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Diff for /imach/src/imach.c between versions 1.163 and 1.177

version 1.163, 2014/12/16 10:30:11 version 1.177, 2015/01/03 18:40:56
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.177  2015/01/03 18:40:56  brouard
     Summary: Still testing ilc32 on OSX
   
     Revision 1.176  2015/01/03 16:45:04  brouard
     *** empty log message ***
   
     Revision 1.175  2015/01/03 16:33:42  brouard
     *** empty log message ***
   
     Revision 1.174  2015/01/03 16:15:49  brouard
     Summary: Still in cross-compilation
   
     Revision 1.173  2015/01/03 12:06:26  brouard
     Summary: trying to detect cross-compilation
   
     Revision 1.172  2014/12/27 12:07:47  brouard
     Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
   
     Revision 1.171  2014/12/23 13:26:59  brouard
     Summary: Back from Visual C
   
     Still problem with utsname.h on Windows
   
     Revision 1.170  2014/12/23 11:17:12  brouard
     Summary: Cleaning some \%% back to %%
   
     The escape was mandatory for a specific compiler (which one?), but too many warnings.
   
     Revision 1.169  2014/12/22 23:08:31  brouard
     Summary: 0.98p
   
     Outputs some informations on compiler used, OS etc. Testing on different platforms.
   
     Revision 1.168  2014/12/22 15:17:42  brouard
     Summary: update
   
     Revision 1.167  2014/12/22 13:50:56  brouard
     Summary: Testing uname and compiler version and if compiled 32 or 64
   
     Testing on Linux 64
   
     Revision 1.166  2014/12/22 11:40:47  brouard
     *** empty log message ***
   
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
     * imach.c (Module): Merging 1.61 to 1.162
   
   Revision 1.163  2014/12/16 10:30:11  brouard    Revision 1.163  2014/12/16 10:30:11  brouard
   * imach.c (Module): Merging 1.61 to 1.162    * imach.c (Module): Merging 1.61 to 1.162
   
Line 492 Line 546
  end   end
 */  */
   
   #define POWELL /* Instead of NLOPT */
   
   
    
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
Line 502 Line 555
   
 #ifdef _WIN32  #ifdef _WIN32
 #include <io.h>  #include <io.h>
   #include <windows.h>
   #include <tchar.h>
 #else  #else
 #include <unistd.h>  #include <unistd.h>
 #endif  #endif
   
 #include <limits.h>  #include <limits.h>
 #include <sys/types.h>  #include <sys/types.h>
   
   #if defined(__GNUC__)
   #include <sys/utsname.h> /* Doesn't work on Windows */
   #endif
   
 #include <sys/stat.h>  #include <sys/stat.h>
 #include <errno.h>  #include <errno.h>
 /* extern int errno; */  /* extern int errno; */
Line 526 Line 586
 #include <gsl/gsl_multimin.h>  #include <gsl/gsl_multimin.h>
 #endif  #endif
   
   
 #ifdef NLOPT  #ifdef NLOPT
 #include <nlopt.h>  #include <nlopt.h>
 typedef struct {  typedef struct {
Line 557  typedef struct { Line 618  typedef struct {
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #define AGESUP 130  #define AGESUP 130
 #define AGEBASE 40  #define AGEBASE 40
 #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */  #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
 #ifdef _WIN32  #ifdef _WIN32
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #define CHARSEPARATOR "\\"  #define CHARSEPARATOR "\\"
Line 571  typedef struct { Line 632  typedef struct {
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";  char version[]="Imach version 0.98p, December 2014,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 686  static double maxarg1,maxarg2; Line 747  static double maxarg1,maxarg2;
       
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 #define rint(a) floor(a+0.5)  #define rint(a) floor(a+0.5)
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
   /* #define mytinydouble 1.0e-16 */
   /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
   /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
   /* static double dsqrarg; */
   /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
 static double sqrarg;  static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
Line 1149  double brent(double ax, double bx, doubl Line 1215  double brent(double ax, double bx, doubl
   int iter;     int iter; 
   double a,b,d,etemp;    double a,b,d,etemp;
   double fu=0,fv,fw,fx;    double fu=0,fv,fw,fx;
   double ftemp;    double ftemp=0.;
   double p,q,r,tol1,tol2,u,v,w,x,xm;     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double e=0.0;     double e=0.0; 
     
