
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  
      cov[1]=1.;
    
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     newm=savm;      newm=savm;
     /* Covariates have to be included here again */      /* Covariates have to be included here again */
     cov[1]=1.;       cov[2]=agefin;
     cov[2]=agefin;   
     if (cptcovn>0){        for (k=1; k<=cptcovn;k++) {
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     }          /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/
         }
         for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
     savm=oldm;      savm=oldm;
Line 756  double ***hpxij(double ***po, int nhstep Line 803  double ***hpxij(double ***po, int nhstep
       /* Covariates have to be included here again */        /* Covariates have to be included here again */
       cov[1]=1.;        cov[1]=1.;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       if (cptcovn>0){        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];  for (k=1; k<=cptcovage;k++)
     }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
      for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[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]);*/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
Line 780  double ***hpxij(double ***po, int nhstep Line 831  double ***hpxij(double ***po, int nhstep
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
 {  {
   int i, ii, j, k, mi, d;    int i, ii, j, k, mi, d, kk;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double **out;    double **out;
   double sw; /* Sum of weights */    double sw; /* Sum of weights */
Line 790  double func( double *x) Line 841  double func( double *x)
   /* We are differentiating ll according to initial status */    /* We are differentiating ll according to initial status */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   /*for(i=1;i<imx;i++)    /*for(i=1;i<imx;i++)
 printf(" %d\n",s[4][i]);      printf(" %d\n",s[4][i]);
   */    */
     cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for(mi=1; mi<= wav[i]-1; mi++){      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (ii=1;ii<=nlstate+ndeath;ii++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             for(d=0; d<dh[mi][i]; d++){        for(d=0; d<dh[mi][i]; d++){
         newm=savm;          newm=savm;
           cov[1]=1.;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          for (kk=1; kk<=cptcovage;kk++) {
           if (cptcovn>0){            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];          }
             }         
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;          savm=oldm;
           oldm=newm;          oldm=newm;
          
          
       } /* end mult */        } /* end mult */
           
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
       ipmx +=1;        ipmx +=1;
Line 1113  void  freqsummary(char fileres[], int ag Line 1166  void  freqsummary(char fileres[], int ag
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
   j1=0;    j1=0;
   
   j=cptcovn;    j=cptcoveff;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
   for(k1=1; k1<=j;k1++){    for(k1=1; k1<=j;k1++){
    for(i1=1; i1<=ncodemax[k1];i1++){     for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;         j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
            scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)            for (i=-1; i<=nlstate+ndeath; i++)  
          for (jk=-1; jk<=nlstate+ndeath; jk++)             for (jk=-1; jk<=nlstate+ndeath; jk++)  
            for(m=agemin; m <= agemax+3; m++)             for(m=agemin; m <= agemax+3; m++)
Line 1128  void  freqsummary(char fileres[], int ag Line 1182  void  freqsummary(char fileres[], int ag
        for (i=1; i<=imx; i++) {         for (i=1; i<=imx; i++) {
          bool=1;           bool=1;
          if  (cptcovn>0) {           if  (cptcovn>0) {
            for (z1=1; z1<=cptcovn; z1++)             for (z1=1; z1<=cptcoveff; z1++)
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
                  bool=0;
          }           }
           if (bool==1) {            if (bool==1) {
            for(m=firstpass; m<=lastpass-1; m++){             for(m=firstpass; m<=lastpass-1; m++){
Line 1141  void  freqsummary(char fileres[], int ag Line 1196  void  freqsummary(char fileres[], int ag
          }           }
        }         }
         if  (cptcovn>0) {          if  (cptcovn>0) {
          fprintf(ficresp, "\n#Variable");           fprintf(ficresp, "\n#********** Variable ");
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
        }         fprintf(ficresp, "**********\n#");
        fprintf(ficresp, "\n#");          }
        for(i=1; i<=nlstate;i++)         for(i=1; i<=nlstate;i++)
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        fprintf(ficresp, "\n");         fprintf(ficresp, "\n");
Line 1212  void  concatwav(int wav[], int **dh, int Line 1267  void  concatwav(int wav[], int **dh, int
      */       */
   
   int i, mi, m;    int i, mi, m;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 float sum=0.;       double sum=0., jmean=0.;*/
   
