/* $Id$
$State$
$Log$
+ Revision 1.278 2017/07/19 14:09:02 brouard
+ Summary: Bug for mobil_average=0 and prevforecast fixed(?)
+
Revision 1.277 2017/07/17 08:53:49 brouard
Summary: BOM files can be read now
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij, int nres)
{
- /* Computes the prevalence limit in each live state at age x and for covariate combination ij
- (and selected quantitative values in nres)
- by left multiplying the unit
- matrix by transitions matrix until convergence is reached with precision ftolpl */
- /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
- /* Wx is row vector: population in state 1, population in state 2, population dead */
- /* or prevalence in state 1, prevalence in state 2, 0 */
- /* newm is the matrix after multiplications, its rows are identical at a factor */
- /* Initial matrix pimij */
+ /**< Computes the prevalence limit in each live state at age x and for covariate combination ij
+ * (and selected quantitative values in nres)
+ * by left multiplying the unit
+ * matrix by transitions matrix until convergence is reached with precision ftolpl
+ * Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
+ * Wx is row vector: population in state 1, population in state 2, population dead
+ * or prevalence in state 1, prevalence in state 2, 0
+ * newm is the matrix after multiplications, its rows are identical at a factor.
+ * Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
+ * Output is prlim.
+ * Initial matrix pimij
+ */
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
/* 0, 0 , 1} */
/************ 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;
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; */
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\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 ");
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++)
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);
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 */
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);
}
}
- /* 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++)
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;
}
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);
}
}
git://henry.ined.fr / .git / commitdiff