--- imach096d/src/imach.c 2002/07/24 09:07:45 1.54 +++ imach096d/src/imach.c 2003/01/28 17:41:19 1.67 @@ -1,4 +1,4 @@ -/* $Id: imach.c,v 1.54 2002/07/24 09:07:45 brouard Exp $ +/* $Id: imach.c,v 1.67 2003/01/28 17:41:19 brouard Exp $ Interpolated Markov Chain Short summary of the programme: @@ -32,8 +32,8 @@ hPijx is the probability to be observed in state i at age x+h conditional to the observed state i at age x. The delay 'h' can be split into an exact number (nh*stepm) of unobserved intermediate - states. This elementary transition (by month or quarter trimester, - semester or year) is model as a multinomial logistic. The hPx + states. This elementary transition (by month, quarter, + semester or year) is modelled as a multinomial logistic. The hPx matrix is simply the matrix product of nh*stepm elementary matrices and the contribution of each individual to the likelihood is simply hPijx. @@ -60,7 +60,7 @@ /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/ #define FILENAMELENGTH 80 /*#define DEBUG*/ -#define unix +#define windows #define GLOCK_ERROR_NOPATH -1 /* empty path */ #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */ @@ -83,7 +83,7 @@ #define ODIRSEPARATOR '\\' #endif -char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES "; +char version[80]="Imach version 0.91, November 2002, INED-EUROREVES "; int erreur; /* Error number */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -99,6 +99,8 @@ int jmin, jmax; /* min, max spacing betw int mle, weightopt; int **mw; /* mw[mi][i] is number of the mi wave for this individual */ int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */ +int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between + * wave mi and wave mi+1 is not an exact multiple of stepm. */ double jmean; /* Mean space between 2 waves */ double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ @@ -163,7 +165,7 @@ int estepm; int m,nb; int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage; double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint; -double **pmmij, ***probs, ***mobaverage; +double **pmmij, ***probs; double dateintmean=0; double *weight; @@ -177,49 +179,49 @@ double ftolhess; /* Tolerance for comput /**************** split *************************/ static int split( char *path, char *dirc, char *name, char *ext, char *finame ) { - char *s; /* pointer */ - int l1, l2; /* length counters */ + char *ss; /* pointer */ + int l1, l2; /* length counters */ - l1 = strlen( path ); /* length of path */ - if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); - s= strrchr( path, DIRSEPARATOR ); /* find last / */ - if ( s == NULL ) { /* no directory, so use current */ - /*if(strrchr(path, ODIRSEPARATOR )==NULL) - printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ + l1 = strlen(path ); /* length of path */ + if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH ); + ss= strrchr( path, DIRSEPARATOR ); /* find last / */ + if ( ss == NULL ) { /* no directory, so use current */ + /*if(strrchr(path, ODIRSEPARATOR )==NULL) + printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/ #if defined(__bsd__) /* get current working directory */ - extern char *getwd( ); + extern char *getwd( ); - if ( getwd( dirc ) == NULL ) { + if ( getwd( dirc ) == NULL ) { #else - extern char *getcwd( ); + extern char *getcwd( ); - if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { + if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { #endif - return( GLOCK_ERROR_GETCWD ); - } - strcpy( name, path ); /* we've got it */ - } else { /* strip direcotry from path */ - s++; /* after this, the filename */ - l2 = strlen( s ); /* length of filename */ - if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); - strcpy( name, s ); /* save file name */ - strncpy( dirc, path, l1 - l2 ); /* now the directory */ - dirc[l1-l2] = 0; /* add zero */ - } - l1 = strlen( dirc ); /* length of directory */ + return( GLOCK_ERROR_GETCWD ); + } + strcpy( name, path ); /* we've got it */ + } else { /* strip direcotry from path */ + ss++; /* after this, the filename */ + l2 = strlen( ss ); /* length of filename */ + if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH ); + strcpy( name, ss ); /* save file name */ + strncpy( dirc, path, l1 - l2 ); /* now the directory */ + dirc[l1-l2] = 0; /* add zero */ + } + l1 = strlen( dirc ); /* length of directory */ #ifdef windows - if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } + if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; } #else - if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } + if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; } #endif - s = strrchr( name, '.' ); /* find last / */ - s++; - strcpy(ext,s); /* save extension */ - l1= strlen( name); - l2= strlen( s)+1; - strncpy( finame, name, l1-l2); - finame[l1-l2]= 0; - return( 0 ); /* we're done */ + ss = strrchr( name, '.' ); /* find last / */ + ss++; + strcpy(ext,ss); /* save extension */ + l1= strlen( name); + l2= strlen(ss)+1; + strncpy( finame, name, l1-l2); + finame[l1-l2]= 0; + return( 0 ); /* we're done */ } @@ -277,7 +279,7 @@ void nrerror(char error_text[]) { fprintf(stderr,"ERREUR ...\n"); fprintf(stderr,"%s\n",error_text); - exit(1); + exit(EXIT_FAILURE); } /*********************** vector *******************/ double *vector(int nl, int nh) @@ -854,11 +856,13 @@ double **matprod2(double **out, double * double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij ) { - /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month - duration (i.e. until - age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. + /* Computes the transition matrix starting at age 'age' over + 'nhstepm*hstepm*stepm' months (i.e. until + age (in years) age+nhstepm*hstepm*stepm/12) by multiplying + nhstepm*hstepm matrices. Output is stored in matrix po[i][j][h] for h every 'hstepm' step - (typically every 2 years instead of every month which is too big). + (typically every 2 years instead of every month which is too big + for the memory). Model is determined by parameters x and covariates have to be included manually here. @@ -914,6 +918,8 @@ double func( double *x) double **out; double sw; /* Sum of weights */ double lli; /* Individual log likelihood */ + int s1, s2; + double bbh; long ipmx; /*extern weight */ /* We are differentiating ll according to initial status */ @@ -924,34 +930,187 @@ double func( double *x) cov[1]=1.; for(k=1; k<=nlstate; k++) ll[k]=0.; - for (i=1,ipmx=0, sw=0.; i<=imx; i++){ - for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; - for(mi=1; mi<= wav[i]-1; mi++){ - for (ii=1;ii<=nlstate+ndeath;ii++) - for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0); - for(d=0; d 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ + lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + } else if(mle==2){ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d<=dh[mi][i]; d++){ + newm=savm; + cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM; + for (kk=1; kk<=cptcovage;kk++) { + cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; + } + out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, + 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); + savm=oldm; + oldm=newm; + } /* end mult */ + + /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ + /* But now since version 0.9 we anticipate for bias and large stepm. + * If stepm is larger than one month (smallest stepm) and if the exact delay + * (in months) between two waves is not a multiple of stepm, we rounded to + * the nearest (and in case of equal distance, to the lowest) interval but now + * we keep into memory the bias bh[mi][i] and also the previous matrix product + * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the + * probability in order to take into account the bias as a fraction of the way + * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies + * -stepm/2 to stepm/2 . + * For stepm=1 the results are the same as for previous versions of Imach. + * For stepm > 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */ + /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ + /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + } else if(mle==3){ /* exponential inter-extrapolation */ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d 1 the results are less biased than in previous versions. + */ + s1=s[mw[mi][i]][i]; + s2=s[mw[mi+1][i]][i]; + bbh=(double)bh[mi][i]/(double)stepm; + /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */ + lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ + /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ + /*if(lli ==000.0)*/ + /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ + ipmx +=1; + sw += weight[i]; + ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; + } /* end of wave */ + } /* end of individual */ + }else{ /* ml=4 no inter-extrapolation */ + for (i=1,ipmx=0, sw=0.; i<=imx; i++){ + for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i]; + for(mi=1; mi<= wav[i]-1; mi++){ + for (ii=1;ii<=nlstate+ndeath;ii++) + for (j=1;j<=nlstate+ndeath;j++){ + oldm[ii][j]=(ii==j ? 1.0 : 0.0); + savm[ii][j]=(ii==j ? 1.0 : 0.0); + } + for(d=0; d=dateprev1) && (k2<=dateprev2)) { @@ -1482,12 +1641,12 @@ void prevalence(int agemin, float agemax /************* Waves Concatenation ***************/ -void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) +void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm) { /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i. Death is a valid wave (if date is known). mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i - dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i] + dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i] and mw[mi+1][i]. dh depends on stepm. */ @@ -1558,14 +1717,35 @@ void concatwav(int wav[], int **dh, int jk= j/stepm; jl= j -jk*stepm; ju= j -(jk+1)*stepm; - if(jl <= -ju) - dh[mi][i]=jk; - else - dh[mi][i]=jk+1; - if(dh[mi][i]==0) - dh[mi][i]=1; /* At least one step */ - } - } + if(mle <=1){ + if(jl==0){ + dh[mi][i]=jk; + bh[mi][i]=0; + }else{ /* We want a negative bias in order to only have interpolation ie + * at the price of an extra matrix product in likelihood */ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + }else{ + if(jl <= -ju){ + dh[mi][i]=jk; + bh[mi][i]=jl; /* bias is positive if real duration + * is higher than the multiple of stepm and negative otherwise. + */ + } + else{ + dh[mi][i]=jk+1; + bh[mi][i]=ju; + } + if(dh[mi][i]==0){ + dh[mi][i]=1; /* At least one step */ + bh[mi][i]=ju; /* At least one step */ + printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i); + } + if(i==298 || i==287 || i==763 ||i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm); + } + } /* end if mle */ + } /* end wave */ } jmean=sum/k; printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean); @@ -1575,31 +1755,35 @@ void concatwav(int wav[], int **dh, int /*********** Tricode ****************************/ void tricode(int *Tvar, int **nbcode, int imx) { - int Ndum[20],ij=1, k, j, i; + + int Ndum[20],ij=1, k, j, i, maxncov=19; int cptcode=0; cptcoveff=0; - for (k=0; k<19; k++) Ndum[k]=0; + for (k=0; k cptcode) cptcode=ij; + if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable + Tvar[j]. If V=sex and male is 0 and + female is 1, then cptcode=1.*/ } for (i=0; i<=cptcode; i++) { - if(Ndum[i]!=0) ncodemax[j]++; + if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */ } - ij=1; - + ij=1; for (i=1; i<=ncodemax[j]; i++) { - for (k=0; k<=19; k++) { + for (k=0; k<= maxncov; k++) { if (Ndum[k] != 0) { nbcode[Tvar[j]][ij]=k; + /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */ ij++; } @@ -1608,22 +1792,23 @@ void tricode(int *Tvar, int **nbcode, in } } - for (k=0; k<19; k++) Ndum[k]=0; + for (k=0; k< maxncov; k++) Ndum[k]=0; - for (i=1; i<=ncovmodel-2; i++) { + for (i=1; i<=ncovmodel-2; i++) { + /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/ ij=Tvar[i]; - Ndum[ij]++; + Ndum[ij]++; } ij=1; - for (i=1; i<=10; i++) { + for (i=1; i<= maxncov; i++) { if((Ndum[i]!=0) && (i<=ncovcol)){ - Tvaraff[ij]=i; + Tvaraff[ij]=i; /*For printing */ ij++; } } - cptcoveff=ij-1; + cptcoveff=ij-1; /*Number of simple covariates*/ } /*********** Health Expectancies ****************/ @@ -1661,7 +1846,7 @@ void evsij(char fileres[], double ***eij * This is mainly to measure the difference between two models: for example * if stepm=24 months pijx are given only every 2 years and by summing them * we are calculating an estimate of the Life Expectancy assuming a linear - * progression inbetween and thus overestimating or underestimating according + * progression in between and thus overestimating or underestimating according * to the curvature of the survival function. If, for the same date, we * estimate the model with stepm=1 month, we can keep estepm to 24 months * to compare the new estimate of Life expectancy with the same linear @@ -1819,18 +2004,18 @@ void varevsij(char optionfilefiname[], d double ***mobaverage; int theta; char digit[4]; - char digitp[16]; + char digitp[25]; char fileresprobmorprev[FILENAMELENGTH]; - if(popbased==1) - strcpy(digitp,"-populbased-"); - else + if(popbased==1){ + if(mobilav!=0) + strcpy(digitp,"-populbased-mobilav-"); + else strcpy(digitp,"-populbased-nomobil-"); + } + else strcpy(digitp,"-stablbased-"); - if(mobilav!=0) - strcat(digitp,"mobilav-"); - else - strcat(digitp,"nomobil-"); + if (mobilav!=0) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ @@ -1851,7 +2036,7 @@ void varevsij(char optionfilefiname[], d } printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev); - fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n"); + fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm); fprintf(ficresprobmorprev,"# Age cov=%-d",ij); for(j=nlstate+1; j<=(nlstate+ndeath);j++){ fprintf(ficresprobmorprev," p.%-d SE",j); @@ -1873,8 +2058,8 @@ void varevsij(char optionfilefiname[], d exit(0); } else{ - fprintf(fichtm,"\n

