Datafile=%s Firstpass=%d La
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
} /* end j==0 */
/* bool =0 we keep that guy which corresponds to the combination of dummy values */
- if(bool==1){
+ if(bool==1){ /*Selected */
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
and mw[mi+1][iind]. dh depends on stepm. */
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
@@ -4567,6 +4583,11 @@ Title=%s
Datafile=%s Firstpass=%d La
if(s[m][iind]==-1)
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
+ for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean */
+ idq[z1]=idq[z1]+weight[iind];
+ meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /* Computes mean of quantitative with selected filter */
+ stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /* *weight[iind];*/ /* Computes mean of quantitative with selected filter */
+ }
/* if((int)agev[m][iind] == 55) */
/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
@@ -4582,6 +4603,11 @@ Title=%s
Datafile=%s Firstpass=%d La
bool=1;
}/* end bool 2 */
} /* end m */
+ /* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean *\/ */
+ /* idq[z1]=idq[z1]+weight[iind]; */
+ /* meanq[z1]+=covar[ncovcol+z1][iind]*weight[iind]; /\* Computes mean of quantitative with selected filter *\/ */
+ /* stdq[z1]+=covar[ncovcol+z1][iind]*covar[ncovcol+z1][iind]*weight[iind]*weight[iind]; /\* *weight[iind];*\/ /\* Computes mean of quantitative with selected filter *\/ */
+ /* } */
} /* end bool */
} /* end iind = 1 to imx */
/* prop[s][age] is feeded for any initial and valid live state as well as
@@ -4619,6 +4645,27 @@ Title=%s
Datafile=%s Firstpass=%d La
fprintf(ficresphtmfr, "**********\n");
fprintf(ficlog, "**********\n");
}
+ /*
+ Printing means of quantitative variables if any
+ */
+ for (z1=1; z1<= nqfveff; z1++) {
+ fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.0f individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
+ fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
+ if(weightopt==1){
+ printf(" Weighted mean and standard deviation of");
+ fprintf(ficlog," Weighted mean and standard deviation of");
+ fprintf(ficresphtmfr," Weighted mean and standard deviation of");
+ }
+ printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+ fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+ fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
+ }
+ /* for (z1=1; z1<= nqtveff; z1++) { */
+ /* for(m=1;m<=lastpass;m++){ */
+ /* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f
\n", z1, m, meanqt[m][z1]); */
+ /* } */
+ /* } */
+
fprintf(ficresphtm,"
");
if((cptcoveff==0 && nj==1)|| nj==2 ) /* no covariate and first pass */
fprintf(ficresp, " Age");
@@ -4806,6 +4853,8 @@ Title=%s
Datafile=%s Firstpass=%d La
y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
/* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
}
+ /* Some are not finite, but linreg will ignore these ages */
+ no=0;
linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+b*x with standard errors */
pstart[s1]=b;
pstart[s1-1]=a;
@@ -4851,7 +4900,7 @@ Title=%s
Datafile=%s Firstpass=%d La
fprintf(ficlog,"\n");
}
}
- }
+ } /* end of state i */
printf("#Freqsummary\n");
fprintf(ficlog,"\n");
for(s1=-1; s1 <=nlstate+ndeath; s1++){
@@ -4897,7 +4946,9 @@ Title=%s
Datafile=%s Firstpass=%d La
fclose(ficresp);
fclose(ficresphtm);
fclose(ficresphtmfr);
+ free_vector(idq,1,nqfveff);
free_vector(meanq,1,nqfveff);
+ free_vector(stdq,1,nqfveff);
free_matrix(meanqt,1,lastpass,1,nqtveff);
free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
@@ -4909,6 +4960,72 @@ Title=%s
Datafile=%s Firstpass=%d La
/* End of freqsummary */
}
+/* Simple linear regression */
+int linreg(int ifi, int ila, int *no, const double x[], const double y[], double* a, double* b, double* r, double* sa, double * sb) {
+
+ /* y=a+bx regression */
+ double sumx = 0.0; /* sum of x */
+ double sumx2 = 0.0; /* sum of x**2 */
+ double sumxy = 0.0; /* sum of x * y */
+ double sumy = 0.0; /* sum of y */
+ double sumy2 = 0.0; /* sum of y**2 */
+ double sume2 = 0.0; /* sum of square or residuals */
+ double yhat;
+
+ double denom=0;
+ int i;
+ int ne=*no;
+
+ for ( i=ifi, ne=0;i<=ila;i++) {
+ if(!isfinite(x[i]) || !isfinite(y[i])){
+ /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+ continue;
+ }
+ ne=ne+1;
+ sumx += x[i];
+ sumx2 += x[i]*x[i];
+ sumxy += x[i] * y[i];
+ sumy += y[i];
+ sumy2 += y[i]*y[i];
+ denom = (ne * sumx2 - sumx*sumx);
+ /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+ }
+
+ denom = (ne * sumx2 - sumx*sumx);
+ if (denom == 0) {
+ // vertical, slope m is infinity
+ *b = INFINITY;
+ *a = 0;
+ if (r) *r = 0;
+ return 1;
+ }
+
+ *b = (ne * sumxy - sumx * sumy) / denom;
+ *a = (sumy * sumx2 - sumx * sumxy) / denom;
+ if (r!=NULL) {
+ *r = (sumxy - sumx * sumy / ne) / /* compute correlation coeff */
+ sqrt((sumx2 - sumx*sumx/ne) *
+ (sumy2 - sumy*sumy/ne));
+ }
+ *no=ne;
+ for ( i=ifi, ne=0;i<=ila;i++) {
+ if(!isfinite(x[i]) || !isfinite(y[i])){
+ /* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
+ continue;
+ }
+ ne=ne+1;
+ yhat = y[i] - *a -*b* x[i];
+ sume2 += yhat * yhat ;
+
+ denom = (ne * sumx2 - sumx*sumx);
+ /* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
+ }
+ *sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx * sumx /(double)ne));
+ *sa= *sb * sqrt(sumx2/ne);
+
+ return 0;
+}
+
/************ Prevalence ********************/
void prevalence(double ***probs, 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)
{
@@ -5247,9 +5364,11 @@ void concatwav(int wav[], int **dh, int
/* *cptcov=0; */
for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
+ for (k=1; k <= maxncov; k++)
+ for(j=1; j<=2; j++)
+ nbcode[k][j]=0; /* Valgrind */
/* Loop on covariates without age and products and no quantitative variable */
- /* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only *\/ */
for (k=1; k<=cptcovt; k++) { /* From model V1 + V2*age + V3 + V3*V4 keeps V1 + V3 = 2 only */
for (j=-1; (j < maxncov); j++) Ndum[j]=0;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
@@ -5267,7 +5386,11 @@ void concatwav(int wav[], int **dh, int
modmaxcovj=ij;
else if (ij < modmincovj)
modmincovj=ij;
- if ((ij < -1) && (ij > NCOVMAX)){
+ if (ij <0 || ij >1 ){
+ printf("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
+ fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
+ }
+ if ((ij < -1) || (ij > NCOVMAX)){
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
exit(1);
}else
