From 2b4bb09e9103edfbc1fbe2aab308a4a5487a1f06 Mon Sep 17 00:00:00 2001 From: "N. Brouard" Date: Wed, 9 Sep 2015 16:53:55 +0000 Subject: [PATCH] Summary: Big bug thanks to Flavia Even model=1+age+V2. did not work anymore --- src/imach.c | 81 +++++++++++++++++++++++++++++++---------------------- 1 file changed, 48 insertions(+), 33 deletions(-) diff --git a/src/imach.c b/src/imach.c index c7fe66d..56d2e11 100644 --- a/src/imach.c +++ b/src/imach.c @@ -1,6 +1,9 @@ /* $Id$ $State$ $Log$ + Revision 1.199 2015/09/07 14:09:23 brouard + Summary: 0.98q6 changing default small png format for graph to vectorized svg. + Revision 1.198 2015/09/03 07:14:39 brouard Summary: 0.98q5 Flavia @@ -878,7 +881,7 @@ double idx; int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */ int *Tage; int *Ndum; /** Freq of modality (tricode */ -int **codtab; /**< codtab=imatrix(1,100,1,10); */ +/* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */ int **Tvard, *Tprod, cptcovprod, *Tvaraff; double *lsurv, *lpop, *tpop; @@ -1914,13 +1917,16 @@ double **prevalim(double **prlim, int nlstate, double x[], double age, double ** if(nagesqr==1) cov[3]= agefin*agefin;; for (k=1; k<=cptcovn;k++) { - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ + cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */ } /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; + /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */ + for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2]; for (k=1; k<=cptcovprod;k++) /* Useless */ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; /*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]);*/ @@ -2093,12 +2099,15 @@ double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, in if(nagesqr==1) cov[3]= agexact*agexact; for (k=1; k<=cptcovn;k++) - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; + cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; + /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */ for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */ /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */ - cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; + cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; + /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */ for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */ - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; + /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */ /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/ @@ -3839,7 +3848,8 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double } fprintf(ficresprobmorprev,"\n"); fprintf(ficgp,"\n# Routine varevsij"); - /* fprintf(fichtm, "#Local time at start: %s", strstart);*/ + fprintf(ficgp,"\nunset title \n"); +/* fprintf(fichtm, "#Local time at start: %s", strstart);*/ fprintf(fichtm,"\n

  • Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)

    • \n"); fprintf(fichtm,"\n
    %s
    \n",digitp); /* } */ @@ -4055,6 +4065,7 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480"); /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); + fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",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); */ @@ -4066,7 +4077,7 @@ void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double /* fprintf(fichtm,"\n
    Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year

    \n", stepm,YEARM,digitp,digit); */ /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */ - fprintf(ficgp,"\nset out \"%s%s.svg\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); + fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit); free_vector(xp,1,npar); free_matrix(doldm,1,nlstate,1,nlstate); @@ -4239,7 +4250,7 @@ void varprob(char optionfilefiname[], double **matcov, double x[], double delti[ fprintf(fichtm,"\n

  • Computing and drawing one step probabilities with their confidence intervals

    • \n"); fprintf(fichtm,"\n"); - fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)


    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery
    • \n",optionfilehtmcov); + fprintf(fichtm,"\n

  • Matrix of variance-covariance of one-step probabilities (drawings)

    this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.
    • \n",optionfilehtmcov); fprintf(fichtmcov,"Current page is file %s
    \n\n