     int j, k=0,jk, ju, jl;
     double sum=0.;
     jmin=1e+5;
     jmax=-1;
     jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
     mi=0;      mi=0;
     m=firstpass;      m=firstpass;
Line 1244  float sum=0.; Line 1304  float sum=0.;
         dh[mi][i]=1;          dh[mi][i]=1;
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) {          if (s[mw[mi+1][i]][i] > nlstate) {
             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 */
             k=k+1;
             if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
             sum=sum+j;
             if (j<0) printf("j=%d num=%d ",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));
Line 1266  float sum=0.; Line 1333  float sum=0.;
       }        }
     }      }
   }    }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
 }  }
 /*********** Tricode ****************************/  /*********** Tricode ****************************/
 void tricode(int *Tvar, int **nbcode, int imx)  void tricode(int *Tvar, int **nbcode, int imx)
 {  {
   int Ndum[80],ij, k, j, i;    int Ndum[20],ij=1, k, j, i;
   int cptcode=0;    int cptcode=0;
   for (k=0; k<79; k++) Ndum[k]=0;    cptcoveff=0;
    
     for (k=0; k<19; k++) Ndum[k]=0;
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
    
   for (j=1; j<=cptcovn; j++) {    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<=imx; i++) {      for (i=1; i<=imx; i++) {
       ij=(int)(covar[Tvar[j]][i]);        ij=(int)(covar[Tvar[j]][i]);
       Ndum[ij]++;        Ndum[ij]++;
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       if (ij > cptcode) cptcode=ij;        if (ij > cptcode) cptcode=ij;
     }      }
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/  
     for (i=0; i<=cptcode; i++) {      for (i=0; i<=cptcode; i++) {
       if(Ndum[i]!=0) ncodemax[j]++;        if(Ndum[i]!=0) ncodemax[j]++;
     }      }
    
     ij=1;      ij=1;
   
   
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1; i<=ncodemax[j]; i++) {
       for (k=0; k<=79; k++) {        for (k=0; k<=19; k++) {
         if (Ndum[k] != 0) {          if (Ndum[k] != 0) {
           nbcode[Tvar[j]][ij]=k;            nbcode[Tvar[j]][ij]=k;
           ij++;            ij++;
Line 1297  void tricode(int *Tvar, int **nbcode, in Line 1369  void tricode(int *Tvar, int **nbcode, in
         if (ij > ncodemax[j]) break;          if (ij > ncodemax[j]) break;
       }          }  
     }      }
   }      }  
   
   }   for (k=0; k<19; k++) Ndum[k]=0;
   
    for (i=1; i<=ncovmodel; i++) {
         ij=Tvar[i];
         Ndum[ij]++;
       }
   
    ij=1;
    for (i=1; i<=10; i++) {
      if((Ndum[i]!=0) && (i<=ncov)){
        Tvaraff[ij]=i;
        ij++;
      }
    }
    
       cptcoveff=ij-1;
   }
   
 /*********** Health Expectancies ****************/  /*********** Health Expectancies ****************/
   
Line 1552  void varprevlim(char fileres[], double * Line 1640  void varprevlim(char fileres[], double *
 int main()  int main()
 {  {
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;    int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
   double agedeb, agefin,hf;    double agedeb, agefin,hf;
   double agemin=1.e20, agemax=-1.e20;    double agemin=1.e20, agemax=-1.e20;
   
Line 1564  int main() Line 1652  int main()
   int *indx;    int *indx;
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE], linepar[MAXLINE];
   char title[MAXLINE];    char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];
   char filerest[FILENAMELENGTH];    char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];    char fileregp[FILENAMELENGTH];
Line 1573  int main() Line 1661  int main()
   int sdeb, sfin; /* Status at beginning and end */    int sdeb, sfin; /* Status at beginning and end */
   int c,  h , cpt,l;    int c,  h , cpt,l;
   int ju,jl, mi;    int ju,jl, mi;
   int i1,j1, k1,jk,aa,bb, stepsize;    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
     
   int hstepm, nhstepm;    int hstepm, nhstepm;
Line 1589  int main() Line 1677  int main()
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;    double *epj, vepp;
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";    char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   char z[1]="c", occ;    char z[1]="c", occ;
 #include <sys/time.h>  #include <sys/time.h>
 #include <time.h>  #include <time.h>
Line 1601  int main() Line 1690  int main()
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   
   
   printf("\nIMACH, Version 0.63");    printf("\nIMACH, Version 0.64b");
   printf("\nEnter the parameter file name: ");    printf("\nEnter the parameter file name: ");
   
