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Diff for /imach/src/imach.c between versions 1.183 and 1.186

version 1.183, 2015/03/10 20:34:32 version 1.186, 2015/04/23 12:01:52
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.186  2015/04/23 12:01:52  brouard
     Summary: V1*age is working now, version 0.98q1
   
     Some codes had been disabled in order to simplify and Vn*age was
     working in the optimization phase, ie, giving correct MLE parameters,
     but, as usual, outputs were not correct and program core dumped.
   
     Revision 1.185  2015/03/11 13:26:42  brouard
     Summary: Inclusion of compile and links command line for Intel Compiler
   
     Revision 1.184  2015/03/11 11:52:39  brouard
     Summary: Back from Windows 8. Intel Compiler
   
   Revision 1.183  2015/03/10 20:34:32  brouard    Revision 1.183  2015/03/10 20:34:32  brouard
   Summary: 0.98q0, trying with directest, mnbrak fixed    Summary: 0.98q0, trying with directest, mnbrak fixed
   
Line 573 Line 586
 */  */
   
 #define POWELL /* Instead of NLOPT */  #define POWELL /* Instead of NLOPT */
 /* #define POWELLORIGINAL */ /* Don't use Directest to decide new direction but original Powell test */  /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
   /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
   
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
Line 659  typedef struct { Line 673  typedef struct {
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98q0, March 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 0.98q1, April 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 823  static int split( char *path, char *dirc Line 837  static int split( char *path, char *dirc
      the name of the file (name), its extension only (ext) and its first part of the name (finame)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   */     */ 
   char  *ss;                            /* pointer */    char  *ss;                            /* pointer */
   int   l1, l2;                         /* length counters */    int   l1=0, l2=0;                             /* length counters */
   
   l1 = strlen(path );                   /* length of path */    l1 = strlen(path );                   /* length of path */
   if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
Line 834  static int split( char *path, char *dirc Line 848  static int split( char *path, char *dirc
       printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     /* get current working directory */      /* get current working directory */
     /*    extern  char* getcwd ( char *buf , int len);*/      /*    extern  char* getcwd ( char *buf , int len);*/
     if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #ifdef WIN32
       if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
   #else
           if (getcwd(dirc, FILENAME_MAX) == NULL) {
   #endif
       return( GLOCK_ERROR_GETCWD );        return( GLOCK_ERROR_GETCWD );
     }      }
     /* got dirc from getcwd*/      /* got dirc from getcwd*/
Line 845  static int split( char *path, char *dirc Line 863  static int split( char *path, char *dirc
     if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     strcpy( name, ss );         /* save file name */      strcpy( name, ss );         /* save file name */
     strncpy( dirc, path, l1 - l2 );     /* now the directory */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     dirc[l1-l2] = 0;                    /* add zero */      dirc[l1-l2] = '\0';                 /* add zero */
     printf(" DIRC2 = %s \n",dirc);      printf(" DIRC2 = %s \n",dirc);
   }    }
   /* We add a separator at the end of dirc if not exists */    /* We add a separator at the end of dirc if not exists */
Line 1354  values at the three points, fa, fb , and Line 1372  values at the three points, fa, fb , and
         (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */          (*cx=10.098840694817, *fc=298946.631474258087),  (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
       /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/        /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
 #endif   #endif 
 #ifdef MNBRAKORI  #ifdef MNBRAKORIGINAL
 #else  #else
       if (fu > *fc) {        if (fu > *fc) {
 #ifdef DEBUG  #ifdef DEBUG
Line 1635  void powell(double p[], double **xi, int Line 1653  void powell(double p[], double **xi, int
       if (t < 0.0) { /* Then we use it for new direction */        if (t < 0.0) { /* Then we use it for new direction */
 #else  #else
       if (directest*t < 0.0) { /* Contradiction between both tests */        if (directest*t < 0.0) { /* Contradiction between both tests */
       printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);        printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
       printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);        printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
       fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt);        fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
       fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);        fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
     }       } 
       if (directest < 0.0) { /* Then we use it for new direction */        if (directest < 0.0) { /* Then we use it for new direction */
Line 1696  double **prevalim(double **prlim, int nl Line 1714  double **prevalim(double **prlim, int nl
       cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        cov[2+k]=nbcode[Tvar[k]][codtab[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 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]]);*/
     }      }
     /* 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<=cptcovprod;k++) /\* Useless *\/ */      for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
     /*   cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */      for (k=1; k<=cptcovprod;k++) /* Useless */
         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 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 1868  double ***hpxij(double ***po, int nhstep Line 1887  double ***hpxij(double ***po, int nhstep
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       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]][codtab[ij][Tvar[k]]];
       for (k=1; k<=cptcovage;k++)        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+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[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+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
Line 3096  void tricode(int *Tvar, int **nbcode, in Line 3116  void tricode(int *Tvar, int **nbcode, in
   for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */    for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
   
