Summary: Some updates

diff --git a/src/imach.c b/src/imach.c
index b3774fb6b6ae8b45c0f5e27227ad2164af8e690d..64801252b803b9c0a573a31c2b467149f9375d60 100644 (file)
--- a/src/imach.c
+++ b/src/imach.c
@@ -1,6 +1,9 @@
 /* $Id$
   $State$
   $Log$
+  Revision 1.291  2019/05/09 13:44:18  brouard
+  Summary: Before ncovmax
+
   Revision 1.290  2019/05/09 13:39:37  brouard
   Summary: 0.99r18 unlimited number of individuals
 
@@ -2989,7 +2992,7 @@ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   double **out, **pmij();
   double sumnew=0.;
   double agefin;
-  double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */
+  double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
   double **dnewm, **dsavm, **doldm;
   double **bbmij;
   
@@ -3008,7 +3011,7 @@ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /* outputs pmmij which is a stochastic matrix in row */
 
   /* Diag(w_x) */
-  /* Problem with prevacurrent which can be zero */
+  /* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
   sumnew=0.;
   /*for (ii=1;ii<=nlstate+ndeath;ii++){*/
   for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
@@ -3035,10 +3038,10 @@ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }
   /* End doldm, At the end doldm is diag[(w_i)] */
   
-  /* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */
-  bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */
+  /* Left product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm): diag[(w_i)*Px */
+  bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */
 
-  /* Diag(Sum_i w^i_x p^ij_x */
+  /* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
   /* w1 p11 + w2 p21 only on live states N1./N..*N11/N1. + N2./N..*N21/N2.=(N11+N21)/N..=N.1/N.. */
   for (j=1;j<=nlstate+ndeath;j++){
     sumnew=0.;
@@ -3056,7 +3059,7 @@ double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     } /*End ii */
   } /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */
 
-  ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */
+  ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
   /* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
   /* end bmij */
   return ps; /*pointer is unchanged */
@@ -3888,7 +3891,7 @@ return -l;
 
 
 /*************** function likelione ***********/
-void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
+void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*func)(double []))
 {
   /* This routine should help understanding what is done with 
      the selection of individuals/waves and
@@ -3912,7 +3915,7 @@ void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, lon
     fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   }
 
-  *fretone=(*funcone)(p);
+  *fretone=(*func)(p);
   if(*globpri !=0){
     fclose(ficresilk);
     if (mle ==0)
@@ -6006,7 +6009,7 @@ void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc
        /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
        */                      
        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);  /* Returns p3mat[i][j][h] for h=0 to nhstepm */
-       /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
+       /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
        * at horizon h in state j including mortality.
        */
        for(j=1; j<= nlstate; j++){
@@ -6928,13 +6931,13 @@ divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-
 <img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); 
      /* Survival functions (period) in state j */
      for(cpt=1; cpt<=nlstate;cpt++){
-       fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
+       fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
 <img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
      }
      /* State specific survival functions (period) */
      for(cpt=1; cpt<=nlstate;cpt++){
-       fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
- Or probability to survive in various states (1 to %d) being in state %d at different ages.    \
+       fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
+ And probability to be observed in various states (up to %d) being in state %d at different ages.      \
  <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
      }
      /* Period (forward stable) prevalence in each health state */
@@ -10196,8 +10199,10 @@ BOOL IsWow64()
 #endif
 
 void syscompilerinfo(int logged)
- {
-   /* #include "syscompilerinfo.h"*/
+{
+#include <stdint.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
@@ -10232,6 +10237,8 @@ void syscompilerinfo(int logged)
       /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
       /NOLOGO /TLBID:1
    */
+
+
 #if defined __INTEL_COMPILER
 #if defined(__GNUC__)
        struct utsname sysInfo;  /* For Intel on Linux and OS/X */
@@ -10248,8 +10255,6 @@ void syscompilerinfo(int logged)
    }
 #endif
 
-#include <stdint.h>
-
    printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
 #if defined(__clang__)
    printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM");      /* Clang/LLVM. ---------------------------------------------- */
@@ -10779,7 +10784,7 @@ int main(int argc, char *argv[])
 
   int *tab; 
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
-  int backcast=0;
+  /* int backcast=0; */ /* defined as global for mlikeli and mle */
   int mobilav=0,popforecast=0;
   int hstepm=0, nhstepm=0;
   int agemortsup;
@@ -11204,6 +11209,15 @@ int main(int argc, char *argv[])
       for(jj=1; jj <=nlstate+ndeath; jj++){
        if(jj==i) continue;
        j++;
+       while((c=getc(ficpar))=='#' && c!= EOF){
+         ungetc(c,ficpar);
+         fgets(line, MAXLINE, ficpar);
+         numlinepar++;
+         fputs(line,stdout);
+         fputs(line,ficparo);
+         fputs(line,ficlog);
+       }
+       ungetc(c,ficpar);
        fscanf(ficpar,"%1d%1d",&i1,&j1);
        if ((i1 != i) || (j1 != jj)){
          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
@@ -12818,13 +12832,16 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa
   
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
+  strcpy(pplotcmd,plotcmd);
   
   if((outcmd=system(plotcmd)) != 0){
-    printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
+    printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
-    if((outcmd=system(plotcmd)) != 0)
+    if((outcmd=system(plotcmd)) != 0){
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
+      strcpy(plotcmd,pplotcmd);
+    }
   }
   printf(" Successful, please wait...");
   while (z[0] != 'q') {