-/* $Id$\r
- Interpolated Markov Chain\r
-\r
- Short summary of the programme:\r
- \r
- This program computes Healthy Life Expectancies from\r
- cross-longitudinal data. Cross-longitudinal data consist in: -1- a\r
- first survey ("cross") where individuals from different ages are\r
- interviewed on their health status or degree of disability (in the\r
- case of a health survey which is our main interest) -2- at least a\r
- second wave of interviews ("longitudinal") which measure each change\r
- (if any) in individual health status. Health expectancies are\r
- computed from the time spent in each health state according to a\r
- model. More health states you consider, more time is necessary to reach the\r
- Maximum Likelihood of the parameters involved in the model. The\r
- simplest model is the multinomial logistic model where pij is the\r
- probability to be observed in state j at the second wave\r
- conditional to be observed in state i at the first wave. Therefore\r
- the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where\r
- 'age' is age and 'sex' is a covariate. If you want to have a more\r
- complex model than "constant and age", you should modify the program\r
- where the markup *Covariates have to be included here again* invites\r
- you to do it. More covariates you add, slower the\r
- convergence.\r
-\r
- The advantage of this computer programme, compared to a simple\r
- multinomial logistic model, is clear when the delay between waves is not\r
- identical for each individual. Also, if a individual missed an\r
- intermediate interview, the information is lost, but taken into\r
- account using an interpolation or extrapolation. \r
-\r
- hPijx is the probability to be observed in state i at age x+h\r
- conditional to the observed state i at age x. The delay 'h' can be\r
- split into an exact number (nh*stepm) of unobserved intermediate\r
- states. This elementary transition (by month or quarter trimester,\r
- semester or year) is model as a multinomial logistic. The hPx\r
- matrix is simply the matrix product of nh*stepm elementary matrices\r
- and the contribution of each individual to the likelihood is simply\r
- hPijx.\r
-\r
- Also this programme outputs the covariance matrix of the parameters but also\r
- of the life expectancies. It also computes the prevalence limits. \r
- \r
- Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).\r
- Institut national d'études démographiques, Paris.\r
- This software have been partly granted by Euro-REVES, a concerted action\r
- from the European Union.\r
- It is copyrighted identically to a GNU software product, ie programme and\r
- software can be distributed freely for non commercial use. Latest version\r
- can be accessed at http://euroreves.ined.fr/imach .\r
- **********************************************************************/\r
- \r
-#include <math.h>\r
-#include <stdio.h>\r
-#include <stdlib.h>\r
-#include <unistd.h>\r
-\r
-#define MAXLINE 256\r
-#define GNUPLOTPROGRAM "gnuplot"\r
-/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/\r
-#define FILENAMELENGTH 80\r
-/*#define DEBUG*/\r
-#define windows\r
-#define GLOCK_ERROR_NOPATH -1 /* empty path */\r
-#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */\r
-\r
-#define MAXPARM 30 /* Maximum number of parameters for the optimization */\r
-#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */\r
-\r
-#define NINTERVMAX 8\r
-#define NLSTATEMAX 8 /* Maximum number of live states (for func) */\r
-#define NDEATHMAX 8 /* Maximum number of dead states (for func) */\r
-#define NCOVMAX 8 /* Maximum number of covariates */\r
-#define MAXN 20000\r
-#define YEARM 12. /* Number of months per year */\r
-#define AGESUP 130\r
-#define AGEBASE 40\r
-#ifdef windows\r
-#define DIRSEPARATOR '\\'\r
-#define ODIRSEPARATOR '/'\r
-#else\r
-#define DIRSEPARATOR '/'\r
-#define ODIRSEPARATOR '\\'\r
-#endif\r
-\r
-char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";\r
-int erreur; /* Error number */\r
-int nvar;\r
-int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;\r
-int npar=NPARMAX;\r
-int nlstate=2; /* Number of live states */\r
-int ndeath=1; /* Number of dead states */\r
-int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */\r
-int popbased=0;\r
-\r
-int *wav; /* Number of waves for this individuual 0 is possible */\r
-int maxwav; /* Maxim number of waves */\r
-int jmin, jmax; /* min, max spacing between 2 waves */\r
-int mle, weightopt;\r
-int **mw; /* mw[mi][i] is number of the mi wave for this individual */\r
-int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */\r
-double jmean; /* Mean space between 2 waves */\r
-double **oldm, **newm, **savm; /* Working pointers to matrices */\r
-double **oldms, **newms, **savms; /* Fixed working pointers to matrices */\r
-FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;\r
-FILE *ficlog;\r
-FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;\r
-FILE *ficresprobmorprev;\r
-FILE *fichtm; /* Html File */\r
-FILE *ficreseij;\r
-char filerese[FILENAMELENGTH];\r
-FILE *ficresvij;\r
-char fileresv[FILENAMELENGTH];\r
-FILE *ficresvpl;\r
-char fileresvpl[FILENAMELENGTH];\r
-char title[MAXLINE];\r
-char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];\r
-char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];\r
-\r
-char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];\r
-char filelog[FILENAMELENGTH]; /* Log file */\r
-char filerest[FILENAMELENGTH];\r
-char fileregp[FILENAMELENGTH];\r
-char popfile[FILENAMELENGTH];\r
-\r
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];\r
-\r
-#define NR_END 1\r
-#define FREE_ARG char*\r
-#define FTOL 1.0e-10\r
-\r
-#define NRANSI \r
-#define ITMAX 200 \r
-\r
-#define TOL 2.0e-4 \r
-\r
-#define CGOLD 0.3819660 \r
-#define ZEPS 1.0e-10 \r
-#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); \r
-\r
-#define GOLD 1.618034 \r
-#define GLIMIT 100.0 \r
-#define TINY 1.0e-20 \r
-\r
-static double maxarg1,maxarg2;\r
-#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))\r
-#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))\r
- \r
-#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))\r
-#define rint(a) floor(a+0.5)\r
-\r
-static double sqrarg;\r
-#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)\r
-#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} \r
-\r
-int imx; \r
-int stepm;\r
-/* Stepm, step in month: minimum step interpolation*/\r
-\r
-int estepm;\r
-/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/\r
-\r
-int m,nb;\r
-int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;\r
-double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;\r
-double **pmmij, ***probs, ***mobaverage;\r
-double dateintmean=0;\r
-\r
-double *weight;\r
-int **s; /* Status */\r
-double *agedc, **covar, idx;\r
-int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;\r
-\r
-double ftol=FTOL; /* Tolerance for computing Max Likelihood */\r
-double ftolhess; /* Tolerance for computing hessian */\r
-\r
-/**************** split *************************/\r
-static int split( char *path, char *dirc, char *name, char *ext, char *finame )\r
-{\r
- char *s; /* pointer */\r
- int l1, l2; /* length counters */\r
-\r
- l1 = strlen( path ); /* length of path */\r
- if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );\r
- s= strrchr( path, DIRSEPARATOR ); /* find last / */\r
- if ( s == NULL ) { /* no directory, so use current */\r
- /*if(strrchr(path, ODIRSEPARATOR )==NULL)\r
- printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/\r
-#if defined(__bsd__) /* get current working directory */\r
- extern char *getwd( );\r
-\r
- if ( getwd( dirc ) == NULL ) {\r
-#else\r
- extern char *getcwd( );\r
-\r
- if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {\r
-#endif\r
- return( GLOCK_ERROR_GETCWD );\r
- }\r
- strcpy( name, path ); /* we've got it */\r
- } else { /* strip direcotry from path */\r
- s++; /* after this, the filename */\r
- l2 = strlen( s ); /* length of filename */\r
- if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );\r
- strcpy( name, s ); /* save file name */\r
- strncpy( dirc, path, l1 - l2 ); /* now the directory */\r
- dirc[l1-l2] = 0; /* add zero */\r
- }\r
- l1 = strlen( dirc ); /* length of directory */\r
-#ifdef windows\r
- if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }\r
-#else\r
- if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }\r
-#endif\r
- s = strrchr( name, '.' ); /* find last / */\r
- s++;\r
- strcpy(ext,s); /* save extension */\r
- l1= strlen( name);\r
- l2= strlen( s)+1;\r
- strncpy( finame, name, l1-l2);\r
- finame[l1-l2]= 0;\r
- return( 0 ); /* we're done */\r
-}\r
-\r
-\r
-/******************************************/\r
-\r
-void replace(char *s, char*t)\r
-{\r
- int i;\r
- int lg=20;\r
- i=0;\r
- lg=strlen(t);\r
- for(i=0; i<= lg; i++) {\r
- (s[i] = t[i]);\r
- if (t[i]== '\\') s[i]='/';\r
- }\r
-}\r
-\r
-int nbocc(char *s, char occ)\r
-{\r
- int i,j=0;\r
- int lg=20;\r
- i=0;\r
- lg=strlen(s);\r
- for(i=0; i<= lg; i++) {\r
- if (s[i] == occ ) j++;\r
- }\r
- return j;\r
-}\r
-\r
-void cutv(char *u,char *v, char*t, char occ)\r
-{\r
- /* cuts string t into u and v where u is ended by char occ excluding it\r
- and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)\r
- gives u="abcedf" and v="ghi2j" */\r
- int i,lg,j,p=0;\r
- i=0;\r
- for(j=0; j<=strlen(t)-1; j++) {\r
- if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;\r
- }\r
-\r
- lg=strlen(t);\r
- for(j=0; j<p; j++) {\r
- (u[j] = t[j]);\r
- }\r
- u[p]='\0';\r
-\r
- for(j=0; j<= lg; j++) {\r
- if (j>=(p+1))(v[j-p-1] = t[j]);\r
- }\r
-}\r
-\r
-/********************** nrerror ********************/\r
-\r
-void nrerror(char error_text[])\r
-{\r
- fprintf(stderr,"ERREUR ...\n");\r
- fprintf(stderr,"%s\n",error_text);\r
- exit(1);\r
-}\r
-/*********************** vector *******************/\r
-double *vector(int nl, int nh)\r
-{\r
- double *v;\r
- v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));\r
- if (!v) nrerror("allocation failure in vector");\r
- return v-nl+NR_END;\r
-}\r
-\r
-/************************ free vector ******************/\r
-void free_vector(double*v, int nl, int nh)\r
-{\r
- free((FREE_ARG)(v+nl-NR_END));\r
-}\r
-\r
-/************************ivector *******************************/\r
-int *ivector(long nl,long nh)\r
-{\r
- int *v;\r
- v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));\r
- if (!v) nrerror("allocation failure in ivector");\r
- return v-nl+NR_END;\r
-}\r
-\r
-/******************free ivector **************************/\r
-void free_ivector(int *v, long nl, long nh)\r
-{\r
- free((FREE_ARG)(v+nl-NR_END));\r
-}\r
-\r
-/******************* imatrix *******************************/\r
-int **imatrix(long nrl, long nrh, long ncl, long nch) \r
- /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ \r
-{ \r
- long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; \r
- int **m; \r
- \r
- /* allocate pointers to rows */ \r
- m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); \r
- if (!m) nrerror("allocation failure 1 in matrix()"); \r
- m += NR_END; \r
- m -= nrl; \r
- \r
- \r
- /* allocate rows and set pointers to them */ \r
- m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); \r
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); \r
- m[nrl] += NR_END; \r
- m[nrl] -= ncl; \r
- \r
- for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; \r
- \r
- /* return pointer to array of pointers to rows */ \r
- return m; \r
-} \r
-\r
-/****************** free_imatrix *************************/\r
-void free_imatrix(m,nrl,nrh,ncl,nch)\r
- int **m;\r
- long nch,ncl,nrh,nrl; \r
- /* free an int matrix allocated by imatrix() */ \r
-{ \r
- free((FREE_ARG) (m[nrl]+ncl-NR_END)); \r
- free((FREE_ARG) (m+nrl-NR_END)); \r
-} \r
-\r
-/******************* matrix *******************************/\r
-double **matrix(long nrl, long nrh, long ncl, long nch)\r
-{\r
- long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;\r
- double **m;\r
-\r
- m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));\r
- if (!m) nrerror("allocation failure 1 in matrix()");\r
- m += NR_END;\r
- m -= nrl;\r
-\r
- m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));\r
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()");\r
- m[nrl] += NR_END;\r
- m[nrl] -= ncl;\r
-\r
- for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;\r
- return m;\r
-}\r
-\r
-/*************************free matrix ************************/\r
-void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)\r
-{\r
- free((FREE_ARG)(m[nrl]+ncl-NR_END));\r
- free((FREE_ARG)(m+nrl-NR_END));\r
-}\r
-\r
-/******************* ma3x *******************************/\r
-double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)\r
-{\r
- long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;\r
- double ***m;\r
-\r
- m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));\r
- if (!m) nrerror("allocation failure 1 in matrix()");\r
- m += NR_END;\r
- m -= nrl;\r
-\r
- m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));\r
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()");\r
- m[nrl] += NR_END;\r
- m[nrl] -= ncl;\r
-\r
- for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;\r
-\r
- m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));\r
- if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");\r
- m[nrl][ncl] += NR_END;\r
- m[nrl][ncl] -= nll;\r
- for (j=ncl+1; j<=nch; j++) \r
- m[nrl][j]=m[nrl][j-1]+nlay;\r
- \r
- for (i=nrl+1; i<=nrh; i++) {\r
- m[i][ncl]=m[i-1l][ncl]+ncol*nlay;\r
- for (j=ncl+1; j<=nch; j++) \r
- m[i][j]=m[i][j-1]+nlay;\r
- }\r
- return m;\r
-}\r
-\r
-/*************************free ma3x ************************/\r
-void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)\r
-{\r
- free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));\r
- free((FREE_ARG)(m[nrl]+ncl-NR_END));\r
- free((FREE_ARG)(m+nrl-NR_END));\r
-}\r
-\r
-/***************** f1dim *************************/\r
-extern int ncom; \r
-extern double *pcom,*xicom;\r
-extern double (*nrfunc)(double []); \r
- \r
-double f1dim(double x) \r
-{ \r
- int j; \r
- double f;\r
- double *xt; \r
- \r
- xt=vector(1,ncom); \r
- for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; \r
- f=(*nrfunc)(xt); \r
- free_vector(xt,1,ncom); \r
- return f; \r
-} \r
-\r
-/*****************brent *************************/\r
-double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) \r
-{ \r
- int iter; \r
- double a,b,d,etemp;\r
- double fu,fv,fw,fx;\r
- double ftemp;\r
- double p,q,r,tol1,tol2,u,v,w,x,xm; \r
- double e=0.0; \r
- \r
- a=(ax < cx ? ax : cx); \r
- b=(ax > cx ? ax : cx); \r
- x=w=v=bx; \r
- fw=fv=fx=(*f)(x); \r
- for (iter=1;iter<=ITMAX;iter++) { \r
- xm=0.5*(a+b); \r
- tol2=2.0*(tol1=tol*fabs(x)+ZEPS); \r
- /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/\r
- printf(".");fflush(stdout);\r
- fprintf(ficlog,".");fflush(ficlog);\r
-#ifdef DEBUG\r
- printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);\r
- fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);\r
- /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */\r
-#endif\r
- if (fabs(x-xm) <= (tol2-0.5*(b-a))){ \r
- *xmin=x; \r
- return fx; \r
- } \r
- ftemp=fu;\r
- if (fabs(e) > tol1) { \r
- r=(x-w)*(fx-fv); \r
- q=(x-v)*(fx-fw); \r
- p=(x-v)*q-(x-w)*r; \r
- q=2.0*(q-r); \r
- if (q > 0.0) p = -p; \r
- q=fabs(q); \r
- etemp=e; \r
- e=d; \r
- if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) \r
- d=CGOLD*(e=(x >= xm ? a-x : b-x)); \r
- else { \r
- d=p/q; \r
- u=x+d; \r
- if (u-a < tol2 || b-u < tol2) \r
- d=SIGN(tol1,xm-x); \r
- } \r
- } else { \r
- d=CGOLD*(e=(x >= xm ? a-x : b-x)); \r
- } \r
- u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); \r
- fu=(*f)(u); \r
- if (fu <= fx) { \r
- if (u >= x) a=x; else b=x; \r
- SHFT(v,w,x,u) \r
- SHFT(fv,fw,fx,fu) \r
- } else { \r
- if (u < x) a=u; else b=u; \r
- if (fu <= fw || w == x) { \r
- v=w; \r
- w=u; \r
- fv=fw; \r
- fw=fu; \r
- } else if (fu <= fv || v == x || v == w) { \r
- v=u; \r
- fv=fu; \r
- } \r
- } \r
- } \r
- nrerror("Too many iterations in brent"); \r
- *xmin=x; \r
- return fx; \r
-} \r
-\r
-/****************** mnbrak ***********************/\r
-\r
-void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, \r
- double (*func)(double)) \r
-{ \r
- double ulim,u,r,q, dum;\r
- double fu; \r
- \r
- *fa=(*func)(*ax); \r
- *fb=(*func)(*bx); \r
- if (*fb > *fa) { \r
- SHFT(dum,*ax,*bx,dum) \r
- SHFT(dum,*fb,*fa,dum) \r
- } \r
- *cx=(*bx)+GOLD*(*bx-*ax); \r
- *fc=(*func)(*cx); \r
- while (*fb > *fc) { \r
- r=(*bx-*ax)*(*fb-*fc); \r
- q=(*bx-*cx)*(*fb-*fa); \r
- u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ \r
- (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); \r
- ulim=(*bx)+GLIMIT*(*cx-*bx); \r
- if ((*bx-u)*(u-*cx) > 0.0) { \r
- fu=(*func)(u); \r
- } else if ((*cx-u)*(u-ulim) > 0.0) { \r
- fu=(*func)(u); \r
- if (fu < *fc) { \r
- SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) \r
- SHFT(*fb,*fc,fu,(*func)(u)) \r
- } \r
- } else if ((u-ulim)*(ulim-*cx) >= 0.0) { \r
- u=ulim; \r
- fu=(*func)(u); \r
- } else { \r
- u=(*cx)+GOLD*(*cx-*bx); \r
- fu=(*func)(u); \r
- } \r
- SHFT(*ax,*bx,*cx,u) \r
- SHFT(*fa,*fb,*fc,fu) \r
- } \r
-} \r
-\r
-/*************** linmin ************************/\r
-\r
-int ncom; \r
-double *pcom,*xicom;\r
-double (*nrfunc)(double []); \r
- \r
-void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) \r
-{ \r
- double brent(double ax, double bx, double cx, \r
- double (*f)(double), double tol, double *xmin); \r
- double f1dim(double x); \r
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, \r
- double *fc, double (*func)(double)); \r
- int j; \r
- double xx,xmin,bx,ax; \r
- double fx,fb,fa;\r
- \r
- ncom=n; \r
- pcom=vector(1,n); \r
- xicom=vector(1,n); \r
- nrfunc=func; \r
- for (j=1;j<=n;j++) { \r
- pcom[j]=p[j]; \r
- xicom[j]=xi[j]; \r
- } \r
- ax=0.0; \r
- xx=1.0; \r
- mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); \r
- *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); \r
-#ifdef DEBUG\r
- printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);\r
- fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);\r
-#endif\r
- for (j=1;j<=n;j++) { \r
- xi[j] *= xmin; \r
- p[j] += xi[j]; \r
- } \r
- free_vector(xicom,1,n); \r
- free_vector(pcom,1,n); \r
-} \r
-\r
-/*************** powell ************************/\r
-void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, \r
- double (*func)(double [])) \r
-{ \r
- void linmin(double p[], double xi[], int n, double *fret, \r
- double (*func)(double [])); \r
- int i,ibig,j; \r
- double del,t,*pt,*ptt,*xit;\r
- double fp,fptt;\r
- double *xits;\r
- pt=vector(1,n); \r
- ptt=vector(1,n); \r
- xit=vector(1,n); \r
- xits=vector(1,n); \r
- *fret=(*func)(p); \r
- for (j=1;j<=n;j++) pt[j]=p[j]; \r
- for (*iter=1;;++(*iter)) { \r
- fp=(*fret); \r
- ibig=0; \r
- del=0.0; \r
- printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);\r
- fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);\r
- for (i=1;i<=n;i++) \r
- printf(" %d %.12f",i, p[i]);\r
- fprintf(ficlog," %d %.12f",i, p[i]);\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- for (i=1;i<=n;i++) { \r
- for (j=1;j<=n;j++) xit[j]=xi[j][i]; \r
- fptt=(*fret); \r
-#ifdef DEBUG\r
- printf("fret=%lf \n",*fret);\r
- fprintf(ficlog,"fret=%lf \n",*fret);\r
-#endif\r
- printf("%d",i);fflush(stdout);\r
- fprintf(ficlog,"%d",i);fflush(ficlog);\r
- linmin(p,xit,n,fret,func); \r
- if (fabs(fptt-(*fret)) > del) { \r
- del=fabs(fptt-(*fret)); \r
- ibig=i; \r
- } \r
-#ifdef DEBUG\r
- printf("%d %.12e",i,(*fret));\r
- fprintf(ficlog,"%d %.12e",i,(*fret));\r
- for (j=1;j<=n;j++) {\r
- xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);\r
- printf(" x(%d)=%.12e",j,xit[j]);\r
- fprintf(ficlog," x(%d)=%.12e",j,xit[j]);\r
- }\r
- for(j=1;j<=n;j++) {\r
- printf(" p=%.12e",p[j]);\r
- fprintf(ficlog," p=%.12e",p[j]);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
-#endif\r
- } \r
- if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {\r
-#ifdef DEBUG\r
- int k[2],l;\r
- k[0]=1;\r
- k[1]=-1;\r
- printf("Max: %.12e",(*func)(p));\r
- fprintf(ficlog,"Max: %.12e",(*func)(p));\r
- for (j=1;j<=n;j++) {\r
- printf(" %.12e",p[j]);\r
- fprintf(ficlog," %.12e",p[j]);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- for(l=0;l<=1;l++) {\r
- for (j=1;j<=n;j++) {\r
- ptt[j]=p[j]+(p[j]-pt[j])*k[l];\r
- printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);\r
- fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);\r
- }\r
- printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));\r
- fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));\r
- }\r
-#endif\r
-\r
-\r
- free_vector(xit,1,n); \r
- free_vector(xits,1,n); \r
- free_vector(ptt,1,n); \r
- free_vector(pt,1,n); \r
- return; \r
- } \r
- if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); \r
- for (j=1;j<=n;j++) { \r
- ptt[j]=2.0*p[j]-pt[j]; \r
- xit[j]=p[j]-pt[j]; \r
- pt[j]=p[j]; \r
- } \r
- fptt=(*func)(ptt); \r
- if (fptt < fp) { \r
- t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); \r
- if (t < 0.0) { \r
- linmin(p,xit,n,fret,func); \r
- for (j=1;j<=n;j++) { \r
- xi[j][ibig]=xi[j][n]; \r
- xi[j][n]=xit[j]; \r
- }\r
-#ifdef DEBUG\r
- printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);\r
- fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);\r
- for(j=1;j<=n;j++){\r
- printf(" %.12e",xit[j]);\r
- fprintf(ficlog," %.12e",xit[j]);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
-#endif\r
- } \r
- } \r
- } \r
-} \r
-\r
-/**** Prevalence limit ****************/\r
-\r
-double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)\r
-{\r
- /* Computes the prevalence limit in each live state at age x by left multiplying the unit\r
- matrix by transitions matrix until convergence is reached */\r
-\r
- int i, ii,j,k;\r
- double min, max, maxmin, maxmax,sumnew=0.;\r
- double **matprod2();\r
- double **out, cov[NCOVMAX], **pmij();\r
- double **newm;\r
- double agefin, delaymax=50 ; /* Max number of years to converge */\r
-\r
- for (ii=1;ii<=nlstate+ndeath;ii++)\r
- for (j=1;j<=nlstate+ndeath;j++){\r
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
- }\r
-\r
- cov[1]=1.;\r
- \r
- /* Even if hstepm = 1, at least one multiplication by the unit matrix */\r
- for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){\r
- newm=savm;\r
- /* Covariates have to be included here again */\r
- cov[2]=agefin;\r
- \r
- for (k=1; k<=cptcovn;k++) {\r
- cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];\r
- /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/\r
- }\r
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
- for (k=1; k<=cptcovprod;k++)\r
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
-\r
- /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/\r
- /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/\r
- /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/\r
- out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);\r
-\r
- savm=oldm;\r
- oldm=newm;\r
- maxmax=0.;\r
- for(j=1;j<=nlstate;j++){\r
- min=1.;\r
- max=0.;\r
- for(i=1; i<=nlstate; i++) {\r
- sumnew=0;\r
- for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];\r
- prlim[i][j]= newm[i][j]/(1-sumnew);\r