@@ -5313,12 +5436,18 @@ void concatwav(int wav[], int **dh, int
/* nbcode[Tvar[j]][3]=2; */
/* To be continued (not working yet). */
ij=0; /* ij is similar to i but can jump over null modalities */
- for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+
+ /* for (i=modmincovj; i<=modmaxcovj; i++) { */ /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
+ /* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
+ /* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
+ * nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
+ /*, could be restored in the future */
+ for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;
}
ij++;
- nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
+ nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */
break;
@@ -5334,21 +5463,7 @@ void concatwav(int wav[], int **dh, int
break;
} /* end switch */
} /* end dummy test */
-
- /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
- /* /\*recode from 0 *\/ */
- /* 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; */
- /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
- /* } */
- /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
- /* if (ij > ncodemax[j]) { */
- /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
- /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
- /* break; */
- /* } */
- /* } /\* end of loop on modality k *\/ */
- } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
+ } /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
for (k=-1; k< maxncov; k++) Ndum[k]=0;
/* Look at fixed dummy (single or product) covariates to check empty modalities */
@@ -5441,7 +5556,7 @@ void concatwav(int wav[], int **dh, int
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
+ Look at hpijx to understand the reason which relies in memory size consideration
and note for a fixed period like estepm months */
/* 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
@@ -5672,7 +5787,8 @@ void concatwav(int wav[], int **dh, int
/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
}
-
+
+ /* Standard deviation of expectancies ij */
fprintf(ficresstdeij,"%3.0f",age );
for(i=1; i<=nlstate;i++){
eip=0.;
@@ -5687,6 +5803,7 @@ void concatwav(int wav[], int **dh, int
}
fprintf(ficresstdeij,"\n");
+ /* Variance of expectancies ij */
fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
@@ -5720,10 +5837,11 @@ void concatwav(int wav[], int **dh, int
/************ Variance ******************/
void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
{
- /* Variance of health expectancies */
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- /* double **newm;*/
- /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
+ /** Variance of health expectancies
+ * double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);
+ * double **newm;
+ * int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)
+ */
/* int movingaverage(); */
double **dnewm,**doldm;
@@ -5731,11 +5849,11 @@ void concatwav(int wav[], int **dh, int
int i, j, nhstepm, hstepm, h, nstepm ;
int k;
double *xp;
- double **gp, **gm; /* for var eij */
- double ***gradg, ***trgradg; /*for var eij */
- double **gradgp, **trgradgp; /* for var p point j */
- double *gpp, *gmp; /* for var p point j */
- double **varppt; /* for var p point j nlstate to nlstate+ndeath */
+ double **gp, **gm; /**< for var eij */
+ double ***gradg, ***trgradg; /**< for var eij */
+ double **gradgp, **trgradgp; /**< for var p point j */
+ double *gpp, *gmp; /**< for var p point j */
+ double **varppt; /**< for var p point j nlstate to nlstate+ndeath */
double ***p3mat;
double age,agelim, hf;
/* double ***mobaverage; */
@@ -5796,7 +5914,7 @@ void concatwav(int wav[], int **dh, int
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)
\n");
fprintf(fichtm,"\n
%s
\n",digitp);
- /* } */
+
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
@@ -5851,9 +5969,12 @@ void concatwav(int wav[], int **dh, int
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);
}
-
+ /**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
+ * returns into prlim .
+ */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);
-
+
+ /* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
if (popbased==1) {
if(mobilav ==0){
for(i=1; i<=nlstate;i++)
@@ -5863,23 +5984,28 @@ void concatwav(int wav[], int **dh, int
prlim[i][i]=mobaverage[(int)age][i][ij];
}
}
-
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
+ /**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
+ */
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
+ /**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}_x\f$, which are the probability
+ * at horizon h in state j including mortality.
+ */
for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}
}
- /* Next for computing probability of death (h=1 means
+ /* Next for computing shifted+ probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
+ as a weighted average of prlim(i) * p(i,j) p.3=w1*p13 + w2*p23 .
*/
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 probability of death */
+ }
+
+ /* Again with minus shift */
for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);
@@ -5912,19 +6038,23 @@ void concatwav(int wav[], int **dh, int
for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];
}
- /* end probability of death */
-
+ /* end shifting computations */
+
+ /**< Computing gradient matrix at horizon h
+ */
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 */
+ /**< Gradient of overall mortality p.3 (or p.j)
+ */
+ for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}
} /* End theta */
-
+
+ /* We got the gradient matrix for each theta and state j */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
for(h=0; h<=nhstepm; h++) /* veij */
@@ -5935,13 +6065,19 @@ void concatwav(int wav[], int **dh, int
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];
-
+ /**< as well as its transposed matrix
+ */
hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;
-
+
+ /* Computing trgradg by matcov by gradg at age and summing over h
+ * and k (nhstepm) formula 15 of article
+ * Lievre-Brouard-Heathcote
+ */
+
for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
@@ -5952,7 +6088,11 @@ void concatwav(int wav[], int **dh, int
}
}
- /* pptj */
+ /* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
+ * p.j overall mortality formula 49 but computed directly because
+ * we compute the grad (wix pijx) instead of grad (pijx),even if
+ * wix is independent of theta.