    Matrix of variance-covariance of pairs of step probabilities

    \n",optionfilehtmcov, optionfilehtmcov); fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (pij, pkl) are estimated \ and drawn. It helps understanding how is the covariance between two incidences.\ @@ -4291,7 +4302,8 @@ To be simple, these graphs help to understand the significativity of each parame if(nagesqr==1) cov[3]= age*age; for (k=1; k<=cptcovn;k++) { - cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];/* j1 1 2 3 4 + cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; + /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4 * 1 1 1 1 1 * 2 2 1 1 1 * 3 1 2 1 1 @@ -4299,9 +4311,9 @@ To be simple, these graphs help to understand the significativity of each parame /* 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]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; + for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2]; for (k=1; k<=cptcovprod;k++) - cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; + cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)]; for(theta=1; theta <=npar; theta++){ @@ -4449,6 +4461,7 @@ To be simple, these graphs help to understand the significativity of each parame /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */ if(first==1){ first=0; + fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n"); fprintf(ficgp,"\nset parametric;unset label"); fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2); fprintf(ficgp,"\nset ter svg size 640, 480"); @@ -4476,7 +4489,7 @@ To be simple, these graphs help to understand the significativity of each parame }/* if first */ } /* age mod 5 */ } /* end loop age */ - fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); + fprintf(ficgp,"\nset out;\nset out \"%s%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2); first=1; } /*l12 */ } /* k12 */ @@ -4787,7 +4800,7 @@ plot [%.f:%.f] ", ageminpar, agemaxpar); fprintf(ficgp,"##############\n#\n"); /*goto avoid;*/ - fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n"); + fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n"); fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n"); fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n"); fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n"); @@ -4810,7 +4823,7 @@ plot [%.f:%.f] ", ageminpar, agemaxpar); if (ng==2) fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n"); else - fprintf(ficgp,"\nset title \"Probability\"\n"); + fprintf(ficgp,"\nunset title \n"); fprintf(ficgp,"\nset ter svg size 640, 480\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar); i=1; for(k2=1; k2<=nlstate; k2++) { @@ -4832,7 +4845,8 @@ plot [%.f:%.f] ", ageminpar, agemaxpar); /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */ if(ij <=cptcovage) { /* Bug valgrind */ if((j-2)==Tage[ij]) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); + fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); + /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ ij++; } } @@ -4851,7 +4865,8 @@ plot [%.f:%.f] ", ageminpar, agemaxpar); for(j=3; j <=ncovmodel-nagesqr; j++){ if(ij <=cptcovage) { /* Bug valgrind */ if((j-2)==Tage[ij]) { /* Bug valgrind */ - fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); + fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); + /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */ ij++; } } @@ -6176,9 +6191,9 @@ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxp k=k+1; /* to clean */ //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov)); - fprintf(ficrespl,"\n#******"); - printf("\n#******"); - fprintf(ficlog,"\n#******"); + fprintf(ficrespl,"#******"); + printf("#******"); + fprintf(ficlog,"#******"); for(j=1;j<=cptcoveff;j++) { fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); @@ -6190,7 +6205,7 @@ int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxp fprintf(ficrespl,"#Age "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i); fprintf(ficrespl,"\n"); @@ -6918,7 +6933,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numline 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],codtabm(100,10));*/ /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/ h=0; @@ -6953,10 +6968,10 @@ Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numline */ for(h=1; h <=100 ;h++){ /* printf("h=%2d ", h); */ - for(k=1; k <=10; k++){ + /* for(k=1; k <=10; k++){ */ /* printf("k=%d %d ",k,codtabm(h,k)); */ - codtab[h][k]=codtabm(h,k); - } + /* codtab[h][k]=codtabm(h,k); */ + /* } */ /* printf("\n"); */ } /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */ @@ -7650,7 +7665,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa for (k=1; k <= (int) pow(2,cptcoveff); k++){ fprintf(ficreseij,"\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } fprintf(ficreseij,"******\n"); @@ -7710,21 +7725,21 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa for (k=1; k <= (int) pow(2,cptcoveff); k++){ fprintf(ficrest,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficrest,"******\n"); fprintf(ficresstdeij,"\n#****** "); fprintf(ficrescveij,"\n#****** "); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); + fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); } fprintf(ficresstdeij,"******\n"); fprintf(ficrescveij,"******\n"); fprintf(ficresvij,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficresvij,"******\n"); eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage); @@ -7820,7 +7835,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa for (k=1; k <= (int) pow(2,cptcoveff); k++){ fprintf(ficresvpl,"\n#****** "); for(j=1;j<=cptcoveff;j++) - fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); fprintf(ficresvpl,"******\n"); varpl=matrix(1,nlstate,(int) bage, (int) fage); @@ -7857,7 +7872,7 @@ Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpa free_ivector(Tage,1,NCOVMAX); free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); - free_imatrix(codtab,1,100,1,10); + /* free_imatrix(codtab,1,100,1,10); */ fflush(fichtm); fflush(ficgp); -- 2.43.0