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

    • \n"); - fprintf(fichtm,"\n
    %s (à revoir)
    \n",digitp); + 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); } varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); @@ -1908,7 +2093,7 @@ void varevsij(char optionfilefiname[], d and note for a fixed period like k years */ /* We decided (b) to get a life expectancy respecting the most precise curvature of the survival function given by stepm (the optimization length). Unfortunately it - means that if the survival funtion is printed only each two years of age and if + means that if the survival funtion is printed every two years of age and if you sum them up and add 1 year (area under the trapezoids) you won't get the same results. So we changed our mind and took the option of the best precision. */ @@ -1924,7 +2109,7 @@ void varevsij(char optionfilefiname[], d for(theta=1; theta <=npar; theta++){ - for(i=1; i<=npar; i++){ /* Computes gradient */ + for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/ xp[i] = x[i] + (i==theta ?delti[theta]:0); } hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); @@ -1946,14 +2131,17 @@ void varevsij(char optionfilefiname[], d gp[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - /* This for computing forces of mortality (h=1)as a weighted average */ + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ for(i=1; i<= nlstate; i++) gpp[j] += prlim[i][i]*p3mat[i][j][1]; } - /* end force of mortality */ + /* end probability of death */ - for(i=1; i<=npar; i++) /* Computes gradient */ + for(i=1; i<=npar; i++) /* Computes gradient x - delta */ xp[i] = x[i] - (i==theta ?delti[theta]:0); hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij); @@ -1974,12 +2162,15 @@ void varevsij(char optionfilefiname[], d gm[h][j] += prlim[i][i]*p3mat[i][j][h]; } } - /* This for computing force of mortality (h=1)as a weighted average */ + /* This for computing probability of death (h=1 means + computed over hstepm matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ for(i=1; i<= nlstate; i++) gmp[j] += prlim[i][i]*p3mat[i][j][1]; } - /* end force of mortality */ + /* end probability of death */ for(j=1; j<= nlstate; j++) /* vareij */ for(h=0; h<=nhstepm; h++){ @@ -2024,6 +2215,7 @@ void varevsij(char optionfilefiname[], d for(i=nlstate+1;i<=nlstate+ndeath;i++) varppt[j][i]=doldmp[j][i]; /* end ppptj */ + /* x centered again */ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij); @@ -2037,12 +2229,15 @@ void varevsij(char optionfilefiname[], d } } - /* This for computing force of mortality (h=1)as a weighted average */ + /* This for computing probability of death (h=1 means + computed over hstepm (estepm) matrices product = hstepm*stepm months) + as a weighted average of prlim. + */ for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ for(i=1; i<= nlstate; i++) gmp[j] += prlim[i][i]*p3mat[i][j][1]; } - /* end force of mortality */ + /* end probability of death */ fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij); for(j=nlstate+1; j<=(nlstate+ndeath);j++){ @@ -2072,11 +2267,14 @@ void varevsij(char optionfilefiname[], d fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65"); /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */ fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";"); - 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); +/* 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); */ + fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev); + fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev); fprintf(fichtm,"\n
    File (multiple files are possible if covariates are present): %s\n",fileresprobmorprev,fileresprobmorprev); - fprintf(fichtm,"\n
    Probability is computed over estepm=%d months.

    \n", stepm,digitp,digit); + fprintf(fichtm,"\n
    Probability is computed over estepm=%d months.

    \n", estepm,digitp,digit); /* 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.png\";replot;",digitp,digit); @@ -2087,18 +2285,17 @@ void varevsij(char optionfilefiname[], d free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar); free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath); - free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); fclose(ficresprobmorprev); fclose(ficgp); fclose(fichtm); - } /************ Variance of prevlim ******************/ void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij) { /* 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; int i, j, nhstepm, hstepm; @@ -2270,7 +2467,6 @@ void varprob(char optionfilefiname[], do } - cov[1]=1; tj=cptcoveff; if (cptcovn<1) {tj=1;ncodemax[1]=1;} @@ -2278,7 +2474,6 @@ void varprob(char optionfilefiname[], do for(t=1; t<=tj;t++){ for(i1=1; i1<=ncodemax[t];i1++){ j1++; - if (cptcovn>0) { fprintf(ficresprob, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); @@ -2351,7 +2546,11 @@ void varprob(char optionfilefiname[], do matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg); - + free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); + free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); + pmij(pmmij,cov,ncovmodel,x,nlstate); k=0; @@ -2366,10 +2565,10 @@ void varprob(char optionfilefiname[], do varpij[i][j][(int)age] = doldm[i][j]; /*printf("\n%d ",(int)age); - for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ - printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); - }*/ + for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){ + printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i])); + }*/ fprintf(ficresprob,"\n%d ",(int)age); fprintf(ficresprobcov,"\n%d ",(int)age); @@ -2397,13 +2596,13 @@ void varprob(char optionfilefiname[], do /* Confidence intervalle of pij */ /* - fprintf(ficgp,"\nset noparametric;unset label"); - fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); - fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); - fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); - fprintf(fichtm,"\n