Line 1383  void powell(double p[], double **xi, int Line 1449  void powell(double p[], double **xi, int
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf \n",*fret);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficlog,"fret=%lf \n",*fret);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
       printf("%d",i);fflush(stdout);        printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
Line 1478  void powell(double p[], double **xi, int Line 1544  void powell(double p[], double **xi, int
           xi[j][n]=xit[j];      /* and nth direction by the extrapolated */            xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
         }          }
         printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);          printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
         fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);          fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
   
 #ifdef DEBUG  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for(j=1;j<=n;j++){          for(j=1;j<=n;j++){
           printf(" %.12e",xit[j]);            printf(" %.12e",xit[j]);
           fprintf(ficlog," %.12e",xit[j]);            fprintf(ficlog," %.12e",xit[j]);
Line 1499  double **prevalim(double **prlim, int nl Line 1567  double **prevalim(double **prlim, int nl
 {  {
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      matrix by transitions matrix until convergence is reached */       matrix by transitions matrix until convergence is reached */
     
   int i, ii,j,k;    int i, ii,j,k;
   double min, max, maxmin, maxmax,sumnew=0.;    double min, max, maxmin, maxmax,sumnew=0.;
   /* double **matprod2(); */ /* test */    /* double **matprod2(); */ /* test */
   double **out, cov[NCOVMAX+1], **pmij();    double **out, cov[NCOVMAX+1], **pmij();
   double **newm;    double **newm;
   double agefin, delaymax=50 ; /* Max number of years to converge */    double agefin, delaymax=50 ; /* Max number of years to converge */
     
   for (ii=1;ii<=nlstate+ndeath;ii++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=nlstate+ndeath;j++){      for (j=1;j<=nlstate+ndeath;j++){
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }      }
     
    cov[1]=1.;    cov[1]=1.;
      
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    /* 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 */
Line 1551  double **prevalim(double **prlim, int nl Line 1619  double **prevalim(double **prlim, int nl
       }        }
       maxmin=max-min;        maxmin=max-min;
       maxmax=FMAX(maxmax,maxmin);        maxmax=FMAX(maxmax,maxmin);
     }      } /* j loop */
     if(maxmax < ftolpl){      if(maxmax < ftolpl){
       return prlim;        return prlim;
     }      }
   }    } /* age loop */
     return prlim; /* should not reach here */
 }  }
   
 /*************** transition probabilities ***************/   /*************** transition probabilities ***************/ 
Line 1577  double **pmij(double **ps, double *cov, Line 1646  double **pmij(double **ps, double *cov,
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
   int i,j,j1, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){        for(j=1; j<i;j++){
Line 2140  void likelione(FILE *ficres,double p[], Line 2209  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter;    int i,j, iter=0;
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
Line 2216  void hesscov(double **matcov, double p[] Line 2285  void hesscov(double **matcov, double p[]
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    double **hess;
   int i, j,jk;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
Line 2350  double hessii(double x[], double delta, Line 2419  double hessii(double x[], double delta,
         k=kmax;          k=kmax;
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         k=kmax; l=lmax*10.;          k=kmax; l=lmax*10;
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
Line 2365  double hessii(double x[], double delta, Line 2434  double hessii(double x[], double delta,
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k;
Line 2480  void pstamp(FILE *fichier) Line 2549  void pstamp(FILE *fichier)
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
Line 2504  void  freqsummary(char fileres[], int ia Line 2573  void  freqsummary(char fileres[], int ia
   
   first=1;    first=1;
   
   /* for(k1=1; k1<=j ; k1++){   /* Loop on covariates */    /* for(k1=1; k1<=j ; k1++){ */  /* Loop on covariates */
   /*  for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */    /*  for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
   /*    j1++;    /*    j1++; */
 */  
   for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){    for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         scanf("%d", i);*/          scanf("%d", i);*/
Line 2661  void prevalence(double ***probs, double Line 2729  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, k1, i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   double ***freq; /* Frequencies */  
   double *pp, **prop;    double **prop;
   double pos,posprop;     double posprop; 
   double  y2; /* in fractional years */    double  y2; /* in fractional years */
   int iagemin, iagemax;    int iagemin, iagemax;
   int first; /** to stop verbosity which is redirected to log file */    int first; /** to stop verbosity which is redirected to log file */
Line 2755  void  concatwav(int wav[], int **dh, int Line 2823  void  concatwav(int wav[], int **dh, int
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
   jmin=1e+5;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
Line 2884  void tricode(int *Tvar, int **nbcode, in Line 2952  void tricode(int *Tvar, int **nbcode, in
 {  {
   /**< Uses cptcovn+2*cptcovprod as the number of covariates */    /**< Uses cptcovn+2*cptcovprod as the number of covariates */
   /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1     /*      Tvar[i]=atoi(stre);  find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 
   /* Boring subroutine which should only output nbcode[Tvar[j]][k]     * Boring subroutine which should only output nbcode[Tvar[j]][k]
    * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)     * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
   /* nbcode[Tvar[j]][1]=      * nbcode[Tvar[j]][1]= 
   */    */
   