   /* Loop on covariates without age and products */    /* Loop on covariates without age and products */
   for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */    for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
     for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the       for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the 
                                modality of this covariate Vj*/                                  modality of this covariate Vj*/ 
       ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i        ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
                                     * If product of Vn*Vm, still boolean *:                                      * If product of Vn*Vm, still boolean *:
Line 3134  void tricode(int *Tvar, int **nbcode, in Line 3154  void tricode(int *Tvar, int **nbcode, in
     } /* Ndum[-1] number of undefined modalities */      } /* Ndum[-1] number of undefined modalities */
   
     /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */      /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
     /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */      /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. 
     /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;         If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
        modmincovj=3; modmaxcovj = 7;         modmincovj=3; modmaxcovj = 7;
        There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;         There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
        which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy          which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
        variables V1_1 and V1_2.         defining two dummy variables: variables V1_1 and V1_2.
        nbcode[Tvar[j]][ij]=k;         nbcode[Tvar[j]][ij]=k;
        nbcode[Tvar[j]][1]=0;         nbcode[Tvar[j]][1]=0;
        nbcode[Tvar[j]][2]=1;         nbcode[Tvar[j]][2]=1;
Line 3150  void tricode(int *Tvar, int **nbcode, in Line 3170  void tricode(int *Tvar, int **nbcode, in
       for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */        for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
         /*recode from 0 */          /*recode from 0 */
         if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */          if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
           nbcode[Tvar[j]][ij]=k;  /* stores the modality in an array nbcode.             nbcode[Tvar[j]][ij]=k;  /* stores the modality k in an array nbcode. 
                                      k is a modality. If we have model=V1+V1*sex                                        k is a modality. If we have model=V1+V1*sex 
                                      then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */                                       then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
           ij++;            ij++;
Line 4027  To be simple, these graphs help to under Line 4047  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<=cptcovprod;k++)          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]]];            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                   
Line 4520  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4541  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
              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; j++) {               for(j=3; j <=ncovmodel; j++) {
                /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
                /*        /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                /*        ij++; */                   ij++;
                /* } */                 }
                /* else */                 else
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
              }               }
              fprintf(ficgp,")/(1");               fprintf(ficgp,")/(1");
Line 4533  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4554  plot [%.f:%.f]  ", ageminpar, agemaxpar)
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                ij=1;                 ij=1;
                for(j=3; j <=ncovmodel; j++){                 for(j=3; j <=ncovmodel; j++){
                  /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */                   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]]]); */                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                  /*   ij++; */                     ij++;
                  /* } */                   }
                  /* else */                   else
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }                 }
                fprintf(ficgp,")");                 fprintf(ficgp,")");
Line 5418  int decodemodel ( char model[], int last Line 5439  int decodemodel ( char model[], int last
     /* 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]][codtab[ij][Tvar[k]]]; */
     /*  } */      /*  } */
     /* 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]; */
     /*      /*
      * 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 5438  int decodemodel ( char model[], int last Line 5459  int decodemodel ( char model[], int last
           cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */            cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
           Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */            Tvar[k]=atoi(stre);  /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
           cptcovage++; /* Sums the number of covariates which include age as a product */            cptcovage++; /* Sums the number of covariates which include age as a product */
           Tage[cptcovage]=k;  /* Tage[1] = 4 */            Tage[cptcovage]=k;  /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
           /*printf("stre=%s ", stre);*/            /*printf("stre=%s ", stre);*/
         } else if (strcmp(strd,"age")==0) { /* or age*Vn */          } else if (strcmp(strd,"age")==0) { /* or age*Vn */
           cptcovprod--;            cptcovprod--;
Line 5638  BOOL IsWow64() Line 5659  BOOL IsWow64()
 void syscompilerinfo()  void syscompilerinfo()
  {   {
    /* #include "syscompilerinfo.h"*/     /* #include "syscompilerinfo.h"*/
      /* command line Intel compiler 32bit windows, XP compatible:*/
      /* /GS /W3 /Gy
         /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
         "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
         "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
         /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
      */ 
      /* 64 bits */
      /*
        /GS /W3 /Gy
        /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
        /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
        /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
        "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
      /* Optimization are useless and O3 is slower than O2 */
      /*
        /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32" 
        /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo 
        /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel 
        /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch" 
      */
      /* Link is */ /* /OUT:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
         /PDB:"visual studio
         2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
         "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
         "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
         "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
         /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
         /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
         uiAccess='false'"
         /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
         /NOLOGO /TLBID:1
      */
 #if defined __INTEL_COMPILER  #if defined __INTEL_COMPILER
 #if defined(__GNUC__)  #if defined(__GNUC__)
         struct utsname sysInfo;  /* For Intel on Linux and OS/X */          struct utsname sysInfo;  /* For Intel on Linux and OS/X */
Line 5827  int prevalence_limit(double *p, double * Line 5881  int prevalence_limit(double *p, double *
         } /* Age */          } /* Age */
         /* was end of cptcod */          /* was end of cptcod */
     } /* cptcov */      } /* cptcov */
           return 0;
 }  }
   