    ",optionfilefiname); - fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); - fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); + fprintf(ficgp,"\nset noparametric;unset label"); + fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\""); + fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65"); + fprintf(fichtm,"\n
    Probability with confidence intervals expressed in year-1 :pijgr%s.png, ",optionfilefiname,optionfilefiname); + fprintf(fichtm,"\n
    ",optionfilefiname); + fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname); + fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob); */ /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/ @@ -2475,13 +2674,9 @@ void varprob(char optionfilefiname[], do } /*l1 */ }/* k1 */ } /* loop covariates */ - free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); - free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath)); - free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); - free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); - free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar); } + 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_vector(xp,1,npar); fclose(ficresprob); fclose(ficresprobcov); @@ -2774,14 +2969,20 @@ m=pow(2,cptcoveff); int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){ int i, cpt, cptcod; + int modcovmax =1; int mobilavrange, mob; double age; + + modcovmax=2*cptcoveff;/* Max number of modalities. We suppose + a covariate has 2 modalities */ + if (cptcovn<1) modcovmax=1; /* At least 1 pass */ + if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){ if(mobilav==1) mobilavrange=5; /* default */ else mobilavrange=mobilav; for (age=bage; age<=fage; age++) for (i=1; i<=nlstate;i++) - for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++) + for (cptcod=1;cptcod<=modcovmax;cptcod++) mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod]; /* We keep the original values on the extreme ages bage, fage and for fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2 @@ -2790,7 +2991,7 @@ int movingaverage(double ***probs, doubl for (mob=3;mob <=mobilavrange;mob=mob+2){ for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ for (i=1; i<=nlstate;i++){ - for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ + for (cptcod=1;cptcod<=modcovmax;cptcod++){ mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod]; for (cpt=1;cpt<=(mob-1)/2;cpt++){ mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod]; @@ -2814,10 +3015,11 @@ prevforecast(char fileres[], double anpr double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; double *popeffectif,*popcount; double ***p3mat; + double ***mobaverage; char fileresf[FILENAMELENGTH]; agelim=AGESUP; -calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; + calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM; prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); @@ -2918,9 +3120,10 @@ populforecast(char fileres[], double anp int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; int *popage; - double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double calagedate, agelim, kk1, kk2; double *popeffectif,*popcount; double ***p3mat,***tabpop,***tabpopprev; + double ***mobaverage; char filerespop[FILENAMELENGTH]; tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); @@ -3078,7 +3281,7 @@ populforecast(char fileres[], double anp int main(int argc, char *argv[]) { - + int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod; double agedeb, agefin,hf; double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; @@ -3097,7 +3300,7 @@ int main(int argc, char *argv[]) int c, h , cpt,l; int ju,jl, mi; int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; - int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; + int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; int mobilav=0,popforecast=0; int hstepm, nhstepm; double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; @@ -3116,7 +3319,6 @@ int main(int argc, char *argv[]) double *epj, vepp; double kk1, kk2; double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; - char *alph[]={"a","a","b","c","d","e"}, str[4]; @@ -3127,9 +3329,9 @@ int main(int argc, char *argv[]) char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80]; /* long total_usecs; - struct timeval start_time, end_time; + struct timeval start_time, end_time; - gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ + gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ getcwd(pathcd, size); printf("\n%s",version); @@ -3146,11 +3348,11 @@ int main(int argc, char *argv[]) /* cutv(path,optionfile,pathtot,'\\');*/ split(pathtot,path,optionfile,optionfilext,optionfilefiname); - printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); + printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); chdir(path); replace(pathc,path); -/*-------- arguments in the command line --------*/ + /*-------- arguments in the command line --------*/ /* Log file */ strcat(filelog, optionfilefiname); @@ -3198,7 +3400,7 @@ int main(int argc, char *argv[]) fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model); -while((c=getc(ficpar))=='#' && c!= EOF){ + while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); puts(line); @@ -3208,10 +3410,10 @@ while((c=getc(ficpar))=='#' && c!= EOF){ covar=matrix(0,NCOVMAX,1,n); - cptcovn=0; + cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/ if (strlen(model)>1) cptcovn=nbocc(model,'+')+1; - ncovmodel=2+cptcovn; + ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */ nvar=ncovmodel-1; /* Suppressing age as a basic covariate */ /* Read guess parameters */ @@ -3225,7 +3427,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - for(i=1; i <=nlstate; i++) + for(i=1; i <=nlstate; i++) for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); fprintf(ficparo,"%1d%1d",i1,j1); @@ -3249,7 +3451,7 @@ while((c=getc(ficpar))=='#' && c!= EOF){ fprintf(ficparo,"\n"); } - npar= (nlstate+ndeath-1)*nlstate*ncovmodel; + npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ p=param[1][1]; @@ -3322,73 +3524,72 @@ while((c=getc(ficpar))=='#' && c!