--- imach/src/imach.c 2002/12/11 16:58:19 1.65 +++ imach/src/imach.c 2003/05/03 01:18:24 1.75 @@ -1,4 +1,4 @@ -/* $Id: imach.c,v 1.65 2002/12/11 16:58:19 lievre Exp $ +/* $Id: imach.c,v 1.75 2003/05/03 01:18:24 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. @@ -48,7 +48,43 @@ It is copyrighted identically to a GNU software product, ie programme and software can be distributed freely for non commercial use. Latest version can be accessed at http://euroreves.ined.fr/imach . + + Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach + or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so + **********************************************************************/ +/* + main + read parameterfile + read datafile + concatwav + if (mle >= 1) + mlikeli + print results files + if mle==1 + computes hessian + read end of parameter file: agemin, agemax, bage, fage, estepm + begin-prev-date,... + open gnuplot file + open html file + stable prevalence + for age prevalim() + h Pij x + variance of p varprob + forecasting if prevfcast==1 prevforecast call prevalence() + health expectancies + Variance-covariance of DFLE + prevalence() + movingaverage() + varevsij() + if popbased==1 varevsij(,popbased) + total life expectancies + Variance of stable prevalence + end +*/ + + + #include #include @@ -83,7 +119,7 @@ #define ODIRSEPARATOR '\\' #endif -char version[80]="Imach version 0.9, November 2002, INED-EUROREVES "; +char version[80]="Imach version 0.95, May 2003, INED-EUROREVES "; int erreur; /* Error number */ int nvar; int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov; @@ -188,15 +224,9 @@ static int split( char *path, char *dirc 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( ); - - if ( getwd( dirc ) == NULL ) { -#else - extern char *getcwd( ); - + /* get current working directory */ + /* extern char* getcwd ( char *buf , int len);*/ if ( getcwd( dirc, FILENAME_MAX ) == NULL ) { -#endif return( GLOCK_ERROR_GETCWD ); } strcpy( name, path ); /* we've got it */ @@ -365,6 +395,8 @@ double **matrix(long nrl, long nrh, long for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol; return m; + /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) + */ } /*************************free matrix ************************/ @@ -404,7 +436,10 @@ double ***ma3x(long nrl, long nrh, long for (j=ncl+1; j<=nch; j++) m[i][j]=m[i][j-1]+nlay; } - return m; + return m; + /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1]) + &(m[i][j][k]) <=> *((*(m+i) + j)+k) + */ } /*************************free ma3x ************************/ @@ -856,11 +891,13 @@ 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. @@ -917,7 +954,7 @@ double func( double *x) double sw; /* Sum of weights */ double lli; /* Individual log likelihood */ int s1, s2; - double bbh; + double bbh, survp; long ipmx; /*extern weight */ /* We are differentiating ll according to initial status */ @@ -970,11 +1007,38 @@ double func( double *x) * 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 */ + if( s2 > nlstate){ + /* i.e. if s2 is a death state and if the date of death is known then the contribution + to the likelihood is the probability to die between last step unit time and current + step unit time, which is also the differences between probability to die before dh + and probability to die before dh-stepm . + In version up to 0.92 likelihood was computed + as if date of death was unknown. Death was treated as any other + health state: the date of the interview describes the actual state + and not the date of a change in health state. The former idea was + to consider that at each interview the state was recorded + (healthy, disable or death) and IMaCh was corrected; but when we + introduced the exact date of death then we should have modified + the contribution of an exact death to the likelihood. This new + contribution is smaller and very dependent of the step unit + stepm. It is no more the probability to die between last interview + and month of death but the probability to survive from last + interview up to one month before death multiplied by the + probability to die within a month. Thanks to Chris + Jackson for correcting this bug. Former versions increased + mortality artificially. The bad side is that we add another loop + which slows down the processing. The difference can be up to 10% + lower mortality. + */ + lli=log(out[s1][s2] - savm[s1][s2]); + }else{ + lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */ + /* 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; + ipmx +=1; sw += weight[i]; ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; } /* end of wave */ @@ -1121,7 +1185,7 @@ double func( double *x) void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double [])) { int i,j, iter; - double **xi,*delti; + double **xi; double fret; xi=matrix(1,npar,1,npar); for (i=1;i<=npar;i++) @@ -1394,19 +1458,19 @@ void lubksb(double **a, int n, int *indx } /************ Frequencies ********************/ -void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) +void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2) { /* Some frequencies */ int i, m, jk, k1,i1, j1, bool, z1,z2,j; int first; double ***freq; /* Frequencies */ - double *pp; - double pos, k2, dateintsum=0,k2cpt=0; + double *pp, **prop; + double pos,posprop, k2, dateintsum=0,k2cpt=0; FILE *ficresp; char fileresp[FILENAMELENGTH]; pp=vector(1,nlstate); - probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX); + prop=matrix(1,nlstate,iagemin,iagemax+3); strcpy(fileresp,"p"); strcat(fileresp,fileres); if((ficresp=fopen(fileresp,"w"))==NULL) { @@ -1414,7 +1478,7 @@ void freqsummary(char fileres[], int ag fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp); exit(0); } - freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3); j1=0; j=cptcoveff; @@ -1429,8 +1493,12 @@ void freqsummary(char fileres[], int ag scanf("%d", i);*/ for (i=-1; i<=nlstate+ndeath; i++) for (jk=-1; jk<=nlstate+ndeath; jk++) - for(m=agemin; m <= agemax+3; m++) + for(m=iagemin; m <= iagemax+3; m++) freq[i][jk][m]=0; + + for (i=1; i<=nlstate; i++) + for(m=iagemin; m <= iagemax+3; m++) + prop[i][m]=0; dateintsum=0; k2cpt=0; @@ -1445,14 +1513,15 @@ void freqsummary(char fileres[], int ag for(m=firstpass; m<=lastpass; m++){ k2=anint[m][i]+(mint[m][i]/12.); if ((k2>=dateprev1) && (k2<=dateprev2)) { - if(agev[m][i]==0) agev[m][i]=agemax+1; - if(agev[m][i]==1) agev[m][i]=agemax+2; + if(agev[m][i]==0) agev[m][i]=iagemax+1; + if(agev[m][i]==1) agev[m][i]=iagemax+2; + if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i]; if (m1) && (agev[m][i]< (agemax+3))) { + if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) { dateintsum=dateintsum+k2; k2cpt++; } @@ -1472,8 +1541,8 @@ void freqsummary(char fileres[], int ag fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i); fprintf(ficresp, "\n"); - for(i=(int)agemin; i <= (int)agemax+3; i++){ - if(i==(int)agemax+3){ + for(i=iagemin; i <= iagemax+3; i++){ + if(i==iagemax+3){ fprintf(ficlog,"Total"); }else{ if(first==1){ @@ -1504,10 +1573,11 @@ void freqsummary(char fileres[], int ag for(jk=1; jk <=nlstate ; jk++){ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) pp[jk] += freq[jk][m][i]; - } - - for(jk=1,pos=0; jk <=nlstate ; jk++) + } + for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){ pos += pp[jk]; + posprop += prop[jk][i]; + } for(jk=1; jk <=nlstate ; jk++){ if(pos>=1.e-5){ if(first==1) @@ -1518,14 +1588,14 @@ void freqsummary(char fileres[], int ag printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk); } - if( i <= (int) agemax){ + if( i <= iagemax){ if(pos>=1.e-5){ - fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos); + fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop); probs[i][jk][j1]= pp[jk]/pos; /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/ } else - fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos); + fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop); } } @@ -1536,7 +1606,7 @@ void freqsummary(char fileres[], int ag printf(" %d%d=%.0f",jk,m,freq[jk][m][i]); fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]); } - if(i <= (int) agemax) + if(i <= iagemax) fprintf(ficresp,"\n"); if(first==1) printf("Others in log...