 int hPijx(double *p, int bage, int fage){  int hPijx(double *p, int bage, int fage){
Line 5896  int hPijx(double *p, int bage, int fage) Line 5951  int hPijx(double *p, int bage, int fage)
       }        }
       /*}*/        /*}*/
     }      }
           return 0;
 }  }
   
   
Line 6006  int main(int argc, char *argv[]) Line 6062  int main(int argc, char *argv[])
   
   nberr=0; /* Number of errors and warnings */    nberr=0; /* Number of errors and warnings */
   nbwarn=0;    nbwarn=0;
   #ifdef WIN32
     _getcwd(pathcd, size);
   #else
   getcwd(pathcd, size);    getcwd(pathcd, size);
   #endif
   
   printf("\n%s\n%s",version,fullversion);    printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
Line 6042  int main(int argc, char *argv[]) Line 6102  int main(int argc, char *argv[])
   /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */    /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   #ifdef WIN32
     _chdir(path); /* Can be a relative path */
     if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
   #else
   chdir(path); /* Can be a relative path */    chdir(path); /* Can be a relative path */
   if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */    if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
     printf("Current directory %s!\n",pathcd);  #endif
     printf("Current directory %s!\n",pathcd);
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
Line 6059  int main(int argc, char *argv[]) Line 6124  int main(int argc, char *argv[])
   
   /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
   /* Log file */    /* Main Log file */
   strcat(filelog, optionfilefiname);    strcat(filelog, optionfilefiname);
   strcat(filelog,".log");    /* */    strcat(filelog,".log");    /* */
   if((ficlog=fopen(filelog,"w"))==NULL)    {    if((ficlog=fopen(filelog,"w"))==NULL)    {
Line 6088  int main(int argc, char *argv[]) Line 6153  int main(int argc, char *argv[])
   strcat(fileres, optionfilefiname);    strcat(fileres, optionfilefiname);
   strcat(fileres,".txt");    /* Other files have txt extension */    strcat(fileres,".txt");    /* Other files have txt extension */
   
   /*---------arguments file --------*/    /* Main ---------arguments file --------*/
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));      printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
Line 6123  int main(int argc, char *argv[]) Line 6188  int main(int argc, char *argv[])
   
   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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    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=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
   numlinepar++;    numlinepar++;
   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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);    /* 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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n",title, datafile, lastobs, firstpass,lastpass);
     /*
   
   
   