= EOF){ fprintf(ficlog,"\n"); - /*-------- Rewriting paramater file ----------*/ - strcpy(rfileres,"r"); /* "Rparameterfile */ - strcat(rfileres,optionfilefiname); /* Parameter file first name*/ - strcat(rfileres,"."); /* */ - strcat(rfileres,optionfilext); /* Other files have txt extension */ - if((ficres =fopen(rfileres,"w"))==NULL) { - printf("Problem writing new parameter file: %s\n", fileres);goto end; - fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; - } - fprintf(ficres,"#%s\n",version); + /*-------- Rewriting paramater file ----------*/ + strcpy(rfileres,"r"); /* "Rparameterfile */ + strcat(rfileres,optionfilefiname); /* Parameter file first name*/ + strcat(rfileres,"."); /* */ + strcat(rfileres,optionfilext); /* Other files have txt extension */ + if((ficres =fopen(rfileres,"w"))==NULL) { + printf("Problem writing new parameter file: %s\n", fileres);goto end; + fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end; + } + fprintf(ficres,"#%s\n",version); - /*-------- data file ----------*/ - if((fic=fopen(datafile,"r"))==NULL) { - printf("Problem with datafile: %s\n", datafile);goto end; - fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; - } - - n= lastobs; - severity = vector(1,maxwav); - outcome=imatrix(1,maxwav+1,1,n); - num=ivector(1,n); - moisnais=vector(1,n); - annais=vector(1,n); - moisdc=vector(1,n); - andc=vector(1,n); - agedc=vector(1,n); - cod=ivector(1,n); - weight=vector(1,n); - for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ - mint=matrix(1,maxwav,1,n); - anint=matrix(1,maxwav,1,n); - s=imatrix(1,maxwav+1,1,n); - adl=imatrix(1,maxwav+1,1,n); - tab=ivector(1,NCOVMAX); - ncodemax=ivector(1,8); - - i=1; - while (fgets(line, MAXLINE, fic) != NULL) { - if ((i >= firstobs) && (i <=lastobs)) { + /*-------- data file ----------*/ + if((fic=fopen(datafile,"r"))==NULL) { + printf("Problem with datafile: %s\n", datafile);goto end; + fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end; + } + + n= lastobs; + severity = vector(1,maxwav); + outcome=imatrix(1,maxwav+1,1,n); + num=ivector(1,n); + moisnais=vector(1,n); + annais=vector(1,n); + moisdc=vector(1,n); + andc=vector(1,n); + agedc=vector(1,n); + cod=ivector(1,n); + weight=vector(1,n); + for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */ + mint=matrix(1,maxwav,1,n); + anint=matrix(1,maxwav,1,n); + s=imatrix(1,maxwav+1,1,n); + tab=ivector(1,NCOVMAX); + ncodemax=ivector(1,8); + + i=1; + while (fgets(line, MAXLINE, fic) != NULL) { + if ((i >= firstobs) && (i <=lastobs)) { - for (j=maxwav;j>=1;j--){ - cutv(stra, strb,line,' '); s[j][i]=atoi(strb); - strcpy(line,stra); - cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); - } + for (j=maxwav;j>=1;j--){ + cutv(stra, strb,line,' '); s[j][i]=atoi(strb); + strcpy(line,stra); + cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra); + } - cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); + cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); - cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); - for (j=ncovcol;j>=1;j--){ - cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); - } - num[i]=atol(stra); + cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); + for (j=ncovcol;j>=1;j--){ + cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); + } + num[i]=atol(stra); - /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ - printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ + /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ + printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/ - i=i+1; - } - } - /* printf("ii=%d", ij); - scanf("%d",i);*/ + i=i+1; + } + } + /* printf("ii=%d", ij); + scanf("%d",i);*/ imx=i-1; /* Number of individuals */ /* for (i=1; i<=imx; i++){ @@ -3408,12 +3609,12 @@ while((c=getc(ficpar))=='#' && c!= EOF){ Tvard=imatrix(1,15,1,2); Tage=ivector(1,15); - if (strlen(model) >1){ + if (strlen(model) >1){ /* If there is at least 1 covariate */ j=0, j1=0, k1=1, k2=1; - j=nbocc(model,'+'); - j1=nbocc(model,'*'); - cptcovn=j+1; - cptcovprod=j1; + j=nbocc(model,'+'); /* j=Number of '+' */ + j1=nbocc(model,'*'); /* j1=Number of '*' */ + cptcovn=j+1; + cptcovprod=j1; /*Number of products */ strcpy(modelsav,model); if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){ @@ -3422,9 +3623,11 @@ while((c=getc(ficpar))=='#' && c!= EOF){ goto end; } + /* This loop fills the array Tvar from the string 'model'.*/ + for(i=(j+1); i>=1;i--){ cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ - if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */ + if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/ /*scanf("%d",i);*/ if (strchr(strb,'*')) { /* Model includes a product */ @@ -3471,274 +3674,281 @@ while((c=getc(ficpar))=='#' && c!= EOF){ } /* end of loop + */ } /* end model */ + /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products. + If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/ + /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]); printf("cptcovprod=%d ", cptcovprod); fprintf(ficlog,"cptcovprod=%d ", cptcovprod); - scanf("%d ",i);*/ - fclose(fic); + + scanf("%d ",i); + fclose(fic);*/ /* if(mle==1){*/ - if (weightopt != 1) { /* Maximisation without weights*/ - for(i=1;i<=n;i++) weight[i]=1.0; - } + if (weightopt != 1) { /* Maximisation without weights*/ + for(i=1;i<=n;i++) weight[i]=1.0; + } /*-calculation of age at interview from date of interview and age at death -*/ - agev=matrix(1,maxwav,1,imx); + agev=matrix(1,maxwav,1,imx); - for (i=1; i<=imx; i++) { - for(m=2; (m<= maxwav); m++) { - if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ - anint[m][i]=9999; - s[m][i]=-1; - } - if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; - } + for (i=1; i<=imx; i++) { + for(m=2; (m<= maxwav); m++) { + if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){ + anint[m][i]=9999; + s[m][i]=-1; + } + if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1; } + } - for (i=1; i<=imx; i++) { - agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); - for(m=1; (m<= maxwav); m++){ - if(s[m][i] >0){ - if (s[m][i] >= nlstate+1) { - if(agedc[i]>0) - if(moisdc[i]!=99 && andc[i]!=9999) - agev[m][i]=agedc[i]; - /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ - else { + for (i=1; i<=imx; i++) { + agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); + for(m=1; (m<= maxwav); m++){ + if(s[m][i] >0){ + if (s[m][i] >= nlstate+1) { + if(agedc[i]>0) + if(moisdc[i]!=99 && andc[i]!=9999) + agev[m][i]=agedc[i]; + /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/ + else { if (andc[i]!=9999){ - printf("Warning negative age at death: %d line:%d\n",num[i],i); - fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); - agev[m][i]=-1; + printf("Warning negative age at death: %d line:%d\n",num[i],i); + fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i); + agev[m][i]=-1; } } - } - else if(s[m][i] !