- max=FMAX(max,prlim[i][j]);\r
- min=FMIN(min,prlim[i][j]);\r
- }\r
- maxmin=max-min;\r
- maxmax=FMAX(maxmax,maxmin);\r
- }\r
- if(maxmax < ftolpl){\r
- return prlim;\r
- }\r
- }\r
-}\r
-\r
-/*************** transition probabilities ***************/ \r
-\r
-double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )\r
-{\r
- double s1, s2;\r
- /*double t34;*/\r
- int i,j,j1, nc, ii, jj;\r
-\r
- for(i=1; i<= nlstate; i++){\r
- for(j=1; j<i;j++){\r
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){\r
- /*s2 += param[i][j][nc]*cov[nc];*/\r
- s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];\r
- /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/\r
- }\r
- ps[i][j]=s2;\r
- /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/\r
- }\r
- for(j=i+1; j<=nlstate+ndeath;j++){\r
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){\r
- s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];\r
- /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/\r
- }\r
- ps[i][j]=s2;\r
- }\r
- }\r
- /*ps[3][2]=1;*/\r
-\r
- for(i=1; i<= nlstate; i++){\r
- s1=0;\r
- for(j=1; j<i; j++)\r
- s1+=exp(ps[i][j]);\r
- for(j=i+1; j<=nlstate+ndeath; j++)\r
- s1+=exp(ps[i][j]);\r
- ps[i][i]=1./(s1+1.);\r
- for(j=1; j<i; j++)\r
- ps[i][j]= exp(ps[i][j])*ps[i][i];\r
- for(j=i+1; j<=nlstate+ndeath; j++)\r
- ps[i][j]= exp(ps[i][j])*ps[i][i];\r
- /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */\r
- } /* end i */\r
-\r
- for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){\r
- for(jj=1; jj<= nlstate+ndeath; jj++){\r
- ps[ii][jj]=0;\r
- ps[ii][ii]=1;\r
- }\r
- }\r
-\r
-\r
- /* for(ii=1; ii<= nlstate+ndeath; ii++){\r
- for(jj=1; jj<= nlstate+ndeath; jj++){\r
- printf("%lf ",ps[ii][jj]);\r
- }\r
- printf("\n ");\r
- }\r
- printf("\n ");printf("%lf ",cov[2]);*/\r
-/*\r
- for(i=1; i<= npar; i++) printf("%f ",x[i]);\r
- goto end;*/\r
- return ps;\r
-}\r
-\r
-/**************** Product of 2 matrices ******************/\r
-\r
-double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)\r
-{\r
- /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times\r
- b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */\r
- /* in, b, out are matrice of pointers which should have been initialized \r
- before: only the contents of out is modified. The function returns\r
- a pointer to pointers identical to out */\r
- long i, j, k;\r
- for(i=nrl; i<= nrh; i++)\r
- for(k=ncolol; k<=ncoloh; k++)\r
- for(j=ncl,out[i][k]=0.; j<=nch; j++)\r
- out[i][k] +=in[i][j]*b[j][k];\r
-\r
- return out;\r
-}\r
-\r
-\r
-/************* Higher Matrix Product ***************/\r
-\r
-double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )\r
-{\r
- /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month \r
- duration (i.e. until\r
- age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. \r
- Output is stored in matrix po[i][j][h] for h every 'hstepm' step \r
- (typically every 2 years instead of every month which is too big).\r
- Model is determined by parameters x and covariates have to be \r
- included manually here. \r
-\r
- */\r
-\r
- int i, j, d, h, k;\r
- double **out, cov[NCOVMAX];\r
- double **newm;\r
-\r
- /* Hstepm could be zero and should return the unit matrix */\r
- for (i=1;i<=nlstate+ndeath;i++)\r
- for (j=1;j<=nlstate+ndeath;j++){\r
- oldm[i][j]=(i==j ? 1.0 : 0.0);\r
- po[i][j][0]=(i==j ? 1.0 : 0.0);\r
- }\r
- /* Even if hstepm = 1, at least one multiplication by the unit matrix */\r
- for(h=1; h <=nhstepm; h++){\r
- for(d=1; d <=hstepm; d++){\r
- newm=savm;\r
- /* Covariates have to be included here again */\r
- cov[1]=1.;\r
- cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;\r
- for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];\r
- for (k=1; k<=cptcovage;k++)\r
- cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
- for (k=1; k<=cptcovprod;k++)\r
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
-\r
-\r
- /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/\r
- /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/\r
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, \r
- pmij(pmmij,cov,ncovmodel,x,nlstate));\r
- savm=oldm;\r
- oldm=newm;\r
- }\r
- for(i=1; i<=nlstate+ndeath; i++)\r
- for(j=1;j<=nlstate+ndeath;j++) {\r
- po[i][j][h]=newm[i][j];\r
- /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);\r
- */\r
- }\r
- } /* end h */\r
- return po;\r
-}\r
-\r
-\r
-/*************** log-likelihood *************/\r
-double func( double *x)\r
-{\r
- int i, ii, j, k, mi, d, kk;\r
- double l, ll[NLSTATEMAX], cov[NCOVMAX];\r
- double **out;\r
- double sw; /* Sum of weights */\r
- double lli; /* Individual log likelihood */\r
- long ipmx;\r
- /*extern weight */\r
- /* We are differentiating ll according to initial status */\r
- /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/\r
- /*for(i=1;i<imx;i++) \r
- printf(" %d\n",s[4][i]);\r
- */\r
- cov[1]=1.;\r
-\r
- for(k=1; k<=nlstate; k++) ll[k]=0.;\r
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
- for(mi=1; mi<= wav[i]-1; mi++){\r
- for (ii=1;ii<=nlstate+ndeath;ii++)\r
- for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
- for(d=0; d<dh[mi][i]; d++){\r
- newm=savm;\r
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
- for (kk=1; kk<=cptcovage;kk++) {\r
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
- }\r
- \r
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
- savm=oldm;\r
- oldm=newm;\r
- \r
- \r
- } /* end mult */\r
- \r
- lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);\r
- /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/\r
- ipmx +=1;\r
- sw += weight[i];\r
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
- } /* end of wave */\r
- } /* end of individual */\r
-\r
- for(k=1,l=0.; k<=nlstate; k++) l += ll[k];\r
- /* printf("l1=%f l2=%f ",ll[1],ll[2]); */\r
- l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */\r
- return -l;\r
-}\r
-\r
-\r
-/*********** Maximum Likelihood Estimation ***************/\r
-\r
-void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))\r
-{\r
- int i,j, iter;\r
- double **xi,*delti;\r
- double fret;\r
- xi=matrix(1,npar,1,npar);\r
- for (i=1;i<=npar;i++)\r
- for (j=1;j<=npar;j++)\r
- xi[i][j]=(i==j ? 1.0 : 0.0);\r
- printf("Powell\n"); fprintf(ficlog,"Powell\n");\r
- powell(p,xi,npar,ftol,&iter,&fret,func);\r
-\r
- printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));\r
- fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));\r
- fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));\r
-\r
-}\r
-\r
-/**** Computes Hessian and covariance matrix ***/\r
-void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))\r
-{\r
- double **a,**y,*x,pd;\r
- double **hess;\r
- int i, j,jk;\r
- int *indx;\r
-\r
- double hessii(double p[], double delta, int theta, double delti[]);\r
- double hessij(double p[], double delti[], int i, int j);\r
- void lubksb(double **a, int npar, int *indx, double b[]) ;\r
- void ludcmp(double **a, int npar, int *indx, double *d) ;\r
-\r
- hess=matrix(1,npar,1,npar);\r
-\r
- printf("\nCalculation of the hessian matrix. Wait...\n");\r
- fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");\r
- for (i=1;i<=npar;i++){\r
- printf("%d",i);fflush(stdout);\r
- fprintf(ficlog,"%d",i);fflush(ficlog);\r
- hess[i][i]=hessii(p,ftolhess,i,delti);\r
- /*printf(" %f ",p[i]);*/\r
- /*printf(" %lf ",hess[i][i]);*/\r
- }\r
- \r
- for (i=1;i<=npar;i++) {\r
- for (j=1;j<=npar;j++) {\r
- if (j>i) { \r
- printf(".%d%d",i,j);fflush(stdout);\r
- fprintf(ficlog,".%d%d",i,j);fflush(ficlog);\r
- hess[i][j]=hessij(p,delti,i,j);\r
- hess[j][i]=hess[i][j]; \r
- /*printf(" %lf ",hess[i][j]);*/\r
- }\r
- }\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
-\r
- printf("\nInverting the hessian to get the covariance matrix. Wait...\n");\r
- fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");\r
- \r
- a=matrix(1,npar,1,npar);\r
- y=matrix(1,npar,1,npar);\r
- x=vector(1,npar);\r
- indx=ivector(1,npar);\r
- for (i=1;i<=npar;i++)\r
- for (j=1;j<=npar;j++) a[i][j]=hess[i][j];\r
- ludcmp(a,npar,indx,&pd);\r
-\r
- for (j=1;j<=npar;j++) {\r
- for (i=1;i<=npar;i++) x[i]=0;\r
- x[j]=1;\r
- lubksb(a,npar,indx,x);\r
- for (i=1;i<=npar;i++){ \r
- matcov[i][j]=x[i];\r
- }\r
- }\r
-\r
- printf("\n#Hessian matrix#\n");\r
- fprintf(ficlog,"\n#Hessian matrix#\n");\r
- for (i=1;i<=npar;i++) { \r
- for (j=1;j<=npar;j++) { \r
- printf("%.3e ",hess[i][j]);\r
- fprintf(ficlog,"%.3e ",hess[i][j]);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- }\r
-\r
- /* Recompute Inverse */\r
- for (i=1;i<=npar;i++)\r
- for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];\r
- ludcmp(a,npar,indx,&pd);\r
-\r
- /* printf("\n#Hessian matrix recomputed#\n");\r
-\r
- for (j=1;j<=npar;j++) {\r
- for (i=1;i<=npar;i++) x[i]=0;\r
- x[j]=1;\r
- lubksb(a,npar,indx,x);\r
- for (i=1;i<=npar;i++){ \r
- y[i][j]=x[i];\r
- printf("%.3e ",y[i][j]);\r
- fprintf(ficlog,"%.3e ",y[i][j]);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- }\r
- */\r
-\r
- free_matrix(a,1,npar,1,npar);\r
- free_matrix(y,1,npar,1,npar);\r
- free_vector(x,1,npar);\r
- free_ivector(indx,1,npar);\r
- free_matrix(hess,1,npar,1,npar);\r
-\r
-\r
-}\r
-\r
-/*************** hessian matrix ****************/\r
-double hessii( double x[], double delta, int theta, double delti[])\r
-{\r
- int i;\r
- int l=1, lmax=20;\r
- double k1,k2;\r
- double p2[NPARMAX+1];\r
- double res;\r
- double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;\r
- double fx;\r
- int k=0,kmax=10;\r
- double l1;\r
-\r
- fx=func(x);\r
- for (i=1;i<=npar;i++) p2[i]=x[i];\r
- for(l=0 ; l <=lmax; l++){\r
- l1=pow(10,l);\r
- delts=delt;\r
- for(k=1 ; k <kmax; k=k+1){\r
- delt = delta*(l1*k);\r
- p2[theta]=x[theta] +delt;\r
- k1=func(p2)-fx;\r
- p2[theta]=x[theta]-delt;\r
- k2=func(p2)-fx;\r
- /*res= (k1-2.0*fx+k2)/delt/delt; */\r
- res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */\r
- \r
-#ifdef DEBUG\r
- printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);\r
- fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);\r
-#endif\r
- /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */\r
- if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){\r
- k=kmax;\r
- }\r
- else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */\r
- k=kmax; l=lmax*10.;\r
- }\r
- else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ \r
- delts=delt;\r
- }\r
- }\r
- }\r
- delti[theta]=delts;\r
- return res; \r
- \r
-}\r
-\r
-double hessij( double x[], double delti[], int thetai,int thetaj)\r
-{\r
- int i;\r
- int l=1, l1, lmax=20;\r
- double k1,k2,k3,k4,res,fx;\r
- double p2[NPARMAX+1];\r
- int k;\r
-\r
- fx=func(x);\r
- for (k=1; k<=2; k++) {\r
- for (i=1;i<=npar;i++) p2[i]=x[i];\r
- p2[thetai]=x[thetai]+delti[thetai]/k;\r
- p2[thetaj]=x[thetaj]+delti[thetaj]/k;\r
- k1=func(p2)-fx;\r
- \r
- p2[thetai]=x[thetai]+delti[thetai]/k;\r
- p2[thetaj]=x[thetaj]-delti[thetaj]/k;\r
- k2=func(p2)-fx;\r
- \r
- p2[thetai]=x[thetai]-delti[thetai]/k;\r
- p2[thetaj]=x[thetaj]+delti[thetaj]/k;\r
- k3=func(p2)-fx;\r
- \r
- p2[thetai]=x[thetai]-delti[thetai]/k;\r
- p2[thetaj]=x[thetaj]-delti[thetaj]/k;\r
- k4=func(p2)-fx;\r
- res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */\r
-#ifdef DEBUG\r
- printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);\r
- fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);\r
-#endif\r
- }\r
- return res;\r
-}\r
-\r
-/************** Inverse of matrix **************/\r
-void ludcmp(double **a, int n, int *indx, double *d) \r
-{ \r
- int i,imax,j,k; \r
- double big,dum,sum,temp; \r
- double *vv; \r
- \r
- vv=vector(1,n); \r
- *d=1.0; \r
- for (i=1;i<=n;i++) { \r
- big=0.0; \r
- for (j=1;j<=n;j++) \r
- if ((temp=fabs(a[i][j])) > big) big=temp; \r
- if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); \r
- vv[i]=1.0/big; \r
- } \r
- for (j=1;j<=n;j++) { \r
- for (i=1;i<j;i++) { \r
- sum=a[i][j]; \r
- for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; \r
- a[i][j]=sum; \r
- } \r
- big=0.0; \r
- for (i=j;i<=n;i++) { \r
- sum=a[i][j]; \r
- for (k=1;k<j;k++) \r
- sum -= a[i][k]*a[k][j]; \r
- a[i][j]=sum; \r
- if ( (dum=vv[i]*fabs(sum)) >= big) { \r
- big=dum; \r
- imax=i; \r
- } \r
- } \r
- if (j != imax) { \r
- for (k=1;k<=n;k++) { \r
- dum=a[imax][k]; \r
- a[imax][k]=a[j][k]; \r
- a[j][k]=dum; \r
- } \r
- *d = -(*d); \r
- vv[imax]=vv[j]; \r
- } \r
- indx[j]=imax; \r
- if (a[j][j] == 0.0) a[j][j]=TINY; \r
- if (j != n) { \r
- dum=1.0/(a[j][j]); \r
- for (i=j+1;i<=n;i++) a[i][j] *= dum; \r
- } \r
- } \r
- free_vector(vv,1,n); /* Doesn't work */\r
-;\r
-} \r
-\r
-void lubksb(double **a, int n, int *indx, double b[]) \r
-{ \r
- int i,ii=0,ip,j; \r
- double sum; \r
- \r
- for (i=1;i<=n;i++) { \r
- ip=indx[i]; \r
- sum=b[ip]; \r
- b[ip]=b[i]; \r
- if (ii) \r
- for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; \r
- else if (sum) ii=i; \r
- b[i]=sum; \r
- } \r
- for (i=n;i>=1;i--) { \r
- sum=b[i]; \r
- for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; \r
- b[i]=sum/a[i][i]; \r
- } \r
-} \r
-\r
-/************ Frequencies ********************/\r
-void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)\r
-{ /* Some frequencies */\r
- \r
- int i, m, jk, k1,i1, j1, bool, z1,z2,j;\r
- int first;\r
- double ***freq; /* Frequencies */\r
- double *pp;\r
- double pos, k2, dateintsum=0,k2cpt=0;\r
- FILE *ficresp;\r
- char fileresp[FILENAMELENGTH];\r
- \r
- pp=vector(1,nlstate);\r
- probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- strcpy(fileresp,"p");\r
- strcat(fileresp,fileres);\r
- if((ficresp=fopen(fileresp,"w"))==NULL) {\r
- printf("Problem with prevalence resultfile: %s\n", fileresp);\r
- fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);\r
- exit(0);\r
- }\r
- freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);\r
- j1=0;\r
- \r
- j=cptcoveff;\r
- if (cptcovn<1) {j=1;ncodemax[1]=1;}\r
-\r
- first=1;\r
-\r
- for(k1=1; k1<=j;k1++){\r
- for(i1=1; i1<=ncodemax[k1];i1++){\r
- j1++;\r
- /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);\r
- scanf("%d", i);*/\r
- for (i=-1; i<=nlstate+ndeath; i++) \r
- for (jk=-1; jk<=nlstate+ndeath; jk++) \r
- for(m=agemin; m <= agemax+3; m++)\r
- freq[i][jk][m]=0;\r
- \r
- dateintsum=0;\r
- k2cpt=0;\r
- for (i=1; i<=imx; i++) {\r
- bool=1;\r
- if (cptcovn>0) {\r
- for (z1=1; z1<=cptcoveff; z1++) \r
- if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) \r
- bool=0;\r
- }\r
- if (bool==1) {\r
- for(m=firstpass; m<=lastpass; m++){\r
- k2=anint[m][i]+(mint[m][i]/12.);\r
- if ((k2>=dateprev1) && (k2<=dateprev2)) {\r
- if(agev[m][i]==0) agev[m][i]=agemax+1;\r
- if(agev[m][i]==1) agev[m][i]=agemax+2;\r
- if (m<lastpass) {\r
- freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];\r
- freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];\r
- }\r
- \r
- if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {\r
- dateintsum=dateintsum+k2;\r
- k2cpt++;\r
- }\r
- }\r
- }\r
- }\r
- }\r
- \r
- fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);\r
-\r
- if (cptcovn>0) {\r
- fprintf(ficresp, "\n#********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(ficresp, "**********\n#");\r
- }\r
- for(i=1; i<=nlstate;i++) \r
- fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);\r
- fprintf(ficresp, "\n");\r
- \r
- for(i=(int)agemin; i <= (int)agemax+3; i++){\r
- if(i==(int)agemax+3){\r
- fprintf(ficlog,"Total");\r
- }else{\r
- if(first==1){\r
- first=0;\r
- printf("See log file for details...\n");\r
- }\r
- fprintf(ficlog,"Age %d", i);\r
- }\r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)\r
- pp[jk] += freq[jk][m][i]; \r
- }\r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=-1, pos=0; m <=0 ; m++)\r
- pos += freq[jk][m][i];\r
- if(pp[jk]>=1.e-10){\r
- if(first==1){\r
- printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);\r
- }\r
- fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);\r
- }else{\r
- if(first==1)\r
- printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);\r
- fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);\r
- }\r
- }\r
-\r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)\r
- pp[jk] += freq[jk][m][i];\r
- }\r
-\r
- for(jk=1,pos=0; jk <=nlstate ; jk++)\r
- pos += pp[jk];\r
- for(jk=1; jk <=nlstate ; jk++){\r
- if(pos>=1.e-5){\r
- if(first==1)\r
- printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);\r
- fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);\r
- }else{\r
- if(first==1)\r
- printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);\r
- fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);\r
- }\r
- if( i <= (int) agemax){\r
- if(pos>=1.e-5){\r
- fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);\r
- probs[i][jk][j1]= pp[jk]/pos;\r
- /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/\r
- }\r
- else\r
- fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);\r
- }\r
- }\r
- \r
- for(jk=-1; jk <=nlstate+ndeath; jk++)\r
- for(m=-1; m <=nlstate+ndeath; m++)\r
- if(freq[jk][m][i] !=0 ) {\r
- if(first==1)\r
- printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);\r
- fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);\r
- }\r
- if(i <= (int) agemax)\r
- fprintf(ficresp,"\n");\r
- if(first==1)\r
- printf("Others in log...\n");\r
- fprintf(ficlog,"\n");\r
- }\r
- }\r
- }\r
- dateintmean=dateintsum/k2cpt; \r
- \r
- fclose(ficresp);\r
- free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);\r
- free_vector(pp,1,nlstate);\r
- \r
- /* End of Freq */\r
-}\r
-\r
-/************ Prevalence ********************/\r
-void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)\r
-{ /* Some frequencies */\r
- \r
- int i, m, jk, k1, i1, j1, bool, z1,z2,j;\r
- double ***freq; /* Frequencies */\r
- double *pp;\r
- double pos, k2;\r
-\r
- pp=vector(1,nlstate);\r
- probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- \r
- freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);\r
- j1=0;\r
- \r
- j=cptcoveff;\r
- if (cptcovn<1) {j=1;ncodemax[1]=1;}\r
- \r
- for(k1=1; k1<=j;k1++){\r
- for(i1=1; i1<=ncodemax[k1];i1++){\r
- j1++;\r
- \r
- for (i=-1; i<=nlstate+ndeath; i++) \r
- for (jk=-1; jk<=nlstate+ndeath; jk++) \r
- for(m=agemin; m <= agemax+3; m++)\r
- freq[i][jk][m]=0;\r
- \r
- for (i=1; i<=imx; i++) {\r
- bool=1;\r
- if (cptcovn>0) {\r
- for (z1=1; z1<=cptcoveff; z1++) \r
- if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) \r
- bool=0;\r
- } \r
- if (bool==1) { \r
- for(m=firstpass; m<=lastpass; m++){\r
- k2=anint[m][i]+(mint[m][i]/12.);\r
- if ((k2>=dateprev1) && (k2<=dateprev2)) {\r
- if(agev[m][i]==0) agev[m][i]=agemax+1;\r
- if(agev[m][i]==1) agev[m][i]=agemax+2;\r
- if (m<lastpass) {\r
- if (calagedate>0) \r
- freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];\r
- else\r
- freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];\r
- freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; \r
- }\r
- }\r
- }\r
- }\r
- }\r
- for(i=(int)agemin; i <= (int)agemax+3; i++){ \r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)\r
- pp[jk] += freq[jk][m][i]; \r
- }\r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=-1, pos=0; m <=0 ; m++)\r
- pos += freq[jk][m][i];\r
- }\r
- \r
- for(jk=1; jk <=nlstate ; jk++){\r
- for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)\r
- pp[jk] += freq[jk][m][i];\r
- }\r
- \r
- for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];\r
- \r
- for(jk=1; jk <=nlstate ; jk++){ \r
- if( i <= (int) agemax){\r
- if(pos>=1.e-5){\r
- probs[i][jk][j1]= pp[jk]/pos;\r
- }\r
- }\r
- }/* end jk */\r
- }/* end i */\r
- } /* end i1 */\r
- } /* end k1 */\r
-\r
- \r
- free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);\r
- free_vector(pp,1,nlstate);\r
- \r
-} /* End of Freq */\r
-\r
-/************* Waves Concatenation ***************/\r
-\r
-void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)\r
-{\r
- /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.\r
- Death is a valid wave (if date is known).\r
- mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i\r
- dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]\r
- and mw[mi+1][i]. dh depends on stepm.\r
- */\r
-\r
- int i, mi, m;\r
- /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;\r
- double sum=0., jmean=0.;*/\r
- int first;\r
- int j, k=0,jk, ju, jl;\r
- double sum=0.;\r
- first=0;\r
- jmin=1e+5;\r
- jmax=-1;\r
- jmean=0.;\r
- for(i=1; i<=imx; i++){\r
- mi=0;\r
- m=firstpass;\r
- while(s[m][i] <= nlstate){\r
- if(s[m][i]>=1)\r
- mw[++mi][i]=m;\r
- if(m >=lastpass)\r
- break;\r
- else\r
- m++;\r
- }/* end while */\r
- if (s[m][i] > nlstate){\r
- mi++; /* Death is another wave */\r
- /* if(mi==0) never been interviewed correctly before death */\r
- /* Only death is a correct wave */\r
- mw[mi][i]=m;\r
- }\r
-\r
- wav[i]=mi;\r
- if(mi==0){\r
- if(first==0){\r
- printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);\r
- first=1;\r
- }\r
- if(first==1){\r
- fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);\r
- }\r
- } /* end mi==0 */\r
- }\r
-\r
- for(i=1; i<=imx; i++){\r
- for(mi=1; mi<wav[i];mi++){\r
- if (stepm <=0)\r
- dh[mi][i]=1;\r
- else{\r
- if (s[mw[mi+1][i]][i] > nlstate) {\r
- if (agedc[i] < 2*AGESUP) {\r
- j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); \r
- if(j==0) j=1; /* Survives at least one month after exam */\r
- k=k+1;\r
- if (j >= jmax) jmax=j;\r
- if (j <= jmin) jmin=j;\r
- sum=sum+j;\r
- /*if (j<0) printf("j=%d num=%d \n",j,i); */\r
- }\r
- }\r
- else{\r
- j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));\r
- k=k+1;\r
- if (j >= jmax) jmax=j;\r
- else if (j <= jmin)jmin=j;\r
- /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */\r
- sum=sum+j;\r
- }\r
- jk= j/stepm;\r
- jl= j -jk*stepm;\r
- ju= j -(jk+1)*stepm;\r
- if(jl <= -ju)\r
- dh[mi][i]=jk;\r
- else\r
- dh[mi][i]=jk+1;\r
- if(dh[mi][i]==0)\r
- dh[mi][i]=1; /* At least one step */\r
- }\r
- }\r
- }\r
- jmean=sum/k;\r
- printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);\r
- fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);\r
- }\r
-\r
-/*********** Tricode ****************************/\r
-void tricode(int *Tvar, int **nbcode, int imx)\r
-{\r
- int Ndum[20],ij=1, k, j, i;\r
- int cptcode=0;\r
- cptcoveff=0; \r
- \r
- for (k=0; k<19; k++) Ndum[k]=0;\r
- for (k=1; k<=7; k++) ncodemax[k]=0;\r
-\r
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) {\r
- for (i=1; i<=imx; i++) {\r
- ij=(int)(covar[Tvar[j]][i]);\r
- Ndum[ij]++; \r
- /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/\r
- if (ij > cptcode) cptcode=ij; \r
- }\r
-\r
- for (i=0; i<=cptcode; i++) {\r
- if(Ndum[i]!=0) ncodemax[j]++;\r
- }\r
- ij=1; \r
-\r
-\r
- for (i=1; i<=ncodemax[j]; i++) {\r
- for (k=0; k<=19; k++) {\r
- if (Ndum[k] != 0) {\r
- nbcode[Tvar[j]][ij]=k; \r
- \r
- ij++;\r
- }\r
- if (ij > ncodemax[j]) break; \r
- } \r
- } \r
- } \r
-\r
- for (k=0; k<19; k++) Ndum[k]=0;\r
-\r
- for (i=1; i<=ncovmodel-2; i++) {\r
- ij=Tvar[i];\r
- Ndum[ij]++; \r
- }\r
-\r
- ij=1;\r
- for (i=1; i<=10; i++) {\r
- if((Ndum[i]!=0) && (i<=ncovcol)){\r
- Tvaraff[ij]=i; \r
- ij++;\r
- }\r
- }\r
- \r
- cptcoveff=ij-1;\r
-}\r
-\r
-/*********** Health Expectancies ****************/\r
-\r
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )\r
-\r
-{\r
- /* Health expectancies */\r
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj;\r
- double age, agelim, hf;\r