 #ifdef windows  #ifdef windows
   scanf("%s",pathtot);    scanf("%s",pathtot);
   getcwd(pathcd, size);    getcwd(pathcd, size);
   cutv(path,optionfile,pathtot,'\\');    /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
   split(pathtot, path,optionfile);
   chdir(path);    chdir(path);
   replace(pathc,path);    replace(pathc,path);
 #endif  #endif
Line 1646  int main() Line 1739  int main()
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);
   
   covar=matrix(1,NCOVMAX,1,n);        covar=matrix(0,NCOVMAX,1,n);
   if (strlen(model)<=1) cptcovn=0;    cptcovn=0;
   else {    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
     j=0;  
     j=nbocc(model,'+');  
     cptcovn=j+1;  
   }  
   
   ncovmodel=2+cptcovn;    ncovmodel=2+cptcovn;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
Line 1744  int main() Line 1833  int main()
   printf("\n");    printf("\n");
   
   
    if(mle==1){  
     /*-------- data file ----------*/      /*-------- data file ----------*/
     if((ficres =fopen(fileres,"w"))==NULL) {      if((ficres =fopen(fileres,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileres);goto end;        printf("Problem with resultfile: %s\n", fileres);goto end;
Line 1797  int main() Line 1885  int main()
         }          }
         num[i]=atol(stra);          num[i]=atol(stra);
   
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][i]));*/          /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/
   
         i=i+1;          i=i+1;
       }        }
Line 1807  int main() Line 1895  int main()
   imx=i-1; /* Number of individuals */    imx=i-1; /* Number of individuals */
   
   /* Calculation of the number of parameter from char model*/    /* Calculation of the number of parameter from char model*/
   Tvar=ivector(1,8);        Tvar=ivector(1,15);
     Tprod=ivector(1,15);
     Tvaraff=ivector(1,15);
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
         
   if (strlen(model) >1){    if (strlen(model) >1){
     j=0;      j=0, j1=0, k1=1, k2=1;
     j=nbocc(model,'+');      j=nbocc(model,'+');
       j1=nbocc(model,'*');
     cptcovn=j+1;      cptcovn=j+1;
       cptcovprod=j1;
      
         
     strcpy(modelsav,model);      strcpy(modelsav,model);
     if (j==0) {      if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);        printf("Error. Non available option model=%s ",model);
         goto end;
     }      }
     else {     
       for(i=j; i>=1;i--){      for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+');        cutv(stra,strb,modelsav,'+');
         if (strchr(strb,'*')) {        if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);
           cutv(strd,strc,strb,'*');        /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;        /*scanf("%d",i);*/
         if (strchr(strb,'*')) {
           cutv(strd,strc,strb,'*');
           if (strcmp(strc,"age")==0) {
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) {
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {
             cutv(strb,stre,strc,'V');
             Tvar[i]=ncov+k1;
           cutv(strb,strc,strd,'V');            cutv(strb,strc,strd,'V');
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc);
             Tvard[k1][2]=atoi(stre);
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2];
           for (k=1; k<=lastobs;k++)            for (k=1; k<=lastobs;k++)
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];              covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
         }            k1++;
         else {cutv(strd,strc,strb,'V');            k2=k2+2;
         Tvar[i+1]=atoi(strc);  
         }          }
         strcpy(modelsav,stra);    
       }        }
       cutv(strd,strc,stra,'V');        else {
       Tvar[1]=atoi(strc);          /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
     }      }
   }  }
   /*printf("tvar=%d ",Tvar[1]);   
   scanf("%d ",i);*/    /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     scanf("%d ",i);*/
     fclose(fic);      fclose(fic);
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/      if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;        for(i=1;i<=n;i++) weight[i]=1.0;
     }      }
Line 1855  int main() Line 1984  int main()
             if(agedc[i]>0)              if(agedc[i]>0)
               if(moisdc[i]!=99 && andc[i]!=9999)                if(moisdc[i]!=99 && andc[i]!=9999)
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
             else{              else {
                 if (andc[i]!=9999){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                printf("Warning negative age at death: %d line:%d\n",num[i],i);
               agev[m][i]=-1;                agev[m][i]=-1;
                 }
             }              }
           }            }
           else if(s[m][i] !=9){ /* Should no more exist */            else if(s[m][i] !=9){ /* Should no more exist */
Line 1914  printf("Total number of individuals= %d, Line 2045  printf("Total number of individuals= %d,
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   
 Tcode=ivector(1,100);        Tcode=ivector(1,100);
    nbcode=imatrix(1,nvar,1,8);          nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
    ncodemax[1]=1;        ncodemax[1]=1;
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);        if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
    codtab=imatrix(1,100,1,10);     codtab=imatrix(1,100,1,10);
    h=0;     h=0;
    m=pow(2,cptcovn);     m=pow(2,cptcoveff);
     