      */
     printf("\nftol=%e \n", ftol);
     printf("stepm=%d \n", stepm);
     printf("ncovcol=%d nlstate=%d \n", ncovcol, nlstate);
     printf("ndeath=%d maxwav=%d mle=%d weight=%d\n", ndeath, maxwav, mle, weightopt);
     printf("model=%s\n",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=%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=%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=%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=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
   fflush(ficlog);    fflush(ficlog);
Line 6171  int main(int argc, char *argv[]) Line 6247  int main(int argc, char *argv[])
     goto end;      goto end;
     exit(0);      exit(0);
   }    }
   else if(mle==-3) {    else if(mle==-3) { /* Main Wizard */
     prwizard(ncovmodel, nlstate, ndeath, model, ficparo);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);      fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
Line 6331  run imach with mle=-1 to get a correct t Line 6407  run imach with mle=-1 to get a correct t
     fprintf(ficres,"#%s\n",version);      fprintf(ficres,"#%s\n",version);
   }    /* End of mle != -3 */    }    /* End of mle != -3 */
   
     /*  Main data
      */
   n= lastobs;    n= lastobs;
   num=lvector(1,n);    num=lvector(1,n);
   moisnais=vector(1,n);    moisnais=vector(1,n);
Line 6382  run imach with mle=-1 to get a correct t Line 6459  run imach with mle=-1 to get a correct t
                          Tage[1=V3*age]= 4; Tage[2=age*V4] = 3                           Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
                       */                          */  
   
   /* Main decodemodel */
   
   if(decodemodel(model, lastobs) == 1)    if(decodemodel(model, lastobs) == 1)
     goto end;      goto end;
   
Line 6427  run imach with mle=-1 to get a correct t Line 6506  run imach with mle=-1 to get a correct t
   Ndum =ivector(-1,NCOVMAX);      Ndum =ivector(-1,NCOVMAX);  
   if (ncovmodel > 2)    if (ncovmodel > 2)
     tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */      tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
     /* Nbcode gives the value of the lth modality of jth covariate, in
        V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
     /* 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],codtab[100][10]);*/
     /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
   h=0;    h=0;
   
   
Line 6446  run imach with mle=-1 to get a correct t Line 6529  run imach with mle=-1 to get a correct t
           if (h>m)             if (h>m) 
             h=1;              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
            *     h     1     2     3     4             * For k=4 covariates, h goes from 1 to 2**k
              * codtabm(h,k)=  1 & (h-1) >> (k-1) ;
              *     h\k   1     2     3     4
            *______________________________               *______________________________  
            *     1 i=1 1 i=1 1 i=1 1 i=1 1             *     1 i=1 1 i=1 1 i=1 1 i=1 1
            *     2     2     1     1     1             *     2     2     1     1     1
Line 6466  run imach with mle=-1 to get a correct t Line 6551  run imach with mle=-1 to get a correct t
            *    16     2     2     2     1             *    16     2     2     2     1
            */             */
           codtab[h][k]=j;            codtab[h][k]=j;
             /* codtab[12][3]=1; */
           /*codtab[h][Tvar[k]]=j;*/            /*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("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]]);
         }           } 
Line 6486  run imach with mle=-1 to get a correct t Line 6572  run imach with mle=-1 to get a correct t
   
   
           
   /*------------ gnuplot -------------*/    /* Initialisation of ----------- gnuplot -------------*/
   strcpy(optionfilegnuplot,optionfilefiname);    strcpy(optionfilegnuplot,optionfilefiname);
   if(mle==-3)    if(mle==-3)
     strcat(optionfilegnuplot,"-mort");      strcat(optionfilegnuplot,"-mort");
Line 6502  run imach with mle=-1 to get a correct t Line 6588  run imach with mle=-1 to get a correct t
     fprintf(ficgp,"set datafile missing 'NaNq'\n");      fprintf(ficgp,"set datafile missing 'NaNq'\n");
   }    }
   /*  fclose(ficgp);*/    /*  fclose(ficgp);*/
   /*--------- index.htm --------*/  
   
     /* Initialisation of --------- index.htm --------*/
   
   strcpy(optionfilehtm,optionfilefiname); /* Main html file */    strcpy(optionfilehtm,optionfilefiname); /* Main html file */
   if(mle==-3)    if(mle==-3)
Line 6544  Title=%s <br>Datafile=%s Firstpass=%d La Line 6632  Title=%s <br>Datafile=%s Firstpass=%d La
   
   strcpy(pathr,path);    strcpy(pathr,path);
   strcat(pathr,optionfilefiname);    strcat(pathr,optionfilefiname);
   #ifdef WIN32
     _chdir(optionfilefiname); /* Move to directory named optionfile */
   #else
   chdir(optionfilefiname); /* Move to directory named optionfile */    chdir(optionfilefiname); /* Move to directory named optionfile */
   #endif
             