- double ***p3mat,***varhe;\r
- double **dnewm,**doldm;\r
- double *xp;\r
- double **gp, **gm;\r
- double ***gradg, ***trgradg;\r
- int theta;\r
-\r
- varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);\r
- xp=vector(1,npar);\r
- dnewm=matrix(1,nlstate*2,1,npar);\r
- doldm=matrix(1,nlstate*2,1,nlstate*2);\r
- \r
- fprintf(ficreseij,"# Health expectancies\n");\r
- fprintf(ficreseij,"# Age");\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate;j++)\r
- fprintf(ficreseij," %1d-%1d (SE)",i,j);\r
- fprintf(ficreseij,"\n");\r
-\r
- if(estepm < stepm){\r
- printf ("Problem %d lower than %d\n",estepm, stepm);\r
- }\r
- else hstepm=estepm; \r
- /* We compute the life expectancy from trapezoids spaced every estepm months\r
- * This is mainly to measure the difference between two models: for example\r
- * if stepm=24 months pijx are given only every 2 years and by summing them\r
- * we are calculating an estimate of the Life Expectancy assuming a linear \r
- * progression inbetween and thus overestimating or underestimating according\r
- * to the curvature of the survival function. If, for the same date, we \r
- * estimate the model with stepm=1 month, we can keep estepm to 24 months\r
- * to compare the new estimate of Life expectancy with the same linear \r
- * hypothesis. A more precise result, taking into account a more precise\r
- * curvature will be obtained if estepm is as small as stepm. */\r
-\r
- /* For example we decided to compute the life expectancy with the smallest unit */\r
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. \r
- nhstepm is the number of hstepm from age to agelim \r
- nstepm is the number of stepm from age to agelin. \r
- Look at hpijx to understand the reason of that which relies in memory size\r
- and note for a fixed period like estepm months */\r
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the\r
- survival function given by stepm (the optimization length). Unfortunately it\r
- means that if the survival funtion is printed only each two years of age and if\r
- you sum them up and add 1 year (area under the trapezoids) you won't get the same \r
- results. So we changed our mind and took the option of the best precision.\r
- */\r
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ \r
-\r
- agelim=AGESUP;\r
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */\r
- /* nhstepm age range expressed in number of stepm */\r
- nstepm=(int) rint((agelim-age)*YEARM/stepm); \r
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */ \r
- /* if (stepm >= YEARM) hstepm=1;*/\r
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */\r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);\r
- gp=matrix(0,nhstepm,1,nlstate*2);\r
- gm=matrix(0,nhstepm,1,nlstate*2);\r
-\r
- /* Computed by stepm unit matrices, product of hstepm matrices, stored\r
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */\r
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij); \r
- \r
-\r
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */\r
-\r
- /* Computing Variances of health expectancies */\r
-\r
- for(theta=1; theta <=npar; theta++){\r
- for(i=1; i<=npar; i++){ \r
- xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
- }\r
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
- \r
- cptj=0;\r
- for(j=1; j<= nlstate; j++){\r
- for(i=1; i<=nlstate; i++){\r
- cptj=cptj+1;\r
- for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){\r
- gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;\r
- }\r
- }\r
- }\r
- \r
- \r
- for(i=1; i<=npar; i++) \r
- xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
- \r
- cptj=0;\r
- for(j=1; j<= nlstate; j++){\r
- for(i=1;i<=nlstate;i++){\r
- cptj=cptj+1;\r
- for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){\r
- gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;\r
- }\r
- }\r
- }\r
- for(j=1; j<= nlstate*2; j++)\r
- for(h=0; h<=nhstepm-1; h++){\r
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];\r
- }\r
- } \r
- \r
-/* End theta */\r
-\r
- trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);\r
-\r
- for(h=0; h<=nhstepm-1; h++)\r
- for(j=1; j<=nlstate*2;j++)\r
- for(theta=1; theta <=npar; theta++)\r
- trgradg[h][j][theta]=gradg[h][theta][j];\r
- \r
-\r
- for(i=1;i<=nlstate*2;i++)\r
- for(j=1;j<=nlstate*2;j++)\r
- varhe[i][j][(int)age] =0.;\r
-\r
- printf("%d|",(int)age);fflush(stdout);\r
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);\r
- for(h=0;h<=nhstepm-1;h++){\r
- for(k=0;k<=nhstepm-1;k++){\r
- matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);\r
- matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);\r
- for(i=1;i<=nlstate*2;i++)\r
- for(j=1;j<=nlstate*2;j++)\r
- varhe[i][j][(int)age] += doldm[i][j]*hf*hf;\r
- }\r
- }\r
- /* Computing expectancies */\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate;j++)\r
- for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){\r
- eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;\r
- \r
-/* 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]);*/\r
-\r
- }\r
-\r
- fprintf(ficreseij,"%3.0f",age );\r
- cptj=0;\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate;j++){\r
- cptj++;\r
- fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );\r
- }\r
- fprintf(ficreseij,"\n");\r
- \r
- free_matrix(gm,0,nhstepm,1,nlstate*2);\r
- free_matrix(gp,0,nhstepm,1,nlstate*2);\r
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);\r
- free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
-\r
- free_vector(xp,1,npar);\r
- free_matrix(dnewm,1,nlstate*2,1,npar);\r
- free_matrix(doldm,1,nlstate*2,1,nlstate*2);\r
- free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);\r
-}\r
-\r
-/************ Variance ******************/\r
-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 ij, int estepm, int cptcov, int cptcod, int popbased)\r
-{\r
- /* Variance of health expectancies */\r
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/\r
- /* double **newm;*/\r
- double **dnewm,**doldm;\r
- double **dnewmp,**doldmp;\r
- int i, j, nhstepm, hstepm, h, nstepm ;\r
- int k, cptcode;\r
- double *xp;\r
- double **gp, **gm; /* for var eij */\r
- double ***gradg, ***trgradg; /*for var eij */\r
- double **gradgp, **trgradgp; /* for var p point j */\r
- double *gpp, *gmp; /* for var p point j */\r
- double **varppt; /* for var p point j nlstate to nlstate+ndeath */\r
- double ***p3mat;\r
- double age,agelim, hf;\r
- int theta;\r
- char digit[4];\r
- char digitp[16];\r
-\r
- char fileresprobmorprev[FILENAMELENGTH];\r
-\r
- if(popbased==1)\r
- strcpy(digitp,"-populbased-");\r
- else\r
- strcpy(digitp,"-stablbased-");\r
-\r
- strcpy(fileresprobmorprev,"prmorprev"); \r
- sprintf(digit,"%-d",ij);\r
- /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/\r
- strcat(fileresprobmorprev,digit); /* Tvar to be done */\r
- strcat(fileresprobmorprev,digitp); /* Popbased or not */\r
- strcat(fileresprobmorprev,fileres);\r
- if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {\r
- printf("Problem with resultfile: %s\n", fileresprobmorprev);\r
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);\r
- }\r
- printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);\r
- fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);\r
- fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");\r
- fprintf(ficresprobmorprev,"# Age cov=%-d",ij);\r
- for(j=nlstate+1; j<=(nlstate+ndeath);j++){\r
- fprintf(ficresprobmorprev," p.%-d SE",j);\r
- for(i=1; i<=nlstate;i++)\r
- fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);\r
- } \r
- fprintf(ficresprobmorprev,"\n");\r
- if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {\r
- printf("Problem with gnuplot file: %s\n", optionfilegnuplot);\r
- fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);\r
- exit(0);\r
- }\r
- else{\r
- fprintf(ficgp,"\n# Routine varevsij");\r
- }\r
- if((fichtm=fopen(optionfilehtm,"a"))==NULL) {\r
- printf("Problem with html file: %s\n", optionfilehtm);\r
- fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);\r
- exit(0);\r
- }\r
- else{\r
- fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");\r
- }\r
- varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
-\r
- fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");\r
- fprintf(ficresvij,"# Age");\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate;j++)\r
- fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);\r
- fprintf(ficresvij,"\n");\r
-\r
- xp=vector(1,npar);\r
- dnewm=matrix(1,nlstate,1,npar);\r
- doldm=matrix(1,nlstate,1,nlstate);\r
- dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);\r
- doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
-\r
- gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);\r
- gpp=vector(nlstate+1,nlstate+ndeath);\r
- gmp=vector(nlstate+1,nlstate+ndeath);\r
- trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/\r
- \r
- if(estepm < stepm){\r
- printf ("Problem %d lower than %d\n",estepm, stepm);\r
- }\r
- else hstepm=estepm; \r
- /* For example we decided to compute the life expectancy with the smallest unit */\r
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. \r
- nhstepm is the number of hstepm from age to agelim \r
- nstepm is the number of stepm from age to agelin. \r
- Look at hpijx to understand the reason of that which relies in memory size\r
- and note for a fixed period like k years */\r
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the\r
- survival function given by stepm (the optimization length). Unfortunately it\r
- means that if the survival funtion is printed only each two years of age and if\r
- you sum them up and add 1 year (area under the trapezoids) you won't get the same \r
- results. So we changed our mind and took the option of the best precision.\r
- */\r
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ \r
- agelim = AGESUP;\r
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */\r
- nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */\r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate);\r
- gp=matrix(0,nhstepm,1,nlstate);\r
- gm=matrix(0,nhstepm,1,nlstate);\r
-\r
-\r
- for(theta=1; theta <=npar; theta++){\r
- for(i=1; i<=npar; i++){ /* Computes gradient */\r
- xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
- }\r
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
-\r
- if (popbased==1) {\r
- for(i=1; i<=nlstate;i++)\r
- prlim[i][i]=probs[(int)age][i][ij];\r
- }\r
- \r
- for(j=1; j<= nlstate; j++){\r
- for(h=0; h<=nhstepm; h++){\r
- for(i=1, gp[h][j]=0.;i<=nlstate;i++)\r
- gp[h][j] += prlim[i][i]*p3mat[i][j][h];\r
- }\r
- }\r
- /* This for computing forces of mortality (h=1)as a weighted average */\r
- for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){\r
- for(i=1; i<= nlstate; i++)\r
- gpp[j] += prlim[i][i]*p3mat[i][j][1];\r
- } \r
- /* end force of mortality */\r
-\r
- for(i=1; i<=npar; i++) /* Computes gradient */\r
- xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
- \r
- if (popbased==1) {\r
- for(i=1; i<=nlstate;i++)\r
- prlim[i][i]=probs[(int)age][i][ij];\r
- }\r
-\r
- for(j=1; j<= nlstate; j++){\r
- for(h=0; h<=nhstepm; h++){\r
- for(i=1, gm[h][j]=0.;i<=nlstate;i++)\r
- gm[h][j] += prlim[i][i]*p3mat[i][j][h];\r
- }\r
- }\r
- /* This for computing force of mortality (h=1)as a weighted average */\r
- for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){\r
- for(i=1; i<= nlstate; i++)\r
- gmp[j] += prlim[i][i]*p3mat[i][j][1];\r
- } \r
- /* end force of mortality */\r
-\r
- for(j=1; j<= nlstate; j++) /* vareij */\r
- for(h=0; h<=nhstepm; h++){\r
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];\r
- }\r
- for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */\r
- gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];\r
- }\r
-\r
- } /* End theta */\r
-\r
- trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */\r
-\r
- for(h=0; h<=nhstepm; h++) /* veij */\r
- for(j=1; j<=nlstate;j++)\r
- for(theta=1; theta <=npar; theta++)\r
- trgradg[h][j][theta]=gradg[h][theta][j];\r
-\r
- for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */\r
- for(theta=1; theta <=npar; theta++)\r
- trgradgp[j][theta]=gradgp[theta][j];\r
-\r
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */\r
- for(i=1;i<=nlstate;i++)\r
- for(j=1;j<=nlstate;j++)\r
- vareij[i][j][(int)age] =0.;\r
-\r
- for(h=0;h<=nhstepm;h++){\r
- for(k=0;k<=nhstepm;k++){\r
- matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);\r
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);\r
- for(i=1;i<=nlstate;i++)\r
- for(j=1;j<=nlstate;j++)\r
- vareij[i][j][(int)age] += doldm[i][j]*hf*hf;\r
- }\r
- }\r
-\r
- /* pptj */\r
- matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);\r
- matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);\r
- for(j=nlstate+1;j<=nlstate+ndeath;j++)\r
- for(i=nlstate+1;i<=nlstate+ndeath;i++)\r
- varppt[j][i]=doldmp[j][i];\r
- /* end ppptj */\r
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); \r
- prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);\r
- \r
- if (popbased==1) {\r
- for(i=1; i<=nlstate;i++)\r
- prlim[i][i]=probs[(int)age][i][ij];\r
- }\r
- \r
- /* This for computing force of mortality (h=1)as a weighted average */\r
- for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){\r
- for(i=1; i<= nlstate; i++)\r
- gmp[j] += prlim[i][i]*p3mat[i][j][1]; \r
- } \r
- /* end force of mortality */\r
-\r
- fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);\r
- for(j=nlstate+1; j<=(nlstate+ndeath);j++){\r
- fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));\r
- for(i=1; i<=nlstate;i++){\r
- fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);\r
- }\r
- } \r
- fprintf(ficresprobmorprev,"\n");\r
-\r
- fprintf(ficresvij,"%.0f ",age );\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate;j++){\r
- fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);\r
- }\r
- fprintf(ficresvij,"\n");\r
- free_matrix(gp,0,nhstepm,1,nlstate);\r
- free_matrix(gm,0,nhstepm,1,nlstate);\r
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);\r
- free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- } /* End age */\r
- free_vector(gpp,nlstate+1,nlstate+ndeath);\r
- free_vector(gmp,nlstate+1,nlstate+ndeath);\r
- free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);\r
- free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/\r
- fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");\r
- /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */\r
- fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");\r
- fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);\r
- fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);\r
- fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);\r
- fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);\r
- fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);\r
- /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);\r
-*/\r
- fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);\r
-\r
- free_vector(xp,1,npar);\r
- free_matrix(doldm,1,nlstate,1,nlstate);\r
- free_matrix(dnewm,1,nlstate,1,npar);\r
- free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
- free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);\r
- free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
- fclose(ficresprobmorprev);\r
- fclose(ficgp);\r
- fclose(fichtm);\r
-\r
-}\r
-\r
-/************ Variance of prevlim ******************/\r
-void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)\r
-{\r
- /* Variance of prevalence limit */\r
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/\r
- double **newm;\r
- double **dnewm,**doldm;\r
- int i, j, nhstepm, hstepm;\r
- int k, cptcode;\r
- double *xp;\r
- double *gp, *gm;\r
- double **gradg, **trgradg;\r
- double age,agelim;\r
- int theta;\r
- \r
- fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");\r
- fprintf(ficresvpl,"# Age");\r
- for(i=1; i<=nlstate;i++)\r
- fprintf(ficresvpl," %1d-%1d",i,i);\r
- fprintf(ficresvpl,"\n");\r
-\r
- xp=vector(1,npar);\r
- dnewm=matrix(1,nlstate,1,npar);\r
- doldm=matrix(1,nlstate,1,nlstate);\r
- \r
- hstepm=1*YEARM; /* Every year of age */\r
- hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ \r
- agelim = AGESUP;\r
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */\r
- nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
- if (stepm >= YEARM) hstepm=1;\r
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */\r
- gradg=matrix(1,npar,1,nlstate);\r
- gp=vector(1,nlstate);\r
- gm=vector(1,nlstate);\r
-\r
- for(theta=1; theta <=npar; theta++){\r
- for(i=1; i<=npar; i++){ /* Computes gradient */\r
- xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
- }\r
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
- for(i=1;i<=nlstate;i++)\r
- gp[i] = prlim[i][i];\r
- \r
- for(i=1; i<=npar; i++) /* Computes gradient */\r
- xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
- for(i=1;i<=nlstate;i++)\r
- gm[i] = prlim[i][i];\r
-\r
- for(i=1;i<=nlstate;i++)\r
- gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];\r
- } /* End theta */\r
-\r
- trgradg =matrix(1,nlstate,1,npar);\r
-\r
- for(j=1; j<=nlstate;j++)\r
- for(theta=1; theta <=npar; theta++)\r
- trgradg[j][theta]=gradg[theta][j];\r
-\r
- for(i=1;i<=nlstate;i++)\r
- varpl[i][(int)age] =0.;\r
- matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);\r
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);\r
- for(i=1;i<=nlstate;i++)\r
- varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */\r
-\r
- fprintf(ficresvpl,"%.0f ",age );\r
- for(i=1; i<=nlstate;i++)\r
- fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));\r
- fprintf(ficresvpl,"\n");\r
- free_vector(gp,1,nlstate);\r
- free_vector(gm,1,nlstate);\r
- free_matrix(gradg,1,npar,1,nlstate);\r
- free_matrix(trgradg,1,nlstate,1,npar);\r
- } /* End age */\r
-\r
- free_vector(xp,1,npar);\r
- free_matrix(doldm,1,nlstate,1,npar);\r
- free_matrix(dnewm,1,nlstate,1,nlstate);\r
-\r
-}\r
-\r
-/************ Variance of one-step probabilities ******************/\r
-void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)\r
-{\r
- int i, j=0, i1, k1, l1, t, tj;\r
- int k2, l2, j1, z1;\r
- int k=0,l, cptcode;\r
- int first=1, first1;\r
- double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;\r
- double **dnewm,**doldm;\r
- double *xp;\r
- double *gp, *gm;\r
- double **gradg, **trgradg;\r
- double **mu;\r
- double age,agelim, cov[NCOVMAX];\r
- double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */\r
- int theta;\r
- char fileresprob[FILENAMELENGTH];\r
- char fileresprobcov[FILENAMELENGTH];\r
- char fileresprobcor[FILENAMELENGTH];\r
-\r
- double ***varpij;\r
-\r
- strcpy(fileresprob,"prob"); \r
- strcat(fileresprob,fileres);\r
- if((ficresprob=fopen(fileresprob,"w"))==NULL) {\r
- printf("Problem with resultfile: %s\n", fileresprob);\r
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);\r
- }\r
- strcpy(fileresprobcov,"probcov"); \r
- strcat(fileresprobcov,fileres);\r
- if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {\r
- printf("Problem with resultfile: %s\n", fileresprobcov);\r
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);\r
- }\r
- strcpy(fileresprobcor,"probcor"); \r
- strcat(fileresprobcor,fileres);\r
- if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {\r
- printf("Problem with resultfile: %s\n", fileresprobcor);\r
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);\r
- }\r
- printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);\r
- fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);\r
- printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);\r
- fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);\r
- printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);\r
- fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);\r
- \r
- fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");\r
- fprintf(ficresprob,"# Age");\r
- fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");\r
- fprintf(ficresprobcov,"# Age");\r
- fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");\r
- fprintf(ficresprobcov,"# Age");\r
-\r
-\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=(nlstate+ndeath);j++){\r
- fprintf(ficresprob," p%1d-%1d (SE)",i,j);\r
- fprintf(ficresprobcov," p%1d-%1d ",i,j);\r
- fprintf(ficresprobcor," p%1d-%1d ",i,j);\r
- } \r
- fprintf(ficresprob,"\n");\r
- fprintf(ficresprobcov,"\n");\r
- fprintf(ficresprobcor,"\n");\r
- xp=vector(1,npar);\r
- dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);\r
- doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));\r
- mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);\r
- varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);\r
- first=1;\r
- if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {\r
- printf("Problem with gnuplot file: %s\n", optionfilegnuplot);\r
- fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);\r
- exit(0);\r
- }\r
- else{\r
- fprintf(ficgp,"\n# Routine varprob");\r
- }\r
- if((fichtm=fopen(optionfilehtm,"a"))==NULL) {\r
- printf("Problem with html file: %s\n", optionfilehtm);\r
- fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);\r
- exit(0);\r
- }\r
- else{\r
- fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");\r
- fprintf(fichtm,"\n");\r
-\r
- fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");\r
- fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");\r
- fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");\r
-\r
- }\r
-\r
- \r
- cov[1]=1;\r
- tj=cptcoveff;\r
- if (cptcovn<1) {tj=1;ncodemax[1]=1;}\r
- j1=0;\r
- for(t=1; t<=tj;t++){\r
- for(i1=1; i1<=ncodemax[t];i1++){ \r
- j1++;\r
- \r
- if (cptcovn>0) {\r
- fprintf(ficresprob, "\n#********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(ficresprob, "**********\n#");\r
- fprintf(ficresprobcov, "\n#********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(ficresprobcov, "**********\n#");\r
- \r
- fprintf(ficgp, "\n#********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(ficgp, "**********\n#");\r
- \r
- \r
- fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");\r
- \r
- fprintf(ficresprobcor, "\n#********** Variable "); \r
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
- fprintf(ficgp, "**********\n#"); \r
- }\r
- \r
- for (age=bage; age<=fage; age ++){ \r
- cov[2]=age;\r
- for (k=1; k<=cptcovn;k++) {\r
- cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];\r
- }\r
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
- for (k=1; k<=cptcovprod;k++)\r
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
- \r
- gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));\r
- trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);\r
- gp=vector(1,(nlstate)*(nlstate+ndeath));\r
- gm=vector(1,(nlstate)*(nlstate+ndeath));\r
- \r
- for(theta=1; theta <=npar; theta++){\r
- for(i=1; i<=npar; i++)\r
- xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
- \r
- pmij(pmmij,cov,ncovmodel,xp,nlstate);\r
- \r
- k=0;\r
- for(i=1; i<= (nlstate); i++){\r
- for(j=1; j<=(nlstate+ndeath);j++){\r
- k=k+1;\r
- gp[k]=pmmij[i][j];\r
- }\r
- }\r
- \r
- for(i=1; i<=npar; i++)\r
- xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
- \r
- pmij(pmmij,cov,ncovmodel,xp,nlstate);\r
- k=0;\r
- for(i=1; i<=(nlstate); i++){\r
- for(j=1; j<=(nlstate+ndeath);j++){\r
- k=k+1;\r
