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Diff for /imach/src/imach.c between versions 1.194 and 1.198

version 1.194, 2015/08/18 13:32:00 version 1.198, 2015/09/03 07:14:39
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.198  2015/09/03 07:14:39  brouard
     Summary: 0.98q5 Flavia
   
     Revision 1.197  2015/09/01 18:24:39  brouard
     *** empty log message ***
   
     Revision 1.196  2015/08/18 23:17:52  brouard
     Summary: 0.98q5
   
     Revision 1.195  2015/08/18 16:28:39  brouard
     Summary: Adding a hack for testing purpose
   
     After reading the title, ftol and model lines, if the comment line has
     a q, starting with #q, the answer at the end of the run is quit. It
     permits to run test files in batch with ctest. The former workaround was
     $ echo q | imach foo.imach
   
   Revision 1.194  2015/08/18 13:32:00  brouard    Revision 1.194  2015/08/18 13:32:00  brouard
   Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.    Summary:  Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
   
Line 683  typedef struct { Line 700  typedef struct {
 #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */  #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
 #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */  #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
 #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */  #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
 #define codtabm(h,k)  1 & (h-1) >> (k-1) ;  #define codtabm(h,k)  (1 & (h-1) >> (k-1))+1
 #define MAXN 20000  #define MAXN 20000
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  #define AGESUP 130
Line 702  typedef struct { Line 719  typedef struct {
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   #include "version.h"
 char version[]="Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";  char version[]=__IMACH_VERSION__;
   char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 838  int estepm; Line 856  int estepm;
   
 int m,nb;  int m,nb;
 long *num;  long *num;
 int firstpass=0, lastpass=4,*cod, *Tage,*cens;  int firstpass=0, lastpass=4,*cod, *cens;
 int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th  int *ncodemax;  /* ncodemax[j]= Number of modalities of the j th
                    covariate for which somebody answered excluding                      covariate for which somebody answered excluding 
                    undefined. Usually 2: 0 and 1. */                     undefined. Usually 2: 0 and 1. */
Line 858  double  **covar; /**< covar[j,i], value Line 876  double  **covar; /**< covar[j,i], value
                   * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */                    * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
 double  idx;   double  idx; 
 int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */  int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
   int *Tage;
 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;  int **Tvard, *Tprod, cptcovprod, *Tvaraff;
Line 1895  double **prevalim(double **prlim, int nl Line 1914  double **prevalim(double **prlim, int nl
     if(nagesqr==1)      if(nagesqr==1)
       cov[3]= agefin*agefin;;        cov[3]= agefin*agefin;;
     for (k=1; k<=cptcovn;k++) {      for (k=1; k<=cptcovn;k++) {
       cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])];
       /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/        /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
     }      }
     /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */      /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
     for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];      for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2];
     for (k=1; k<=cptcovprod;k++) /* Useless */      for (k=1; k<=cptcovprod;k++) /* Useless */
       cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[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("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
Line 2074  double ***hpxij(double ***po, int nhstep Line 2093  double ***hpxij(double ***po, int nhstep
       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]][codtab[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]]][codtab[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]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[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);*/
Line 2898  void lubksb(double **a, int n, int *indx Line 2917  void lubksb(double **a, int n, int *indx
   
 void pstamp(FILE *fichier)  void pstamp(FILE *fichier)
 {  {
   fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);    fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
 }  }
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
Line 2950  void  freqsummary(char fileres[], int ia Line 2969  void  freqsummary(char fileres[], int ia
         bool=1;          bool=1;
         if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */          if  (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
           for (z1=1; z1<=cptcoveff; z1++)                   for (z1=1; z1<=cptcoveff; z1++)       
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
                 /* Tests if the value of each of the covariates of i is equal to filter j1 */                  /* Tests if the value of each of the covariates of i is equal to filter j1 */
               bool=0;                bool=0;
               /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",                 /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", 
                 bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],                  bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
                 j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/                  j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
               /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/                /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
             }               } 
         }          }
     