    for(k=1;k<=cptcovn; k++){     for(k=1;k<=cptcoveff; k++){
      for(i=1; i <=(m/pow(2,k));i++){       for(i=1; i <=(m/pow(2,k));i++){
        for(j=1; j <= ncodemax[k]; j++){         for(j=1; j <= ncodemax[k]; j++){
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
            h++;             h++;
            if (h>m) h=1;codtab[h][k]=j;             if (h>m) h=1;codtab[h][k]=j;
          }           }
Line 1934  Tcode=ivector(1,100); Line 2065  Tcode=ivector(1,100);
      }       }
    }     }
   
   
    /*for(i=1; i <=m ;i++){     /*for(i=1; i <=m ;i++){
      for(k=1; k <=cptcovn; k++){       for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);         printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);
      }       }
      printf("\n");       printf("\n");
    }*/     }
    /*scanf("%d",i);*/     scanf("%d",i);*/
         
    /* Calculates basic frequencies. Computes observed prevalence at single age     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */         and prints on file fileres'p'. */
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);
   
   
   /*scanf("%d ",i);*/  
   
   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
Line 1959  Tcode=ivector(1,100); Line 2087  Tcode=ivector(1,100);
     /* For Powell, parameters are in a vector p[] starting at p[1]      /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */      p=param[1][1]; /* *(*(*(param +1)+1)+0) */
      
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
   
       if(mle==1){
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
         
     /*--------- results files --------------*/      /*--------- results files --------------*/
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);
Line 1985  Tcode=ivector(1,100); Line 2114  Tcode=ivector(1,100);
          }           }
      }       }
    }     }
    if(mle==1){
     /* Computing hessian and covariance matrix */      /* Computing hessian and covariance matrix */
     ftolhess=ftol; /* Usually correct */      ftolhess=ftol; /* Usually correct */
     hesscov(matcov, p, npar, delti, ftolhess, func);      hesscov(matcov, p, npar, delti, ftolhess, func);
    }
     fprintf(ficres,"# Scales\n");      fprintf(ficres,"# Scales\n");
     printf("# Scales\n");      printf("# Scales\n");
      for(i=1,jk=1; i <=nlstate; i++){       for(i=1,jk=1; i <=nlstate; i++){
Line 2043  Tcode=ivector(1,100); Line 2173  Tcode=ivector(1,100);
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
   
      
 /*------------ gnuplot -------------*/  /*------------ gnuplot -------------*/
 chdir(pathcd);  chdir(pathcd);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    if((ficgp=fopen("graph.plt","w"))==NULL) {
Line 2051  chdir(pathcd); Line 2183  chdir(pathcd);
 #ifdef windows  #ifdef windows
   fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
 #endif  #endif
 m=pow(2,cptcovn);  m=pow(2,cptcoveff);
     
  /* 1eme*/   /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
Line 2118  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2250  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
     
   /*3eme*/    /*3eme*/
   
    for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(cpt-1);        k=2+nlstate*(cpt-1);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);
Line 2127  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2259  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       }        }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
     }      }
    }    }
     
   /* CV preval stat */    /* CV preval stat */
     for (k1=1; k1<= m ; k1 ++) {    for (k1=1; k1<= m ; k1 ++) {
     for (cpt=1; cpt<nlstate ; cpt ++) {      for (cpt=1; cpt<nlstate ; cpt ++) {
       k=3;        k=3;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);
Line 2148  fprintf(ficgp,"\nset out \"v%s%d%d.gif\" Line 2280  fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
     }      }
   }    }
    