+ */
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);
for(j=nlstate+1;j<=nlstate+ndeath;j++)
@@ -6040,12 +6180,12 @@ void concatwav(int wav[], int **dh, int
} /* end varevsij */
/************ 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 *ncvyearp, int ij, char strstart[], int nres)
+ void varprevlim(char fileresvpl[], FILE *ficresvpl, 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 *ncvyearp, int ij, char strstart[], int nres)
{
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- double **dnewm,**doldm;
+ double **dnewmpar,**doldm;
int i, j, nhstepm, hstepm;
double *xp;
double *gp, *gm;
@@ -6064,7 +6204,7 @@ void concatwav(int wav[], int **dh, int
fprintf(ficresvpl,"\n");
xp=vector(1,npar);
- dnewm=matrix(1,nlstate,1,npar);
+ dnewmpar=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);
hstepm=1*YEARM; /* Every year of age */
@@ -6134,11 +6274,11 @@ void concatwav(int wav[], int **dh, int
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;
if((int)age==79 ||(int)age== 80 ||(int)age== 81){
- matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}else{
- matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}
for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
@@ -6159,36 +6299,161 @@ void concatwav(int wav[], int **dh, int
free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);
- free_matrix(dnewm,1,nlstate,1,nlstate);
+ free_matrix(dnewmpar,1,nlstate,1,nlstate);
}
-/************ Variance of one-step probabilities ******************/
-void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
- {
- int i, j=0, k1, l1, tj;
- int k2, l2, j1, z1;
- int k=0, l;
- int first=1, first1, first2;
- double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- double **dnewm,**doldm;
- double *xp;
- double *gp, *gm;
- double **gradg, **trgradg;
- double **mu;
- double age, cov[NCOVMAX+1];
- double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
- int theta;
- char fileresprob[FILENAMELENGTH];
- char fileresprobcov[FILENAMELENGTH];
- char fileresprobcor[FILENAMELENGTH];
- double ***varpij;
- strcpy(fileresprob,"PROB_");
- strcat(fileresprob,fileres);
- if((ficresprob=fopen(fileresprob,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprob);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
+/************ Variance of backprevalence limit ******************/
+ void varbrevlim(char fileresvbl[], FILE *ficresvbl, double **varbpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **bprlim, double ftolpl, int mobilavproj, int *ncvyearp, int ij, char strstart[], int nres)
+{
+ /* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
+ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
+
+ double **dnewmpar,**doldm;
+ int i, j, nhstepm, hstepm;
+ double *xp;
+ double *gp, *gm;
+ double **gradg, **trgradg;
+ double **mgm, **mgp;
+ double age,agelim;
+ int theta;
+
+ pstamp(ficresvbl);
+ fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
+ fprintf(ficresvbl,"# Age ");
+ if(nresult >=1)
+ fprintf(ficresvbl," Result# ");
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresvbl," %1d-%1d",i,i);
+ fprintf(ficresvbl,"\n");
+
+ xp=vector(1,npar);
+ dnewmpar=matrix(1,nlstate,1,npar);
+ doldm=matrix(1,nlstate,1,nlstate);
+
+ hstepm=1*YEARM; /* Every year of age */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
+ agelim = AGEINF;
+ for (age=fage; age>=bage; age --){ /* If stepm=6 months */
+ nhstepm=(int) rint((age-agelim)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ if (stepm >= YEARM) hstepm=1;
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+ gradg=matrix(1,npar,1,nlstate);
+ mgp=matrix(1,npar,1,nlstate);
+ mgm=matrix(1,npar,1,nlstate);
+ gp=vector(1,nlstate);
+ gm=vector(1,nlstate);
+
+ for(theta=1; theta <=npar; theta++){
+ for(i=1; i<=npar; i++){ /* Computes gradient */
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ }
+ if(mobilavproj > 0 )
+ bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+ else
+ bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+ for(i=1;i<=nlstate;i++){
+ gp[i] = bprlim[i][i];
+ mgp[theta][i] = bprlim[i][i];
+ }
+ for(i=1; i<=npar; i++) /* Computes gradient */
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ if(mobilavproj > 0 )
+ bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+ else
+ bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
+ for(i=1;i<=nlstate;i++){
+ gm[i] = bprlim[i][i];
+ mgm[theta][i] = bprlim[i][i];
+ }
+ for(i=1;i<=nlstate;i++)
+ gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+ /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
+ } /* End theta */
+
+ trgradg =matrix(1,nlstate,1,npar);
+
+ for(j=1; j<=nlstate;j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[j][theta]=gradg[theta][j];
+ /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+ /* printf("\nmgm mgp %d ",(int)age); */
+ /* for(j=1; j<=nlstate;j++){ */
+ /* printf(" %d ",j); */
+ /* for(theta=1; theta <=npar; theta++) */
+ /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
+ /* printf("\n "); */
+ /* } */
+ /* } */
+ /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
+ /* printf("\n gradg %d ",(int)age); */
+ /* for(j=1; j<=nlstate;j++){ */
+ /* printf("%d ",j); */
+ /* for(theta=1; theta <=npar; theta++) */
+ /* printf("%d %lf ",theta,gradg[theta][j]); */
+ /* printf("\n "); */
+ /* } */
+ /* } */
+
+ for(i=1;i<=nlstate;i++)
+ varbpl[i][(int)age] =0.;
+ if((int)age==79 ||(int)age== 80 ||(int)age== 81){
+ matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+ }else{
+ matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
+ }
+ for(i=1;i<=nlstate;i++)
+ varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+
+ fprintf(ficresvbl,"%.0f ",age );
+ if(nresult >=1)
+ fprintf(ficresvbl,"%d ",nres );
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
+ fprintf(ficresvbl,"\n");
+ free_vector(gp,1,nlstate);
+ free_vector(gm,1,nlstate);
+ free_matrix(mgm,1,npar,1,nlstate);
+ free_matrix(mgp,1,npar,1,nlstate);
+ free_matrix(gradg,1,npar,1,nlstate);
+ free_matrix(trgradg,1,nlstate,1,npar);
+ } /* End age */
+
+ free_vector(xp,1,npar);
+ free_matrix(doldm,1,nlstate,1,npar);
+ free_matrix(dnewmpar,1,nlstate,1,nlstate);
+
+}
+
+/************ Variance of one-step probabilities ******************/
+void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
+ {
+ int i, j=0, k1, l1, tj;
+ int k2, l2, j1, z1;
+ int k=0, l;
+ int first=1, first1, first2;
+ double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
+ double **dnewm,**doldm;
+ double *xp;
+ double *gp, *gm;
+ double **gradg, **trgradg;
+ double **mu;
+ double age, cov[NCOVMAX+1];
+ double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
+ int theta;
+ char fileresprob[FILENAMELENGTH];
+ char fileresprobcov[FILENAMELENGTH];
+ char fileresprobcor[FILENAMELENGTH];
+ double ***varpij;
+
+ strcpy(fileresprob,"PROB_");
+ strcat(fileresprob,fileres);
+ if((ficresprob=fopen(fileresprob,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprob);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
}
strcpy(fileresprobcov,"PROBCOV_");
strcat(fileresprobcov,fileresu);
@@ -6436,7 +6701,12 @@ To be simple, these graphs help to under
}
/* Eigen vectors */
- v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+ if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
+ printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
+ v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
+ }else
+ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/*v21=sqrt(1.-v11*v11); *//* error */
v21=(lc1-v1)/cv12*v11;
v12=-v21;
@@ -6467,8 +6737,8 @@ To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not", \
- mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
- mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */
+ mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
+ mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{
first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
@@ -6505,8 +6775,8 @@ void printinghtml(char fileresu[], char
int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
- double jprev1, double mprev1,double anprev1, double dateprev1, \
- double jprev2, double mprev2,double anprev2, double dateprev2){
+ double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
+ double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){
int jj1, k1, i1, cpt, k4, nres;
fprintf(fichtm,"- Result files (first order: no variance)\n \
@@ -6643,7 +6913,7 @@ divided by h: hPij
for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"
\n- Survival functions from state %d in each live state and total.\
Or probability to survive in various states (1 to %d) being in state %d at different ages. \
- %s_%d%d-%d.svg