=9){ /* Should no more exist */ - agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); - if(mint[m][i]==99 || anint[m][i]==9999) - agev[m][i]=1; - else if(agev[m][i] agemax){ - agemax=agev[m][i]; - /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ - } - /*agev[m][i]=anint[m][i]-annais[i];*/ - /* agev[m][i] = age[i]+2*m;*/ - } - else { /* =9 */ + } + else if(s[m][i] !=9){ /* Should no more exist */ + agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]); + if(mint[m][i]==99 || anint[m][i]==9999) agev[m][i]=1; - s[m][i]=-1; + else if(agev[m][i] agemax){ + agemax=agev[m][i]; + /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/ } + /*agev[m][i]=anint[m][i]-annais[i];*/ + /* agev[m][i] = age[i]+2*m;*/ } - else /*= 0 Unknown */ + else { /* =9 */ agev[m][i]=1; + s[m][i]=-1; + } } - + else /*= 0 Unknown */ + agev[m][i]=1; } - for (i=1; i<=imx; i++) { - for(m=1; (m<= maxwav); m++){ - if (s[m][i] > (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); - goto end; - } + + } + for (i=1; i<=imx; i++) { + for(m=1; (m<= maxwav); m++){ + if (s[m][i] > (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); + goto end; } } + } -printf("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); - - free_vector(severity,1,maxwav); - free_imatrix(outcome,1,maxwav+1,1,n); - free_vector(moisnais,1,n); - free_vector(annais,1,n); - /* free_matrix(mint,1,maxwav,1,n); - free_matrix(anint,1,maxwav,1,n);*/ - free_vector(moisdc,1,n); - free_vector(andc,1,n); + printf("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); + + free_vector(severity,1,maxwav); + free_imatrix(outcome,1,maxwav+1,1,n); + free_vector(moisnais,1,n); + free_vector(annais,1,n); + /* free_matrix(mint,1,maxwav,1,n); + free_matrix(anint,1,maxwav,1,n);*/ + free_vector(moisdc,1,n); + free_vector(andc,1,n); - wav=ivector(1,imx); - dh=imatrix(1,lastpass-firstpass+1,1,imx); - mw=imatrix(1,lastpass-firstpass+1,1,imx); + wav=ivector(1,imx); + dh=imatrix(1,lastpass-firstpass+1,1,imx); + bh=imatrix(1,lastpass-firstpass+1,1,imx); + mw=imatrix(1,lastpass-firstpass+1,1,imx); - /* Concatenates waves */ - concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); + /* Concatenates waves */ + concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm); + /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */ - Tcode=ivector(1,100); - nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); - ncodemax[1]=1; - if (cptcovn > 0) tricode(Tvar,nbcode,imx); + Tcode=ivector(1,100); + nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); + ncodemax[1]=1; + if (cptcovn > 0) tricode(Tvar,nbcode,imx); - codtab=imatrix(1,100,1,10); - h=0; - m=pow(2,cptcoveff); + codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of + the estimations*/ + h=0; + m=pow(2,cptcoveff); - for(k=1;k<=cptcoveff; k++){ - for(i=1; i <=(m/pow(2,k));i++){ - for(j=1; j <= ncodemax[k]; j++){ - for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ - h++; - if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; - /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ - } - } - } - } - /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); - codtab[1][2]=1;codtab[2][2]=2; */ - /* for(i=1; i <=m ;i++){ - for(k=1; k <=cptcovn; k++){ - printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); - } - printf("\n"); + for(k=1;k<=cptcoveff; k++){ + for(i=1; i <=(m/pow(2,k));i++){ + for(j=1; j <= ncodemax[k]; j++){ + for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ + h++; + if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j; + /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/ + } } - scanf("%d",i);*/ + } + } + /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); + codtab[1][2]=1;codtab[2][2]=2; */ + /* for(i=1; i <=m ;i++){ + for(k=1; k <=cptcovn; k++){ + printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); + } + printf("\n"); + } + scanf("%d",i);*/ - /* Calculates basic frequencies. Computes observed prevalence at single age - and prints on file fileres'p'. */ + /* Calculates basic frequencies. Computes observed prevalence at single age + and prints on file fileres'p'. */ - - pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ - - /* For Powell, parameters are in a vector p[] starting at p[1] - so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ - p=param[1][1]; /* *(*(*(param +1)+1)+0) */ + + + /* For Powell, parameters are in a vector p[] starting at p[1] + so we point p on param[1][1] so that p[1] maps on param[1][1][1] */ + p=param[1][1]; /* *(*(*(param +1)+1)+0) */ - if(mle==1){ + if(mle>=1){ /* Could be 1 or 2 */ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func); - } + } - /*--------- results files --------------*/ - fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); + /*--------- results files --------------*/ + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model); - jk=1; - fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(k=1; k <=(nlstate+ndeath); k++){ - if (k != i) - { - printf("%d%d ",i,k); - fprintf(ficlog,"%d%d ",i,k); - fprintf(ficres,"%1d%1d ",i,k); - for(j=1; j <=ncovmodel; j++){ - printf("%f ",p[jk]); - fprintf(ficlog,"%f ",p[jk]); - fprintf(ficres,"%f ",p[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } - if(mle==1){ - /* Computing hessian and covariance matrix */ - ftolhess=ftol; /* Usually correct */ - hesscov(matcov, p, npar, delti, ftolhess, func); - } - fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); - printf("# Scales (for hessian or gradient estimation)\n"); - fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); - for(i=1,jk=1; i <=nlstate; i++){ - for(j=1; j <=nlstate+ndeath; j++){ - if (j!=i) { - fprintf(ficres,"%1d%1d",i,j); - printf("%1d%1d",i,j); - fprintf(ficlog,"%1d%1d",i,j); - for(k=1; k<=ncovmodel;k++){ - printf(" %.5e",delti[jk]); - fprintf(ficlog," %.5e",delti[jk]); - fprintf(ficres," %.5e",delti[jk]); - jk++; - } - printf("\n"); - fprintf(ficlog,"\n"); - fprintf(ficres,"\n"); - } - } - } + jk=1; + fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(k=1; k <=(nlstate+ndeath); k++){ + if (k != i) + { + printf("%d%d ",i,k); + fprintf(ficlog,"%d%d ",i,k); + fprintf(ficres,"%1d%1d ",i,k); + for(j=1; j <=ncovmodel; j++){ + printf("%f ",p[jk]); + fprintf(ficlog,"%f ",p[jk]); + fprintf(ficres,"%f ",p[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } + } + } + if(mle==1){ + /* Computing hessian and covariance matrix */ + ftolhess=ftol; /* Usually correct */ + hesscov(matcov, p, npar, delti, ftolhess, func); + } + fprintf(ficres,"# Scales (for hessian or gradient estimation)\n"); + printf("# Scales (for hessian or gradient estimation)\n"); + fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n"); + for(i=1,jk=1; i <=nlstate; i++){ + for(j=1; j <=nlstate+ndeath; j++){ + if (j!