   int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;    int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
Line 2995  void evsij(double ***eij, double x[], in Line 3063  void evsij(double ***eij, double x[], in
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
Line 3314  void varevsij(char optionfilefiname[], d Line 3382  void varevsij(char optionfilefiname[], d
   /* Variance of health expectancies */    /* Variance of health expectancies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   /* double **newm;*/    /* double **newm;*/
     /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
     
     int movingaverage();
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double **dnewmp,**doldmp;    double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k;
   double *xp;    double *xp;
   double **gp, **gm;  /* for var eij */    double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */    double ***gradg, ***trgradg; /*for var eij */
Line 3591  void varevsij(char optionfilefiname[], d Line 3662  void varevsij(char optionfilefiname[], d
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
Line 3617  void varprevlim(char fileres[], double * Line 3688  void varprevlim(char fileres[], double *
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;  
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   int k, cptcode;  
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
Line 3699  void varprevlim(char fileres[], double * Line 3769  void varprevlim(char fileres[], double *
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;    int k2, l2, j1,  z1;
   int k=0,l, cptcode;    int k=0, l;
   int first=1, first1, first2;    int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 3709  void varprob(char optionfilefiname[], do Line 3779  void varprob(char optionfilefiname[], do
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double **mu;    double **mu;
   double age,agelim, cov[NCOVMAX+1];    double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char fileresprob[FILENAMELENGTH];
Line 4013  To be simple, these graphs help to under Line 4083  To be simple, these graphs help to under
           } /* k12 */            } /* k12 */
         } /*l1 */          } /*l1 */
       }/* k1 */        }/* k1 */
       /* } /* loop covariates */        /* } */ /* loop covariates */
   }    }
   free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
Line 4081  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4151  fprintf(fichtm," \n<ul><li><b>Graphs</b>
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Period (stable) prevalence in each health state */         /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \           fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
 <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);  <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \          fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
Line 4167  true period expectancies (those weighted Line 4237  true period expectancies (those weighted
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;    int ng=0;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 4190  void printinggnuplot(char fileres[], cha Line 4260  void printinggnuplot(char fileres[], cha
      fprintf(ficgp,"set xlabel \"Age\" \n\       fprintf(ficgp,"set xlabel \"Age\" \n\
 set ylabel \"Probability\" \n\  set ylabel \"Probability\" \n\
 set ter png small size 320, 240\n\  set ter png small size 320, 240\n\
 plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else        fprintf(ficgp," \%%*lf (\%%*lf)");         else        fprintf(ficgp," %%*lf (%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);       fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);        fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," %%*lf (%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }     }
Line 4217  plot [%.f:%.f] \"%s\" every :::%d::%d u Line 4287  plot [%.f:%.f] \"%s\" every :::%d::%d u
           
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       fprintf(ficgp,"\" t\"\" w l lt 0,");        fprintf(ficgp,"\" t\"\" w l lt 0,");
       fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," %%lf (%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," %%*lf (%%*lf)");
       }           }   
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
       else fprintf(ficgp,"\" t\"\" w l lt 0,");        else fprintf(ficgp,"\" t\"\" w l lt 0,");
Line 4353  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4423  plot [%.f:%.f]  ", ageminpar, agemaxpar)
        } /* end k2 */         } /* end k2 */
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
  avoid:   /* avoid: */
    fflush(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
Line 4401  int movingaverage(double ***probs, doubl Line 4471  int movingaverage(double ***probs, doubl
   
   
 /************** Forecasting ******************/  /************** Forecasting ******************/
 prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){  void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
   /* proj1, year, month, day of starting projection     /* proj1, year, month, day of starting projection 
      agemin, agemax range of age       agemin, agemax range of age
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
   int *popage;  
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
Line 4525  prevforecast(char fileres[], double anpr Line 4594  prevforecast(char fileres[], double anpr
 }  }
   
 /************** Forecasting *****not tested NB*************/  /************** Forecasting *****not tested NB*************/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){  void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
       