\n"); @@ -1547,24 +1617,32 @@ void freqsummary(char fileres[], int ag dateintmean=dateintsum/k2cpt; fclose(ficresp); - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3); free_vector(pp,1,nlstate); - + free_matrix(prop,1,nlstate,iagemin, iagemax+3); /* End of Freq */ } /************ Prevalence ********************/ -void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate) -{ /* Some frequencies */ +void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass) +{ + /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people + in each health status at the date of interview (if between dateprev1 and dateprev2). + We still use firstpass and lastpass as another selection. + */ int i, m, jk, k1, i1, j1, bool, z1,z2,j; double ***freq; /* Frequencies */ - double *pp; - double pos, k2; - - pp=vector(1,nlstate); - - freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + double *pp, **prop; + double pos,posprop; + double y2; /* in fractional years */ + int iagemin, iagemax; + + iagemin= (int) agemin; + iagemax= (int) agemax; + /*pp=vector(1,nlstate);*/ + prop=matrix(1,nlstate,iagemin,iagemax+3); + /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/ j1=0; j=cptcoveff; @@ -1574,12 +1652,11 @@ void prevalence(int agemin, float agemax for(i1=1; i1<=ncodemax[k1];i1++){ j1++; - for (i=-1; i<=nlstate+ndeath; i++) - for (jk=-1; jk<=nlstate+ndeath; jk++) - for(m=agemin; m <= agemax+3; m++) - freq[i][jk][m]=0; + for (i=1; i<=nlstate; i++) + for(m=iagemin; m <= iagemax+3; m++) + prop[i][m]=0.0; - for (i=1; i<=imx; i++) { + for (i=1; i<=imx; i++) { /* Each individual */ bool=1; if (cptcovn>0) { for (z1=1; z1<=cptcoveff; z1++) @@ -1587,55 +1664,42 @@ void prevalence(int agemin, float agemax bool=0; } if (bool==1) { - for(m=firstpass; m<=lastpass; m++){ - k2=anint[m][i]+(mint[m][i]/12.); - if ((k2>=dateprev1) && (k2<=dateprev2)) { - if(agev[m][i]==0) agev[m][i]=agemax+1; - if(agev[m][i]==1) agev[m][i]=agemax+2; - if (m0) - freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i]; - else - freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; - freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; - } + for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/ + y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */ + if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */ + if(agev[m][i]==0) agev[m][i]=iagemax+1; + if(agev[m][i]==1) agev[m][i]=iagemax+2; + if((int)agev[m][i] iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); + if (s[m][i]>0 && s[m][i]<=nlstate) { + /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/ + prop[s[m][i]][(int)agev[m][i]] += weight[i]; + prop[s[m][i]][iagemax+3] += weight[i]; + } } - } + } /* end selection of waves */ } } - for(i=(int)agemin; i <= (int)agemax+3; i++){ - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++) - pp[jk] += freq[jk][m][i]; - } - for(jk=1; jk <=nlstate ; jk++){ - for(m=-1, pos=0; m <=0 ; m++) - pos += freq[jk][m][i]; - } - - for(jk=1; jk <=nlstate ; jk++){ - for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++) - pp[jk] += freq[jk][m][i]; - } - - for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk]; + for(i=iagemin; i <= iagemax+3; i++){ - for(jk=1; jk <=nlstate ; jk++){ - if( i <= (int) agemax){ - if(pos>=1.e-5){ - probs[i][jk][j1]= pp[jk]/pos; - } - } - }/* end jk */ - }/* end i */ + for(jk=1,posprop=0; jk <=nlstate ; jk++) { + posprop += prop[jk][i]; + } + + for(jk=1; jk <=nlstate ; jk++){ + if( i <= iagemax){ + if(posprop>=1.e-5){ + probs[i][jk][j1]= prop[jk][i]/posprop; + } + } + }/* end jk */ + }/* end i */ } /* end i1 */ } /* end k1 */ - - - free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); - free_vector(pp,1,nlstate); -} /* End of Freq */ + /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/ + /*free_vector(pp,1,nlstate);*/ + free_matrix(prop,1,nlstate, iagemin,iagemax+3); +} /* End of prevalence */ /************* Waves Concatenation ***************/ @@ -1702,14 +1766,18 @@ void concatwav(int wav[], int **dh, int if (j <= jmin) jmin=j; sum=sum+j; /*if (j<0) printf("j=%d num=%d \n",j,i); */ + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ + /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ } } else{ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12)); + /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ k=k+1; if (j >= jmax) jmax=j; else if (j <= jmin)jmin=j; /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */ + /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/ sum=sum+j; } jk= j/stepm; @@ -1738,9 +1806,8 @@ void concatwav(int wav[], int **dh, int 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); + /* 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 */ @@ -1824,10 +1891,10 @@ void evsij(char fileres[], double ***eij double ***gradg, ***trgradg; int