=i) { + fprintf(ficres,"%1d%1d",i,j); + printf("%1d%1d",i,j); + fprintf(ficlog,"%1d%1d",i,j); + for(k=1; k<=ncovmodel;k++){ + printf(" %.5e",delti[jk]); + fprintf(ficlog," %.5e",delti[jk]); + fprintf(ficres," %.5e",delti[jk]); + jk++; + } + printf("\n"); + fprintf(ficlog,"\n"); + fprintf(ficres,"\n"); + } + } + } - k=1; - fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - if(mle==1) - printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); - for(i=1;i<=npar;i++){ - /* if (k>nlstate) k=1; - i1=(i-1)/(ncovmodel*nlstate)+1; - fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); - printf("%s%d%d",alph[k],i1,tab[i]);*/ - fprintf(ficres,"%3d",i); - if(mle==1) - printf("%3d",i); - fprintf(ficlog,"%3d",i); - for(j=1; j<=i;j++){ - fprintf(ficres," %.5e",matcov[i][j]); - if(mle==1) - printf(" %.5e",matcov[i][j]); - fprintf(ficlog," %.5e",matcov[i][j]); - } - fprintf(ficres,"\n"); - if(mle==1) - printf("\n"); - fprintf(ficlog,"\n"); - k++; - } + fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + if(mle==1) + printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n"); + for(i=1,k=1;i<=npar;i++){ + /* if (k>nlstate) k=1; + i1=(i-1)/(ncovmodel*nlstate)+1; + fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]); + printf("%s%d%d",alph[k],i1,tab[i]); + */ + fprintf(ficres,"%3d",i); + if(mle==1) + printf("%3d",i); + fprintf(ficlog,"%3d",i); + for(j=1; j<=i;j++){ + fprintf(ficres," %.5e",matcov[i][j]); + if(mle==1) + printf(" %.5e",matcov[i][j]); + fprintf(ficlog," %.5e",matcov[i][j]); + } + fprintf(ficres,"\n"); + if(mle==1) + printf("\n"); + fprintf(ficlog,"\n"); + k++; + } - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); - estepm=0; - fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); - if (estepm==0 || estepm < stepm) estepm=stepm; - if (fage <= 2) { - bage = ageminpar; - fage = agemaxpar; - } + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + estepm=0; + fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); + if (estepm==0 || estepm < stepm) estepm=stepm; + if (fage <= 2) { + bage = ageminpar; + fage = agemaxpar; + } - fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); - fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n"); + fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); + fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm); - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); - fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); - fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav); - fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav); + fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); + fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); + fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav); - while((c=getc(ficpar))=='#' && c!= EOF){ - ungetc(c,ficpar); - fgets(line, MAXLINE, ficpar); - puts(line); - fputs(line,ficparo); - } - ungetc(c,ficpar); + while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); - dateprev1=anprev1+mprev1/12.+jprev1/365.; - dateprev2=anprev2+mprev2/12.+jprev2/365.; + dateprev1=anprev1+mprev1/12.+jprev1/365.; + dateprev2=anprev2+mprev2/12.+jprev2/365.; fscanf(ficpar,"pop_based=%d\n",&popbased); fprintf(ficparo,"pop_based=%d\n",popbased); @@ -3753,11 +3963,11 @@ printf("Total number of individuals= %d, ungetc(c,ficpar); fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2); -fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); -fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); + fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); + fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2); -while((c=getc(ficpar))=='#' && c!= EOF){ + while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); puts(line); @@ -3769,21 +3979,22 @@ while((c=getc(ficpar))=='#' && c!= EOF){ fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1); - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); -/*------------ gnuplot -------------*/ - strcpy(optionfilegnuplot,optionfilefiname); - strcat(optionfilegnuplot,".gp"); - if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { - printf("Problem with file %s",optionfilegnuplot); - } - else{ - fprintf(ficgp,"\n# %s\n", version); - fprintf(ficgp,"# %s\n", optionfilegnuplot); - fprintf(ficgp,"set missing 'NaNq'\n"); -} - fclose(ficgp); - printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); -/*--------- index.htm --------*/ + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); + + /*------------ gnuplot -------------*/ + strcpy(optionfilegnuplot,optionfilefiname); + strcat(optionfilegnuplot,".gp"); + if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) { + printf("Problem with file %s",optionfilegnuplot); + } + else{ + fprintf(ficgp,"\n# %s\n", version); + fprintf(ficgp,"# %s\n", optionfilegnuplot); + fprintf(ficgp,"set missing 'NaNq'\n"); + } + fclose(ficgp); + printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p); + /*--------- index.htm --------*/ strcpy(optionfilehtm,optionfile); strcat(optionfilehtm,".htm"); @@ -3803,19 +4014,21 @@ Interval (in months) between two waves: - Gnuplot file name: %s\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot); fclose(fichtm); - printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); + printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); -/*------------ free_vector -------------*/ - chdir(path); + /*------------ free_vector -------------*/ + chdir(path); - free_ivector(wav,1,imx); - free_imatrix(dh,1,lastpass-firstpass+1,1,imx); - free_imatrix(mw,1,lastpass-firstpass+1,1,imx); - free_ivector(num,1,n); - free_vector(agedc,1,n); - /*free_matrix(covar,1,NCOVMAX,1,n);*/ - fclose(ficparo); - fclose(ficres); + free_ivector(wav,1,imx); + free_imatrix(dh,1,lastpass-firstpass+1,1,imx); + free_imatrix(bh,1,lastpass-firstpass+1,1,imx); + free_imatrix(mw,1,lastpass-firstpass+1,1,imx); + free_ivector(num,1,n); + free_vector(agedc,1,n); + /*free_matrix(covar,0,NCOVMAX,1,n);*/ + /*free_matrix(covar,1,NCOVMAX,1,n);*/ + fclose(ficparo); + fclose(ficres); /*--------------- Prevalence limit (stable prevalence) --------------*/ @@ -3834,43 +4047,38 @@ Interval (in months) between two waves: fprintf(ficrespl,"\n"); prlim=matrix(1,nlstate,1,nlstate); - pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ - oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */ - k=0; + agebase=ageminpar; agelim=agemaxpar; ftolpl=1.e-10; i1=cptcoveff; if (cptcovn < 1){i1=1;} - for(cptcov=1;cptcov<=i1;cptcov++){ + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ - k=k+1; - /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ - fprintf(ficrespl,"\n#******"); - printf("\n#******"); - fprintf(ficlog,"\n#******"); - for(j=1;j<=cptcoveff;j++) { - fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - } - fprintf(ficrespl,"******\n"); - printf("******\n"); - fprintf(ficlog,"******\n"); + k=k+1; + /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/ + fprintf(ficrespl,"\n#******"); + printf("\n#******"); + fprintf(ficlog,"\n#******"); + for(j=1;j<=cptcoveff;j++) { + fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + } + fprintf(ficrespl,"******\n"); + printf("******\n"); + fprintf(ficlog,"******\n"); - for (age=agebase; age<=agelim; age++){ - prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); - fprintf(ficrespl,"%.0f",age ); - for(i=1; i<=nlstate;i++) + for (age=agebase; age<=agelim; age++){ + prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); + fprintf(ficrespl,"%.0f",age ); + for(i=1; i<=nlstate;i++) fprintf(ficrespl," %.5f", prlim[i][i]); - fprintf(ficrespl,"\n"); - } + fprintf(ficrespl,"\n"); } } + } fclose(ficrespl); /*------------- h Pij x at various ages ------------*/ @@ -3892,39 +4100,38 @@ Interval (in months) between two waves: /* hstepm=1; aff par mois*/ - k=0; - for(cptcov=1;cptcov<=i1;cptcov++){ + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; - fprintf(ficrespij,"\n#****** "); - for(j=1;j<=cptcoveff;j++) - fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); - fprintf(ficrespij,"******\n"); + fprintf(ficrespij,"\n#****** "); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficrespij,"******\n"); - for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ - nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ - - /* nhstepm=nhstepm*YEARM; aff par mois*/ - - p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - oldm=oldms;savm=savms; - hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); - fprintf(ficrespij,"# Age"); + for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */ + nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ + nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */ + + /* nhstepm=nhstepm*YEARM; aff par mois*/ + + p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + oldm=oldms;savm=savms; + hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); + fprintf(ficrespij,"# Age"); + for(i=1; i<=nlstate;i++) + for(j=1; j<=nlstate+ndeath;j++) + fprintf(ficrespij," %1d-%1d",i,j); + fprintf(ficrespij,"\n"); + for (h=0; h<=nhstepm; h++){ + fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); for(i=1; i<=nlstate;i++) for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %1d-%1d",i,j); - fprintf(ficrespij,"\n"); - for (h=0; h<=nhstepm; h++){ - fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm ); - for(i=1; i<=nlstate;i++) - for(j=1; j<=nlstate+ndeath;j++) - fprintf(ficrespij," %.5f", p3mat[i][j][h]); - fprintf(ficrespij,"\n"); - } - free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespij," %.5f", p3mat[i][j][h]); fprintf(ficrespij,"\n"); } + free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); + fprintf(ficrespij,"\n"); + } } } @@ -3974,8 +4181,11 @@ Interval (in months) between two waves: } printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv); + calagedate=-1; + prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + if (mobilav!=0) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){ @@ -3984,8 +4194,7 @@ Interval (in months) between two waves: } } - k=0; - for(cptcov=1;cptcov<=i1;cptcov++){ + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; fprintf(ficrest,"\n#****** "); @@ -4012,7 +4221,7 @@ Interval (in months) between two waves: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav); if(popbased==1){ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav); - } + } fprintf(ficrest,"#Total LEs with variances: e.. (std) "); @@ -4050,16 +4259,22 @@ Interval (in months) between two waves: } fprintf(ficrest,"\n"); } + free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); + free_vector(epj,1,nlstate+1); } } -free_matrix(mint,1,maxwav,1,n); - free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n); - free_vector(weight,1,n); + free_vector(weight,1,n); + free_imatrix(Tvard,1,15,1,2); + free_imatrix(s,1,maxwav+1,1,n); + free_matrix(anint,1,maxwav,1,n); + free_matrix(mint,1,maxwav,1,n); + free_ivector(cod,1,n); + free_ivector(tab,1,NCOVMAX); fclose(ficreseij); fclose(ficresvij); fclose(ficrest); fclose(ficpar); - free_vector(epj,1,nlstate+1); /*------- Variance of stable prevalence------*/ @@ -4071,8 +4286,7 @@ free_matrix(mint,1,maxwav,1,n); } printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl); - k=0; - for(cptcov=1;cptcov<=i1;cptcov++){ + for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; fprintf(ficresvpl,"\n#****** "); @@ -4082,29 +4296,31 @@ free_matrix(mint,1,maxwav,1,n); varpl=matrix(1,nlstate,(int) bage, (int) fage); oldm=oldms;savm=savms; - varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); + varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k); + free_matrix(varpl,1,nlstate,(int) bage, (int)fage); } - } + } fclose(ficresvpl); /*---------- End : free ----------------*/ - free_matrix(varpl,1,nlstate,(int) bage, (int)fage); - - free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage); - free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage); - - free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); - + + free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); free_vector(delti,1,npar); free_matrix(agev,1,maxwav,1,imx); free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); + free_ivector(ncodemax,1,8); + free_ivector(Tvar,1,15); + free_ivector(Tprod,1,15); + free_ivector(Tvaraff,1,15); + free_ivector(Tage,1,15); + free_ivector(Tcode,1,100); fprintf(fichtm,"\n"); fclose(fichtm); @@ -4126,8 +4342,7 @@ free_matrix(mint,1,maxwav,1,n); /*printf("Total time was %d uSec.\n", total_usecs);*/ /*------ End -----------*/ - - end: + end: #ifdef windows /* chdir(pathcd);*/ #endif @@ -4135,11 +4350,11 @@ free_matrix(mint,1,maxwav,1,n); /*system("../gp37mgw/wgnuplot graph.plt");*/ /*system("cd ../gp37mgw");*/ /* system("..\\gp37mgw\\wgnuplot graph.plt");*/ - strcpy(plotcmd,GNUPLOTPROGRAM); - strcat(plotcmd," "); - strcat(plotcmd,optionfilegnuplot); - printf("Starting: %s\n",plotcmd);fflush(stdout); - system(plotcmd); + strcpy(plotcmd,GNUPLOTPROGRAM); + strcat(plotcmd," "); + strcat(plotcmd,optionfilegnuplot); + printf("Starting: %s\n",plotcmd);fflush(stdout); + system(plotcmd); /*#ifdef windows*/ while (z[0] != 'q') {