Line 2985  void  freqsummary(char fileres[], int ia Line 3004  void  freqsummary(char fileres[], int ia
       pstamp(ficresp);        pstamp(ficresp);
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresp, "**********\n#");          fprintf(ficresp, "**********\n#");
         fprintf(ficlog, "\n#********** Variable ");           fprintf(ficlog, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[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#");
       }        }
       for(i=1; i<=nlstate;i++)         for(i=1; i<=nlstate;i++) 
Line 3116  void prevalence(double ***probs, double Line 3135  void prevalence(double ***probs, double
         bool=1;          bool=1;
         if  (cptcovn>0) {          if  (cptcovn>0) {
           for (z1=1; z1<=cptcoveff; z1++)             for (z1=1; z1<=cptcoveff; z1++) 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) 
               bool=0;                bool=0;
         }           } 
         if (bool==1) {           if (bool==1) { 
Line 3382  void tricode(int *Tvar, int **nbcode, in Line 3401  void tricode(int *Tvar, int **nbcode, in
        nbcode[Tvar[j]][1]=0;         nbcode[Tvar[j]][1]=0;
        nbcode[Tvar[j]][2]=1;         nbcode[Tvar[j]][2]=1;
        nbcode[Tvar[j]][3]=2;         nbcode[Tvar[j]][3]=2;
          To be continued (not working yet).
     */      */
     ij=0; /* ij is similar to i but can jumps over null modalities */      ij=0; /* ij is similar to i but can jump over null modalities */
     for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/      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 at least one individual responded to this modality k */          if (Ndum[i] == 0) { /* If nobody responded to this modality k */
           break;            break;
         }          }
         ij++;          ij++;
         nbcode[Tvar[j]][ij]=i;  /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/          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 */          cptcode = ij; /* New max modality for covar j */
     } /* end of loop on modality i=-1 to 1 or more */      } /* end of loop on modality i=-1 to 1 or more */
               
Line 4218  void varprob(char optionfilefiname[], do Line 4238  void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\    fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
   file %s<br>\n",optionfilehtmcov);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\  
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
  They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
Line 4242  To be simple, these graphs help to under Line 4261  To be simple, these graphs help to under
     /*j1++;*/      /*j1++;*/
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresprob, "\n#********** Variable ");           fprintf(ficresprob, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprob, "**********\n#\n");          fprintf(ficresprob, "**********\n#\n");
         fprintf(ficresprobcov, "\n#********** Variable ");           fprintf(ficresprobcov, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcov, "**********\n#\n");          fprintf(ficresprobcov, "**********\n#\n");
                   
         fprintf(ficgp, "\n#********** Variable ");           fprintf(ficgp, "\n#********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficgp, "**********\n#\n");          fprintf(ficgp, "**********\n#\n");
                   
                   
         fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   
         fprintf(ficresprobcor, "\n#********** Variable ");              fprintf(ficresprobcor, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
         fprintf(ficresprobcor, "**********\n#");              fprintf(ficresprobcor, "**********\n#");    
       }        }
               
Line 4271  To be simple, these graphs help to under Line 4290  To be simple, these graphs help to under
         if(nagesqr==1)          if(nagesqr==1)
           cov[3]= age*age;            cov[3]= age*age;
         for (k=1; k<=cptcovn;k++) {          for (k=1; k<=cptcovn;k++) {
           cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4            cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4
                                                          * 1  1 1 1 1                                                           * 1  1 1 1 1
                                                          * 2  2 1 1 1                                                           * 2  2 1 1 1
                                                          * 3  1 2 1 1                                                           * 3  1 2 1 1
Line 4279  To be simple, these graphs help to under Line 4298  To be simple, these graphs help to under
           /* nbcode[1][1]=0 nbcode[1][2]=1;*/            /* nbcode[1][1]=0 nbcode[1][2]=1;*/
         }          }
         /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */          /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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];
         for (k=1; k<=cptcovprod;k++)          for (k=1; k<=cptcovprod;k++)
           cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[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])];
                   
           
         for(theta=1; theta <=npar; theta++){          for(theta=1; theta <=npar; theta++){
Line 4518  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4537  fprintf(fichtm," \n<ul><li><b>Graphs</b>
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++){          for (cpt=1; cpt<=cptcoveff;cpt++){ 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
          printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);           printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
        }         }
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
Line 4546  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4565  fprintf(fichtm," \n<ul><li><b>Graphs</b>
  fprintf(fichtm,"\   fprintf(fichtm,"\
 \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
  - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);   - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
   But because parameters are usually highly correlated (a higher incidence of disability \
   and a higher incidence of recovery can give very close observed transition) it might \
   be very useful to look not only at linear confidence intervals estimated from the \
   variances but at the covariance matrix. And instead of looking at the estimated coefficients \
   (parameters) of the logistic regression, it might be more meaningful to visualize the \
   covariance matrix of the one-step probabilities. \
   See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
   
  fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",   fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
          subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
Line 4594  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4620  fprintf(fichtm," \n<ul><li><b>Graphs</b>
      if (cptcovn > 0) {       if (cptcovn > 0) {
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
        for (cpt=1; cpt<=cptcoveff;cpt++)          for (cpt=1; cpt<=cptcoveff;cpt++) 
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
Line 4802  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4828  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                  fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);                   fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
              ij=1;/* To be checked else nbcode[0][0] wrong */               ij=1;/* To be checked else nbcode[0][0] wrong */
              for(j=3; j <=ncovmodel-nagesqr; j++) {               for(j=3; j <=ncovmodel-nagesqr; j++) {
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */                 /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
                  fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                 if(ij <=cptcovage) { /* Bug valgrind */
                  ij++;                   if((j-2)==Tage[ij]) { /* Bug valgrind */
                      fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                      ij++;
                    }
                }                 }
                else                 else
                  fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
              }               }
              fprintf(ficgp,")/(1");               fprintf(ficgp,")/(1");
                             
Line 4819  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4848  plot [%.f:%.f]  ", ageminpar, agemaxpar)
       
                ij=1;                 ij=1;
                for(j=3; j <=ncovmodel-nagesqr; j++){                 for(j=3; j <=ncovmodel-nagesqr; j++){
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                   if(ij <=cptcovage) { /* Bug valgrind */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                     if((j-2)==Tage[ij]) { /* Bug valgrind */
                    ij++;                       fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]);
                        ij++;
                      }
                  }                   }
                  else                   else
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
              }               }
Line 4951  void prevforecast(char fileres[], double Line 4982  void prevforecast(char fileres[], double
       k=k+1;        k=k+1;
       fprintf(ficresf,"\n#******");        fprintf(ficresf,"\n#******");
       for(j=1;j<=cptcoveff;j++) {        for(j=1;j<=cptcoveff;j++) {
         fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
       }        }
       fprintf(ficresf,"******\n");        fprintf(ficresf,"******\n");
       fprintf(ficresf,"# Covariate valuofcovar yearproj age");        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
Line 4975  void prevforecast(char fileres[], double Line 5006  void prevforecast(char fileres[], double
             if (h*hstepm/YEARM*stepm ==yearp) {              if (h*hstepm/YEARM*stepm ==yearp) {
               fprintf(ficresf,"\n");                fprintf(ficresf,"\n");
               for(j=1;j<=cptcoveff;j++)                 for(j=1;j<=cptcoveff;j++) 
                 fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
               fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             }               } 
             for(j=1; j<=nlstate+ndeath;j++) {              for(j=1; j<=nlstate+ndeath;j++) {
Line 5073  void populforecast(char fileres[], doubl Line 5104  void populforecast(char fileres[], doubl
       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]][codtab[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");
Line 5440  int readdata(char datafile[], int firsto Line 5471  int readdata(char datafile[], int firsto
   
   
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem while opening datafile: %s\n", datafile);return 1;      printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
     fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;      fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
   }    }
   
   i=1;    i=1;
Line 5730  int decodemodel ( char model[], int last Line 5761  int decodemodel ( char model[], int last
       /*        k=1 Tvar[1]=2 (from V2) */        /*        k=1 Tvar[1]=2 (from V2) */
       /*        k=5 Tvar[5] */        /*        k=5 Tvar[5] */
       /* for (k=1; k<=cptcovn;k++) { */        /* for (k=1; k<=cptcovn;k++) { */
       /*        cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */        /*        cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
       /*        } */        /*        } */
       /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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 */        for(k=cptcovt; k>=1;k--) /**< Number of covariates */
Line 6143  int prevalence_limit(double *p, double * Line 6174  int prevalence_limit(double *p, double *
       //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;          k=k+1;
         /* to clean */          /* to clean */
         //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);          //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
         fprintf(ficrespl,"\n#******");          fprintf(ficrespl,"\n#******");
         printf("\n#******");          printf("\n#******");
         fprintf(ficlog,"\n#******");          fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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");
Line 6158  int prevalence_limit(double *p, double * Line 6189  int prevalence_limit(double *p, double *
   