       
   /* 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'. */
Line 6567  Interval (in months) between two waves: Line 6660  Interval (in months) between two waves:
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   globpr=0; /* To get the number ipmx of contributions and the sum of weights*/    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     /* For mortality only */
   if (mle==-3){    if (mle==-3){
     ximort=matrix(1,NDIM,1,NDIM);       ximort=matrix(1,NDIM,1,NDIM); 
 /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */      /*     ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
     cens=ivector(1,n);      cens=ivector(1,n);
     ageexmed=vector(1,n);      ageexmed=vector(1,n);
     agecens=vector(1,n);      agecens=vector(1,n);
Line 6660  Interval (in months) between two waves: Line 6753  Interval (in months) between two waves:
       
     /* Initialize method and iterate */      /* Initialize method and iterate */
     /*     p[1]=0.0268; p[NDIM]=0.083; */      /*     p[1]=0.0268; p[NDIM]=0.083; */
 /*     gsl_vector_set(x, 0, 0.0268); */      /*     gsl_vector_set(x, 0, 0.0268); */
 /*     gsl_vector_set(x, 1, 0.083); */      /*     gsl_vector_set(x, 1, 0.083); */
     gsl_vector_set(x, 0, p[1]);      gsl_vector_set(x, 0, p[1]);
     gsl_vector_set(x, 1, p[2]);      gsl_vector_set(x, 1, p[2]);
   
Line 6778  Interval (in months) between two waves: Line 6871  Interval (in months) between two waves:
     free_ivector(dcwave,1,n);      free_ivector(dcwave,1,n);
     free_matrix(ximort,1,NDIM,1,NDIM);      free_matrix(ximort,1,NDIM,1,NDIM);
 #endif  #endif
   } /* Endof if mle==-3 */    } /* Endof if mle==-3 mortality only */
       /* Standard maximisation */
   else{ /* For mle >=1 */    else{ /* For mle >=1 */
     globpr=0;/* debug */      globpr=0;/* debug */
       /* Computes likelihood for initial parameters */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     globpr=1; /* to print the contributions */      globpr=1; /* again, to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */      likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);      printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)      for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);        printf(" %d %8.5f",k,p[k]);
     printf("\n");      printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */      if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }      }
           
Line 6954  Interval (in months) between two waves: Line 7048  Interval (in months) between two waves:
     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 estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       /* Other stuffs, more or less useful */    
     while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);        ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);        fgets(line, MAXLINE, ficpar);
Line 7027  Interval (in months) between two waves: Line 7122  Interval (in months) between two waves:
     fclose(ficres);      fclose(ficres);
   
   
       /* Other results (useful)*/
   
   
     /*--------------- Prevalence limit  (period or stable prevalence) --------------*/      /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */      /*#include "prevlim.h"*/  /* Use ficrespl, ficlog */
     prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
Line 7066  Interval (in months) between two waves: Line 7164  Interval (in months) between two waves:
       /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */        /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
       /*      } */        /*      } */
     }      }
      
       /* ------ Other prevalence ratios------------ */
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   
Line 7341  Interval (in months) between two waves: Line 7440  Interval (in months) between two waves:
   
   
    printf("Before Current directory %s!\n",pathcd);     printf("Before Current directory %s!\n",pathcd);
   #ifdef WIN32
      if (_chdir(pathcd) != 0)
              printf("Can't move to directory %s!\n",path);
      if(_getcwd(pathcd,MAXLINE) > 0)
   #else
    if(chdir(pathcd) != 0)     if(chdir(pathcd) != 0)
     printf("Can't move to directory %s!\n",path);             printf("Can't move to directory %s!\n", path);
   if(getcwd(pathcd,MAXLINE) > 0)     if (getcwd(pathcd, MAXLINE) > 0)
   #endif 
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");
Removed from v.1.183  
changed lines
  Added in v.1.186

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