   /* proba elementaires */    /* proba elementaires */
   for(i=1,jk=1; i <=nlstate; i++){     for(i=1,jk=1; i <=nlstate; i++){
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i) {        if (k != i) {
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/  
         for(j=1; j <=ncovmodel; j++){          for(j=1; j <=ncovmodel; j++){
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);            /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/
             /*fprintf(ficgp,"%s",alph[1]);*/
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           jk++;            jk++;
           fprintf(ficgp,"\n");            fprintf(ficgp,"\n");
         }          }
       }        }
     }      }
   }      }
   
   for(jk=1; jk <=m; jk++) {    for(jk=1; jk <=m; jk++) {
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);
   for(i=1; i <=nlstate; i++) {     i=1;
     for(k=1; k <=(nlstate+ndeath); k++){     for(k2=1; k2<=nlstate; k2++) {
       if (k != i) {       k3=i;
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);       for(k=1; k<=(nlstate+ndeath); k++) {
         for(j=3; j <=ncovmodel; j++)         if (k != k2){
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
         fprintf(ficgp,")/(1");  ij=1;
         for(k1=1; k1 <=(nlstate+ndeath); k1++)          for(j=3; j <=ncovmodel; j++) {
           if (k1 != i) {            if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);              fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
             for(j=3; j <=ncovmodel; j++)              ij++;
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
             fprintf(ficgp,")");  
           }            }
         fprintf(ficgp,") t \"p%d%d\" ", i,k);            else
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");            fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       }          }
     }            fprintf(ficgp,")/(1");
   }         
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            for(k1=1; k1 <=nlstate; k1++){  
             fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   ij=1;
             for(j=3; j <=ncovmodel; j++){
             if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
               fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
               ij++;
             }
             else
               fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
             }
             fprintf(ficgp,")");
           }
           fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           i=i+ncovmodel;
          }
        }
      }
      fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
   }    }
       
  fclose(ficgp);    fclose(ficgp);
      
     chdir(path);  chdir(path);
     free_matrix(agev,1,maxwav,1,imx);      free_matrix(agev,1,maxwav,1,imx);
     free_ivector(wav,1,imx);      free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
Line 2203  fprintf(ficgp,"\nset out \"pe%s%d.gif\" Line 2354  fprintf(ficgp,"\nset out \"pe%s%d.gif\"
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);      fclose(ficparo);
     fclose(ficres);      fclose(ficres);
    }      /*  }*/
         
    /*________fin mle=1_________*/     /*________fin mle=1_________*/
         
Line 2219  fprintf(ficgp,"\nset out \"pe%s%d.gif\" Line 2370  fprintf(ficgp,"\nset out \"pe%s%d.gif\"
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
     
   
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
 /*--------- index.htm --------*/  /*--------- index.htm --------*/
   
   if((fichtm=fopen("index.htm","w"))==NULL)    {    strcpy(optionfilehtm,optionfile);
     printf("Problem with index.htm \n");goto end;    strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm);goto end;
   }    }
   
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n   fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">
   Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>
   Total number of observations=%d <br>
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
   <hr  size=\"2\" color=\"#EC5E5E\">
   <li>Outputs files<br><br>\n
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
Line 2238  fprintf(ficgp,"\nset out \"pe%s%d.gif\" Line 2395  fprintf(ficgp,"\nset out \"pe%s%d.gif\"
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);
   
  fprintf(fichtm," <li>Graphs</li>\n<p>");   fprintf(fichtm," <li>Graphs</li><p>");
   