         fprintf(ficrespl,"#Age ");          fprintf(ficrespl,"#Age ");
         for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[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,"\n");          fprintf(ficrespl,"\n");
Line 6168  int prevalence_limit(double *p, double * Line 6199  int prevalence_limit(double *p, double *
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );            fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)            for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);              fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");            fprintf(ficrespl,"\n");
Line 6215  int hPijx(double *p, int bage, int fage) Line 6246  int hPijx(double *p, int bage, int fage)
     for (k=1; k <= (int) pow(2,cptcoveff); k++){      for (k=1; k <= (int) pow(2,cptcoveff); k++){
       fprintf(ficrespij,"\n#****** ");        fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)         for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(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 6267  int main(int argc, char *argv[]) Line 6298  int main(int argc, char *argv[])
   
   int jj, ll, li, lj, lk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
     int num_filled;
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
Line 6285  int main(int argc, char *argv[]) Line 6317  int main(int argc, char *argv[])
   double ***mobaverage;    double ***mobaverage;
   
   char line[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
   
     char model[MAXLINE], modeltemp[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int c,  h , cpt;    int c,  h , cpt, c2;
   int jl=0;    int jl=0;
   int i1, j1, jk, stepsize=0;    int i1, j1, jk, stepsize=0;
   int count=0;    int count=0;
Line 6365  int main(int argc, char *argv[]) Line 6399  int main(int argc, char *argv[])
   getcwd(pathcd, size);    getcwd(pathcd, size);
 #endif  #endif
   syscompilerinfo(0);    syscompilerinfo(0);
   printf("\n%s\n%s",version,fullversion);    printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     fgets(pathr,FILENAMELENGTH,stdin);      fgets(pathr,FILENAMELENGTH,stdin);
Line 6429  int main(int argc, char *argv[]) Line 6463  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s\n%s",version,fullversion);    fprintf(ficlog,"Version %s %s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: \n");    fprintf(ficlog,"\nEnter the parameter file name: \n");
   fprintf(ficlog,"pathimach=%s\npathtot=%s\n\    fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
  path=%s \n\   path=%s \n\
Line 6437  int main(int argc, char *argv[]) Line 6471  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   syscompilerinfo(0);    syscompilerinfo(1);
   
   printf("Local time (at start):%s",strstart);    printf("Local time (at start):%s",strstart);
   fprintf(ficlog,"Local time (at start): %s",strstart);    fprintf(ficlog,"Local time (at start): %s",strstart);
Line 6473  int main(int argc, char *argv[]) Line 6507  int main(int argc, char *argv[])
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
   numlinepar=0;    numlinepar=0;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      /* First parameter line */
     fgets(line, MAXLINE, ficpar);    while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
                           title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
       if (num_filled != 5) {
         printf("Should be 5 parameters\n");
       }
     numlinepar++;      numlinepar++;
     fputs(line,stdout);      printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
     fputs(line,ficparo);    }
     fputs(line,ficlog);    /* Second parameter line */
     while(fgets(line, MAXLINE, ficpar)) {
       /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
                           &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
       if (num_filled != 8) {
         printf("Not 8\n");
       }
       printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
   }    }
   ungetc(c,ficpar);  
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    /* Third parameter line */
   numlinepar=numlinepar+3; /* In general */    while(fgets(line, MAXLINE, ficpar)) {
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);      /* If line starts with a # it is a comment */
       if (line[0] == '#') {
         numlinepar++;
         fputs(line,stdout);
         fputs(line,ficparo);
         fputs(line,ficlog);
         continue;
       }else
         break;
     }
     if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
       if (num_filled != 1) {
         printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
         model[0]='\0';
         goto end;
       }
       else{
         if (model[0]=='+'){
           for(i=1; i<=strlen(model);i++)
             modeltemp[i-1]=model[i];
         }
         strcpy(model,modeltemp); 
       }
       printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
     }
     /* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
     /* numlinepar=numlinepar+3; /\* In general *\/ */
     /* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
   if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */    if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
     model[strlen(model)-1]='\0';      model[strlen(model)-1]='\0';
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);    fflush(ficlog);
   /* if(model[0]=='#'|| model[0]== '\0'){ */    /* if(model[0]=='#'|| model[0]== '\0'){ */
   if(model[0]=='#'){    if(model[0]=='#'){
Line 6505  int main(int argc, char *argv[]) Line 6598  int main(int argc, char *argv[])
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
     numlinepar++;      numlinepar++;
       if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
         z[0]=line[1];
       }
       /* printf("****line [1] = %c \n",line[1]); */
     fputs(line, stdout);      fputs(line, stdout);
     //puts(line);      //puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
Line 6821  Please run with mle=-1 to get a correct Line 6918  Please run with mle=-1 to get a correct
   /* 1 to ncodemax[j] is the maximum value of this jth covariate */    /* 1 to ncodemax[j] 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],codtab[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).*/
   h=0;    h=0;
   