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   int *popage;    int *popage;
Line 4702  void prwizard(int ncovmodel, int nlstate Line 4771  void prwizard(int ncovmodel, int nlstate
   
   /* Wizard to print covariance matrix template */    /* Wizard to print covariance matrix template */
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;    int i,j, k, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;    int numlinepar;
   
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 4924  fprintf(fichtm,"<ul><li><h4>Life table</ Line 4993  fprintf(fichtm,"<ul><li><h4>Life table</
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;    int ng;
   
   
Line 4949  int readdata(char datafile[], int firsto Line 5018  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i, j, n;    int i=0, j=0, n=0;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[80], strb[80];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;    int lstra;
   
Line 4980  int readdata(char datafile[], int firsto Line 5049  int readdata(char datafile[], int firsto
       continue;        continue;
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     for (j=0; line[j]!='\0';j++){      strcpy(line, linetmp);
       line[j]=linetmp[j];  
     }  
       
   
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
Line 5003  int readdata(char datafile[], int firsto Line 5070  int readdata(char datafile[], int firsto
               
       strcpy(line,stra);        strcpy(line,stra);
       cutv(stra, strb,line,' ');        cutv(stra, strb,line,' ');
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){        if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
       }        }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){        else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
         month=99;          month=99;
         year=9999;          year=9999;
       }else{        }else{
Line 5019  int readdata(char datafile[], int firsto Line 5086  int readdata(char datafile[], int firsto
     } /* ENd Waves */      } /* ENd Waves */
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.",dummy) != 0){      else  if( (iout=sscanf(strb,"%s.",dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }else{
Line 5034  int readdata(char datafile[], int firsto Line 5101  int readdata(char datafile[], int firsto
     strcpy(line,stra);      strcpy(line,stra);
           
     cutv(stra, strb,line,' ');       cutv(stra, strb,line,' '); 
     if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){      if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
     }      }
     else  if(iout=sscanf(strb,"%s.", dummy) != 0){      else  if( (iout=sscanf(strb,"%s.", dummy)) != 0){
       month=99;        month=99;
       year=9999;        year=9999;
     }else{      }else{
Line 5121  int readdata(char datafile[], int firsto Line 5188  int readdata(char datafile[], int firsto
   fclose(fic);    fclose(fic);
     
   return (0);    return (0);
   endread:    /* endread: */
     printf("Exiting readdata: ");      printf("Exiting readdata: ");
     fclose(fic);      fclose(fic);
     return (1);      return (1);
Line 5134  void removespace(char *str) { Line 5201  void removespace(char *str) {
   do    do
     while (*p2 == ' ')      while (*p2 == ' ')
       p2++;        p2++;
   while (*p1++ = *p2++);    while (*p1++ == *p2++);
 }  }
   
 int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:  int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
Line 5152  int decodemodel ( char model[], int last Line 5219  int decodemodel ( char model[], int last
  */   */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int i1, j1, k1, k2;    int  j1, k1, k2;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
Line 5164  int decodemodel ( char model[], int last Line 5231  int decodemodel ( char model[], int last
     cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */      cptcovs=j+1-j1; /**<  Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2  */
     cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/      cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
                   /* including age products which are counted in cptcovage.                    /* including age products which are counted in cptcovage.
                   /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */                    * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
     cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */      cptcovprod=j1; /**< Number of products  V1*V2 +v3*age = 2 */
     cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */      cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1  */
     strcpy(modelsav,model);       strcpy(modelsav,model); 
Line 5301  int decodemodel ( char model[], int last Line 5368  int decodemodel ( char model[], int last
   
   
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   endread:    /*endread:*/
     printf("Exiting decodemodel: ");      printf("Exiting decodemodel: ");
     return (1);      return (1);
 }  }
   
 calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )  int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
 {  {
   int i, m;    int i, m;
   