- gm[k]=pmmij[i][j];\r
- }\r
- }\r
- \r
- for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) \r
- gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta]; \r
- }\r
-\r
- for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)\r
- for(theta=1; theta <=npar; theta++)\r
- trgradg[j][theta]=gradg[theta][j];\r
- \r
- matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); \r
- matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);\r
- \r
- pmij(pmmij,cov,ncovmodel,x,nlstate);\r
- \r
- k=0;\r
- for(i=1; i<=(nlstate); i++){\r
- for(j=1; j<=(nlstate+ndeath);j++){\r
- k=k+1;\r
- mu[k][(int) age]=pmmij[i][j];\r
- }\r
- }\r
- for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)\r
- for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)\r
- varpij[i][j][(int)age] = doldm[i][j];\r
-\r
- /*printf("\n%d ",(int)age);\r
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){\r
- printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));\r
- fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));\r
- }*/\r
-\r
- fprintf(ficresprob,"\n%d ",(int)age);\r
- fprintf(ficresprobcov,"\n%d ",(int)age);\r
- fprintf(ficresprobcor,"\n%d ",(int)age);\r
-\r
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)\r
- fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));\r
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){\r
- fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);\r
- fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);\r
- }\r
- i=0;\r
- for (k=1; k<=(nlstate);k++){\r
- for (l=1; l<=(nlstate+ndeath);l++){ \r
- i=i++;\r
- fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);\r
- fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);\r
- for (j=1; j<=i;j++){\r
- fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);\r
- fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));\r
- }\r
- }\r
- }/* end of loop for state */\r
- } /* end of loop for age */\r
-\r
- /* Confidence intervalle of pij */\r
- /*\r
- fprintf(ficgp,"\nset noparametric;unset label");\r
- fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");\r
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");\r
- fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);\r
- fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);\r
- fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);\r
- fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);\r
- */\r
-\r
- /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/\r
- first1=1;\r
- for (k2=1; k2<=(nlstate);k2++){\r
- for (l2=1; l2<=(nlstate+ndeath);l2++){ \r
- if(l2==k2) continue;\r
- j=(k2-1)*(nlstate+ndeath)+l2;\r
- for (k1=1; k1<=(nlstate);k1++){\r
- for (l1=1; l1<=(nlstate+ndeath);l1++){ \r
- if(l1==k1) continue;\r
- i=(k1-1)*(nlstate+ndeath)+l1;\r
- if(i<=j) continue;\r
- for (age=bage; age<=fage; age ++){ \r
- if ((int)age %5==0){\r
- v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;\r
- v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;\r
- cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;\r
- mu1=mu[i][(int) age]/stepm*YEARM ;\r
- mu2=mu[j][(int) age]/stepm*YEARM;\r
- c12=cv12/sqrt(v1*v2);\r
- /* Computing eigen value of matrix of covariance */\r
- lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;\r
- lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;\r
- /* Eigen vectors */\r
- v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));\r
- /*v21=sqrt(1.-v11*v11); *//* error */\r
- v21=(lc1-v1)/cv12*v11;\r
- v12=-v21;\r
- v22=v11;\r
- tnalp=v21/v11;\r
- if(first1==1){\r
- first1=0;\r
- printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);\r
- }\r
- fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);\r
- /*printf(fignu*/\r
- /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */\r
- /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */\r
- if(first==1){\r
- first=0;\r
- fprintf(ficgp,"\nset parametric;unset label");\r
- fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);\r
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");\r
- fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);\r
- fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);\r
- fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);\r
- fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);\r
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);\r
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);\r
- 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",\\r
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\\r
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));\r
- }else{\r
- first=0;\r
- fprintf(fichtm," %d (%.3f),",(int) age, c12);\r
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);\r
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);\r
- fprintf(ficgp,"\nreplot %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",\\r
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\\r
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));\r
- }/* if first */\r
- } /* age mod 5 */\r
- } /* end loop age */\r
- fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);\r
- first=1;\r
- } /*l12 */\r
- } /* k12 */\r
- } /*l1 */\r
- }/* k1 */\r
- } /* loop covariates */\r
- free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);\r
- free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));\r
- free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));\r
- free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);\r
- free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);\r
- free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);\r
- }\r
- free_vector(xp,1,npar);\r
- fclose(ficresprob);\r
- fclose(ficresprobcov);\r
- fclose(ficresprobcor);\r
- fclose(ficgp);\r
- fclose(fichtm);\r
-}\r
-\r
-\r
-/******************* Printing html file ***********/\r
-void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \\r
- int lastpass, int stepm, int weightopt, char model[],\\r
- int imx,int jmin, int jmax, double jmeanint,char rfileres[],\\r
- int popforecast, int estepm ,\\r
- double jprev1, double mprev1,double anprev1, \\r
- double jprev2, double mprev2,double anprev2){\r
- int jj1, k1, i1, cpt;\r
- /*char optionfilehtm[FILENAMELENGTH];*/\r
- if((fichtm=fopen(optionfilehtm,"a"))==NULL) {\r
- printf("Problem with %s \n",optionfilehtm), exit(0);\r
- fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);\r
- }\r
-\r
- fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n\r
- - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n\r
- - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n\r
- - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n\r
- - Life expectancies by age and initial health status (estepm=%2d months): \r
- <a href=\"e%s\">e%s</a> <br>\n</li>", \\r
- jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);\r
-\r
-fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");\r
-\r
- m=cptcoveff;\r
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}\r
-\r
- jj1=0;\r
- for(k1=1; k1<=m;k1++){\r
- for(i1=1; i1<=ncodemax[k1];i1++){\r
- jj1++;\r
- if (cptcovn > 0) {\r
- fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");\r
- for (cpt=1; cpt<=cptcoveff;cpt++) \r
- fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);\r
- fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");\r
- }\r
- /* Pij */\r
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>\r
-<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); \r
- /* Quasi-incidences */\r
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>\r
-<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); \r
- /* Stable prevalence in each health state */\r
- for(cpt=1; cpt<nlstate;cpt++){\r
- fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>\r
-<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);\r
- }\r
- for(cpt=1; cpt<=nlstate;cpt++) {\r
- fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>\r
-<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);\r
- }\r
- fprintf(fichtm,"\n<br>- Total life expectancy by age and\r
-health expectancies in states (1) and (2): e%s%d.png<br>\r
-<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);\r
- } /* end i1 */\r
- }/* End k1 */\r
- fprintf(fichtm,"</ul>");\r
-\r
-\r
- fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\r
- - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\r
- - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\r
- - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\r
- - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\r
- - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n \r
- - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\r
- - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);\r
-\r
- if(popforecast==1) fprintf(fichtm,"\n\r
- - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n\r
- - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n\r
- <br>",fileres,fileres,fileres,fileres);\r
- else \r
- fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);\r
-fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");\r
-\r
- m=cptcoveff;\r
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}\r
-\r
- jj1=0;\r
- for(k1=1; k1<=m;k1++){\r
- for(i1=1; i1<=ncodemax[k1];i1++){\r
- jj1++;\r
- if (cptcovn > 0) {\r
- fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");\r
- for (cpt=1; cpt<=cptcoveff;cpt++) \r
- fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);\r
- fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");\r
- }\r
- for(cpt=1; cpt<=nlstate;cpt++) {\r
- fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident\r
-interval) in state (%d): v%s%d%d.png <br>\r
-<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1); \r
- }\r
- } /* end i1 */\r
- }/* End k1 */\r
- fprintf(fichtm,"</ul>");\r
-fclose(fichtm);\r
-}\r
-\r
-/******************* Gnuplot file **************/\r
-void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){\r
-\r
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;\r
- int ng;\r
- if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {\r
- printf("Problem with file %s",optionfilegnuplot);\r
- fprintf(ficlog,"Problem with file %s",optionfilegnuplot);\r
- }\r
-\r
-#ifdef windows\r
- fprintf(ficgp,"cd \"%s\" \n",pathc);\r
-#endif\r
-m=pow(2,cptcoveff);\r
- \r
- /* 1eme*/\r
- for (cpt=1; cpt<= nlstate ; cpt ++) {\r
- for (k1=1; k1<= m ; k1 ++) {\r
-\r
-#ifdef windows\r
- fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);\r
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);\r
-#endif\r
-#ifdef unix\r
-fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);\r
-fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);\r
-#endif\r
-\r
-for (i=1; i<= nlstate ; i ++) {\r
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-}\r
- fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);\r
- for (i=1; i<= nlstate ; i ++) {\r
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-} \r
- fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); \r
- for (i=1; i<= nlstate ; i ++) {\r
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-} \r
- fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));\r
-#ifdef unix\r
-fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");\r
-#endif\r
- }\r
- }\r
- /*2 eme*/\r
-\r
- for (k1=1; k1<= m ; k1 ++) { \r
- fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);\r
- fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);\r
- \r
- for (i=1; i<= nlstate+1 ; i ++) {\r
- k=2*i;\r
- fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);\r
- for (j=1; j<= nlstate+1 ; j ++) {\r
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-} \r
- if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");\r
- else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);\r
- fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);\r
- for (j=1; j<= nlstate+1 ; j ++) {\r
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-} \r
- fprintf(ficgp,"\" t\"\" w l 0,");\r
- fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);\r
- for (j=1; j<= nlstate+1 ; j ++) {\r
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
- else fprintf(ficgp," \%%*lf (\%%*lf)");\r
-} \r
- if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");\r
- else fprintf(ficgp,"\" t\"\" w l 0,");\r
- }\r
- }\r
- \r
- /*3eme*/\r
-\r
- for (k1=1; k1<= m ; k1 ++) { \r
- for (cpt=1; cpt<= nlstate ; cpt ++) {\r
- k=2+nlstate*(2*cpt-2);\r
- fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);\r
- fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);\r
- /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);\r
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");\r
-fprintf(ficgp,"\" t \"e%d1\" w l",cpt);\r
-fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);\r
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");\r
-fprintf(ficgp,"\" t \"e%d1\" w l",cpt);\r
-\r
-*/\r
- for (i=1; i< nlstate ; i ++) {\r
- fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);\r
-\r
- } \r
- }\r
- }\r
- \r
- /* CV preval stat */\r
- for (k1=1; k1<= m ; k1 ++) { \r
- for (cpt=1; cpt<nlstate ; cpt ++) {\r
- k=3;\r
- fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);\r
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);\r
-\r
- for (i=1; i< nlstate ; i ++)\r
- fprintf(ficgp,"+$%d",k+i+1);\r
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);\r
- \r
- l=3+(nlstate+ndeath)*cpt;\r
- fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);\r
- for (i=1; i< nlstate ; i ++) {\r
- l=3+(nlstate+ndeath)*cpt;\r
- fprintf(ficgp,"+$%d",l+i+1);\r
- }\r
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); \r
- } \r
- } \r
- \r
- /* proba elementaires */\r
- for(i=1,jk=1; i <=nlstate; i++){\r
- for(k=1; k <=(nlstate+ndeath); k++){\r
- if (k != i) {\r
- for(j=1; j <=ncovmodel; j++){\r
- fprintf(ficgp,"p%d=%f ",jk,p[jk]);\r
- jk++; \r
- fprintf(ficgp,"\n");\r
- }\r
- }\r
- }\r
- }\r
-\r
- for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/\r
- for(jk=1; jk <=m; jk++) {\r
- fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); \r
- if (ng==2)\r
- fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");\r
- else\r
- fprintf(ficgp,"\nset title \"Probability\"\n");\r
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);\r
- i=1;\r
- for(k2=1; k2<=nlstate; k2++) {\r
- k3=i;\r
- for(k=1; k<=(nlstate+ndeath); k++) {\r
- if (k != k2){\r
- if(ng==2)\r
- fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);\r
- else\r
- fprintf(ficgp," exp(p%d+p%d*x",i,i+1);\r
- ij=1;\r
- for(j=3; j <=ncovmodel; j++) {\r
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {\r
- fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\r
- ij++;\r
- }\r
- else\r
- fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);\r
- }\r
- fprintf(ficgp,")/(1");\r
- \r
- for(k1=1; k1 <=nlstate; k1++){ \r
- fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);\r
- ij=1;\r
- for(j=3; j <=ncovmodel; j++){\r
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {\r
- fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\r
- ij++;\r
- }\r
- else\r
- fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);\r
- }\r
- fprintf(ficgp,")");\r
- }\r
- fprintf(ficgp,") t \"p%d%d\" ", k2,k);\r
- if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");\r
- i=i+ncovmodel;\r
- }\r
- } /* end k */\r
- } /* end k2 */\r
- } /* end jk */\r
- } /* end ng */\r
- fclose(ficgp); \r
-} /* end gnuplot */\r
-\r
-\r
-/*************** Moving average **************/\r
-void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){\r
-\r
- int i, cpt, cptcod;\r
- for (agedeb=ageminpar; agedeb<=fage; agedeb++)\r
- for (i=1; i<=nlstate;i++)\r
- for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)\r
- mobaverage[(int)agedeb][i][cptcod]=0.;\r
- \r
- for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){\r
- for (i=1; i<=nlstate;i++){\r
- for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){\r
- for (cpt=0;cpt<=4;cpt++){\r
- mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];\r
- }\r
- mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;\r
- }\r
- }\r
- }\r
- \r
-}\r
-\r
-\r
-/************** Forecasting ******************/\r
-prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){\r
- \r
- int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;\r
- int *popage;\r
- double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;\r
- double *popeffectif,*popcount;\r
- double ***p3mat;\r
- char fileresf[FILENAMELENGTH];\r
-\r
- agelim=AGESUP;\r
-calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;\r
-\r
- prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);\r
- \r
- \r
- strcpy(fileresf,"f"); \r
- strcat(fileresf,fileres);\r
- if((ficresf=fopen(fileresf,"w"))==NULL) {\r
- printf("Problem with forecast resultfile: %s\n", fileresf);\r
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);\r
- }\r
- printf("Computing forecasting: result on file '%s' \n", fileresf);\r
- fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);\r
-\r
- if (cptcoveff==0) ncodemax[cptcoveff]=1;\r
-\r
- if (mobilav==1) {\r
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- movingaverage(agedeb, fage, ageminpar, mobaverage);\r
- }\r
-\r
- stepsize=(int) (stepm+YEARM-1)/YEARM;\r
- if (stepm<=12) stepsize=1;\r
- \r
- agelim=AGESUP;\r
- \r
- hstepm=1;\r
- hstepm=hstepm/stepm; \r
- yp1=modf(dateintmean,&yp);\r
- anprojmean=yp;\r
- yp2=modf((yp1*12),&yp);\r
- mprojmean=yp;\r
- yp1=modf((yp2*30.5),&yp);\r
- jprojmean=yp;\r
- if(jprojmean==0) jprojmean=1;\r
- if(mprojmean==0) jprojmean=1;\r
- \r
- fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); \r
- \r
- for(cptcov=1;cptcov<=i2;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){\r
- k=k+1;\r
- fprintf(ficresf,"\n#******");\r
- for(j=1;j<=cptcoveff;j++) {\r
- fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- }\r
- fprintf(ficresf,"******\n");\r
- fprintf(ficresf,"# StartingAge FinalAge");\r
- for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);\r
- \r
- \r
- for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { \r
- fprintf(ficresf,"\n");\r
- fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt); \r
-\r
- for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ \r
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); \r
- nhstepm = nhstepm/hstepm; \r
- \r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- oldm=oldms;savm=savms;\r
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
- \r
- for (h=0; h<=nhstepm; h++){\r
- if (h==(int) (calagedate+YEARM*cpt)) {\r
- fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);\r
- } \r
- for(j=1; j<=nlstate+ndeath;j++) {\r
- kk1=0.;kk2=0;\r
- for(i=1; i<=nlstate;i++) { \r
- if (mobilav==1) \r
- kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];\r
- else {\r
- kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];\r
- }\r
- \r
- }\r
- if (h==(int)(calagedate+12*cpt)){\r
- fprintf(ficresf," %.3f", kk1);\r
- \r
- }\r
- }\r
- }\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- }\r
- }\r
- }\r
- }\r
- \r
- if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
-\r
- fclose(ficresf);\r
-}\r
-/************** Forecasting ******************/\r
-populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){\r
- \r
- int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;\r
- int *popage;\r
- double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;\r
- double *popeffectif,*popcount;\r
- double ***p3mat,***tabpop,***tabpopprev;\r
- char filerespop[FILENAMELENGTH];\r
-\r
- tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- agelim=AGESUP;\r
- calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;\r
- \r
- prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);\r
- \r
- \r
- strcpy(filerespop,"pop"); \r
- strcat(filerespop,fileres);\r
- if((ficrespop=fopen(filerespop,"w"))==NULL) {\r
- printf("Problem with forecast resultfile: %s\n", filerespop);\r
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);\r
- }\r
- printf("Computing forecasting: result on file '%s' \n", filerespop);\r
- fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);\r
-\r
- if (cptcoveff==0) ncodemax[cptcoveff]=1;\r
-\r
- if (mobilav==1) {\r
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- movingaverage(agedeb, fage, ageminpar, mobaverage);\r
- }\r
-\r
- stepsize=(int) (stepm+YEARM-1)/YEARM;\r
- if (stepm<=12) stepsize=1;\r
- \r
- agelim=AGESUP;\r
- \r
- hstepm=1;\r
- hstepm=hstepm/stepm; \r
- \r
- if (popforecast==1) {\r
- if((ficpop=fopen(popfile,"r"))==NULL) {\r
- printf("Problem with population file : %s\n",popfile);exit(0);\r
- fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);\r
- } \r
- popage=ivector(0,AGESUP);\r
- popeffectif=vector(0,AGESUP);\r
- popcount=vector(0,AGESUP);\r
- \r
- i=1; \r
- while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;\r
- \r
- imx=i;\r
- for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];\r
- }\r
-\r
- for(cptcov=1;cptcov<=i2;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){\r
- k=k+1;\r
- fprintf(ficrespop,"\n#******");\r
- for(j=1;j<=cptcoveff;j++) {\r
- fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- }\r
- fprintf(ficrespop,"******\n");\r
- fprintf(ficrespop,"# Age");\r
- for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);\r
- if (popforecast==1) fprintf(ficrespop," [Population]");\r
- \r
- for (cpt=0; cpt<=0;cpt++) { \r
- fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); \r
- \r
- for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ \r
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); \r
- nhstepm = nhstepm/hstepm; \r
- \r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- oldm=oldms;savm=savms;\r
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
- \r
- for (h=0; h<=nhstepm; h++){\r
- if (h==(int) (calagedate+YEARM*cpt)) {\r
- fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);\r
- } \r
- for(j=1; j<=nlstate+ndeath;j++) {\r
- kk1=0.;kk2=0;\r
- for(i=1; i<=nlstate;i++) { \r
- if (mobilav==1) \r
- kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];\r
- else {\r
- kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];\r
- }\r
- }\r
- if (h==(int)(calagedate+12*cpt)){\r
- tabpop[(int)(agedeb)][j][cptcod]=kk1;\r
- /*fprintf(ficrespop," %.3f", kk1);\r
- if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/\r
- }\r
- }\r
- for(i=1; i<=nlstate;i++){\r
- kk1=0.;\r
- for(j=1; j<=nlstate;j++){\r
- kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; \r
- }\r
- tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];\r
- }\r
-\r
- if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) \r
- fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);\r
- }\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- }\r
- }\r
- \r
- /******/\r
-\r
- for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { \r
- fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); \r
- for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){ \r
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); \r
- nhstepm = nhstepm/hstepm; \r
- \r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- oldm=oldms;savm=savms;\r
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
- for (h=0; h<=nhstepm; h++){\r
- if (h==(int) (calagedate+YEARM*cpt)) {\r
- fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);\r
- } \r
- for(j=1; j<=nlstate+ndeath;j++) {\r
