version 1.291, 2019/05/09 13:44:18
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version 1.294, 2019/05/16 14:54:33
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.294 2019/05/16 14:54:33 brouard |
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Summary: There was some wrong lines added |
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Revision 1.293 2019/05/09 15:17:34 brouard |
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*** empty log message *** |
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Revision 1.292 2019/05/09 14:17:20 brouard |
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Summary: Some updates |
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Revision 1.291 2019/05/09 13:44:18 brouard |
Revision 1.291 2019/05/09 13:44:18 brouard |
Summary: Before ncovmax |
Summary: Before ncovmax |
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Line 2963 double **pmij(double **ps, double *cov,
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Line 2972 double **pmij(double **ps, double *cov,
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ps[ii][ii]=1; |
ps[ii][ii]=1; |
} |
} |
} |
} |
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/* for(ii=1; ii<= nlstate+ndeath; ii++){ */ |
/* for(ii=1; ii<= nlstate+ndeath; ii++){ */ |
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */ |
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */ |
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ |
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */ |
Line 2992 double **pmij(double **ps, double *cov,
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Line 3001 double **pmij(double **ps, double *cov,
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double **out, **pmij(); |
double **out, **pmij(); |
double sumnew=0.; |
double sumnew=0.; |
double agefin; |
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 **dnewm, **dsavm, **doldm; |
double **bbmij; |
double **bbmij; |
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Line 3011 double **pmij(double **ps, double *cov,
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Line 3020 double **pmij(double **ps, double *cov,
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/* outputs pmmij which is a stochastic matrix in row */ |
/* outputs pmmij which is a stochastic matrix in row */ |
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/* Diag(w_x) */ |
/* Diag(w_x) */ |
/* Problem with prevacurrent which can be zero */ |
/* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */ |
sumnew=0.; |
sumnew=0.; |
/*for (ii=1;ii<=nlstate+ndeath;ii++){*/ |
/*for (ii=1;ii<=nlstate+ndeath;ii++){*/ |
for (ii=1;ii<=nlstate;ii++){ /* Only on live states */ |
for (ii=1;ii<=nlstate;ii++){ /* Only on live states */ |
Line 3038 double **pmij(double **ps, double *cov,
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Line 3047 double **pmij(double **ps, double *cov,
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} |
} |
/* End doldm, At the end doldm is diag[(w_i)] */ |
/* End doldm, At the end doldm is diag[(w_i)] */ |
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/* left Product of this diag matrix by pmmij=Px (dnewm=dsavm*doldm) */ |
/* 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); /* Bug Valgrind */ |
bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */ |
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/* 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.. */ |
/* 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++){ |
for (j=1;j<=nlstate+ndeath;j++){ |
sumnew=0.; |
sumnew=0.; |
Line 3059 double **pmij(double **ps, double *cov,
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Line 3068 double **pmij(double **ps, double *cov,
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} /*End ii */ |
} /*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 */ |
} /* 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 */ |
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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)] */ |
/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */ |
/* end bmij */ |
/* end bmij */ |
return ps; /*pointer is unchanged */ |
return ps; /*pointer is unchanged */ |
Line 3891 return -l;
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Line 3900 return -l;
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/*************** function likelione ***********/ |
/*************** 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 |
/* This routine should help understanding what is done with |
the selection of individuals/waves and |
the selection of individuals/waves and |
Line 3915 void likelione(FILE *ficres,double p[],
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Line 3924 void likelione(FILE *ficres,double p[],
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fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); |
fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n"); |
} |
} |
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*fretone=(*funcone)(p); |
*fretone=(*func)(p); |
if(*globpri !=0){ |
if(*globpri !=0){ |
fclose(ficresilk); |
fclose(ficresilk); |
if (mle ==0) |
if (mle ==0) |
Line 6009 void concatwav(int wav[], int **dh, int
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Line 6018 void concatwav(int wav[], int **dh, int
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/**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h. |
/**< 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 */ |
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. |
* at horizon h in state j including mortality. |
*/ |
*/ |
for(j=1; j<= nlstate; j++){ |
for(j=1; j<= nlstate; j++){ |
Line 6931 divided by h: <sub>h</sub>P<sub>ij</sub>