theta; - varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage); + varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage); xp=vector(1,npar); - dnewm=matrix(1,nlstate*2,1,npar); - doldm=matrix(1,nlstate*2,1,nlstate*2); + dnewm=matrix(1,nlstate*nlstate,1,npar); + doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate); fprintf(ficreseij,"# Health expectancies\n"); fprintf(ficreseij,"# Age"); @@ -1844,7 +1911,7 @@ 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 @@ -1873,9 +1940,9 @@ void evsij(char fileres[], double ***eij /* if (stepm >= YEARM) hstepm=1;*/ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2); - gp=matrix(0,nhstepm,1,nlstate*2); - gm=matrix(0,nhstepm,1,nlstate*2); + gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate); + gp=matrix(0,nhstepm,1,nlstate*nlstate); + gm=matrix(0,nhstepm,1,nlstate*nlstate); /* Computed by stepm unit matrices, product of hstepm matrices, stored in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */ @@ -1916,7 +1983,7 @@ void evsij(char fileres[], double ***eij } } } - for(j=1; j<= nlstate*2; j++) + for(j=1; j<= nlstate*nlstate; j++) for(h=0; h<=nhstepm-1; h++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } @@ -1924,26 +1991,26 @@ void evsij(char fileres[], double ***eij /* End theta */ - trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar); + trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar); for(h=0; h<=nhstepm-1; h++) - for(j=1; j<=nlstate*2;j++) + for(j=1; j<=nlstate*nlstate;j++) for(theta=1; theta <=npar; theta++) trgradg[h][j][theta]=gradg[h][theta][j]; - for(i=1;i<=nlstate*2;i++) - for(j=1;j<=nlstate*2;j++) + for(i=1;i<=nlstate*nlstate;i++) + for(j=1;j<=nlstate*nlstate;j++) varhe[i][j][(int)age] =0.; printf("%d|",(int)age);fflush(stdout); fprintf(ficlog,"%d|",(int)age);fflush(ficlog); for(h=0;h<=nhstepm-1;h++){ for(k=0;k<=nhstepm-1;k++){ - matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov); - matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]); - for(i=1;i<=nlstate*2;i++) - for(j=1;j<=nlstate*2;j++) + matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov); + matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]); + for(i=1;i<=nlstate*nlstate;i++) + for(j=1;j<=nlstate*nlstate;j++) varhe[i][j][(int)age] += doldm[i][j]*hf*hf; } } @@ -1966,19 +2033,19 @@ void evsij(char fileres[], double ***eij } fprintf(ficreseij,"\n"); - free_matrix(gm,0,nhstepm,1,nlstate*2); - free_matrix(gp,0,nhstepm,1,nlstate*2); - free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2); - free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar); + free_matrix(gm,0,nhstepm,1,nlstate*nlstate); + free_matrix(gp,0,nhstepm,1,nlstate*nlstate); + free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate); + free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar); free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); } printf("\n"); fprintf(ficlog,"\n"); free_vector(xp,1,npar); - free_matrix(dnewm,1,nlstate*2,1,npar); - free_matrix(doldm,1,nlstate*2,1,nlstate*2); - free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage); + free_matrix(dnewm,1,nlstate*nlstate,1,npar); + free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate); + free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage); } /************ Variance ******************/ @@ -2034,7 +2101,7 @@ 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); @@ -2056,8 +2123,8 @@ 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); @@ -2091,7 +2158,7 @@ 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. */ @@ -2107,7 +2174,7 @@ 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); @@ -2129,14 +2196,17 @@ 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 */ - for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) + /* 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;j<=nlstate+ndeath;j++){ + for(i=1,gpp[j]=0.; 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); @@ -2157,17 +2227,21 @@ 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 */ - 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]; + /* 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;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.; 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++){ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta]; } + for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */ gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta]; } @@ -2184,6 +2258,7 @@ void