Line 5317  calandcheckages(int imx, int maxwav, dou Line 5384  calandcheckages(int imx, int maxwav, dou
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         *nberr++;          *nberr = *nberr + 1;
         printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         *nberr++;          (*nberr)++;
         printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
         fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
         s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */          s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
Line 5336  calandcheckages(int imx, int maxwav, dou Line 5403  calandcheckages(int imx, int maxwav, dou
     for(m=firstpass; (m<= lastpass); m++){      for(m=firstpass; (m<= lastpass); m++){
       if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){        if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
         if (s[m][i] >= nlstate+1) {          if (s[m][i] >= nlstate+1) {
           if(agedc[i]>0)            if(agedc[i]>0){
             if((int)moisdc[i]!=99 && (int)andc[i]!=9999)              if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
               agev[m][i]=agedc[i];                agev[m][i]=agedc[i];
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             else {              }else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 nbwarn++;                  nbwarn++;
                 printf("Warning negative age at death: %ld line:%d\n",num[i],i);                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
Line 5348  calandcheckages(int imx, int maxwav, dou Line 5415  calandcheckages(int imx, int maxwav, dou
                 agev[m][i]=-1;                  agev[m][i]=-1;
               }                }
             }              }
             } /* agedc > 0 */
         }          }
         else if(s[m][i] !=9){ /* Standard case, age in fractional          else if(s[m][i] !=9){ /* Standard case, age in fractional
                                  years but with the precision of a month */                                   years but with the precision of a month */
Line 5378  calandcheckages(int imx, int maxwav, dou Line 5446  calandcheckages(int imx, int maxwav, dou
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
         *nberr++;          (*nberr)++;
         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         return 1;          return 1;
Line 5398  calandcheckages(int imx, int maxwav, dou Line 5466  calandcheckages(int imx, int maxwav, dou
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
   return (0);    return (0);
   endread:   /* endread:*/
     printf("Exiting calandcheckages: ");      printf("Exiting calandcheckages: ");
     return (1);      return (1);
 }  }
   
   #if defined(_MSC_VER)
   /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
   //#include "stdafx.h"
   //#include <stdio.h>
   //#include <tchar.h>
   //#include <windows.h>
   //#include <iostream>
   typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
   
   LPFN_ISWOW64PROCESS fnIsWow64Process;
   
   BOOL IsWow64()
   {
           BOOL bIsWow64 = FALSE;
   
           //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
           //  (HANDLE, PBOOL);
   
           //LPFN_ISWOW64PROCESS fnIsWow64Process;
   
           HMODULE module = GetModuleHandle(_T("kernel32"));
           const char funcName[] = "IsWow64Process";
           fnIsWow64Process = (LPFN_ISWOW64PROCESS)
                   GetProcAddress(module, funcName);
   
           if (NULL != fnIsWow64Process)
           {
                   if (!fnIsWow64Process(GetCurrentProcess(),
                           &bIsWow64))
                           //throw std::exception("Unknown error");
                           printf("Unknown error\n");
           }
           return bIsWow64 != FALSE;
   }
   #endif
   
   void syscompilerinfo()
    {
      /* #include "syscompilerinfo.h"*/
   
   #if defined __INTEL_COMPILER
      struct utsname sysInfo;
   #elif defined(__GNUC__) 
   #include <gnu/libc-version.h>  /* Only on gnu */
      struct utsname sysInfo;
   #endif
   
   #include <stdint.h>
      int cross = CROSS;
      if (cross){
        printf("Cross-");
        fprintf(ficlog,"Cross-");
      }
      printf("Compiled with:");fprintf(ficlog,"Compiled with:");
   #if defined(__clang__)
      printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
   #endif
   #if defined(__ICC) || defined(__INTEL_COMPILER)
      printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
   #endif
   #if defined(__GNUC__) || defined(__GNUG__)
      printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
   #endif
   #if defined(__HP_cc) || defined(__HP_aCC)
      printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
   #endif
   #if defined(__IBMC__) || defined(__IBMCPP__)
      printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
   #endif
   #if defined(_MSC_VER)
      printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
   #endif
   #if defined(__PGI)
      printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
   #endif
   #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
      printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
   #endif
      printf(" for ");fprintf(ficlog," for ");
      
   // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
   #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
       // Windows (x64 and x86)
      printf("Windows (x64 and x86) ");fprintf(ficlog,"Windows (x64 and x86) ");
   #elif __unix__ // all unices, not all compilers
       // Unix
      printf("Unix ");fprintf(ficlog,"Unix ");
   #elif __linux__
       // linux
      printf("linux ");fprintf(ficlog,"linux ");
   #elif __APPLE__
       // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
      printf("Mac OS ");fprintf(ficlog,"Mac OS ");
   #endif
   
   /*  __MINGW32__   */
   /*  __CYGWIN__   */
   /* __MINGW64__  */
   // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
   /* _MSC_VER  //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /?  */
   /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
   /* _WIN64  // Defined for applications for Win64. */
   /* _M_X64 // Defined for compilations that target x64 processors. */
   /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
   