- kk1=0.;kk2=0;\r
- for(i=1; i<=nlstate;i++) { \r
- kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; \r
- }\r
- if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1); \r
- }\r
- }\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- }\r
- }\r
- } \r
- }\r
- \r
- if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
-\r
- if (popforecast==1) {\r
- free_ivector(popage,0,AGESUP);\r
- free_vector(popeffectif,0,AGESUP);\r
- free_vector(popcount,0,AGESUP);\r
- }\r
- free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
- fclose(ficrespop);\r
-}\r
-\r
-/***********************************************/\r
-/**************** Main Program *****************/\r
-/***********************************************/\r
-\r
-int main(int argc, char *argv[])\r
-{\r
-\r
- int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;\r
- double agedeb, agefin,hf;\r
- double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;\r
-\r
- double fret;\r
- double **xi,tmp,delta;\r
-\r
- double dum; /* Dummy variable */\r
- double ***p3mat;\r
- int *indx;\r
- char line[MAXLINE], linepar[MAXLINE];\r
- char path[80],pathc[80],pathcd[80],pathtot[80],model[80];\r
- int firstobs=1, lastobs=10;\r
- int sdeb, sfin; /* Status at beginning and end */\r
- int c, h , cpt,l;\r
- int ju,jl, mi;\r
- int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;\r
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab; \r
- int mobilav=0,popforecast=0;\r
- int hstepm, nhstepm;\r
- double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;\r
-\r
- double bage, fage, age, agelim, agebase;\r
- double ftolpl=FTOL;\r
- double **prlim;\r
- double *severity;\r
- double ***param; /* Matrix of parameters */\r
- double *p;\r
- double **matcov; /* Matrix of covariance */\r
- double ***delti3; /* Scale */\r
- double *delti; /* Scale */\r
- double ***eij, ***vareij;\r
- double **varpl; /* Variances of prevalence limits by age */\r
- double *epj, vepp;\r
- double kk1, kk2;\r
- double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;\r
- \r
-\r
- char *alph[]={"a","a","b","c","d","e"}, str[4];\r
-\r
-\r
- char z[1]="c", occ;\r
-#include <sys/time.h>\r
-#include <time.h>\r
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];\r
- \r
- /* long total_usecs;\r
- struct timeval start_time, end_time;\r
- \r
- gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */\r
- getcwd(pathcd, size);\r
-\r
- printf("\n%s",version);\r
- if(argc <=1){\r
- printf("\nEnter the parameter file name: ");\r
- scanf("%s",pathtot);\r
- }\r
- else{\r
- strcpy(pathtot,argv[1]);\r
- }\r
- /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/\r
- /*cygwin_split_path(pathtot,path,optionfile);\r
- printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/\r
- /* cutv(path,optionfile,pathtot,'\\');*/\r
-\r
- split(pathtot,path,optionfile,optionfilext,optionfilefiname);\r
- printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);\r
- chdir(path);\r
- replace(pathc,path);\r
-\r
-/*-------- arguments in the command line --------*/\r
-\r
- /* Log file */\r
- strcat(filelog, optionfilefiname);\r
- strcat(filelog,".log"); /* */\r
- if((ficlog=fopen(filelog,"w"))==NULL) {\r
- printf("Problem with logfile %s\n",filelog);\r
- goto end;\r
- }\r
- fprintf(ficlog,"Log filename:%s\n",filelog);\r
- fprintf(ficlog,"\n%s",version);\r
- fprintf(ficlog,"\nEnter the parameter file name: ");\r
- fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);\r
- fflush(ficlog);\r
-\r
- /* */\r
- strcpy(fileres,"r");\r
- strcat(fileres, optionfilefiname);\r
- strcat(fileres,".txt"); /* Other files have txt extension */\r
-\r
- /*---------arguments file --------*/\r
-\r
- if((ficpar=fopen(optionfile,"r"))==NULL) {\r
- printf("Problem with optionfile %s\n",optionfile);\r
- fprintf(ficlog,"Problem with optionfile %s\n",optionfile);\r
- goto end;\r
- }\r
-\r
- strcpy(filereso,"o");\r
- strcat(filereso,fileres);\r
- if((ficparo=fopen(filereso,"w"))==NULL) {\r
- printf("Problem with Output resultfile: %s\n", filereso);\r
- fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);\r
- goto end;\r
- }\r
-\r
- /* Reads comments: lines beginning with '#' */\r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
-\r
- fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);\r
- printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);\r
- fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);\r
-while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- \r
- \r
- covar=matrix(0,NCOVMAX,1,n); \r
- cptcovn=0; \r
- if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;\r
-\r
- ncovmodel=2+cptcovn;\r
- nvar=ncovmodel-1; /* Suppressing age as a basic covariate */\r
- \r
- /* Read guess parameters */\r
- /* Reads comments: lines beginning with '#' */\r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- \r
- param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);\r
- for(i=1; i <=nlstate; i++)\r
- for(j=1; j <=nlstate+ndeath-1; j++){\r
- fscanf(ficpar,"%1d%1d",&i1,&j1);\r
- fprintf(ficparo,"%1d%1d",i1,j1);\r
- if(mle==1)\r
- printf("%1d%1d",i,j);\r
- fprintf(ficlog,"%1d%1d",i,j);\r
- for(k=1; k<=ncovmodel;k++){\r
- fscanf(ficpar," %lf",¶m[i][j][k]);\r
- if(mle==1){\r
- printf(" %lf",param[i][j][k]);\r
- fprintf(ficlog," %lf",param[i][j][k]);\r
- }\r
- else\r
- fprintf(ficlog," %lf",param[i][j][k]);\r
- fprintf(ficparo," %lf",param[i][j][k]);\r
- }\r
- fscanf(ficpar,"\n");\r
- if(mle==1)\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- fprintf(ficparo,"\n");\r
- }\r
- \r
- npar= (nlstate+ndeath-1)*nlstate*ncovmodel;\r
-\r
- p=param[1][1];\r
- \r
- /* Reads comments: lines beginning with '#' */\r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
-\r
- delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);\r
- delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */\r
- for(i=1; i <=nlstate; i++){\r
- for(j=1; j <=nlstate+ndeath-1; j++){\r
- fscanf(ficpar,"%1d%1d",&i1,&j1);\r
- printf("%1d%1d",i,j);\r
- fprintf(ficparo,"%1d%1d",i1,j1);\r
- for(k=1; k<=ncovmodel;k++){\r
- fscanf(ficpar,"%le",&delti3[i][j][k]);\r
- printf(" %le",delti3[i][j][k]);\r
- fprintf(ficparo," %le",delti3[i][j][k]);\r
- }\r
- fscanf(ficpar,"\n");\r
- printf("\n");\r
- fprintf(ficparo,"\n");\r
- }\r
- }\r
- delti=delti3[1][1];\r
- \r
- /* Reads comments: lines beginning with '#' */\r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- \r
- matcov=matrix(1,npar,1,npar);\r
- for(i=1; i <=npar; i++){\r
- fscanf(ficpar,"%s",&str);\r
- if(mle==1)\r
- printf("%s",str);\r
- fprintf(ficlog,"%s",str);\r
- fprintf(ficparo,"%s",str);\r
- for(j=1; j <=i; j++){\r
- fscanf(ficpar," %le",&matcov[i][j]);\r
- if(mle==1){\r
- printf(" %.5le",matcov[i][j]);\r
- fprintf(ficlog," %.5le",matcov[i][j]);\r
- }\r
- else\r
- fprintf(ficlog," %.5le",matcov[i][j]);\r
- fprintf(ficparo," %.5le",matcov[i][j]);\r
- }\r
- fscanf(ficpar,"\n");\r
- if(mle==1)\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- fprintf(ficparo,"\n");\r
- }\r
- for(i=1; i <=npar; i++)\r
- for(j=i+1;j<=npar;j++)\r
- matcov[i][j]=matcov[j][i];\r
- \r
- if(mle==1)\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
-\r
-\r
- /*-------- Rewriting paramater file ----------*/\r
- strcpy(rfileres,"r"); /* "Rparameterfile */\r
- strcat(rfileres,optionfilefiname); /* Parameter file first name*/\r
- strcat(rfileres,"."); /* */\r
- strcat(rfileres,optionfilext); /* Other files have txt extension */\r
- if((ficres =fopen(rfileres,"w"))==NULL) {\r
- printf("Problem writing new parameter file: %s\n", fileres);goto end;\r
- fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;\r
- }\r
- fprintf(ficres,"#%s\n",version);\r
- \r
- /*-------- data file ----------*/\r
- if((fic=fopen(datafile,"r"))==NULL) {\r
- printf("Problem with datafile: %s\n", datafile);goto end;\r
- fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;\r
- }\r
-\r
- n= lastobs;\r
- severity = vector(1,maxwav);\r
- outcome=imatrix(1,maxwav+1,1,n);\r
- num=ivector(1,n);\r
- moisnais=vector(1,n);\r
- annais=vector(1,n);\r
- moisdc=vector(1,n);\r
- andc=vector(1,n);\r
- agedc=vector(1,n);\r
- cod=ivector(1,n);\r
- weight=vector(1,n);\r
- for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */\r
- mint=matrix(1,maxwav,1,n);\r
- anint=matrix(1,maxwav,1,n);\r
- s=imatrix(1,maxwav+1,1,n);\r
- adl=imatrix(1,maxwav+1,1,n); \r
- tab=ivector(1,NCOVMAX);\r
- ncodemax=ivector(1,8);\r
-\r
- i=1;\r
- while (fgets(line, MAXLINE, fic) != NULL) {\r
- if ((i >= firstobs) && (i <=lastobs)) {\r
- \r
- for (j=maxwav;j>=1;j--){\r
- cutv(stra, strb,line,' '); s[j][i]=atoi(strb); \r
- strcpy(line,stra);\r
- cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);\r
- cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);\r
- }\r
- \r
- cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);\r
- cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);\r
-\r
- cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);\r
- cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);\r
-\r
- cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);\r
- for (j=ncovcol;j>=1;j--){\r
- cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);\r
- } \r
- num[i]=atol(stra);\r
- \r
- /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){\r
- printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/\r
-\r
- i=i+1;\r
- }\r
- } \r
- /* printf("ii=%d", ij);\r
- scanf("%d",i);*/\r
- imx=i-1; /* Number of individuals */\r
-\r
- /* for (i=1; i<=imx; i++){\r
- if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;\r
- if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;\r
- if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;\r
- }*/\r
- /* for (i=1; i<=imx; i++){\r
- if (s[4][i]==9) s[4][i]=-1; \r
- printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/\r
- \r
- \r
- /* Calculation of the number of parameter from char model*/\r
- Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */\r
- Tprod=ivector(1,15); \r
- Tvaraff=ivector(1,15); \r
- Tvard=imatrix(1,15,1,2);\r
- Tage=ivector(1,15); \r
- \r
- if (strlen(model) >1){\r
- j=0, j1=0, k1=1, k2=1;\r
- j=nbocc(model,'+');\r
- j1=nbocc(model,'*');\r
- cptcovn=j+1;\r
- cptcovprod=j1;\r
- \r
- strcpy(modelsav,model); \r
- if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){\r
- printf("Error. Non available option model=%s ",model);\r
- fprintf(ficlog,"Error. Non available option model=%s ",model);\r
- goto end;\r
- }\r
- \r
- for(i=(j+1); i>=1;i--){\r
- cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ \r
- if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */\r
- /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/\r
- /*scanf("%d",i);*/\r
- if (strchr(strb,'*')) { /* Model includes a product */\r
- cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/\r
- if (strcmp(strc,"age")==0) { /* Vn*age */\r
- cptcovprod--;\r
- cutv(strb,stre,strd,'V');\r
- Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/\r
- cptcovage++;\r
- Tage[cptcovage]=i;\r
- /*printf("stre=%s ", stre);*/\r
- }\r
- else if (strcmp(strd,"age")==0) { /* or age*Vn */\r
- cptcovprod--;\r
- cutv(strb,stre,strc,'V');\r
- Tvar[i]=atoi(stre);\r
- cptcovage++;\r
- Tage[cptcovage]=i;\r
- }\r
- else { /* Age is not in the model */\r
- cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/\r
- Tvar[i]=ncovcol+k1;\r
- cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */\r
- Tprod[k1]=i;\r
- Tvard[k1][1]=atoi(strc); /* m*/\r
- Tvard[k1][2]=atoi(stre); /* n */\r
- Tvar[cptcovn+k2]=Tvard[k1][1];\r
- Tvar[cptcovn+k2+1]=Tvard[k1][2]; \r
- for (k=1; k<=lastobs;k++) \r
- covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];\r
- k1++;\r
- k2=k2+2;\r
- }\r
- }\r
- else { /* no more sum */\r
- /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/\r
- /* scanf("%d",i);*/\r
- cutv(strd,strc,strb,'V');\r
- Tvar[i]=atoi(strc);\r
- }\r
- strcpy(modelsav,stra); \r
- /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);\r
- scanf("%d",i);*/\r
- } /* end of loop + */\r
- } /* end model */\r
- \r
- /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);\r
- printf("cptcovprod=%d ", cptcovprod);\r
- fprintf(ficlog,"cptcovprod=%d ", cptcovprod);\r
- scanf("%d ",i);*/\r
- fclose(fic);\r
-\r
- /* if(mle==1){*/\r
- if (weightopt != 1) { /* Maximisation without weights*/\r
- for(i=1;i<=n;i++) weight[i]=1.0;\r
- }\r
- /*-calculation of age at interview from date of interview and age at death -*/\r
- agev=matrix(1,maxwav,1,imx);\r
-\r
- for (i=1; i<=imx; i++) {\r
- for(m=2; (m<= maxwav); m++) {\r
- if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){\r
- anint[m][i]=9999;\r
- s[m][i]=-1;\r
- }\r
- if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;\r
- }\r
- }\r
-\r
- for (i=1; i<=imx; i++) {\r
- agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);\r
- for(m=1; (m<= maxwav); m++){\r
- if(s[m][i] >0){\r
- if (s[m][i] >= nlstate+1) {\r
- if(agedc[i]>0)\r
- if(moisdc[i]!=99 && andc[i]!=9999)\r
- agev[m][i]=agedc[i];\r
- /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/\r
- else {\r
- if (andc[i]!=9999){\r
- printf("Warning negative age at death: %d line:%d\n",num[i],i);\r
- fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);\r
- agev[m][i]=-1;\r
- }\r
- }\r
- }\r
- else if(s[m][i] !=9){ /* Should no more exist */\r
- agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);\r
- if(mint[m][i]==99 || anint[m][i]==9999)\r
- agev[m][i]=1;\r
- else if(agev[m][i] <agemin){ \r
- agemin=agev[m][i];\r
- /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/\r
- }\r
- else if(agev[m][i] >agemax){\r
- agemax=agev[m][i];\r
- /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/\r
- }\r
- /*agev[m][i]=anint[m][i]-annais[i];*/\r
- /* agev[m][i] = age[i]+2*m;*/\r
- }\r
- else { /* =9 */\r
- agev[m][i]=1;\r
- s[m][i]=-1;\r
- }\r
- }\r
- else /*= 0 Unknown */\r
- agev[m][i]=1;\r
- }\r
- \r
- }\r
- for (i=1; i<=imx; i++) {\r
- for(m=1; (m<= maxwav); m++){\r
- if (s[m][i] > (nlstate+ndeath)) {\r
- printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); \r
- fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath); \r
- goto end;\r
- }\r
- }\r
- }\r
-\r
-printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);\r
- fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); \r
-\r
- free_vector(severity,1,maxwav);\r
- free_imatrix(outcome,1,maxwav+1,1,n);\r
- free_vector(moisnais,1,n);\r
- free_vector(annais,1,n);\r
- /* free_matrix(mint,1,maxwav,1,n);\r
- free_matrix(anint,1,maxwav,1,n);*/\r
- free_vector(moisdc,1,n);\r
- free_vector(andc,1,n);\r
-\r
- \r
- wav=ivector(1,imx);\r
- dh=imatrix(1,lastpass-firstpass+1,1,imx);\r
- mw=imatrix(1,lastpass-firstpass+1,1,imx);\r
- \r
- /* Concatenates waves */\r
- concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);\r
-\r
-\r
- Tcode=ivector(1,100);\r
- nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); \r
- ncodemax[1]=1;\r
- if (cptcovn > 0) tricode(Tvar,nbcode,imx);\r
- \r
- codtab=imatrix(1,100,1,10);\r
- h=0;\r
- m=pow(2,cptcoveff);\r
- \r
- for(k=1;k<=cptcoveff; k++){\r
- for(i=1; i <=(m/pow(2,k));i++){\r
- for(j=1; j <= ncodemax[k]; j++){\r
- for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){\r
- h++;\r
- if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;\r
- /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/\r
- } \r
- }\r
- }\r
- } \r
- /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); \r
- codtab[1][2]=1;codtab[2][2]=2; */\r
- /* for(i=1; i <=m ;i++){ \r
- for(k=1; k <=cptcovn; k++){\r
- printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);\r
- }\r
- printf("\n");\r
- }\r
- scanf("%d",i);*/\r
- \r
- /* Calculates basic frequencies. Computes observed prevalence at single age\r
- and prints on file fileres'p'. */\r
-\r
- \r
- \r
- pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */\r
- \r
- /* For Powell, parameters are in a vector p[] starting at p[1]\r
- so we point p on param[1][1] so that p[1] maps on param[1][1][1] */\r
- p=param[1][1]; /* *(*(*(param +1)+1)+0) */\r
-\r
- if(mle==1){\r
- mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);\r
- }\r
- \r
- /*--------- results files --------------*/\r
- fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);\r
- \r
-\r
- jk=1;\r
- fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
- printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
- fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
- for(i=1,jk=1; i <=nlstate; i++){\r
- for(k=1; k <=(nlstate+ndeath); k++){\r
- if (k != i) \r
- {\r
- printf("%d%d ",i,k);\r
- fprintf(ficlog,"%d%d ",i,k);\r
- fprintf(ficres,"%1d%1d ",i,k);\r
- for(j=1; j <=ncovmodel; j++){\r
- printf("%f ",p[jk]);\r
- fprintf(ficlog,"%f ",p[jk]);\r
- fprintf(ficres,"%f ",p[jk]);\r
- jk++; \r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- fprintf(ficres,"\n");\r
- }\r
- }\r
- }\r
- if(mle==1){\r
- /* Computing hessian and covariance matrix */\r
- ftolhess=ftol; /* Usually correct */\r
- hesscov(matcov, p, npar, delti, ftolhess, func);\r
- }\r
- fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");\r
- printf("# Scales (for hessian or gradient estimation)\n");\r
- fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");\r
- for(i=1,jk=1; i <=nlstate; i++){\r
- for(j=1; j <=nlstate+ndeath; j++){\r
- if (j!=i) {\r
- fprintf(ficres,"%1d%1d",i,j);\r
- printf("%1d%1d",i,j);\r
- fprintf(ficlog,"%1d%1d",i,j);\r
- for(k=1; k<=ncovmodel;k++){\r
- printf(" %.5e",delti[jk]);\r
- fprintf(ficlog," %.5e",delti[jk]);\r
- fprintf(ficres," %.5e",delti[jk]);\r
- jk++;\r
- }\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- fprintf(ficres,"\n");\r
- }\r
- }\r
- }\r
- \r
- k=1;\r
- fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");\r
- if(mle==1)\r
- printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");\r
- fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");\r
- for(i=1;i<=npar;i++){\r
- /* if (k>nlstate) k=1;\r
- i1=(i-1)/(ncovmodel*nlstate)+1; \r
- fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);\r
- printf("%s%d%d",alph[k],i1,tab[i]);*/\r
- fprintf(ficres,"%3d",i);\r
- if(mle==1)\r
- printf("%3d",i);\r
- fprintf(ficlog,"%3d",i);\r
- for(j=1; j<=i;j++){\r
- fprintf(ficres," %.5e",matcov[i][j]);\r
- if(mle==1)\r
- printf(" %.5e",matcov[i][j]);\r
- fprintf(ficlog," %.5e",matcov[i][j]);\r
- }\r
- fprintf(ficres,"\n");\r
- if(mle==1)\r
- printf("\n");\r
- fprintf(ficlog,"\n");\r
- k++;\r
- }\r
- \r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- estepm=0;\r
- fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);\r
- if (estepm==0 || estepm < stepm) estepm=stepm;\r
- if (fage <= 2) {\r
- bage = ageminpar;\r
- fage = agemaxpar;\r
- }\r
- \r
- fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");\r
- fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);\r
- fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);\r
- \r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- \r
- fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);\r
- fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);\r
- fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);\r
- \r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
- \r
-\r
- dateprev1=anprev1+mprev1/12.+jprev1/365.;\r
- dateprev2=anprev2+mprev2/12.+jprev2/365.;\r
-\r
- fscanf(ficpar,"pop_based=%d\n",&popbased);\r
- fprintf(ficparo,"pop_based=%d\n",popbased); \r
- fprintf(ficres,"pop_based=%d\n",popbased); \r
- \r
- while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
-\r
- fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);\r
-fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);\r
-fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);\r
-\r
-\r
-while((c=getc(ficpar))=='#' && c!= EOF){\r
- ungetc(c,ficpar);\r
- fgets(line, MAXLINE, ficpar);\r
- puts(line);\r
- fputs(line,ficparo);\r
- }\r
- ungetc(c,ficpar);\r
-\r
- fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);\r
- fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);\r
- fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);\r
-\r
- freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);\r
-\r
-/*------------ gnuplot -------------*/\r
- strcpy(optionfilegnuplot,optionfilefiname);\r
- strcat(optionfilegnuplot,".gp");\r
- if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {\r
- printf("Problem with file %s",optionfilegnuplot);\r
- }\r
- fclose(ficgp);\r
- printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);\r
-/*--------- index.htm --------*/\r
-\r
- strcpy(optionfilehtm,optionfile);\r
- strcat(optionfilehtm,".htm");\r
- if((fichtm=fopen(optionfilehtm,"w"))==NULL) {\r
- printf("Problem with %s \n",optionfilehtm), exit(0);\r
- }\r
-\r
- fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n\r
-Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\r
-\n\r
-Total number of observations=%d <br>\n\r
-Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n\r
-<hr size=\"2\" color=\"#EC5E5E\">\r
- <ul><li><h4>Parameter files</h4>\n\r
- - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\r
- - Log file of the run: <a href=\"%s\">%s</a><br>\n\r
- - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);\r
- fclose(fichtm);\r
-\r
- printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);\r
- \r
-/*------------ free_vector -------------*/\r
- chdir(path);\r
- \r
- free_ivector(wav,1,imx);\r
- free_imatrix(dh,1,lastpass-firstpass+1,1,imx);\r
- free_imatrix(mw,1,lastpass-firstpass+1,1,imx); \r
- free_ivector(num,1,n);\r
- free_vector(agedc,1,n);\r
- /*free_matrix(covar,1,NCOVMAX,1,n);*/\r
- fclose(ficparo);\r
- fclose(ficres);\r
-\r
-\r
- /*--------------- Prevalence limit --------------*/\r
- \r
- strcpy(filerespl,"pl");\r
- strcat(filerespl,fileres);\r
- if((ficrespl=fopen(filerespl,"w"))==NULL) {\r
- printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;\r
- fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;\r
- }\r
- printf("Computing prevalence limit: result on file '%s' \n", filerespl);\r
- fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);\r
- fprintf(ficrespl,"#Prevalence limit\n");\r
- fprintf(ficrespl,"#Age ");\r
- for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);\r
- fprintf(ficrespl,"\n");\r
- \r
- prlim=matrix(1,nlstate,1,nlstate);\r
- pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
- oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */\r
- k=0;\r
- agebase=ageminpar;\r
- agelim=agemaxpar;\r
- ftolpl=1.e-10;\r
- i1=cptcoveff;\r
- if (cptcovn < 1){i1=1;}\r
-\r
- for(cptcov=1;cptcov<=i1;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
- k=k+1;\r
- /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/\r
- fprintf(ficrespl,"\n#******");\r
- printf("\n#******");\r
- fprintf(ficlog,"\n#******");\r
- for(j=1;j<=cptcoveff;j++) {\r
- fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- }\r
- fprintf(ficrespl,"******\n");\r
- printf("******\n");\r
- fprintf(ficlog,"******\n");\r
- \r
- for (age=agebase; age<=agelim; age++){\r
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);\r
- fprintf(ficrespl,"%.0f",age );\r
- for(i=1; i<=nlstate;i++)\r
- fprintf(ficrespl," %.5f", prlim[i][i]);\r
- fprintf(ficrespl,"\n");\r
- }\r
- }\r
- }\r
- fclose(ficrespl);\r
-\r
- /*------------- h Pij x at various ages ------------*/\r
- \r
- strcpy(filerespij,"pij"); strcat(filerespij,fileres);\r
