--- imach/src/imach.c 2002/02/20 17:05:44 1.14 +++ imach/src/imach.c 2002/02/20 17:12:32 1.16 @@ -73,7 +73,7 @@ int npar=NPARMAX; int nlstate=2; /* Number of live states */ int ndeath=1; /* Number of dead states */ int ncovmodel, ncov; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */ -int popbased=0, fprev,lprev; +int popbased=0; int *wav; /* Number of waves for this individuual 0 is possible */ int maxwav; /* Maxim number of waves */ @@ -85,7 +85,7 @@ double jmean; /* Mean space between 2 wa double **oldm, **newm, **savm; /* Working pointers to matrices */ double **oldms, **newms, **savms; /* Fixed working pointers to matrices */ FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf; -FILE *ficgp, *fichtm,*ficresprob; +FILE *ficgp, *fichtm,*ficresprob,*ficpop; FILE *ficreseij; char filerese[FILENAMELENGTH]; FILE *ficresvij; @@ -1150,7 +1150,7 @@ 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 *Tvar, int **nbcode, int *ncodemax) +void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1) { /* Some frequencies */ int i, m, jk, k1, i1, j1, bool, z1,z2,j; @@ -1192,7 +1192,7 @@ void freqsummary(char fileres[], int ag bool=0; } if (bool==1) { - for(m=fprev; m<=lprev; m++){ + for(m=fprev1; m<=lprev1; m++){ if(agev[m][i]==0) agev[m][i]=agemax+1; if(agev[m][i]==1) agev[m][i]=agemax+2; freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; @@ -1265,6 +1265,83 @@ void freqsummary(char fileres[], int ag } /* End of Freq */ +/************ Prevalence ********************/ +void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1) +{ /* Some frequencies */ + + int i, m, jk, k1, i1, j1, bool, z1,z2,j; + double ***freq; /* Frequencies */ + double *pp; + double pos; + + pp=vector(1,nlstate); + probs= ma3x(1,130 ,1,8, 1,8); + + freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3); + j1=0; + + j=cptcoveff; + if (cptcovn<1) {j=1;ncodemax[1]=1;} + + for(k1=1; k1<=j;k1++){ + 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<=imx; i++) { + bool=1; + if (cptcovn>0) { + for (z1=1; z1<=cptcoveff; z1++) + if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) + bool=0; + } + if (bool==1) { + for(m=fprev1; m<=lprev1; m++){ + if(agev[m][i]==0) agev[m][i]=agemax+1; + if(agev[m][i]==1) agev[m][i]=agemax+2; + 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(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(jk=1; jk <=nlstate ; jk++){ + if( i <= (int) agemax){ + if(pos>=1.e-5){ + probs[i][jk][j1]= pp[jk]/pos; + } + } + } + + } + } + } + + + free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3); + free_vector(pp,1,nlstate); + +} /* End of Freq */ /************* 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) @@ -1783,6 +1860,7 @@ int main() char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH]; char filerest[FILENAMELENGTH]; char fileregp[FILENAMELENGTH]; + char popfile[FILENAMELENGTH]; char path[80],pathc[80],pathcd[80],pathtot[80],model[20]; int firstobs=1, lastobs=10; int sdeb, sfin; /* Status at beginning and end */ @@ -1790,8 +1868,9 @@ int main() 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 mobilav=0, fprevfore=1, lprevfore=1; + int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0; int hstepm, nhstepm; + int *popage; double bage, fage, age, agelim, agebase; double ftolpl=FTOL; @@ -1805,7 +1884,8 @@ int main() double ***eij, ***vareij; double **varpl; /* Variances of prevalence limits by age */ double *epj, vepp; - double kk1; + double kk1, kk2; + double *popeffectif,*popcount; char version[80]="Imach version 64b, May 2001, INED-EUROREVES "; char *alph[]={"a","a","b","c","d","e"}, str[4]; @@ -1821,7 +1901,7 @@ int main() gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */ - printf("\nIMACH, Version 0.64b"); + printf("\nIMACH, Version 0.7"); printf("\nEnter the parameter file name: "); #ifdef windows @@ -1878,6 +1958,8 @@ while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased); + fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased); + while((c=getc(ficpar))=='#' && c!= EOF){ ungetc(c,ficpar); fgets(line, MAXLINE, ficpar); @@ -1886,7 +1968,19 @@ while((c=getc(ficpar))=='#' && c!= EOF){ } ungetc(c,ficpar); - fscanf(ficpar,"fprevalence=%d lprevalence=%d mob_average=%d\n",&fprevfore,&lprevfore,&mobilav); + fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav); + fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav); + + +while((c=getc(ficpar))=='#' && c!= EOF){ + ungetc(c,ficpar); + fgets(line, MAXLINE, ficpar); + puts(line); + fputs(line,ficparo); + } + ungetc(c,ficpar); + + fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile); covar=matrix(0,NCOVMAX,1,n); cptcovn=0; @@ -2241,7 +2335,7 @@ printf("Total number of individuals= %d, /* Calculates basic frequencies. Computes observed prevalence at single age and prints on file fileres'p'. */ - freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax); + freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev); pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */ @@ -2258,8 +2352,10 @@ printf("Total number of individuals= %d, } /*--------- results files --------------*/ - fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model); - + fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model); + fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased); + fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav); + jk=1; fprintf(ficres,"# Parameters\n"); printf("# Parameters\n"); @@ -2505,17 +2601,12 @@ ij=1; fclose(ficgp); chdir(path); - free_matrix(agev,1,maxwav,1,imx); + free_ivector(wav,1,imx); free_imatrix(dh,1,lastpass-firstpass+1,1,imx); - free_imatrix(mw,1,lastpass-firstpass+1,1,imx); - - free_imatrix(s,1,maxwav+1,1,n); - - + free_imatrix(mw,1,lastpass-firstpass+1,1,imx); free_ivector(num,1,n); free_vector(agedc,1,n); - free_vector(weight,1,n); /*free_matrix(covar,1,NCOVMAX,1,n);*/ fclose(ficparo); fclose(ficres); @@ -2546,7 +2637,7 @@ chdir(path); printf("Problem with %s \n",optionfilehtm);goto end; } - fprintf(fichtm,"