![](\"%s_%d-%d-%d.svg\")
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
+ %s_%d-%d-%d.svg
", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
}
/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
@@ -6660,8 +6930,18 @@ divided by h: hPij
if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){
- fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. %s_%d-%d-%d.svg
\
-", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ fprintf(fichtm,"
\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). %s_%d-%d-%d.svg
\
+", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
+ }
+ }
+ if(backcast==1){
+ /* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
+ for(cpt=1; cpt<=nlstate;cpt++){
+ fprintf(fichtm,"
\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
+ from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
+ account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
+with weights corresponding to observed prevalence at different ages. %s_%d-%d-%d.svg
\
+ ", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
}
}
@@ -6767,7 +7047,7 @@ true period expectancies (those weighted
}
/******************* Gnuplot file **************/
- void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear){
+void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear, int offbyear){
char dirfileres[132],optfileres[132];
char gplotcondition[132], gplotlabel[132];
@@ -6776,6 +7056,8 @@ true period expectancies (those weighted
int ng=0;
int vpopbased;
int ioffset; /* variable offset for columns */
+ int iyearc=1; /* variable column for year of projection */
+ int iagec=1; /* variable column for age of projection */
int nres=0; /* Index of resultline */
int istart=1; /* For starting graphs in projections */
@@ -6789,6 +7071,20 @@ true period expectancies (those weighted
/*#endif */
m=pow(2,cptcoveff);
+ /* diagram of the model */
+ fprintf(ficgp,"\n#Diagram of the model \n");
+ fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
+ fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
+ fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i*10+j from cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.95*(cos(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) - cos(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta2:0)), -0.95*(sin(pi*((1-(%d/2)*2./%d)/2+(i-1)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) - sin(pi*((1-(%d/2)*2./%d)/2+(j-1)*2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+
+ fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)*10+i from cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))-(i!=j?(i-j)/abs(i-j)*delta:0), yoff +sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) rto -0.80*(cos(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d))+(i!=j?(i-j)/abs(i-j)*delta:0) ), -0.80*(sin(pi*((1-(%d/2)*2./%d)/2+(1-i)*2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+ fprintf(ficgp,"\n#show arrow\nunset label\n");
+ fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)), yoff+sin(pi*((1-(%d/2)*2./%d)/2+(2-i)*2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
+ fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
+ fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
+ fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
+ fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");
+
/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
@@ -6858,7 +7154,8 @@ true period expectancies (those weighted
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
- fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ /* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
+ fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
/* k1-1 error should be nres-1*/
@@ -6880,7 +7177,7 @@ true period expectancies (those weighted
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
if(cptcoveff ==0){
- fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
+ fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
}else{
kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
@@ -6931,8 +7228,28 @@ true period expectancies (those weighted
}
} /* end covariate */
} /* end if no covariate */
+ if(backcast == 1){
+ fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ /* k1-1 error should be nres-1*/
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ 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 lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
+ else fprintf(ficgp," %%*lf (%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"\" w l lt 4");
+ } /* end if backprojcast */
} /* end if backcast */
- fprintf(ficgp,"\nset out ;unset label;\n");
+ /* fprintf(ficgp,"\nset out ;unset label;\n"); */
+ fprintf(ficgp,"\nset out ;unset title;\n");
} /* nres */
} /* k1 */
} /* cpt */
@@ -7224,7 +7541,7 @@ set ter svg size 640, 480\nunset log y\n
for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)
continue;
- for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
@@ -7248,11 +7565,11 @@ set ter svg size 640, 480\nunset log y\n
}
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
- fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */
- for (i=1; i<= nlstate ; i ++){ /* State of origin */
+ for (i=1; i<= nlstate ; i ++){ /* State of arrival */
if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else
@@ -7265,7 +7582,7 @@ set ter svg size 640, 480\nunset log y\n
/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */
/* /\* fprintf(ficgp,"+$%d",k+l+j-1); *\/ */
- fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
+ fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
} /* nlstate */
fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/
@@ -7330,24 +7647,22 @@ set ter svg size 640, 480\nunset log y\n
/*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
fprintf(ficgp," u %d:(", ioffset);
if(i==nlstate+1){
- fprintf(ficgp," $%d/(1.-$%d)):5 t 'pw.%d' with line lc variable ", \
+ fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
fprintf(ficgp,",\\\n '' ");
fprintf(ficgp," u %d:(",ioffset);
- fprintf(ficgp," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", \
+ fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
offyear, \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate );
}else
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
}else{ /* more than 2 covariates */
- if(cptcoveff ==1){
- ioffset=4; /* Age is in 4 */
- }else{
- ioffset=6; /* Age is in 6 */
- /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
- /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
- }
+ ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+ /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
+ iyearc=ioffset-1;
+ iagec=ioffset;
fprintf(ficgp," u %d:(",ioffset);
kl=0;
strcpy(gplotcondition,"(");
@@ -7369,13 +7684,13 @@ set ter svg size 640, 480\nunset log y\n
/*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(i==nlstate+1){
- fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):5 t 'p.%d' with line lc variable", gplotcondition, \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,iyearc, cpt );
fprintf(ficgp,",\\\n '' ");
- fprintf(ficgp," u %d:(",ioffset);
- fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \
- offyear, \
- ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ fprintf(ficgp," u %d:(",iagec);
+ fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
+ iyearc, iagec, offyear, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate, iyearc );
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
}else{
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
@@ -7388,6 +7703,121 @@ set ter svg size 640, 480\nunset log y\n
} /* end covariate */
} /* End if prevfcast */
+ if(backcast==1){
+ /* Back projection from cross-sectional to stable (mixed) for each covariate */
+
+ for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
+ for(nres=1; nres <= nresult; nres++){ /* For each resultline */
+ if(m != 1 && TKresult[nres]!= k1)
+ continue;
+ for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
+ strcpy(gplotlabel,"(");
+ fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
+ for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
+ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
+ /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv];
+ fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
+ }
+ for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
+ fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
+ }
+ strcpy(gplotlabel+strlen(gplotlabel),")");
+ fprintf(ficgp,"\n#\n");
+ if(invalidvarcomb[k1]){
+ fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
+ continue;
+ }
+
+ fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
+ fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
+ fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
+set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
+
+ /* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 *\/ */
+ istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
+ /*istart=1;*/ /* Could be one if by state, but nlstate+1 is w.i projection only */
+ for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
+ /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
+ /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
+ if(i==istart){
+ fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
+ }else{
+ fprintf(ficgp,",\\\n '' ");
+ }
+ if(cptcoveff ==0){ /* No covariate */
+ ioffset=2; /* Age is in 2 */
+ /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
+ /*# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
+ fprintf(ficgp," u %d:(", ioffset);
+ if(i==nlstate+1){
+ fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt );
+ fprintf(ficgp,",\\\n '' ");
+ fprintf(ficgp," u %d:(",ioffset);
+ fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
+ offbyear, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
+ }else
+ fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)*nlstate,cpt,i );
+ }else{ /* more than 2 covariates */
+ ioffset=2*cptcoveff+2; /* Age is in 4 or 6 or etc.*/
+ /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
+ /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
+ iyearc=ioffset-1;
+ iagec=ioffset;
+ fprintf(ficgp," u %d:(",ioffset);
+ kl=0;
+ strcpy(gplotcondition,"(");
+ for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
+ lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
+ /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
+ /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
+ /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
+ vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
+ kl++;
+ sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
+ kl++;
+ if(k 1)
+ sprintf(gplotcondition+strlen(gplotcondition)," && ");
+ }
+ strcpy(gplotcondition+strlen(gplotcondition),")");
+ /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
+ /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
+ /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
+ /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
+ if(i==nlstate+1){
+ fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
+ fprintf(ficgp,",\\\n '' ");
+ fprintf(ficgp," u %d:(",iagec);
+ /* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
+ fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
+ iyearc,iagec,offbyear, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
+/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
+ }else{
+ /* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
+ fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
+ ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
+ }
+ } /* end if covariate */
+ } /* nlstate */
+ fprintf(ficgp,"\nset out; unset label;\n");
+ } /* end cpt state*/
+ } /* end covariate */
+ } /* End if backcast */
+
/* 9eme writing MLE parameters */
fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
@@ -7433,7 +7863,7 @@ set ter svg size 640, 480\nunset log y\n
continue;
fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
strcpy(gplotlabel,"(");
- sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);
+ /*sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);*/
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
@@ -7450,7 +7880,9 @@ set ter svg size 640, 480\nunset log y\n
strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
- fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
+ fprintf(ficgp,"\nset key outside ");
+ /* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
+ fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
@@ -7494,36 +7926,40 @@ set ter svg size 640, 480\nunset log y\n
/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
- if(j==Tage[ij]) { /* Product by age */
- if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
- if(DummyV[j]==0){
- fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
- }else{ /* quantitative */
- fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
- /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
- }
- ij++;
- }
- }else if(j==Tprod[ijp]) { /* */
- /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
- if(ijp <=cptcovprod) { /* Product */
- if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
- if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
- /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
- fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
- }else{ /* Vn is dummy and Vm is quanti */
- /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
- fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+ if(cptcovage >0){ /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+ if(j==Tage[ij]) { /* Product by age To be looked at!!*/
+ if(ij <=cptcovage) { /* V5+V4+V3+V4*V3+V5*age+V2+V1*V2+V1*age+V1, 2 V5 and V1 */
+ if(DummyV[j]==0){
+ fprintf(ficgp,"+p%d*%d*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
+ }else{ /* quantitative */
+ fprintf(ficgp,"+p%d*%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
+ /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}
- }else{ /* Vn*Vm Vn is quanti */
- if(DummyV[Tvard[ijp][2]]==0){
- fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
- }else{ /* Both quanti */
- fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+ ij++;
+ }
+ }
+ }else if(cptcovprod >0){
+ if(j==Tprod[ijp]) { /* */
+ /* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
+ if(ijp <=cptcovprod) { /* Product */
+ if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
+ if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
+ /* fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
+ fprintf(ficgp,"+p%d*%d*%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
+ }else{ /* Vn is dummy and Vm is quanti */
+ /* fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
+ fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+ }
+ }else{ /* Vn*Vm Vn is quanti */
+ if(DummyV[Tvard[ijp][2]]==0){
+ fprintf(ficgp,"+p%d*%d*%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
+ }else{ /* Both quanti */
+ fprintf(ficgp,"+p%d*%f*%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
+ }
}
+ ijp++;
}
- ijp++;
- }
+ } /* end Tprod */
} else{ /* simple covariate */
/* fprintf(ficgp,"+p%d*%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\* Valgrind bug nbcode *\/ */
if(Dummy[j]==0){
@@ -7551,26 +7987,27 @@ set ter svg size 640, 480\nunset log y\n
ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){
- if((j-2)==Tage[ij]) { /* Bug valgrind */
- if(ij <=cptcovage) { /* Bug valgrind */
- fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
- /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
- ij++;
- }
- }
- else
- fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
+ if(cptcovage >0){
+ if((j-2)==Tage[ij]) { /* Bug valgrind */
+ if(ij <=cptcovage) { /* Bug valgrind */
+ fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
+ /* fprintf(ficgp,"+p%d*%d*x",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
+ ij++;
+ }
+ }
+ }else
+ fprintf(ficgp,"+p%d*%d",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
}
fprintf(ficgp,")");
}
fprintf(ficgp,")");
if(ng ==2)
- fprintf(ficgp," t \"p%d%d\" ", k2,k);
+ fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
else /* ng= 3 */
- fprintf(ficgp," t \"i%d%d\" ", k2,k);
+ fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */
- fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
+ fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}
if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
fprintf(ficgp,",");
@@ -7579,7 +8016,8 @@ set ter svg size 640, 480\nunset log y\n
i=i+ncovmodel;
} /* end k */
} /* end k2 */
- fprintf(ficgp,"\n set out; unset label;\n");
+ /* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
+ fprintf(ficgp,"\n set out; unset title;set key default;\n");
} /* end k1 */
} /* end ng */
/* avoid: */
@@ -7603,8 +8041,8 @@ set ter svg size 640, 480\nunset log y\n
double *agemingoodr, *agemaxgoodr;
- /* modcovmax=2*cptcoveff;/\* Max number of modalities. We suppose */
- /* a covariate has 2 modalities, should be equal to ncovcombmax *\/ */
+ /* modcovmax=2*cptcoveff; Max number of modalities. We suppose */
+ /* a covariate has 2 modalities, should be equal to ncovcombmax */
sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);
@@ -7724,11 +8162,11 @@ set ter svg size 640, 480\nunset log y\n
sumr+=probs[(int)age][i][cptcod];
}
if(fabs(sum - 1.) > 1.e-3) { /* bad */
- printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);
+ printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
if(fabs(sumr - 1.) > 1.e-3) { /* bad */
- printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);
+ printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
} /* end bad */
}/* age */
@@ -7764,11 +8202,11 @@ set ter svg size 640, 480\nunset log y\n
sumr+=mobaverage[(int)age][i][cptcod];
}
if(fabs(sum - 1.) > 1.e-3) { /* bad */
- printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, fage);
+ printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest *\/ */
if(fabs(sumr - 1.) > 1.e-3) { /* bad */
- printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, fage);
+ printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, (int)fage);
} /* end bad */
}/* age */
@@ -7817,7 +8255,7 @@ set ter svg size 640, 480\nunset log y\n
/************** Forecasting ******************/
-void 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){
+ void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, 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
@@ -7856,7 +8294,12 @@ void prevforecast(char fileres[], double
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
- else hstepm=estepm;
+ else{
+ hstepm=estepm;
+ }
+ if(estepm > stepm){ /* Yes every two year */
+ stepsize=2;
+ }
hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
@@ -7901,37 +8344,37 @@ void prevforecast(char fileres[], double
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
- for (agec=fage; agec>=(ageminpar-1); agec--){
+ /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
+ for (agec=fage; agec>=(bage); 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;
+ /* We compute pii at age agec over nhstepm);*/
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
-
+ /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
for (h=0; h<=nhstepm; h++){
if (h*hstepm/YEARM*stepm ==yearp) {
- fprintf(ficresf,"\n");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- ppij=0.;
- for(i=1; i<=nlstate;i++) {
- /* if (mobilav>=1) */
- ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
- /* else { */ /* even if mobilav==-1 we use mobaverage */
- /* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
- /* } */
- 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);
+ break;
+ }
+ }
+ fprintf(ficresf,"\n");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
+
+ for(j=1; j<=nlstate+ndeath;j++) {
+ ppij=0.;
+ for(i=1; i<=nlstate;i++) {
+ if (mobilav>=1)
+ ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
+ else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
+ ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
}
- }/* end j */
- } /* end h */
+ fprintf(ficresf," %.3f", p3mat[i][j][h]);
+ } /* end i */
+ fprintf(ficresf," %.3f", ppij);
+ }/* end j */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */
/* diffyear=(int) anproj1+yearp-ageminpar-1; */
@@ -7945,22 +8388,23 @@ void prevforecast(char fileres[], double
}
-/* /\************** Back Forecasting ******************\/ */
-void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
+/************** Back Forecasting ******************/
+ void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){
/* back1, year, month, day of starting backection
agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed
- anback2 year of en of backection (same day and month as back1).
+ anback2 year of end of backprojection (same day and month as back1).
+ prevacurrent and prev are prevalences.
*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
double agec; /* generic age */
- double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double *popeffectif,*popcount;
double ***p3mat;
/* double ***mobaverage; */
char fileresfb[FILENAMELENGTH];
- agelim=AGESUP;
+ agelim=AGEINF;
/* 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.
@@ -7989,7 +8433,12 @@ void prevbackforecast(char fileres[], do
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
- else hstepm=estepm;
+ else{
+ hstepm=estepm;
+ }
+ if(estepm >= stepm){ /* Yes every two year */
+ stepsize=2;
+ }
hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
@@ -8006,13 +8455,10 @@ void prevbackforecast(char fileres[], do
if (cptcovn < 1){i1=1;}
fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
+ printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
fprintf(ficresfb,"#****** Routine prevbackforecast **\n");
- /* if (h==(int)(YEARM*yearp)){ */
- /* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
- /* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
- /* k=k+1; */
for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){
if(i1 != 1 && TKresult[nres]!= k)
@@ -8021,7 +8467,7 @@ void prevbackforecast(char fileres[], do
printf("\nCombination (%d) projection ignored because no cases \n",k);
continue;
}
- fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#");
+ fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
@@ -8031,46 +8477,55 @@ void prevbackforecast(char fileres[], do
fprintf(ficresfb," yearbproj age");
for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)
- fprintf(ficresfb," p%d%d",i,j);
- fprintf(ficresfb," p.%d",j);
+ fprintf(ficresfb," b%d%d",i,j);
+ fprintf(ficresfb," b.%d",j);
}
for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
fprintf(ficresfb,"\n");
fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
- /* for (agec=fage; agec>=(ageminpar-1); agec--){ */
- /* nhstepm=(int) rint((agelim-agec)*YEARM/stepm); */
- for (agec=fage; agec>=fage-20; agec--){ /* testing up to 10 */
- nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
+ /* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
+ /* for (agec=bage; agec<=agemax-1; agec++){ /\* testing *\/ */
+ for (agec=bage; agec<=fage; agec++){ /* testing */
+ /* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
+ nhstepm=(int) (agec-agelim) *YEARM/stepm;/* nhstepm=(int) rint((agec-agelim)*YEARM/stepm);*/
nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;
+ /* computes hbxij at age agec over 1 to nhstepm */
+ /* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
-
+ /* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
+ /* Then we print p3mat for h corresponding to the right agec+h*stepms=yearp */
+ /* printf(" agec=%.2f\n",agec);fflush(stdout); */
for (h=0; h<=nhstepm; h++){
- if (h*hstepm/YEARM*stepm ==yearp) {
- fprintf(ficresfb,"\n");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- ppij=0.;
- for(i=1; i<=nlstate;i++) {
- /* if (mobilav==1) */
- ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
+ if (h*hstepm/YEARM*stepm ==-yearp) {
+ break;
+ }
+ }
+ fprintf(ficresfb,"\n");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-h*hstepm/YEARM*stepm);
+ for(i=1; i<=nlstate+ndeath;i++) {
+ ppij=0.;ppi=0.;
+ for(j=1; j<=nlstate;j++) {
+ /* if (mobilav==1) */
+ ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
+ ppi=ppi+prevacurrent[(int)agec][j][k];
+ /* ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][j][k]; */
+ /* ppi=ppi+mobaverage[(int)agec][j][k]; */
/* else { */
/* ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k]; */
/* } */
- if (h*hstepm/YEARM*stepm== yearp) {
- fprintf(ficresfb," %.3f", p3mat[i][j][h]);
- }
- } /* end i */
- if (h*hstepm/YEARM*stepm==yearp) {
- fprintf(ficresfb," %.3f", ppij);
- }
- }/* end j */
- } /* end h */
+ fprintf(ficresfb," %.3f", p3mat[i][j][h]);
+ } /* end j */
+ if(ppi <0.99){
+ printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+ fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
+ }
+ fprintf(ficresfb," %.3f", ppij);
+ }/* end j */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */
} /* end yearp */
@@ -8084,6 +8539,123 @@ void prevbackforecast(char fileres[], do
}
+/* Variance of prevalence limit: varprlim */
+ void varprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **prlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+ /*------- Variance of period (stable) prevalence------*/
+
+ char fileresvpl[FILENAMELENGTH];
+ FILE *ficresvpl;
+ double **oldm, **savm;
+ double **varpl; /* Variances of prevalence limits by age */
+ int i1, k, nres, j ;
+
+ strcpy(fileresvpl,"VPL_");
+ strcat(fileresvpl,fileresu);
+ if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+ printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
+ exit(0);
+ }
+ printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
+ fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
+
+ /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficresvpl,"\n#****** ");
+ printf("\n#****** ");
+ fprintf(ficlog,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresvpl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+