  m=cptcovn;   m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
  j1=0;   j1=0;
Line 2250  fprintf(ficgp,"\nset out \"pe%s%d.gif\" Line 2407  fprintf(ficgp,"\nset out \"pe%s%d.gif\"
    for(i1=1; i1<=ncodemax[k1];i1++){     for(i1=1; i1<=ncodemax[k1];i1++){
        j1++;         j1++;
        if (cptcovn > 0) {         if (cptcovn > 0) {
          fprintf(fichtm,"<hr>************ Results for covariates");           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcovn;cpt++)           for (cpt=1; cpt<=cptcoveff;cpt++)
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);
          fprintf(fichtm," ************\n<hr>");           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }         }
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>         fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    
Line 2268  interval) in state (%d): v%s%d%d.gif <br Line 2425  interval) in state (%d): v%s%d%d.gif <br
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       fprintf(fichtm,"\n<br>- Total life expectancy by age and
 health expectancies in states (1) and (2): e%s%d.gif<br>  health expectancies in states (1) and (2): e%s%d.gif<br>
Line 2301  fclose(fichtm); Line 2458  fclose(fichtm);
   agebase=agemin;    agebase=agemin;
   agelim=agemax;    agelim=agemax;
   ftolpl=1.e-10;    ftolpl=1.e-10;
   i1=cptcovn;    i1=cptcoveff;
   if (cptcovn < 1){i1=1;}    if (cptcovn < 1){i1=1;}
   
   for(cptcov=1;cptcov<=i1;cptcov++){    for(cptcov=1;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;          k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#****** ");          fprintf(ficrespl,"\n#******");
         for(j=1;j<=cptcovn;j++)          for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespl,"******\n");          fprintf(ficrespl,"******\n");
                 
         for (age=agebase; age<=agelim; age++){          for (age=agebase; age<=agelim; age++){
Line 2343  fclose(fichtm); Line 2500  fclose(fichtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;        k=k+1;
         fprintf(ficrespij,"\n#****** ");          fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcovn;j++)          for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");          fprintf(ficrespij,"******\n");
                 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 2402  fclose(fichtm); Line 2559  fclose(fichtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;        k=k+1;
       fprintf(ficrest,"\n#****** ");        fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcovn;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrest,"******\n");        fprintf(ficrest,"******\n");
   
       fprintf(ficreseij,"\n#****** ");        fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcovn;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
       fprintf(ficreseij,"******\n");        fprintf(ficreseij,"******\n");
   
       fprintf(ficresvij,"\n#****** ");        fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcovn;j++)        for(j=1;j<=cptcoveff;j++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);
       fprintf(ficresvij,"******\n");        fprintf(ficresvij,"******\n");
   
Line 2456  fclose(fichtm); Line 2613  fclose(fichtm);
   fclose(ficrest);    fclose(ficrest);
   fclose(ficpar);    fclose(ficpar);
   free_vector(epj,1,nlstate+1);    free_vector(epj,1,nlstate+1);
   /*scanf("%d ",i); */    /*  scanf("%d ",i); */
   
   /*------- Variance limit prevalence------*/      /*------- Variance limit prevalence------*/  
   
Line 2473  strcpy(fileresvpl,"vpl"); Line 2630  strcpy(fileresvpl,"vpl");
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
      k=k+1;       k=k+1;
      fprintf(ficresvpl,"\n#****** ");       fprintf(ficresvpl,"\n#****** ");
      for(j=1;j<=cptcovn;j++)       for(j=1;j<=cptcoveff;j++)
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
      fprintf(ficresvpl,"******\n");       fprintf(ficresvpl,"******\n");
             
      varpl=matrix(1,nlstate,(int) bage, (int) fage);       varpl=matrix(1,nlstate,(int) bage, (int) fage);
Line 2513  strcpy(fileresvpl,"vpl"); Line 2670  strcpy(fileresvpl,"vpl");
 #ifdef windows  #ifdef windows
  chdir(pathcd);   chdir(pathcd);
 #endif  #endif
  system("wgnuplot graph.plt");   /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    system("..\\gp37mgw\\wgnuplot graph.plt");
   
 #ifdef windows  #ifdef windows
   while (z[0] != 'q') {    while (z[0] != 'q') {
Line 2523  strcpy(fileresvpl,"vpl"); Line 2683  strcpy(fileresvpl,"vpl");
     if (z[0] == 'c') system("./imach");      if (z[0] == 'c') system("./imach");
     else if (z[0] == 'e') {      else if (z[0] == 'e') {
       chdir(path);        chdir(path);
       system("index.htm");        system(optionfilehtm);
     }      }
     else if (z[0] == 'q') exit(0);      else if (z[0] == 'q') exit(0);
   }    }
Removed from v.1.3  
changed lines
  Added in v.1.11

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