   #if UINTPTR_MAX == 0xffffffff
      printf(" 32-bit"); fprintf(ficlog," 32-bit");/* 32-bit */
   #elif UINTPTR_MAX == 0xffffffffffffffff
      printf(" 64-bit"); fprintf(ficlog," 64-bit");/* 64-bit */
   #else
      printf(" wtf-bit"); fprintf(ficlog," wtf-bit");/* wtf */
   #endif
   
   #if defined(__GNUC__)
   # if defined(__GNUC_PATCHLEVEL__)
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100 \
                               + __GNUC_PATCHLEVEL__)
   # else
   #  define __GNUC_VERSION__ (__GNUC__ * 10000 \
                               + __GNUC_MINOR__ * 100)
   # endif
      printf(" using GNU C version %d.\n", __GNUC_VERSION__);
      fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
   
      if (uname(&sysInfo) != -1) {
        printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
        fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
      }
      else
         perror("uname() error");
   #ifndef __INTEL_COMPILER
      printf("GNU libc version: %s\n", gnu_get_libc_version()); 
      fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version()); 
   #endif
   #endif
   
      //   void main()
      //   {
   #if defined(_MSC_VER)
      if (IsWow64()){
              printf("The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
              fprintf(ficlog, "The program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
      }
      else{
              printf("The process is not running under WOW64 (i.e probably on a 64bit Windows).\n");
              frintf(ficlog,"The programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
      }
      //      printf("\nPress Enter to continue...");
      //      getchar();
      //   }
   
   #endif
      
   
    }
   
 /***********************************************/  /***********************************************/
 /**************** Main Program *****************/  /**************** Main Program *****************/
Line 5418  int main(int argc, char *argv[]) Line 5643  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;    int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
   int linei, month, year,iout;  
   int jj, ll, li, lj, lk, imk;    int jj, ll, li, lj, lk;
   int numlinepar=0; /* Current linenumber of parameter file */    int numlinepar=0; /* Current linenumber of parameter file */
   int itimes;    int itimes;
   int NDIM=2;    int NDIM=2;
   int vpopbased=0;    int vpopbased=0;
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb, agefin,hf;    double agedeb;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   double fret;    double fret;
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */    double dum; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    char line[MAXLINE];
   char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
   char pathr[MAXLINE], pathimach[MAXLINE];     char pathr[MAXLINE], pathimach[MAXLINE]; 
   char **bp, *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int c,  h , cpt;
   int c,  h , cpt,l;    int jl;
   int ju,jl, mi;    int i1, j1, jk, stepsize;
   int i1,j1, jk,aa,bb, stepsize, ij;    int *tab; 
   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;   
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
Line 5458  int main(int argc, char *argv[]) Line 5680  int main(int argc, char *argv[])
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   double bage, fage, age, agelim, agebase;    double bage=0, fage=110, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
Line 5469  int main(int argc, char *argv[]) Line 5691  int main(int argc, char *argv[])
   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;
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
   
   char z[1]="c", occ;    char z[1]="c";
   
   /*char  *strt;*/    /*char  *strt;*/
   char strtend[80];    char strtend[80];
   
   long total_usecs;  
    
 /*   setlocale (LC_ALL, ""); */  /*   setlocale (LC_ALL, ""); */
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 /*   textdomain (PACKAGE); */  /*   textdomain (PACKAGE); */
Line 5557  int main(int argc, char *argv[]) Line 5778  int main(int argc, char *argv[])
   strcpy(command,"mkdir ");    strcpy(command,"mkdir ");
   strcat(command,optionfilefiname);    strcat(command,optionfilefiname);
   if((outcmd=system(command)) != 0){    if((outcmd=system(command)) != 0){
     printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);      printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
     /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
     /* fclose(ficlog); */      /* fclose(ficlog); */
 /*     exit(1); */  /*     exit(1); */
Line 5584  int main(int argc, char *argv[]) Line 5805  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();
   
   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);
   fflush(ficlog);    fflush(ficlog);
Line 5752  run imach with mle=-1 to get a correct t Line 5975  run imach with mle=-1 to get a correct t
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){          if ( (i1-i) * (j1-j) != 0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
Line 6787  Interval (in months) between two waves: Line 7010  Interval (in months) between two waves:
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   }  /* mle==-3 arrives here for freeing */    }  /* mle==-3 arrives here for freeing */
  endfree:   /* endfree:*/
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
Removed from v.1.163  
changed lines
  Added in v.1.177

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