varevsij(char optionfilefiname[], d for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */ for(theta=1; theta <=npar; theta++) trgradgp[j][theta]=gradgp[theta][j]; + hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */ for(i=1;i<=nlstate;i++) @@ -2199,7 +2274,7 @@ void varevsij(char optionfilefiname[], d vareij[i][j][(int)age] += doldm[i][j]*hf*hf; } } - + /* pptj */ matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov); matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp); @@ -2207,6 +2282,7 @@ 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); @@ -2219,13 +2295,16 @@ void varevsij(char optionfilefiname[], d prlim[i][i]=mobaverage[(int)age][i][ij]; } } - - /* This for computing force of mortality (h=1)as a weighted average */ - for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){ - for(i=1; i<= nlstate; i++) + + /* 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;j<=nlstate+ndeath;j++){ + for(i=1,gmp[j]=0.;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++){ @@ -2255,14 +2334,17 @@ 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,optionfilefiname,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); + fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); free_vector(xp,1,npar); free_matrix(doldm,1,nlstate,1,nlstate); @@ -2274,7 +2356,7 @@ void varevsij(char optionfilefiname[], d 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) @@ -2420,10 +2502,11 @@ void varprob(char optionfilefiname[], do fprintf(ficresprobcov," p%1d-%1d ",i,j); fprintf(ficresprobcor," p%1d-%1d ",i,j); } - fprintf(ficresprob,"\n"); + /* fprintf(ficresprob,"\n"); fprintf(ficresprobcov,"\n"); fprintf(ficresprobcor,"\n"); - xp=vector(1,npar); + */ + xp=vector(1,npar); dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar); doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage); @@ -2462,14 +2545,14 @@ void varprob(char optionfilefiname[], do 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]]); - fprintf(ficresprob, "**********\n#"); + fprintf(ficresprob, "**********\n#\n"); fprintf(ficresprobcov, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficresprobcov, "**********\n#"); + fprintf(ficresprobcov, "**********\n#\n"); fprintf(ficgp, "\n#********** Variable "); - for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); + for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); + fprintf(ficgp, "**********\n#\n"); fprintf(fichtm, "\n
    ********** Variable "); @@ -2478,7 +2561,7 @@ void varprob(char optionfilefiname[], do fprintf(ficresprobcor, "\n#********** Variable "); for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]); - fprintf(ficgp, "**********\n#"); + fprintf(ficresprobcor, "**********\n#"); } for (age=bage; age<=fage; age ++){ @@ -2497,7 +2580,7 @@ void varprob(char optionfilefiname[], do for(theta=1; theta <=npar; theta++){ for(i=1; i<=npar; i++) - xp[i] = x[i] + (i==theta ?delti[theta]:0); + xp[i] = x[i] + (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); @@ -2510,7 +2593,7 @@ void varprob(char optionfilefiname[], do } for(i=1; i<=npar; i++) - xp[i] = x[i] - (i==theta ?delti[theta]:0); + xp[i] = x[i] - (i==theta ?delti[theta]:(double)0); pmij(pmmij,cov,ncovmodel,xp,nlstate); k=0; @@ -2522,7 +2605,7 @@ void varprob(char optionfilefiname[], do } for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) - gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; + gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; } for(j=1; j<=(nlstate)*(nlstate+ndeath);j++) @@ -2797,12 +2880,12 @@ m=pow(2,cptcoveff); if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1); + fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); } - fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); + fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); for (i=1; i<= nlstate ; i ++) { if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)"); else fprintf(ficgp," \%%*lf (\%%*lf)"); @@ -2993,21 +3076,23 @@ int movingaverage(double ***probs, doubl /************** Forecasting ******************/ -prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){ - - int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; +prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){ + /* proj1, year, month, day of starting projection + agemin, agemax range of age + dateprev1 dateprev2 range of dates during which prevalence is computed + anproj2 year of en of projection (same day and month as proj1). + */ + int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1; int *popage; - double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; + double agec; /* generic age */ + double agelim, ppij, 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; - - prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); - + agelim=AGESUP; + prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); strcpy(fileresf,"f"); strcat(fileresf,fileres); @@ -3030,12 +3115,14 @@ prevforecast(char fileres[], double anpr stepsize=(int) (stepm+YEARM-1)/YEARM; if (stepm<=12) stepsize=1; - - agelim=AGESUP; - - hstepm=1; + if(estepm < stepm){ + printf ("Problem %d lower than %d\n",estepm, stepm); + } + else hstepm=estepm; + hstepm=hstepm/stepm; - yp1=modf(dateintmean,&yp); + yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and + fractional in yp1 */ anprojmean=yp; yp2=modf((yp1*12),&yp); mprojmean=yp; @@ -3043,69 +3130,81 @@ prevforecast(char fileres[], double anpr jprojmean=yp; if(jprojmean==0) jprojmean=1; if(mprojmean==0) jprojmean=1; + + i1=cptcoveff; + if (cptcovn < 1){i1=1;} - fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); + fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); - for(cptcov=1;cptcov<=i2;cptcov++){ + fprintf(ficresf,"#****** Routine prevforecast **\n"); + +/* if (h==(int)(YEARM*yearp)){ */ + for(cptcov=1, k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ k=k+1; fprintf(ficresf,"\n#******"); for(j=1;j<=cptcoveff;j++) { - fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); } fprintf(ficresf,"******\n"); - fprintf(ficresf,"# StartingAge FinalAge"); - for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j); - - - for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { + fprintf(ficresf,"# Covariate valuofcovar yearproj age"); + for(j=1; j<=nlstate+ndeath;j++){ + for(i=1; i<=nlstate;i++) + fprintf(ficresf," p%d%d",i,j); + fprintf(ficresf," p.%d",j); + } + for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { fprintf(ficresf,"\n"); - fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt); + fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); - for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ - nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); + for (agec=fage; agec>=(ageminpar-1); agec--){ + nhstepm=(int) rint((agelim-agec)*YEARM/stepm); nhstepm = nhstepm/hstepm; - 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); + hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { - fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm); + if (h*hstepm/YEARM*stepm ==yearp) { + fprintf(ficresf,"\n"); + for(j=1;j<=cptcoveff;j++) + fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); + fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm); } for(j=1; j<=nlstate+ndeath;j++) { - kk1=0.;kk2=0; - for(i=1; i<=nlstate;i++) { + ppij=0.; + for(i=1; i<=nlstate;i++) { if (mobilav==1) - kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod]; + ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod]; else { - kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; + ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod]; } - - } - if (h==(int)(calagedate+12*cpt)){ - fprintf(ficresf," %.3f", kk1); - + if (h*hstepm/YEARM*stepm== yearp) { + fprintf(ficresf," %.3f", p3mat[i][j][h]); + } + } /* end i */ + if (h*hstepm/YEARM*stepm==yearp) { + fprintf(ficresf," %.3f", ppij); } - } - } + }/* end j */ + } /* end h */ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); - } - } - } - } + } /* end agec */ + } /* end yearp */ + } /* end cptcod */ + } /* end cptcov */ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); fclose(ficresf); } -/************** Forecasting ******************/ + +/************** Forecasting *****not tested NB*************/ populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h; int *popage; - double calagedate, agelim, kk1, kk2; + double calagedatem, agelim, kk1, kk2; double *popeffectif,*popcount; double ***p3mat,***tabpop,***tabpopprev; double ***mobaverage; @@ -3114,9 +3213,9 @@ populforecast(char fileres[], double anp tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); agelim=AGESUP; - calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; + calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM; - prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate); + prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); strcpy(filerespop,"pop"); @@ -3162,7 +3261,7 @@ populforecast(char fileres[], double anp for (i=1; i=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); nhstepm = nhstepm/hstepm; @@ -3186,7 +3285,7 @@ populforecast(char fileres[], double anp hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { + if (h==(int) (calagedatem+YEARM*cpt)) { fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); } for(j=1; j<=nlstate+ndeath;j++) { @@ -3198,7 +3297,7 @@ populforecast(char fileres[], double anp kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod]; } } - if (h==(int)(calagedate+12*cpt)){ + if (h==(int)(calagedatem+12*cpt)){ tabpop[(int)(agedeb)][j][cptcod]=kk1; /*fprintf(ficrespop," %.3f", kk1); if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/ @@ -3209,10 +3308,10 @@ populforecast(char fileres[], double anp for(j=1; j<=nlstate;j++){ kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; } - tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)]; + tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)]; } - if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) + if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]); } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); @@ -3223,7 +3322,7 @@ populforecast(char fileres[], double anp for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); - for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ + for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); nhstepm = nhstepm/hstepm; @@ -3231,7 +3330,7 @@ populforecast(char fileres[], double anp oldm=oldms;savm=savms; hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); for (h=0; h<=nhstepm; h++){ - if (h==(int) (calagedate+YEARM*cpt)) { + if (h==(int) (calagedatem+YEARM*cpt)) { fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm); } for(j=1; j<=nlstate+ndeath;j++) { @@ -3239,7 +3338,7 @@ populforecast(char fileres[], double anp for(i=1; i<=nlstate;i++) { kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; } - if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); + if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); } } free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); @@ -3267,7 +3366,7 @@ 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; + int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; double agedeb, agefin,hf; double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20; @@ -3286,9 +3385,11 @@ int main(int argc, char *argv[]) int ju,jl, mi; int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij; int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; + int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */ int mobilav=0,popforecast=0; int hstepm, nhstepm; - double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate; + double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000; + double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000; double bage, fage, age, agelim, agebase; double ftolpl=FTOL; @@ -3303,7 +3404,7 @@ int main(int argc, char *argv[]) double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; double kk1, kk2; - double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2; + double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000; char *alph[]={"a","a","b","c","d","e"}, str[4]; @@ -3450,7 +3551,7 @@ int main(int argc, char *argv[]) ungetc(c,ficpar); delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); - delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */ + /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */ for(i=1; i <=nlstate; i++){ for(j=1; j <=nlstate+ndeath-1; j++){ fscanf(ficpar,"%1d%1d",&i1,&j1); @@ -3467,6 +3568,9 @@ int main(int argc, char *argv[]) } } delti=delti3[1][1]; + + + /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */ /* Reads comments: lines beginning with '#' */ while((c=getc(ficpar))=='#' && c!= EOF){ @@ -3586,7 +3690,11 @@ int main(int argc, char *argv[]) if (s[4][i]==9) s[4][i]=-1; 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]));}*/ + for (i=1; i<=imx; i++) + /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08; + else weight[i]=1;*/ + /* Calculation of the number of parameter from char model*/ Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */ Tprod=ivector(1,15); @@ -3688,7 +3796,7 @@ int main(int argc, char *argv[]) for (i=1; i<=imx; i++) { agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]); - for(m=1; (m<= maxwav); m++){ + for(m=firstpass; (m<= lastpass); m++){ if(s[m][i] >0){ if (s[m][i] >= nlstate+1) { if(agedc[i]>0) @@ -3703,7 +3811,9 @@ int main(int argc, char *argv[]) } } } - else if(s[m][i] !