- if((ficrespij=fopen(filerespij,"w"))==NULL) {\r
- printf("Problem with Pij resultfile: %s\n", filerespij);goto end;\r
- fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;\r
- }\r
- printf("Computing pij: result on file '%s' \n", filerespij);\r
- fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);\r
- \r
- stepsize=(int) (stepm+YEARM-1)/YEARM;\r
- /*if (stepm<=24) stepsize=2;*/\r
-\r
- agelim=AGESUP;\r
- hstepm=stepsize*YEARM; /* Every year of age */\r
- hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ \r
-\r
- /* hstepm=1; aff par mois*/\r
-\r
- k=0;\r
- for(cptcov=1;cptcov<=i1;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
- k=k+1;\r
- fprintf(ficrespij,"\n#****** ");\r
- for(j=1;j<=cptcoveff;j++) \r
- fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficrespij,"******\n");\r
- \r
- for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */\r
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */\r
-\r
- /* nhstepm=nhstepm*YEARM; aff par mois*/\r
-\r
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- oldm=oldms;savm=savms;\r
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
- fprintf(ficrespij,"# Age");\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate+ndeath;j++)\r
- fprintf(ficrespij," %1d-%1d",i,j);\r
- fprintf(ficrespij,"\n");\r
- for (h=0; h<=nhstepm; h++){\r
- fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );\r
- for(i=1; i<=nlstate;i++)\r
- for(j=1; j<=nlstate+ndeath;j++)\r
- fprintf(ficrespij," %.5f", p3mat[i][j][h]);\r
- fprintf(ficrespij,"\n");\r
- }\r
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
- fprintf(ficrespij,"\n");\r
- }\r
- }\r
- }\r
-\r
- varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);\r
-\r
- fclose(ficrespij);\r
-\r
-\r
- /*---------- Forecasting ------------------*/\r
- if((stepm == 1) && (strcmp(model,".")==0)){\r
- prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);\r
- if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);\r
- } \r
- else{\r
- erreur=108;\r
- printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);\r
- fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);\r
- }\r
- \r
-\r
- /*---------- Health expectancies and variances ------------*/\r
-\r
- strcpy(filerest,"t");\r
- strcat(filerest,fileres);\r
- if((ficrest=fopen(filerest,"w"))==NULL) {\r
- printf("Problem with total LE resultfile: %s\n", filerest);goto end;\r
- fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;\r
- }\r
- printf("Computing Total LEs with variances: file '%s' \n", filerest); \r
- fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); \r
-\r
-\r
- strcpy(filerese,"e");\r
- strcat(filerese,fileres);\r
- if((ficreseij=fopen(filerese,"w"))==NULL) {\r
- printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);\r
- fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);\r
- }\r
- printf("Computing Health Expectancies: result on file '%s' \n", filerese);\r
- fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);\r
-\r
- strcpy(fileresv,"v");\r
- strcat(fileresv,fileres);\r
- if((ficresvij=fopen(fileresv,"w"))==NULL) {\r
- printf("Problem with variance resultfile: %s\n", fileresv);exit(0);\r
- fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);\r
- }\r
- printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);\r
- fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);\r
- calagedate=-1;\r
- prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);\r
-\r
- k=0;\r
- for(cptcov=1;cptcov<=i1;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
- k=k+1; \r
- fprintf(ficrest,"\n#****** ");\r
- for(j=1;j<=cptcoveff;j++) \r
- fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficrest,"******\n");\r
-\r
- fprintf(ficreseij,"\n#****** ");\r
- for(j=1;j<=cptcoveff;j++) \r
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficreseij,"******\n");\r
-\r
- fprintf(ficresvij,"\n#****** ");\r
- for(j=1;j<=cptcoveff;j++) \r
- fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficresvij,"******\n");\r
-\r
- eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);\r
- oldm=oldms;savm=savms;\r
- evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov); \r
- \r
- vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);\r
- oldm=oldms;savm=savms;\r
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);\r
- if(popbased==1){\r
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);\r
- }\r
-\r
- \r
- fprintf(ficrest,"#Total LEs with variances: e.. (std) ");\r
- for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);\r
- fprintf(ficrest,"\n");\r
-\r
- epj=vector(1,nlstate+1);\r
- for(age=bage; age <=fage ;age++){\r
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);\r
- if (popbased==1) {\r
- for(i=1; i<=nlstate;i++)\r
- prlim[i][i]=probs[(int)age][i][k];\r
- }\r
- \r
- fprintf(ficrest," %4.0f",age);\r
- for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){\r
- for(i=1, epj[j]=0.;i <=nlstate;i++) {\r
- epj[j] += prlim[i][i]*eij[i][j][(int)age];\r
- /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/\r
- }\r
- epj[nlstate+1] +=epj[j];\r
- }\r
-\r
- for(i=1, vepp=0.;i <=nlstate;i++)\r
- for(j=1;j <=nlstate;j++)\r
- vepp += vareij[i][j][(int)age];\r
- fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));\r
- for(j=1;j <=nlstate;j++){\r
- fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));\r
- }\r
- fprintf(ficrest,"\n");\r
- }\r
- }\r
- }\r
-free_matrix(mint,1,maxwav,1,n);\r
- free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);\r
- free_vector(weight,1,n);\r
- fclose(ficreseij);\r
- fclose(ficresvij);\r
- fclose(ficrest);\r
- fclose(ficpar);\r
- free_vector(epj,1,nlstate+1);\r
- \r
- /*------- Variance limit prevalence------*/ \r
-\r
- strcpy(fileresvpl,"vpl");\r
- strcat(fileresvpl,fileres);\r
- if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {\r
- printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);\r
- exit(0);\r
- }\r
- printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);\r
-\r
- k=0;\r
- for(cptcov=1;cptcov<=i1;cptcov++){\r
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
- k=k+1;\r
- fprintf(ficresvpl,"\n#****** ");\r
- for(j=1;j<=cptcoveff;j++) \r
- fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
- fprintf(ficresvpl,"******\n");\r
- \r
- varpl=matrix(1,nlstate,(int) bage, (int) fage);\r
- oldm=oldms;savm=savms;\r
- varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);\r
- }\r
- }\r
-\r
- fclose(ficresvpl);\r
-\r
- /*---------- End : free ----------------*/\r
- free_matrix(varpl,1,nlstate,(int) bage, (int)fage);\r
- \r
- free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);\r
- free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);\r
- \r
- \r
- free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);\r
- free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
- free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
- free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
- \r
- free_matrix(matcov,1,npar,1,npar);\r
- free_vector(delti,1,npar);\r
- free_matrix(agev,1,maxwav,1,imx);\r
- free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);\r
-\r
- fprintf(fichtm,"\n</body>");\r
- fclose(fichtm);\r
- fclose(ficgp);\r
- \r
-\r
- if(erreur >0){\r
- printf("End of Imach with error or warning %d\n",erreur);\r
- fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);\r
- }else{\r
- printf("End of Imach\n");\r
- fprintf(ficlog,"End of Imach\n");\r
- }\r
- printf("See log file on %s\n",filelog);\r
- fclose(ficlog);\r
- /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */\r
- \r
- /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/\r
- /*printf("Total time was %d uSec.\n", total_usecs);*/\r
- /*------ End -----------*/\r
-\r
-\r
- end:\r
-#ifdef windows\r
- /* chdir(pathcd);*/\r
-#endif \r
- /*system("wgnuplot graph.plt");*/\r
- /*system("../gp37mgw/wgnuplot graph.plt");*/\r
- /*system("cd ../gp37mgw");*/\r
- /* system("..\\gp37mgw\\wgnuplot graph.plt");*/\r
- strcpy(plotcmd,GNUPLOTPROGRAM);\r
- strcat(plotcmd," ");\r
- strcat(plotcmd,optionfilegnuplot);\r
- system(plotcmd);\r
-\r
-#ifdef windows\r
- while (z[0] != 'q') {\r
- /* chdir(path); */\r
- printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");\r
- scanf("%s",z);\r
- if (z[0] == 'c') system("./imach");\r
- else if (z[0] == 'e') system(optionfilehtm);\r
- else if (z[0] == 'g') system(plotcmd);\r
- else if (z[0] == 'q') exit(0);\r
- }\r
-#endif \r
-}\r
-\r
-\r
+/* $Id$
+ Interpolated Markov Chain
+
+ Short summary of the programme:
+
+ This program computes Healthy Life Expectancies from
+ cross-longitudinal data. Cross-longitudinal data consist in: -1- a
+ first survey ("cross") where individuals from different ages are
+ interviewed on their health status or degree of disability (in the
+ case of a health survey which is our main interest) -2- at least a
+ second wave of interviews ("longitudinal") which measure each change
+ (if any) in individual health status. Health expectancies are
+ computed from the time spent in each health state according to a
+ model. More health states you consider, more time is necessary to reach the
+ Maximum Likelihood of the parameters involved in the model. The
+ simplest model is the multinomial logistic model where pij is the
+ probability to be observed in state j at the second wave
+ conditional to be observed in state i at the first wave. Therefore
+ the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
+ 'age' is age and 'sex' is a covariate. If you want to have a more
+ complex model than "constant and age", you should modify the program
+ where the markup *Covariates have to be included here again* invites
+ you to do it. More covariates you add, slower the
+ convergence.
+
+ The advantage of this computer programme, compared to a simple
+ multinomial logistic model, is clear when the delay between waves is not
+ identical for each individual. Also, if a individual missed an
+ intermediate interview, the information is lost, but taken into
+ account using an interpolation or extrapolation.
+
+ hPijx is the probability to be observed in state i at age x+h
+ conditional to the observed state i at age x. The delay 'h' can be
+ split into an exact number (nh*stepm) of unobserved intermediate
+ states. This elementary transition (by month or quarter trimester,
+ semester or year) is model as a multinomial logistic. The hPx
+ matrix is simply the matrix product of nh*stepm elementary matrices
+ and the contribution of each individual to the likelihood is simply
+ hPijx.
+
+ Also this programme outputs the covariance matrix of the parameters but also
+ of the life expectancies. It also computes the prevalence limits.
+
+ Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
+ Institut national d'études démographiques, Paris.
+ This software have been partly granted by Euro-REVES, a concerted action
+ from the European Union.
+ It is copyrighted identically to a GNU software product, ie programme and
+ software can be distributed freely for non commercial use. Latest version
+ can be accessed at http://euroreves.ined.fr/imach .
+ **********************************************************************/
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#define MAXLINE 256
+#define GNUPLOTPROGRAM "gnuplot"
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
+#define FILENAMELENGTH 80
+/*#define DEBUG*/
+#define unix
+#define GLOCK_ERROR_NOPATH -1 /* empty path */
+#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
+
+#define MAXPARM 30 /* Maximum number of parameters for the optimization */
+#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
+
+#define NINTERVMAX 8
+#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
+#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
+#define NCOVMAX 8 /* Maximum number of covariates */
+#define MAXN 20000
+#define YEARM 12. /* Number of months per year */
+#define AGESUP 130
+#define AGEBASE 40
+#ifdef windows
+#define DIRSEPARATOR '\\'
+#define ODIRSEPARATOR '/'
+#else
+#define DIRSEPARATOR '/'
+#define ODIRSEPARATOR '\\'
+#endif
+
+char version[80]="Imach version 0.8j, July 2002, INED-EUROREVES ";
+int erreur; /* Error number */
+int nvar;
+int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
+int npar=NPARMAX;
+int nlstate=2; /* Number of live states */
+int ndeath=1; /* Number of dead states */
+int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
+int popbased=0;
+
+int *wav; /* Number of waves for this individuual 0 is possible */
+int maxwav; /* Maxim number of waves */
+int jmin, jmax; /* min, max spacing between 2 waves */
+int mle, weightopt;
+int **mw; /* mw[mi][i] is number of the mi wave for this individual */
+int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
+double jmean; /* Mean space between 2 waves */
+double **oldm, **newm, **savm; /* Working pointers to matrices */
+double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
+FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *ficlog;
+FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
+FILE *ficresprobmorprev;
+FILE *fichtm; /* Html File */
+FILE *ficreseij;
+char filerese[FILENAMELENGTH];
+FILE *ficresvij;
+char fileresv[FILENAMELENGTH];
+FILE *ficresvpl;
+char fileresvpl[FILENAMELENGTH];
+char title[MAXLINE];
+char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
+char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+
+char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
+char filelog[FILENAMELENGTH]; /* Log file */
+char filerest[FILENAMELENGTH];
+char fileregp[FILENAMELENGTH];
+char popfile[FILENAMELENGTH];
+
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
+
+#define NR_END 1
+#define FREE_ARG char*
+#define FTOL 1.0e-10
+
+#define NRANSI
+#define ITMAX 200
+
+#define TOL 2.0e-4
+
+#define CGOLD 0.3819660
+#define ZEPS 1.0e-10
+#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
+
+#define GOLD 1.618034
+#define GLIMIT 100.0
+#define TINY 1.0e-20
+
+static double maxarg1,maxarg2;
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
+#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
+
+#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
+#define rint(a) floor(a+0.5)
+
+static double sqrarg;
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
+#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
+
+int imx;
+int stepm;
+/* Stepm, step in month: minimum step interpolation*/
+
+int estepm;
+/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
+
+int m,nb;
+int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
+double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
+double **pmmij, ***probs, ***mobaverage;
+double dateintmean=0;
+
+double *weight;
+int **s; /* Status */
+double *agedc, **covar, idx;
+int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
+
+double ftol=FTOL; /* Tolerance for computing Max Likelihood */
+double ftolhess; /* Tolerance for computing hessian */
+
+/**************** split *************************/
+static int split( char *path, char *dirc, char *name, char *ext, char *finame )
+{
+ char *s; /* pointer */
+ int l1, l2; /* length counters */
+
+ l1 = strlen( path ); /* length of path */
+ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
+ s= strrchr( path, DIRSEPARATOR ); /* find last / */
+ if ( s == NULL ) { /* no directory, so use current */
+ /*if(strrchr(path, ODIRSEPARATOR )==NULL)
+ printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
+#if defined(__bsd__) /* get current working directory */
+ extern char *getwd( );
+
+ if ( getwd( dirc ) == NULL ) {
+#else
+ extern char *getcwd( );
+
+ if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
+#endif
+ return( GLOCK_ERROR_GETCWD );
+ }
+ strcpy( name, path ); /* we've got it */
+ } else { /* strip direcotry from path */
+ s++; /* after this, the filename */
+ l2 = strlen( s ); /* length of filename */
+ if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
+ strcpy( name, s ); /* save file name */
+ strncpy( dirc, path, l1 - l2 ); /* now the directory */
+ dirc[l1-l2] = 0; /* add zero */
+ }
+ l1 = strlen( dirc ); /* length of directory */
+#ifdef windows
+ if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
+#else
+ if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
+#endif
+ s = strrchr( name, '.' ); /* find last / */
+ s++;
+ strcpy(ext,s); /* save extension */
+ l1= strlen( name);
+ l2= strlen( s)+1;
+ strncpy( finame, name, l1-l2);
+ finame[l1-l2]= 0;
+ return( 0 ); /* we're done */
+}
+
+
+/******************************************/
+
+void replace(char *s, char*t)
+{
+ int i;
+ int lg=20;
+ i=0;
+ lg=strlen(t);
+ for(i=0; i<= lg; i++) {
+ (s[i] = t[i]);
+ if (t[i]== '\\') s[i]='/';
+ }
+}
+
+int nbocc(char *s, char occ)
+{
+ int i,j=0;
+ int lg=20;
+ i=0;
+ lg=strlen(s);
+ for(i=0; i<= lg; i++) {
+ if (s[i] == occ ) j++;
+ }
+ return j;
+}
+
+void cutv(char *u,char *v, char*t, char occ)
+{
+ /* cuts string t into u and v where u is ended by char occ excluding it
+ and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
+ gives u="abcedf" and v="ghi2j" */
+ int i,lg,j,p=0;
+ i=0;
+ for(j=0; j<=strlen(t)-1; j++) {
+ if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
+ }
+
+ lg=strlen(t);
+ for(j=0; j<p; j++) {
+ (u[j] = t[j]);
+ }
+ u[p]='\0';
+
+ for(j=0; j<= lg; j++) {
+ if (j>=(p+1))(v[j-p-1] = t[j]);
+ }
+}
+
+/********************** nrerror ********************/
+
+void nrerror(char error_text[])
+{
+ fprintf(stderr,"ERREUR ...\n");
+ fprintf(stderr,"%s\n",error_text);
+ exit(1);
+}
+/*********************** vector *******************/
+double *vector(int nl, int nh)
+{
+ double *v;
+ v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
+ if (!v) nrerror("allocation failure in vector");
+ return v-nl+NR_END;
+}
+
+/************************ free vector ******************/
+void free_vector(double*v, int nl, int nh)
+{
+ free((FREE_ARG)(v+nl-NR_END));
+}
+
+/************************ivector *******************************/
+int *ivector(long nl,long nh)
+{
+ int *v;
+ v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
+ if (!v) nrerror("allocation failure in ivector");
+ return v-nl+NR_END;
+}
+
+/******************free ivector **************************/
+void free_ivector(int *v, long nl, long nh)
+{
+ free((FREE_ARG)(v+nl-NR_END));
+}
+
+/******************* imatrix *******************************/
+int **imatrix(long nrl, long nrh, long ncl, long nch)
+ /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
+{
+ long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
+ int **m;
+
+ /* allocate pointers to rows */
+ m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+
+ /* allocate rows and set pointers to them */
+ m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
+
+ /* return pointer to array of pointers to rows */
+ return m;
+}
+
+/****************** free_imatrix *************************/
+void free_imatrix(m,nrl,nrh,ncl,nch)
+ int **m;
+ long nch,ncl,nrh,nrl;
+ /* free an int matrix allocated by imatrix() */
+{
+ free((FREE_ARG) (m[nrl]+ncl-NR_END));
+ free((FREE_ARG) (m+nrl-NR_END));
+}
+
+/******************* matrix *******************************/
+double **matrix(long nrl, long nrh, long ncl, long nch)
+{
+ long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
+ double **m;
+
+ m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+ m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+ return m;
+}
+
+/*************************free matrix ************************/
+void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
+{
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ free((FREE_ARG)(m+nrl-NR_END));
+}
+
+/******************* ma3x *******************************/
+double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
+{
+ long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
+ double ***m;
+
+ m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
+ if (!m) nrerror("allocation failure 1 in matrix()");
+ m += NR_END;
+ m -= nrl;
+
+ m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
+ m[nrl] += NR_END;
+ m[nrl] -= ncl;
+
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
+
+ m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
+ if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
+ m[nrl][ncl] += NR_END;
+ m[nrl][ncl] -= nll;
+ for (j=ncl+1; j<=nch; j++)
+ m[nrl][j]=m[nrl][j-1]+nlay;
+
+ for (i=nrl+1; i<=nrh; i++) {
+ m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
+ for (j=ncl+1; j<=nch; j++)
+ m[i][j]=m[i][j-1]+nlay;
+ }
+ return m;
+}
+
+/*************************free ma3x ************************/
+void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
+{
+ free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));
+ free((FREE_ARG)(m+nrl-NR_END));
+}
+
+/***************** f1dim *************************/
+extern int ncom;
+extern double *pcom,*xicom;
+extern double (*nrfunc)(double []);
+
+double f1dim(double x)
+{
+ int j;
+ double f;
+ double *xt;
+
+ xt=vector(1,ncom);
+ for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
+ f=(*nrfunc)(xt);
+ free_vector(xt,1,ncom);
+ return f;
+}
+
+/*****************brent *************************/
+double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
+{
+ int iter;
+ double a,b,d,etemp;
+ double fu,fv,fw,fx;
+ double ftemp;
+ double p,q,r,tol1,tol2,u,v,w,x,xm;
+ double e=0.0;
+
+ a=(ax < cx ? ax : cx);
+ b=(ax > cx ? ax : cx);
+ x=w=v=bx;
+ fw=fv=fx=(*f)(x);
+ for (iter=1;iter<=ITMAX;iter++) {
+ xm=0.5*(a+b);
+ tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
+ /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
+ printf(".");fflush(stdout);
+ fprintf(ficlog,".");fflush(ficlog);
+#ifdef DEBUG
+ printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
+ /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
+#endif
+ if (fabs(x-xm) <= (tol2-0.5*(b-a))){
+ *xmin=x;
+ return fx;
+ }
+ ftemp=fu;
+ if (fabs(e) > tol1) {
+ r=(x-w)*(fx-fv);
+ q=(x-v)*(fx-fw);
+ p=(x-v)*q-(x-w)*r;
+ q=2.0*(q-r);
+ if (q > 0.0) p = -p;
+ q=fabs(q);
+ etemp=e;
+ e=d;
+ if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
+ d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ else {
+ d=p/q;
+ u=x+d;
+ if (u-a < tol2 || b-u < tol2)
+ d=SIGN(tol1,xm-x);
+ }
+ } else {
+ d=CGOLD*(e=(x >= xm ? a-x : b-x));
+ }
+ u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
+ fu=(*f)(u);
+ if (fu <= fx) {
+ if (u >= x) a=x; else b=x;
+ SHFT(v,w,x,u)
+ SHFT(fv,fw,fx,fu)
+ } else {
+ if (u < x) a=u; else b=u;
+ if (fu <= fw || w == x) {
+ v=w;
+ w=u;
+ fv=fw;
+ fw=fu;
+ } else if (fu <= fv || v == x || v == w) {
+ v=u;
+ fv=fu;
+ }
+ }
+ }
+ nrerror("Too many iterations in brent");
+ *xmin=x;
+ return fx;
+}
+
+/****************** mnbrak ***********************/
+
+void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
+ double (*func)(double))
+{
+ double ulim,u,r,q, dum;
+ double fu;
+
+ *fa=(*func)(*ax);
+ *fb=(*func)(*bx);
+ if (*fb > *fa) {
+ SHFT(dum,*ax,*bx,dum)
+ SHFT(dum,*fb,*fa,dum)
+ }
+ *cx=(*bx)+GOLD*(*bx-*ax);
+ *fc=(*func)(*cx);
+ while (*fb > *fc) {
+ r=(*bx-*ax)*(*fb-*fc);
+ q=(*bx-*cx)*(*fb-*fa);
+ u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
+ (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
+ ulim=(*bx)+GLIMIT*(*cx-*bx);
+ if ((*bx-u)*(u-*cx) > 0.0) {
+ fu=(*func)(u);