+ varpl=matrix(1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
+ free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+ /*}*/
+ }
+
+ fclose(ficresvpl);
+ printf("done variance-covariance of period prevalence\n");fflush(stdout);
+ fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
+
+ }
+/* Variance of back prevalence: varbprlim */
+ void varbprlim(char fileresu[], int nresult, double ***prevacurrent, int mobilavproj, double bage, double fage, double **bprlim, int *ncvyearp, double ftolpl, double p[], double **matcov, double *delti, int stepm, int cptcoveff){
+ /*------- Variance of back (stable) prevalence------*/
+
+ char fileresvbl[FILENAMELENGTH];
+ FILE *ficresvbl;
+
+ double **oldm, **savm;
+ double **varbpl; /* Variances of back prevalence limits by age */
+ int i1, k, nres, j ;
+
+ strcpy(fileresvbl,"VBL_");
+ strcat(fileresvbl,fileresu);
+ if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
+ printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
+ exit(0);
+ }
+ printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
+ fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);
+
+
+ i1=pow(2,cptcoveff);
+ if (cptcovn < 1){i1=1;}
+
+ for(nres=1; nres <= nresult; nres++) /* For each resultline */
+ for(k=1; k<=i1;k++){
+ if(i1 != 1 && TKresult[nres]!= k)
+ continue;
+ fprintf(ficresvbl,"\n#****** ");
+ printf("\n#****** ");
+ fprintf(ficlog,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
+ }
+ for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
+ printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
+ }
+ fprintf(ficresvbl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+
+ varbpl=matrix(1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+
+ varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
+ free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
+ /*}*/
+ }
+
+ fclose(ficresvbl);
+ printf("done variance-covariance of back prevalence\n");fflush(stdout);
+ fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);
+
+ } /* End of varbprlim */
+
/************** Forecasting *****not tested NB*************/
/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
@@ -9165,7 +9737,7 @@ Dummy[k] 0=dummy (0 1), 1 quantitative (
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
- for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
+ for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;
@@ -9415,11 +9987,12 @@ Dummy[k] 0=dummy (0 1), 1 quantitative (
/* Searching for doublons in the model */
for(k1=1; k1<= cptcovt;k1++){
for(k2=1; k2 maxwav){
+ printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+ fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
+ fflush(ficlog);
+ goto end;
+ }
+ printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+ fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
+ fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
+ fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
}
/* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
/*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
@@ -10413,22 +11045,18 @@ int main(int argc, char *argv[])
/* If line starts with a # it is a comment */
if (line[0] == '#') {
numlinepar++;
- fputs(line,stdout);
- fputs(line,ficparo);
- fputs(line,ficlog);
+ printf("%s",line);
+ fprintf(ficres,"%s",line);
+ fprintf(ficparo,"%s",line);
+ fprintf(ficlog,"%s",line);
continue;
}else
break;
}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
- if (num_filled == 0){
- printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
- fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
- model[0]='\0';
- goto end;
- } else if (num_filled != 1){
- printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
- fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
+ if (num_filled != 1){
+ printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
+ fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
model[0]='\0';
goto end;
}
@@ -10441,20 +11069,23 @@ int main(int argc, char *argv[])
}
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
printf("model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
+ fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
}
/* 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
/* numlinepar=numlinepar+3; /\* In general *\/ */
/* 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=1+age+%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 nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
- fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);
+ /* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
+ /* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fflush(ficlog);
/* if(model[0]=='#'|| model[0]== '\0'){ */
if(model[0]=='#'){
- printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
- 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
- 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
+ printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
+ 'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age' or \n \
+ 'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
if(mle != -1){
- printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
+ printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
exit(1);
}
}
@@ -10475,9 +11106,9 @@ int main(int argc, char *argv[])
covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
- coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
- cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
- cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
+ if(nqv>=1)coqvar=matrix(1,nqv,1,n); /**< Fixed quantitative covariate */
+ if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /**< Time varying quantitative covariate */
+ if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /**< Time varying covariate (dummy and quantitative)*/
cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
/* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
v1+v2*age+v2*v3 makes cptcovn = 3
@@ -10676,16 +11307,6 @@ Please run with mle=-1 to get a correct
fflush(ficlog);
- /*-------- Rewriting parameter 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", rfileres);goto end;
- fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
- }
- fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */
/* Main data
@@ -11023,15 +11644,36 @@ Title=%s
Datafile=%s Firstpass=%d La
firstpass, lastpass, stepm, weightopt, model);
fprintf(fichtm,"\n");
- fprintf(fichtm,"
Total number of observations=%d
\n\
+ fprintf(fichtm,"Parameter line 2
- Tolerance for the convergence of the likelihood: ftol=%g \n
- Interval for the elementary matrix (in month): stepm=%d",\
+ ftol, stepm);
+ fprintf(fichtm,"\n
- Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
+ ncurrv=1;
+ for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
+ fprintf(fichtm,"\n
- Number of fixed quantitative variables: nqv=%d ", nqv);
+ ncurrv=i;
+ for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
+ fprintf(fichtm,"\n
- Number of time varying (wave varying) covariates: ntv=%d ", ntv);
+ ncurrv=i;
+ for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
+ fprintf(fichtm,"\n
- Number of quantitative time varying covariates: nqtv=%d ", nqtv);
+ ncurrv=i;
+ for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
+ fprintf(fichtm,"\n
- Weights column \n
Number of alive states: nlstate=%d
Number of death states (not really implemented): ndeath=%d \n - Number of waves: maxwav=%d \n
- Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n
- Does the weight column be taken into account (1), or not (0): weight=%d
\n", \
+ nlstate, ndeath, maxwav, mle, weightopt);
+
+ fprintf(fichtm," Diagram of states %s_.svg
\n\
+![](\"%s_.svg\")
", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));
+
+
+ fprintf(fichtm,"\nSome descriptive statistics
\n
Total number of observations=%d
\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f
\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf
\n",\
- imx,agemin,agemax,jmin,jmax,jmean);
+ imx,agemin,agemax,jmin,jmax,jmean);
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 */
+ 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] */
@@ -11298,7 +11940,7 @@ Please run with mle=-1 to get a correct
printf("\n");
/*--------- results files --------------*/
- fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);
+ /* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */
fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
@@ -11586,6 +12228,9 @@ Please run with mle=-1 to get a correct
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/
+ dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
+ dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
+
}
break;
case 12:
@@ -11601,6 +12246,8 @@ Please run with mle=-1 to get a correct
fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/
+ dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
+ dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
}
break;
case 13:
@@ -11651,11 +12298,12 @@ Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else{
- printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)ageminpar);
+ /* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
+ printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);
}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
- jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
+ jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);
/*------------ free_vector -------------*/
/* chdir(path); */
@@ -11691,17 +12339,18 @@ Please run with mle=-1 to get a correct
k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
- /* Prevalence for each covariates in probs[age][status][cov] */
- probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
- for(i=1;i<=AGESUP;i++)
+ /* Prevalence for each covariate combination in probs[age][status][cov] */
+ probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ for(i=AGEINF;i<=AGESUP;i++)
for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
for(k=1;k<=ncovcombmax;k++)
probs[i][j][k]=0.;
- prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
+ prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
+ ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
if (mobilav!=0 ||mobilavproj !=0 ) {
- mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
- for(i=1;i<=AGESUP;i++)
- for(j=1;j<=nlstate;j++)
+ mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ for(i=AGEINF;i<=AGESUP;i++)
+ for(j=1;j<=nlstate+ndeath;j++)
for(k=1;k<=ncovcombmax;k++)
mobaverages[i][j][k]=0.;
mobaverage=mobaverages;
@@ -11712,31 +12361,27 @@ Please run with mle=-1 to get a correct
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);
}
- }
- /* else if(mobilavproj==-1){ /\* Forcing raw observed prevalences *\/ */
- /* for(i=1;i<=AGESUP;i++) */
- /* for(j=1;j<=nlstate;j++) */
- /* for(k=1;k<=ncovcombmax;k++) */
- /* mobaverages[i][j][k]=probs[i][j][k]; */
- /* /\* /\\* Prevalence for each covariates in probs[age][status][cov] *\\/ *\/ */
- /* /\* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); *\/ */
- /* } */
- else if (mobilavproj !=0) {
+ } else if (mobilavproj !=0) {
printf("Movingaveraging projected observed prevalence\n");
fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
}
+ }else{
+ printf("Internal error moving average\n");
+ fflush(stdout);
+ exit(1);
}
}/* end if moving average */
/*---------- Forecasting ------------------*/
- /*if((stepm == 1) && (strcmp(model,".")==0)){*/
if(prevfcast==1){
/* if(stepm ==1){*/
- prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
+ prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
}
+
+ /* Backcasting */
if(backcast==1){
ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
@@ -11745,20 +12390,24 @@ Please run with mle=-1 to get a correct
/*--------------- Back Prevalence limit (period or stable prevalence) --------------*/
bprlim=matrix(1,nlstate,1,nlstate);
+
back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
fclose(ficresplb);
hBijx(p, bage, fage, mobaverage);
fclose(ficrespijb);
- free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
- prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,
- bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
+ prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
+ mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
+ varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
+
+
+ free_matrix(bprlim,1,nlstate,1,nlstate); /*here or after loop ? */
free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
- }
-
+ } /* end Backcasting */
+
/* ------ Other prevalence ratios------------ */
@@ -11810,10 +12459,10 @@ Please run with mle=-1 to get a correct
fclose(ficreseij);
printf("done evsij\n");fflush(stdout);
fprintf(ficlog,"done evsij\n");fflush(ficlog);
+
/*---------- State-specific expectancies and variances ------------*/
-
strcpy(filerest,"T_");
strcat(filerest,fileresu);
if((ficrest=fopen(filerest,"w"))==NULL) {
@@ -11822,8 +12471,6 @@ Please run with mle=-1 to get a correct
}
printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
-
-
strcpy(fileresstde,"STDE_");
strcat(fileresstde,fileresu);
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
@@ -11851,9 +12498,6 @@ Please run with mle=-1 to get a correct
printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);
- /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-
i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}
@@ -11915,7 +12559,7 @@ Please run with mle=-1 to get a correct
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);
-
+ epj=vector(1,nlstate+1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms; /* ZZ Segmentation fault */
cptcod= 0; /* To be deleted */
@@ -11931,7 +12575,6 @@ Please run with mle=-1 to get a correct
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
- epj=vector(1,nlstate+1);
printf("Computing age specific period (stable) prevalences in each health state \n");
fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
for(age=bage; age <=fage ;age++){
@@ -11969,66 +12612,20 @@ Please run with mle=-1 to get a correct
fprintf(ficrest,"\n");
}
} /* End vpopbased */
+ free_vector(epj,1,nlstate+1);
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);
printf("done selection\n");fflush(stdout);
fprintf(ficlog,"done selection\n");fflush(ficlog);
- /*}*/
} /* End k selection */
printf("done State-specific expectancies\n");fflush(stdout);
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
- /*------- Variance of period (stable) prevalence------*/
-
- strcpy(fileresvpl,"VPL_");
- strcat(fileresvpl,fileresu);
- if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
- exit(0);
- }
- printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
- fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
-
- /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
-
- i1=pow(2,cptcoveff);
- if (cptcovn < 1){i1=1;}
+ /* variance-covariance of period prevalence*/
+ varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
- for(nres=1; nres <= nresult; nres++) /* For each resultline */
- for(k=1; k<=i1;k++){
- if(i1 != 1 && TKresult[nres]!= k)
- continue;
- fprintf(ficresvpl,"\n#****** ");
- printf("\n#****** ");
- fprintf(ficlog,"\n#****** ");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
- }
- for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
- printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
- fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
- fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
- }
- fprintf(ficresvpl,"******\n");
- printf("******\n");
- fprintf(ficlog,"******\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, &ncvyear, k, strstart, nres);
- free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
- /*}*/
- }
-
- fclose(ficresvpl);
- printf("done variance-covariance of period prevalence\n");fflush(stdout);
- fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
free_vector(weight,1,n);
free_imatrix(Tvard,1,NCOVMAX,1,2);
@@ -12046,8 +12643,8 @@ Please run with mle=-1 to get a correct
/*---------- End : free ----------------*/
if (mobilav!=0 ||mobilavproj !=0)
- free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
- free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
+ free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
+ free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
} /* mle==-3 arrives here for freeing */
@@ -12055,15 +12652,16 @@ Please run with mle=-1 to get a correct
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_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
- free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
- free_matrix(coqvar,1,maxwav,1,n);
+ if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
+ if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
+ if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);
free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);
free_matrix(hess,1,npar,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(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_ivector(ncodemax,1,NCOVMAX);
@@ -12140,6 +12738,8 @@ Please run with mle=-1 to get a correct
fclose(ficlog);
/*------ End -----------*/
+
+/* Executes gnuplot */
printf("Before Current directory %s!\n",pathcd);
#ifdef WIN32
@@ -12208,4 +12808,6 @@ end:
printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);
}
+ printf("End\n");
+ exit(0);
}
![%s-p%dj.png](\"%s-p%dj.png\"){kind=link}