Line 6831  Please run with mle=-1 to get a correct Line 6928  Please run with mle=-1 to get a correct
     
   m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
   for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */  
     for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */   
       for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/  
         for(cpt=1; cpt <=pow(2,k-1); cpt++){  /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */   
           h++;  
           if (h>m)   
             h=1;  
           /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1            /**< codtab(h,k)  k   = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
            * For k=4 covariates, h goes from 1 to 2**k             * For k=4 covariates, h goes from 1 to 2**k
            * codtabm(h,k)=  1 & (h-1) >> (k-1) ;             * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
Line 6851  Please run with mle=-1 to get a correct Line 6941  Please run with mle=-1 to get a correct
            *     6     2     1     2     1             *     6     2     1     2     1
            *     7 i=4 1     2     2     1             *     7 i=4 1     2     2     1
            *     8     2     2     2     1             *     8     2     2     2     1
            *     9 i=5 1 i=3 1 i=2 1     1             *     9 i=5 1 i=3 1 i=2 1     2
            *    10     2     1     1     1             *    10     2     1     1     2
            *    11 i=6 1     2     1     1             *    11 i=6 1     2     1     2
            *    12     2     2     1     1             *    12     2     2     1     2
            *    13 i=7 1 i=4 1     2     1                 *    13 i=7 1 i=4 1     2     2    
            *    14     2     1     2     1             *    14     2     1     2     2
            *    15 i=8 1     2     2     1             *    15 i=8 1     2     2     2
            *    16     2     2     2     1             *    16     2     2     2     2
            */             */
           codtab[h][k]=j;    for(h=1; h <=100 ;h++){ 
           /* codtab[12][3]=1; */      /* printf("h=%2d ", h); */
           /*codtab[h][Tvar[k]]=j;*/       for(k=1; k <=10; k++){
           printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);         /* printf("k=%d %d ",k,codtabm(h,k)); */
         }          codtab[h][k]=codtabm(h,k);
       }       }
     }       /* printf("\n"); */
   }     }
     /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
     /*   for(i=1; i <=pow(2,cptcoveff-k);i++){ /\* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 *\/  */
     /*     for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
     /*    for(cpt=1; cpt <=pow(2,k-1); cpt++){  /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/  */
     /*      h++; */
     /*      if (h>m)  */
     /*        h=1; */
     /*      codtab[h][k]=j; */
     /*      /\* codtab[12][3]=1; *\/ */
     /*      /\*codtab[h][Tvar[k]]=j;*\/ */
     /*      /\* printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]); *\/ */
     /*    }  */
     /*     } */
     /*   } */
     /* }  */
   /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
      codtab[1][2]=1;codtab[2][2]=2; */       codtab[1][2]=1;codtab[2][2]=2; */
   /* 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 %d ",i,k,codtab[i][k], cptcoveff);    /*      printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
      }    /*    } */
      printf("\n");    /*    printf("\n"); */
      }    /* } */
      scanf("%d",i);*/    /*   scanf("%d",i);*/
   
  free_ivector(Ndum,-1,NCOVMAX);   free_ivector(Ndum,-1,NCOVMAX);
   
Line 7239  Please run with mle=-1 to get a correct Line 7344  Please run with mle=-1 to get a correct
       ftolhess=ftol; /* Usually correct */        ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);        hesscov(matcov, p, npar, delti, ftolhess, func);
     }      }
     printf("Parameters and 95%% confidence intervals\n");      printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
     fprintf(ficlog, "Parameters, T and confidence intervals\n");      fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n  It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
     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) {
           printf("%d%d ",i,k);            printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);            fprintf(ficlog,"%d%d ",i,k);
           for(j=1; j <=ncovmodel; j++){            for(j=1; j <=ncovmodel; j++){
             printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));              printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
             fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));              fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
             jk++;               jk++; 
           }            }
           printf("\n");            printf("\n");
Line 7849  Please run with mle=-1 to get a correct Line 7954  Please run with mle=-1 to get a correct
   }    }
   end:    end:
   while (z[0] != 'q') {    while (z[0] != 'q') {
     printf("\nType  q for exiting: ");      printf("\nType  q for exiting: "); fflush(stdout);
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }
Removed from v.1.194  
changed lines
  Added in v.1.198

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