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Line 6940 divided by h: <sub>h</sub>P<sub>ij</sub>
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<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres); |
<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 */ |
/* Survival functions (period) in state j */ |
for(cpt=1; cpt<=nlstate;cpt++){ |
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); |
<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) */ |
/* State specific survival functions (period) */ |
for(cpt=1; cpt<=nlstate;cpt++){ |
for(cpt=1; cpt<=nlstate;cpt++){ |
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\ |
fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\ |
Or probability to survive in various states (1 to %d) being in state %d at different ages. \ |
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); |
<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 */ |
/* Period (forward stable) prevalence in each health state */ |
Line 10199 BOOL IsWow64()
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Line 10208 BOOL IsWow64()
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#endif |
#endif |
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void syscompilerinfo(int logged) |
void syscompilerinfo(int logged) |
{ |
{ |
/* #include "syscompilerinfo.h"*/ |
#include <stdint.h> |
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/* #include "syscompilerinfo.h"*/ |
/* command line Intel compiler 32bit windows, XP compatible:*/ |
/* command line Intel compiler 32bit windows, XP compatible:*/ |
/* /GS /W3 /Gy |
/* /GS /W3 /Gy |
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D |
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D |
Line 10235 void syscompilerinfo(int logged)
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Line 10246 void syscompilerinfo(int logged)
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/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF |
/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF |
/NOLOGO /TLBID:1 |
/NOLOGO /TLBID:1 |
*/ |
*/ |
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#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 10251 void syscompilerinfo(int logged)
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Line 10264 void syscompilerinfo(int logged)
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} |
} |
#endif |
#endif |
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#include <stdint.h> |
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printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); |
printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:"); |
#if defined(__clang__) |
#if defined(__clang__) |
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */ |
Line 10782 int main(int argc, char *argv[])
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Line 10793 int main(int argc, char *argv[])
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int *tab; |
int *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 backcast=0; |
int backcast=0; /* defined as global for mlikeli and mle*/ |
int mobilav=0,popforecast=0; |
int mobilav=0,popforecast=0; |
int hstepm=0, nhstepm=0; |
int hstepm=0, nhstepm=0; |
int agemortsup; |
int agemortsup; |
Line 11207 int main(int argc, char *argv[])
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Line 11218 int main(int argc, char *argv[])
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for(jj=1; jj <=nlstate+ndeath; jj++){ |
for(jj=1; jj <=nlstate+ndeath; jj++){ |
if(jj==i) continue; |
if(jj==i) continue; |
j++; |
j++; |
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while((c=getc(ficpar))=='#' && c!= EOF){ |
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ungetc(c,ficpar); |
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fgets(line, MAXLINE, ficpar); |
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numlinepar++; |
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fputs(line,stdout); |
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fputs(line,ficparo); |
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fputs(line,ficlog); |
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} |
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ungetc(c,ficpar); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
fscanf(ficpar,"%1d%1d",&i1,&j1); |
if ((i1 != i) || (j1 != jj)){ |
if ((i1 != i) || (j1 != jj)){ |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ |
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \ |
Line 12821 Please run with mle=-1 to get a correct
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Line 12841 Please run with mle=-1 to get a correct
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sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); |
sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); |
printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); |
printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout); |
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strcpy(pplotcmd,plotcmd); |
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if((outcmd=system(plotcmd)) != 0){ |
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"); |
printf("\n Trying if gnuplot resides on the same directory that IMaCh\n"); |
sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot); |
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); |
printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd); |
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strcpy(plotcmd,pplotcmd); |
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} |
} |
} |
printf(" Successful, please wait..."); |
printf(" Successful, please wait..."); |
while (z[0] != 'q') { |
while (z[0] != 'q') { |