=9){ /* Should no more exist */ + else if(s[m][i] !=9){ /* Standard case, age in fractional + years but with the precision of a + month */ 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; @@ -3729,7 +3839,7 @@ int main(int argc, char *argv[]) } for (i=1; i<=imx; i++) { - for(m=1; (m<= maxwav); m++){ + for(m=firstpass; (m<=lastpass); 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); @@ -3738,6 +3848,13 @@ int main(int argc, char *argv[]) } } + /*for (i=1; i<=imx; i++){ + for (m=firstpass; (mo%s
    \n - Log file of the run: %s
    \n - 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); + fclose(fichtm); printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2); @@ -4057,7 +4179,9 @@ Interval (in months) between two waves: for (age=agebase; age<=agelim; age++){ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k); - fprintf(ficrespl,"%.0f",age ); + fprintf(ficrespl,"%.0f ",age ); + for(j=1;j<=cptcoveff;j++) + fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]); for(i=1; i<=nlstate;i++) fprintf(ficrespl," %.5f", prlim[i][i]); fprintf(ficrespl,"\n"); @@ -4085,6 +4209,7 @@ Interval (in months) between two waves: /* hstepm=1; aff par mois*/ + fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x "); for(cptcov=1,k=0;cptcov<=i1;cptcov++){ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){ k=k+1; @@ -4102,13 +4227,13 @@ Interval (in months) between two waves: 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"); + fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j="); 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 ); + fprintf(ficrespij,"%d %3.f %3.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]); @@ -4120,20 +4245,23 @@ Interval (in months) between two waves: } } - varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax); + varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax); fclose(ficrespij); /*---------- Forecasting ------------------*/ - if((stepm == 1) && (strcmp(model,".")==0)){ - prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1); - if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1); - } - else{ - erreur=108; - printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); - fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); + /*if((stepm == 1) && (strcmp(model,".")==0)){*/ + if(prevfcast==1){ + /* if(stepm ==1){*/ + prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff); + /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/ +/* } */ +/* else{ */ +/* erreur=108; */ +/* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ +/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */ +/* } */ } @@ -4167,9 +4295,11 @@ 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); + /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */ + prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); + /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\ +ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass); + */ if (mobilav!=0) { mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); @@ -4296,10 +4426,13 @@ Interval (in months) between two waves: free_matrix(covar,0,NCOVMAX,1,n); free_matrix(matcov,1,npar,1,npar); - free_vector(delti,1,npar); + /*free_vector(delti,1,npar);*/ + free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 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_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); + free_ivector(ncodemax,1,8); free_ivector(Tvar,1,15); free_ivector(Tprod,1,15); @@ -4307,9 +4440,8 @@ Interval (in months) between two waves: free_ivector(Tage,1,15); free_ivector(Tcode,1,100); - fprintf(fichtm,"\n"); - fclose(fichtm); - fclose(ficgp); + /* fclose(fichtm);*/ + /* fclose(ficgp);*/ /* ALready done */ if(erreur >0){ @@ -4338,8 +4470,9 @@ Interval (in months) between two waves: strcpy(plotcmd,GNUPLOTPROGRAM); strcat(plotcmd," "); strcat(plotcmd,optionfilegnuplot); - printf("Starting: %s\n",plotcmd);fflush(stdout); + printf("Starting graphs with: %s",plotcmd);fflush(stdout); system(plotcmd); + printf(" Wait..."); /*#ifdef windows*/ while (z[0] != 'q') {