+ } else if ((*cx-u)*(u-ulim) > 0.0) {
+ fu=(*func)(u);
+ if (fu < *fc) {
+ SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
+ SHFT(*fb,*fc,fu,(*func)(u))
+ }
+ } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
+ u=ulim;
+ fu=(*func)(u);
+ } else {
+ u=(*cx)+GOLD*(*cx-*bx);
+ fu=(*func)(u);
+ }
+ SHFT(*ax,*bx,*cx,u)
+ SHFT(*fa,*fb,*fc,fu)
+ }
+}
+
+/*************** linmin ************************/
+
+int ncom;
+double *pcom,*xicom;
+double (*nrfunc)(double []);
+
+void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
+{
+ double brent(double ax, double bx, double cx,
+ double (*f)(double), double tol, double *xmin);
+ double f1dim(double x);
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
+ double *fc, double (*func)(double));
+ int j;
+ double xx,xmin,bx,ax;
+ double fx,fb,fa;
+
+ ncom=n;
+ pcom=vector(1,n);
+ xicom=vector(1,n);
+ nrfunc=func;
+ for (j=1;j<=n;j++) {
+ pcom[j]=p[j];
+ xicom[j]=xi[j];
+ }
+ ax=0.0;
+ xx=1.0;
+ mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
+ *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
+#ifdef DEBUG
+ printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+ fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
+#endif
+ for (j=1;j<=n;j++) {
+ xi[j] *= xmin;
+ p[j] += xi[j];
+ }
+ free_vector(xicom,1,n);
+ free_vector(pcom,1,n);
+}
+
+/*************** powell ************************/
+void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
+ double (*func)(double []))
+{
+ void linmin(double p[], double xi[], int n, double *fret,
+ double (*func)(double []));
+ int i,ibig,j;
+ double del,t,*pt,*ptt,*xit;
+ double fp,fptt;
+ double *xits;
+ pt=vector(1,n);
+ ptt=vector(1,n);
+ xit=vector(1,n);
+ xits=vector(1,n);
+ *fret=(*func)(p);
+ for (j=1;j<=n;j++) pt[j]=p[j];
+ for (*iter=1;;++(*iter)) {
+ fp=(*fret);
+ ibig=0;
+ del=0.0;
+ printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
+ for (i=1;i<=n;i++)
+ printf(" %d %.12f",i, p[i]);
+ fprintf(ficlog," %d %.12f",i, p[i]);
+ printf("\n");
+ fprintf(ficlog,"\n");
+ for (i=1;i<=n;i++) {
+ for (j=1;j<=n;j++) xit[j]=xi[j][i];
+ fptt=(*fret);
+#ifdef DEBUG
+ printf("fret=%lf \n",*fret);
+ fprintf(ficlog,"fret=%lf \n",*fret);
+#endif
+ printf("%d",i);fflush(stdout);
+ fprintf(ficlog,"%d",i);fflush(ficlog);
+ linmin(p,xit,n,fret,func);
+ if (fabs(fptt-(*fret)) > del) {
+ del=fabs(fptt-(*fret));
+ ibig=i;
+ }
+#ifdef DEBUG
+ printf("%d %.12e",i,(*fret));
+ fprintf(ficlog,"%d %.12e",i,(*fret));
+ for (j=1;j<=n;j++) {
+ xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
+ printf(" x(%d)=%.12e",j,xit[j]);
+ fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
+ }
+ for(j=1;j<=n;j++) {
+ printf(" p=%.12e",p[j]);
+ fprintf(ficlog," p=%.12e",p[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+#endif
+ }
+ if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
+#ifdef DEBUG
+ int k[2],l;
+ k[0]=1;
+ k[1]=-1;
+ printf("Max: %.12e",(*func)(p));
+ fprintf(ficlog,"Max: %.12e",(*func)(p));
+ for (j=1;j<=n;j++) {
+ printf(" %.12e",p[j]);
+ fprintf(ficlog," %.12e",p[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ for(l=0;l<=1;l++) {
+ for (j=1;j<=n;j++) {
+ ptt[j]=p[j]+(p[j]-pt[j])*k[l];
+ printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
+ }
+ printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
+ }
+#endif
+
+
+ free_vector(xit,1,n);
+ free_vector(xits,1,n);
+ free_vector(ptt,1,n);
+ free_vector(pt,1,n);
+ return;
+ }
+ if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
+ for (j=1;j<=n;j++) {
+ ptt[j]=2.0*p[j]-pt[j];
+ xit[j]=p[j]-pt[j];
+ pt[j]=p[j];
+ }
+ fptt=(*func)(ptt);
+ if (fptt < fp) {
+ t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
+ if (t < 0.0) {
+ linmin(p,xit,n,fret,func);
+ for (j=1;j<=n;j++) {
+ xi[j][ibig]=xi[j][n];
+ xi[j][n]=xit[j];
+ }
+#ifdef DEBUG
+ printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
+ for(j=1;j<=n;j++){
+ printf(" %.12e",xit[j]);
+ fprintf(ficlog," %.12e",xit[j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+#endif
+ }
+ }
+ }
+}
+
+/**** Prevalence limit ****************/
+
+double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
+{
+ /* Computes the prevalence limit in each live state at age x by left multiplying the unit
+ matrix by transitions matrix until convergence is reached */
+
+ int i, ii,j,k;
+ double min, max, maxmin, maxmax,sumnew=0.;
+ double **matprod2();
+ double **out, cov[NCOVMAX], **pmij();
+ double **newm;
+ double agefin, delaymax=50 ; /* Max number of years to converge */
+
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ }
+
+ cov[1]=1.;
+
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
+ newm=savm;
+ /* Covariates have to be included here again */
+ cov[2]=agefin;
+
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ /* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
+ }
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ for (k=1; k<=cptcovprod;k++)
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+
+ /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
+ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
+ /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
+ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
+
+ savm=oldm;
+ oldm=newm;
+ maxmax=0.;
+ for(j=1;j<=nlstate;j++){
+ min=1.;
+ max=0.;
+ for(i=1; i<=nlstate; i++) {
+ sumnew=0;
+ for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
+ prlim[i][j]= newm[i][j]/(1-sumnew);
+ max=FMAX(max,prlim[i][j]);
+ min=FMIN(min,prlim[i][j]);
+ }
+ maxmin=max-min;
+ maxmax=FMAX(maxmax,maxmin);
+ }
+ if(maxmax < ftolpl){
+ return prlim;
+ }
+ }
+}
+
+/*************** transition probabilities ***************/
+
+double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
+{
+ double s1, s2;
+ /*double t34;*/
+ int i,j,j1, nc, ii, jj;
+
+ for(i=1; i<= nlstate; i++){
+ for(j=1; j<i;j++){
+ for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ /*s2 += param[i][j][nc]*cov[nc];*/
+ s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
+ }
+ ps[i][j]=s2;
+ /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
+ }
+ for(j=i+1; j<=nlstate+ndeath;j++){
+ for (nc=1, s2=0.;nc <=ncovmodel; nc++){
+ s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
+ /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
+ }
+ ps[i][j]=s2;
+ }
+ }
+ /*ps[3][2]=1;*/
+
+ for(i=1; i<= nlstate; i++){
+ s1=0;
+ for(j=1; j<i; j++)
+ s1+=exp(ps[i][j]);
+ for(j=i+1; j<=nlstate+ndeath; j++)
+ s1+=exp(ps[i][j]);
+ ps[i][i]=1./(s1+1.);
+ for(j=1; j<i; j++)
+ ps[i][j]= exp(ps[i][j])*ps[i][i];
+ for(j=i+1; j<=nlstate+ndeath; j++)
+ ps[i][j]= exp(ps[i][j])*ps[i][i];
+ /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
+ } /* end i */
+
+ for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
+ for(jj=1; jj<= nlstate+ndeath; jj++){
+ ps[ii][jj]=0;
+ ps[ii][ii]=1;
+ }
+ }
+
+
+ /* for(ii=1; ii<= nlstate+ndeath; ii++){
+ for(jj=1; jj<= nlstate+ndeath; jj++){
+ printf("%lf ",ps[ii][jj]);
+ }
+ printf("\n ");
+ }
+ printf("\n ");printf("%lf ",cov[2]);*/
+/*
+ for(i=1; i<= npar; i++) printf("%f ",x[i]);
+ goto end;*/
+ return ps;
+}
+
+/**************** Product of 2 matrices ******************/
+
+double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
+{
+ /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
+ b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
+ /* in, b, out are matrice of pointers which should have been initialized
+ before: only the contents of out is modified. The function returns
+ a pointer to pointers identical to out */
+ long i, j, k;
+ for(i=nrl; i<= nrh; i++)
+ for(k=ncolol; k<=ncoloh; k++)
+ for(j=ncl,out[i][k]=0.; j<=nch; j++)
+ out[i][k] +=in[i][j]*b[j][k];
+
+ return out;
+}
+
+
+/************* Higher Matrix Product ***************/
+
+double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
+{
+ /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month
+ duration (i.e. until
+ age (in years) age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.
+ Output is stored in matrix po[i][j][h] for h every 'hstepm' step
+ (typically every 2 years instead of every month which is too big).
+ Model is determined by parameters x and covariates have to be
+ included manually here.
+
+ */
+
+ int i, j, d, h, k;
+ double **out, cov[NCOVMAX];
+ double **newm;
+
+ /* Hstepm could be zero and should return the unit matrix */
+ for (i=1;i<=nlstate+ndeath;i++)
+ for (j=1;j<=nlstate+ndeath;j++){
+ oldm[i][j]=(i==j ? 1.0 : 0.0);
+ po[i][j][0]=(i==j ? 1.0 : 0.0);
+ }
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */
+ for(h=1; h <=nhstepm; h++){
+ for(d=1; d <=hstepm; d++){
+ newm=savm;
+ /* Covariates have to be included here again */
+ cov[1]=1.;
+ cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
+ for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
+ for (k=1; k<=cptcovage;k++)
+ cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ for (k=1; k<=cptcovprod;k++)
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+
+
+ /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
+ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
+ pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+ }
+ for(i=1; i<=nlstate+ndeath; i++)
+ for(j=1;j<=nlstate+ndeath;j++) {
+ po[i][j][h]=newm[i][j];
+ /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
+ */
+ }
+ } /* end h */
+ return po;
+}
+
+
+/*************** log-likelihood *************/
+double func( double *x)
+{
+ int i, ii, j, k, mi, d, kk;
+ double l, ll[NLSTATEMAX], cov[NCOVMAX];
+ double **out;
+ double sw; /* Sum of weights */
+ double lli; /* Individual log likelihood */
+ long ipmx;
+ /*extern weight */
+ /* We are differentiating ll according to initial status */
+ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
+ /*for(i=1;i<imx;i++)
+ printf(" %d\n",s[4][i]);
+ */
+ cov[1]=1.;
+
+ for(k=1; k<=nlstate; k++) ll[k]=0.;
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
+ for(mi=1; mi<= wav[i]-1; mi++){
+ for (ii=1;ii<=nlstate+ndeath;ii++)
+ for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
+ for(d=0; d<dh[mi][i]; d++){
+ newm=savm;
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
+ for (kk=1; kk<=cptcovage;kk++) {
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
+ }
+
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
+ savm=oldm;
+ oldm=newm;
+
+
+ } /* end mult */
+
+ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
+ /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
+ ipmx +=1;
+ sw += weight[i];
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
+ } /* end of wave */
+ } /* end of individual */
+
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
+ return -l;
+}
+
+
+/*********** Maximum Likelihood Estimation ***************/
+
+void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
+{
+ int i,j, iter;
+ double **xi,*delti;
+ double fret;
+ xi=matrix(1,npar,1,npar);
+ for (i=1;i<=npar;i++)
+ for (j=1;j<=npar;j++)
+ xi[i][j]=(i==j ? 1.0 : 0.0);
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");
+ powell(p,xi,npar,ftol,&iter,&fret,func);
+
+ printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
+ fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+ fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
+
+}
+
+/**** Computes Hessian and covariance matrix ***/
+void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
+{
+ double **a,**y,*x,pd;
+ double **hess;
+ int i, j,jk;
+ int *indx;
+
+ double hessii(double p[], double delta, int theta, double delti[]);
+ double hessij(double p[], double delti[], int i, int j);
+ void lubksb(double **a, int npar, int *indx, double b[]) ;
+ void ludcmp(double **a, int npar, int *indx, double *d) ;
+
+ hess=matrix(1,npar,1,npar);
+
+ printf("\nCalculation of the hessian matrix. Wait...\n");
+ fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
+ for (i=1;i<=npar;i++){
+ printf("%d",i);fflush(stdout);
+ fprintf(ficlog,"%d",i);fflush(ficlog);
+ hess[i][i]=hessii(p,ftolhess,i,delti);
+ /*printf(" %f ",p[i]);*/
+ /*printf(" %lf ",hess[i][i]);*/
+ }
+
+ for (i=1;i<=npar;i++) {
+ for (j=1;j<=npar;j++) {
+ if (j>i) {
+ printf(".%d%d",i,j);fflush(stdout);
+ fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
+ hess[i][j]=hessij(p,delti,i,j);
+ hess[j][i]=hess[i][j];
+ /*printf(" %lf ",hess[i][j]);*/
+ }
+ }
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+ printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
+ fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
+
+ a=matrix(1,npar,1,npar);
+ y=matrix(1,npar,1,npar);
+ x=vector(1,npar);
+ indx=ivector(1,npar);
+ for (i=1;i<=npar;i++)
+ for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
+ ludcmp(a,npar,indx,&pd);
+
+ for (j=1;j<=npar;j++) {
+ for (i=1;i<=npar;i++) x[i]=0;
+ x[j]=1;
+ lubksb(a,npar,indx,x);
+ for (i=1;i<=npar;i++){
+ matcov[i][j]=x[i];
+ }
+ }
+
+ printf("\n#Hessian matrix#\n");
+ fprintf(ficlog,"\n#Hessian matrix#\n");
+ for (i=1;i<=npar;i++) {
+ for (j=1;j<=npar;j++) {
+ printf("%.3e ",hess[i][j]);
+ fprintf(ficlog,"%.3e ",hess[i][j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ }
+
+ /* Recompute Inverse */
+ for (i=1;i<=npar;i++)
+ for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
+ ludcmp(a,npar,indx,&pd);
+
+ /* printf("\n#Hessian matrix recomputed#\n");
+
+ for (j=1;j<=npar;j++) {
+ for (i=1;i<=npar;i++) x[i]=0;
+ x[j]=1;
+ lubksb(a,npar,indx,x);
+ for (i=1;i<=npar;i++){
+ y[i][j]=x[i];
+ printf("%.3e ",y[i][j]);
+ fprintf(ficlog,"%.3e ",y[i][j]);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ }
+ */
+
+ free_matrix(a,1,npar,1,npar);
+ free_matrix(y,1,npar,1,npar);
+ free_vector(x,1,npar);
+ free_ivector(indx,1,npar);
+ free_matrix(hess,1,npar,1,npar);
+
+
+}
+
+/*************** hessian matrix ****************/
+double hessii( double x[], double delta, int theta, double delti[])
+{
+ int i;
+ int l=1, lmax=20;
+ double k1,k2;
+ double p2[NPARMAX+1];
+ double res;
+ double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
+ double fx;
+ int k=0,kmax=10;
+ double l1;
+
+ fx=func(x);
+ for (i=1;i<=npar;i++) p2[i]=x[i];
+ for(l=0 ; l <=lmax; l++){
+ l1=pow(10,l);
+ delts=delt;
+ for(k=1 ; k <kmax; k=k+1){
+ delt = delta*(l1*k);
+ p2[theta]=x[theta] +delt;
+ k1=func(p2)-fx;
+ p2[theta]=x[theta]-delt;
+ k2=func(p2)-fx;
+ /*res= (k1-2.0*fx+k2)/delt/delt; */
+ res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
+
+#ifdef DEBUG
+ printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+ fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
+#endif
+ /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
+ if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
+ k=kmax;
+ }
+ else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
+ k=kmax; l=lmax*10.;
+ }
+ else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
+ delts=delt;
+ }
+ }
+ }
+ delti[theta]=delts;
+ return res;
+
+}
+
+double hessij( double x[], double delti[], int thetai,int thetaj)
+{
+ int i;
+ int l=1, l1, lmax=20;
+ double k1,k2,k3,k4,res,fx;
+ double p2[NPARMAX+1];
+ int k;
+
+ fx=func(x);
+ for (k=1; k<=2; k++) {
+ for (i=1;i<=npar;i++) p2[i]=x[i];
+ p2[thetai]=x[thetai]+delti[thetai]/k;
+ p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+ k1=func(p2)-fx;
+
+ p2[thetai]=x[thetai]+delti[thetai]/k;
+ p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ k2=func(p2)-fx;
+
+ p2[thetai]=x[thetai]-delti[thetai]/k;
+ p2[thetaj]=x[thetaj]+delti[thetaj]/k;
+ k3=func(p2)-fx;
+
+ p2[thetai]=x[thetai]-delti[thetai]/k;
+ p2[thetaj]=x[thetaj]-delti[thetaj]/k;
+ k4=func(p2)-fx;
+ res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
+#ifdef DEBUG
+ printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+ fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
+#endif
+ }
+ return res;
+}
+
+/************** Inverse of matrix **************/
+void ludcmp(double **a, int n, int *indx, double *d)
+{
+ int i,imax,j,k;
+ double big,dum,sum,temp;
+ double *vv;
+
+ vv=vector(1,n);
+ *d=1.0;
+ for (i=1;i<=n;i++) {
+ big=0.0;
+ for (j=1;j<=n;j++)
+ if ((temp=fabs(a[i][j])) > big) big=temp;
+ if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
+ vv[i]=1.0/big;
+ }
+ for (j=1;j<=n;j++) {
+ for (i=1;i<j;i++) {
+ sum=a[i][j];
+ for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
+ a[i][j]=sum;
+ }
+ big=0.0;
+ for (i=j;i<=n;i++) {
+ sum=a[i][j];
+ for (k=1;k<j;k++)
+ sum -= a[i][k]*a[k][j];
+ a[i][j]=sum;
+ if ( (dum=vv[i]*fabs(sum)) >= big) {
+ big=dum;
+ imax=i;
+ }
+ }
+ if (j != imax) {
+ for (k=1;k<=n;k++) {
+ dum=a[imax][k];
+ a[imax][k]=a[j][k];
+ a[j][k]=dum;
+ }
+ *d = -(*d);
+ vv[imax]=vv[j];
+ }
+ indx[j]=imax;
+ if (a[j][j] == 0.0) a[j][j]=TINY;
+ if (j != n) {
+ dum=1.0/(a[j][j]);
+ for (i=j+1;i<=n;i++) a[i][j] *= dum;
+ }
+ }
+ free_vector(vv,1,n); /* Doesn't work */
+;
+}
+
+void lubksb(double **a, int n, int *indx, double b[])
+{
+ int i,ii=0,ip,j;
+ double sum;
+
+ for (i=1;i<=n;i++) {
+ ip=indx[i];
+ sum=b[ip];
+ b[ip]=b[i];
+ if (ii)
+ for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
+ else if (sum) ii=i;
+ b[i]=sum;
+ }
+ for (i=n;i>=1;i--) {
+ sum=b[i];
+ for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
+ b[i]=sum/a[i][i];
+ }
+}
+
+/************ Frequencies ********************/
+void freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
+{ /* Some frequencies */
+
+ int i, m, jk, k1,i1, j1, bool, z1,z2,j;
+ int first;
+ double ***freq; /* Frequencies */
+ double *pp;
+ double pos, k2, dateintsum=0,k2cpt=0;
+ FILE *ficresp;
+ char fileresp[FILENAMELENGTH];
+
+ pp=vector(1,nlstate);
+ probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ strcpy(fileresp,"p");
+ strcat(fileresp,fileres);
+ if((ficresp=fopen(fileresp,"w"))==NULL) {
+ printf("Problem with prevalence resultfile: %s\n", fileresp);
+ fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
+ exit(0);
+ }
+ freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+ j1=0;
+
+ j=cptcoveff;
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}
+
+ first=1;
+
+ for(k1=1; k1<=j;k1++){
+ for(i1=1; i1<=ncodemax[k1];i1++){
+ j1++;
+ /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
+ scanf("%d", i);*/
+ for (i=-1; i<=nlstate+ndeath; i++)
+ for (jk=-1; jk<=nlstate+ndeath; jk++)
+ for(m=agemin; m <= agemax+3; m++)
+ freq[i][jk][m]=0;
+
+ dateintsum=0;
+ k2cpt=0;
+ for (i=1; i<=imx; i++) {
+ bool=1;
+ if (cptcovn>0) {
+ for (z1=1; z1<=cptcoveff; z1++)
+ if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+ bool=0;
+ }
+ if (bool==1) {
+ for(m=firstpass; m<=lastpass; m++){
+ k2=anint[m][i]+(mint[m][i]/12.);
+ if ((k2>=dateprev1) && (k2<=dateprev2)) {
+ if(agev[m][i]==0) agev[m][i]=agemax+1;
+ if(agev[m][i]==1) agev[m][i]=agemax+2;
+ if (m<lastpass) {
+ freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+ freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
+ }
+
+ if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
+ dateintsum=dateintsum+k2;
+ k2cpt++;
+ }
+ }
+ }
+ }
+ }
+
+ fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+
+ if (cptcovn>0) {
+ fprintf(ficresp, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(ficresp, "**********\n#");
+ }
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
+ fprintf(ficresp, "\n");
+
+ for(i=(int)agemin; i <= (int)agemax+3; i++){
+ if(i==(int)agemax+3){
+ fprintf(ficlog,"Total");
+ }else{
+ if(first==1){
+ first=0;
+ printf("See log file for details...\n");
+ }
+ fprintf(ficlog,"Age %d", i);
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+ pp[jk] += freq[jk][m][i];
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pos=0; m <=0 ; m++)
+ pos += freq[jk][m][i];
+ if(pp[jk]>=1.e-10){
+ if(first==1){
+ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }
+ fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
+ }else{
+ if(first==1)
+ printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+ fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
+ }
+ }
+
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+ pp[jk] += freq[jk][m][i];
+ }
+
+ for(jk=1,pos=0; jk <=nlstate ; jk++)
+ pos += pp[jk];
+ for(jk=1; jk <=nlstate ; jk++){
+ if(pos>=1.e-5){
+ if(first==1)
+ printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
+ }else{
+ if(first==1)
+ printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+ fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
+ }
+ if( i <= (int) agemax){
+ if(pos>=1.e-5){
+ fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
+ probs[i][jk][j1]= pp[jk]/pos;
+ /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
+ }
+ else
+ fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
+ }
+ }
+
+ for(jk=-1; jk <=nlstate+ndeath; jk++)
+ for(m=-1; m <=nlstate+ndeath; m++)
+ if(freq[jk][m][i] !=0 ) {
+ if(first==1)
+ printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
+ fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
+ }
+ if(i <= (int) agemax)
+ fprintf(ficresp,"\n");
+ if(first==1)
+ printf("Others in log...\n");
+ fprintf(ficlog,"\n");
+ }
+ }
+ }
+ dateintmean=dateintsum/k2cpt;
+
+ fclose(ficresp);
+ free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+ free_vector(pp,1,nlstate);
+
+ /* End of Freq */
+}
+
+/************ Prevalence ********************/
+void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
+{ /* Some frequencies */
+
+ int i, m, jk, k1, i1, j1, bool, z1,z2,j;
+ double ***freq; /* Frequencies */
+ double *pp;
+ double pos, k2;
+
+ pp=vector(1,nlstate);
+
+ freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
+ j1=0;
+
+ j=cptcoveff;
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}
+
+ for(k1=1; k1<=j;k1++){
+ for(i1=1; i1<=ncodemax[k1];i1++){
+ j1++;
+
+ for (i=-1; i<=nlstate+ndeath; i++)
+ for (jk=-1; jk<=nlstate+ndeath; jk++)
+ for(m=agemin; m <= agemax+3; m++)
+ freq[i][jk][m]=0;
+
+ for (i=1; i<=imx; i++) {
+ bool=1;
+ if (cptcovn>0) {
+ for (z1=1; z1<=cptcoveff; z1++)
+ if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
+ bool=0;
+ }
+ if (bool==1) {
+ for(m=firstpass; m<=lastpass; m++){
+ k2=anint[m][i]+(mint[m][i]/12.);
+ if ((k2>=dateprev1) && (k2<=dateprev2)) {
+ if(agev[m][i]==0) agev[m][i]=agemax+1;
+ if(agev[m][i]==1) agev[m][i]=agemax+2;
+ if (m<lastpass) {
+ if (calagedate>0)
+ freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
+ else
+ freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
+ freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];
+ }
+ }
+ }
+ }
+ }
+ for(i=(int)agemin; i <= (int)agemax+3; i++){
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
+ pp[jk] += freq[jk][m][i];
+ }
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=-1, pos=0; m <=0 ; m++)
+ pos += freq[jk][m][i];
+ }
+
+ for(jk=1; jk <=nlstate ; jk++){
+ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
+ pp[jk] += freq[jk][m][i];
+ }
+
+ for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
+
+ for(jk=1; jk <=nlstate ; jk++){
+ if( i <= (int) agemax){
+ if(pos>=1.e-5){
+ probs[i][jk][j1]= pp[jk]/pos;
+ }
+ }
+ }/* end jk */
+ }/* end i */
+ } /* end i1 */
+ } /* end k1 */
+
+
+ free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
+ free_vector(pp,1,nlstate);
+
+} /* End of Freq */
+
+/************* Waves Concatenation ***************/
+
+void concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
+{
+ /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
+ Death is a valid wave (if date is known).
+ mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
+ dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]
+ and mw[mi+1][i]. dh depends on stepm.
+ */
+
+ int i, mi, m;
+ /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
+ double sum=0., jmean=0.;*/
+ int first;
+ int j, k=0,jk, ju, jl;
+ double sum=0.;
+ first=0;
+ jmin=1e+5;
+ jmax=-1;
+ jmean=0.;
+ for(i=1; i<=imx; i++){
+ mi=0;
+ m=firstpass;
+ while(s[m][i] <= nlstate){
+ if(s[m][i]>=1)
+ mw[++mi][i]=m;
+ if(m >=lastpass)
+ break;
+ else
+ m++;
+ }/* end while */
+ if (s[m][i] > nlstate){
+ mi++; /* Death is another wave */
+ /* if(mi==0) never been interviewed correctly before death */
+ /* Only death is a correct wave */
+ mw[mi][i]=m;
+ }
+
+ wav[i]=mi;
+ if(mi==0){
+ if(first==0){
+ printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
+ first=1;
+ }
+ if(first==1){
+ fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
+ }
+ } /* end mi==0 */
+ }
+
+ for(i=1; i<=imx; i++){
+ for(mi=1; mi<wav[i];mi++){
+ if (stepm <=0)
+ dh[mi][i]=1;
+ else{
+ if (s[mw[mi+1][i]][i] > nlstate) {
+ if (agedc[i] < 2*AGESUP) {
+ j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
+ if(j==0) j=1; /* Survives at least one month after exam */
+ k=k+1;
+ if (j >= jmax) jmax=j;
+ if (j <= jmin) jmin=j;
+ sum=sum+j;
+ /*if (j<0) printf("j=%d num=%d \n",j,i); */
+ }
+ }
+ else{
+ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
+ k=k+1;
+ if (j >= jmax) jmax=j;
+ else if (j <= jmin)jmin=j;
+ /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
+ sum=sum+j;
+ }
+ jk= j/stepm;
+ jl= j -jk*stepm;
+ ju= j -(jk+1)*stepm;
+ if(jl <= -ju)
+ dh[mi][i]=jk;
+ else
+ dh[mi][i]=jk+1;
+ if(dh[mi][i]==0)
+ dh[mi][i]=1; /* At least one step */
+ }
+ }
+ }
+ jmean=sum/k;
+ printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+ fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+ }
+
+/*********** Tricode ****************************/
+void tricode(int *Tvar, int **nbcode, int imx)
+{
+ int Ndum[20],ij=1, k, j, i;
+ int cptcode=0;
+ cptcoveff=0;
+
+ for (k=0; k<19; k++) Ndum[k]=0;
+ for (k=1; k<=7; k++) ncodemax[k]=0;
+
+ for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
+ for (i=1; i<=imx; i++) {
+ ij=(int)(covar[Tvar[j]][i]);
+ Ndum[ij]++;
+ /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
+ if (ij > cptcode) cptcode=ij;
+ }
+
+ for (i=0; i<=cptcode; i++) {
+ if(Ndum[i]!=0) ncodemax[j]++;
+ }
+ ij=1;
+
+
+ for (i=1; i<=ncodemax[j]; i++) {
+ for (k=0; k<=19; k++) {
+ if (Ndum[k] != 0) {
+ nbcode[Tvar[j]][ij]=k;
+
+ ij++;
+ }
+ if (ij > ncodemax[j]) break;
+ }
+ }
+ }
+
+ for (k=0; k<19; k++) Ndum[k]=0;
+
+ for (i=1; i<=ncovmodel-2; i++) {
+ ij=Tvar[i];
+ Ndum[ij]++;
+ }
+
+ ij=1;
+ for (i=1; i<=10; i++) {
+ if((Ndum[i]!=0) && (i<=ncovcol)){
+ Tvaraff[ij]=i;
+ ij++;
+ }
+ }
+
+ cptcoveff=ij-1;
+}
+
+/*********** Health Expectancies ****************/
+
+void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
+
+{
+ /* Health expectancies */
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+ double age, agelim, hf;
+ double ***p3mat,***varhe;
+ double **dnewm,**doldm;
+ double *xp;
+ double **gp, **gm;
+ double ***gradg, ***trgradg;
+ int theta;
+
+ varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
+ xp=vector(1,npar);
+ dnewm=matrix(1,nlstate*2,1,npar);
+ doldm=matrix(1,nlstate*2,1,nlstate*2);
+
+ fprintf(ficreseij,"# Health expectancies\n");
+ fprintf(ficreseij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++)
+ fprintf(ficreseij," %1d-%1d (SE)",i,j);
+ fprintf(ficreseij,"\n");
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* We compute the life expectancy from trapezoids spaced every estepm months
+ * This is mainly to measure the difference between two models: for example
+ * if stepm=24 months pijx are given only every 2 years and by summing them
+ * we are calculating an estimate of the Life Expectancy assuming a linear
+ * progression inbetween and thus overestimating or underestimating according
+ * to the curvature of the survival function. If, for the same date, we
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ * to compare the new estimate of Life expectancy with the same linear
+ * hypothesis. A more precise result, taking into account a more precise
+ * curvature will be obtained if estepm is as small as stepm. */
+
+ /* For example we decided to compute the life expectancy with the smallest unit */
+ /* 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
+ 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
+ means that if the survival funtion is printed only each two years of age and if
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same
+ results. So we changed our mind and took the option of the best precision.
+ */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+
+ agelim=AGESUP;
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
+ nstepm=(int) rint((agelim-age)*YEARM/stepm);
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
+ gp=matrix(0,nhstepm,1,nlstate*2);
+ gm=matrix(0,nhstepm,1,nlstate*2);
+
+ /* Computed by stepm unit matrices, product of hstepm matrices, stored
+ in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
+ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
+
+
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+
+ /* Computing Variances of health expectancies */
+
+ for(theta=1; theta <=npar; theta++){
+ for(i=1; i<=npar; i++){
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ }
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+
+ cptj=0;
+ for(j=1; j<= nlstate; j++){
+ for(i=1; i<=nlstate; i++){
+ cptj=cptj+1;
+ for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
+ gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+ }
+ }
+ }
+
+
+ for(i=1; i<=npar; i++)
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+
+ cptj=0;
+ for(j=1; j<= nlstate; j++){
+ for(i=1;i<=nlstate;i++){
+ cptj=cptj+1;
+ for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
+ gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+ }
+ }
+ }
+ for(j=1; j<= nlstate*2; j++)
+ for(h=0; h<=nhstepm-1; h++){
+ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+ }
+ }
+
+/* End theta */
+
+ trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
+
+ for(h=0; h<=nhstepm-1; h++)
+ for(j=1; j<=nlstate*2;j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[h][j][theta]=gradg[h][theta][j];
+
+
+ for(i=1;i<=nlstate*2;i++)
+ for(j=1;j<=nlstate*2;j++)
+ varhe[i][j][(int)age] =0.;
+
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+ for(h=0;h<=nhstepm-1;h++){
+ for(k=0;k<=nhstepm-1;k++){
+ matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
+ for(i=1;i<=nlstate*2;i++)
+ for(j=1;j<=nlstate*2;j++)
+ varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+ }
+ }
+ /* Computing expectancies */
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++)
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+ eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+
+/* 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]);*/
+
+ }
+
+ fprintf(ficreseij,"%3.0f",age );
+ cptj=0;
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++){
+ cptj++;
+ fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+ }
+ fprintf(ficreseij,"\n");
+
+ free_matrix(gm,0,nhstepm,1,nlstate*2);
+ free_matrix(gp,0,nhstepm,1,nlstate*2);
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
+ free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+ free_vector(xp,1,npar);
+ free_matrix(dnewm,1,nlstate*2,1,npar);
+ free_matrix(doldm,1,nlstate*2,1,nlstate*2);
+ free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
+}
+
+/************ 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 ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
+{
+ /* Variance of health expectancies */
+ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+ /* double **newm;*/
+ double **dnewm,**doldm;
+ double **dnewmp,**doldmp;
+ int i, j, nhstepm, hstepm, h, nstepm ;
+ int k, cptcode;
+ 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 ***p3mat;
+ double age,agelim, hf;
+ double ***mobaverage;
+ int theta;
+ char digit[4];
+ char digitp[16];
+
+ char fileresprobmorprev[FILENAMELENGTH];
+
+ if(popbased==1)
+ strcpy(digitp,"-populbased-");
+ else
+ strcpy(digitp,"-stablbased-");
+ if(mobilav==1)
+ strcat(digitp,"mobilav-");
+ else
+ strcat(digitp,"nomobil-");
+ if (mobilav==1) {
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ movingaverage(probs, bage, fage, mobaverage);
+ }
+
+ strcpy(fileresprobmorprev,"prmorprev");
+ sprintf(digit,"%-d",ij);
+ /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
+ strcat(fileresprobmorprev,digit); /* Tvar to be done */
+ strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
+ strcat(fileresprobmorprev,fileres);
+ if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprobmorprev);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
+ }
+ printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
+ fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
+ fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
+ for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+ fprintf(ficresprobmorprev," p.%-d SE",j);
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
+ }
+ fprintf(ficresprobmorprev,"\n");
+ if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+ printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+ fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+ exit(0);
+ }
+ else{
+ fprintf(ficgp,"\n# Routine varevsij");
+ }
+ if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ printf("Problem with html file: %s\n", optionfilehtm);
+ fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+ exit(0);
+ }
+ else{
+ fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
+ fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
+ }
+ varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+
+ fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
+ fprintf(ficresvij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++)
+ fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+ fprintf(ficresvij,"\n");
+
+ xp=vector(1,npar);
+ dnewm=matrix(1,nlstate,1,npar);
+ doldm=matrix(1,nlstate,1,nlstate);
+ dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
+ doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+
+ gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
+ gpp=vector(nlstate+1,nlstate+ndeath);
+ gmp=vector(nlstate+1,nlstate+ndeath);
+ trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* For example we decided to compute the life expectancy with the smallest unit */
+ /* 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
+ and note for a fixed period like k years */
+ /* We decided (b) to get a life expectancy respecting the most precise curvature of the
+ survival function given by stepm (the optimization length). Unfortunately it
+ means that if the survival funtion is printed only each two years of age and if
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same
+ results. So we changed our mind and took the option of the best precision.
+ */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ agelim = AGESUP;
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
+ gp=matrix(0,nhstepm,1,nlstate);
+ gm=matrix(0,nhstepm,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);
+ }
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+
+ if (popbased==1) {
+ if(mobilav !=1){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][ij];
+ }else{ /* mobilav=1 */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][ij];
+ }
+ }
+
+ 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];
+ }
+ }
+ /* This for computing forces of mortality (h=1)as a weighted average */
+ for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
+ for(i=1; i<= nlstate; i++)
+ gpp[j] += prlim[i][i]*p3mat[i][j][1];
+ }
+ /* end force of mortality */
+
+ for(i=1; i<=npar; i++) /* Computes gradient */
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+
+ if (popbased==1) {
+ if(mobilav !=1){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][ij];
+ }else{ /* mobilav=1 */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][ij];
+ }
+ }
+
+ for(j=1; j<= nlstate; j++){
+ for(h=0; h<=nhstepm; h++){
+ for(i=1, gm[h][j]=0.;i<=nlstate;i++)
+ gm[h][j] += prlim[i][i]*p3mat[i][j][h];
+ }
+ }
+ /* This for computing force of mortality (h=1)as a weighted average */
+ for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+ for(i=1; i<= nlstate; i++)
+ gmp[j] += prlim[i][i]*p3mat[i][j][1];
+ }
+ /* end force of mortality */
+
+ for(j=1; j<= nlstate; j++) /* vareij */
+ for(h=0; h<=nhstepm; h++){
+ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+ }
+ for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
+ gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
+ }
+
+ } /* End theta */
+
+ trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
+
+ for(h=0; h<=nhstepm; h++) /* veij */
+ for(j=1; j<=nlstate;j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[h][j][theta]=gradg[h][theta][j];
+
+ for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
+ for(theta=1; theta <=npar; theta++)
+ trgradgp[j][theta]=gradgp[theta][j];
+
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+ for(i=1;i<=nlstate;i++)
+ for(j=1;j<=nlstate;j++)
+ vareij[i][j][(int)age] =0.;
+
+ for(h=0;h<=nhstepm;h++){
+ for(k=0;k<=nhstepm;k++){
+ matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
+ for(i=1;i<=nlstate;i++)
+ for(j=1;j<=nlstate;j++)
+ vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
+ }
+ }
+
+ /* pptj */
+ matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
+ matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
+ for(j=nlstate+1;j<=nlstate+ndeath;j++)
+ for(i=nlstate+1;i<=nlstate+ndeath;i++)
+ varppt[j][i]=doldmp[j][i];
+ /* end ppptj */
+ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
+ prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
+
+ if (popbased==1) {
+ if(mobilav !=1){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][ij];
+ }else{ /* mobilav=1 */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][ij];
+ }
+ }
+
+ /* This for computing force of mortality (h=1)as a weighted average */
+ for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
+ for(i=1; i<= nlstate; i++)
+ gmp[j] += prlim[i][i]*p3mat[i][j][1];
+ }
+ /* end force of mortality */
+
+ fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
+ for(j=nlstate+1; j<=(nlstate+ndeath);j++){
+ fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
+ for(i=1; i<=nlstate;i++){
+ fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
+ }
+ }
+ fprintf(ficresprobmorprev,"\n");
+
+ fprintf(ficresvij,"%.0f ",age );
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++){
+ fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
+ }
+ fprintf(ficresvij,"\n");
+ free_matrix(gp,0,nhstepm,1,nlstate);
+ free_matrix(gm,0,nhstepm,1,nlstate);
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
+ free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ } /* End age */
+ free_vector(gpp,nlstate+1,nlstate+ndeath);
+ free_vector(gmp,nlstate+1,nlstate+ndeath);
+ free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
+ free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
+ fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
+ /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
+ fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
+ fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
+ fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
+ fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
+ fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
+ fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
+ /* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
+*/
+ fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
+
+ free_vector(xp,1,npar);
+ free_matrix(doldm,1,nlstate,1,nlstate);
+ free_matrix(dnewm,1,nlstate,1,npar);
+ free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
+ free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
+ free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ fclose(ficresprobmorprev);
+ fclose(ficgp);
+ fclose(fichtm);
+
+}
+
+/************ Variance of prevlim ******************/
+void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
+{
+ /* Variance of prevalence limit */
+ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
+ double **newm;
+ double **dnewm,**doldm;
+ int i, j, nhstepm, hstepm;
+ int k, cptcode;
+ double *xp;
+ double *gp, *gm;
+ double **gradg, **trgradg;
+ double age,agelim;
+ int theta;
+
+ fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
+ fprintf(ficresvpl,"# Age");
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresvpl," %1d-%1d",i,i);
+ fprintf(ficresvpl,"\n");
+
+ xp=vector(1,npar);
+ dnewm=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 = AGESUP;
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
+ nhstepm=(int) rint((agelim-age)*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);
+ 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);
+ }
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ for(i=1;i<=nlstate;i++)
+ gp[i] = prlim[i][i];
+
+ for(i=1; i<=npar; i++) /* Computes gradient */
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
+ for(i=1;i<=nlstate;i++)
+ gm[i] = prlim[i][i];
+
+ for(i=1;i<=nlstate;i++)
+ gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
+ } /* 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];
+
+ for(i=1;i<=nlstate;i++)
+ varpl[i][(int)age] =0.;
+ matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
+ for(i=1;i<=nlstate;i++)
+ varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
+
+ fprintf(ficresvpl,"%.0f ",age );
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
+ fprintf(ficresvpl,"\n");
+ free_vector(gp,1,nlstate);
+ free_vector(gm,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(dnewm,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)
+{
+ int i, j=0, i1, k1, l1, t, tj;
+ int k2, l2, j1, z1;
+ int k=0,l, cptcode;
+ int first=1, first1;
+ 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,agelim, cov[NCOVMAX];
+ 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,fileres);
+ if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprobcov);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
+ }
+ strcpy(fileresprobcor,"probcor");
+ strcat(fileresprobcor,fileres);
+ if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", fileresprobcor);
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
+ }
+ printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
+ printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
+ printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+ fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
+
+ fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
+ fprintf(ficresprob,"# Age");
+ fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
+ fprintf(ficresprobcov,"# Age");
+ fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
+ fprintf(ficresprobcov,"# Age");
+
+
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=(nlstate+ndeath);j++){
+ fprintf(ficresprob," p%1d-%1d (SE)",i,j);
+ fprintf(ficresprobcov," p%1d-%1d ",i,j);
+ fprintf(ficresprobcor," p%1d-%1d ",i,j);
+ }
+ fprintf(ficresprob,"\n");
+ fprintf(ficresprobcov,"\n");
+ fprintf(ficresprobcor,"\n");
+ xp=vector(1,npar);
+ dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
+ varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
+ first=1;
+ if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+ printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
+ fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
+ exit(0);
+ }
+ else{
+ fprintf(ficgp,"\n# Routine varprob");
+ }
+ if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ printf("Problem with html file: %s\n", optionfilehtm);
+ fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
+ exit(0);
+ }
+ else{
+ fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
+ fprintf(fichtm,"\n");
+
+ fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
+ fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
+ fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
+
+ }
+
+
+ cov[1]=1;
+ tj=cptcoveff;
+ if (cptcovn<1) {tj=1;ncodemax[1]=1;}
+ j1=0;
+ for(t=1; t<=tj;t++){
+ for(i1=1; i1<=ncodemax[t];i1++){
+ j1++;
+
+ if (cptcovn>0) {
+ fprintf(ficresprob, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(ficresprob, "**********\n#");
+ fprintf(ficresprobcov, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(ficresprobcov, "**********\n#");
+
+ fprintf(ficgp, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(ficgp, "**********\n#");
+
+
+ fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
+
+ fprintf(ficresprobcor, "\n#********** Variable ");
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
+ fprintf(ficgp, "**********\n#");
+ }
+
+ for (age=bage; age<=fage; age ++){
+ cov[2]=age;
+ for (k=1; k<=cptcovn;k++) {
+ cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
+ }
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
+ for (k=1; k<=cptcovprod;k++)
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
+
+ gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
+ trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
+ gp=vector(1,(nlstate)*(nlstate+ndeath));
+ gm=vector(1,(nlstate)*(nlstate+ndeath));
+
+ for(theta=1; theta <=npar; theta++){
+ for(i=1; i<=npar; i++)
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);
+
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);
+
+ k=0;
+ for(i=1; i<= (nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ gp[k]=pmmij[i][j];
+ }
+ }
+
+ for(i=1; i<=npar; i++)
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);
+
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);
+ k=0;
+ for(i=1; i<=(nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ gm[k]=pmmij[i][j];
+ }
+ }
+
+ for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
+ gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];
+ }
+
+ for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
+ for(theta=1; theta <=npar; theta++)
+ trgradg[j][theta]=gradg[theta][j];
+
+ matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
+ matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
+
+ pmij(pmmij,cov,ncovmodel,x,nlstate);
+
+ k=0;
+ for(i=1; i<=(nlstate); i++){
+ for(j=1; j<=(nlstate+ndeath);j++){
+ k=k+1;
+ mu[k][(int) age]=pmmij[i][j];
+ }
+ }
+ for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
+ for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
+ varpij[i][j][(int)age] = doldm[i][j];
+
+ /*printf("\n%d ",(int)age);
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+ fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
+ }*/
+
+ fprintf(ficresprob,"\n%d ",(int)age);
+ fprintf(ficresprobcov,"\n%d ",(int)age);
+ fprintf(ficresprobcor,"\n%d ",(int)age);
+
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
+ fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
+ fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
+ fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
+ }
+ i=0;
+ for (k=1; k<=(nlstate);k++){
+ for (l=1; l<=(nlstate+ndeath);l++){
+ i=i++;
+ fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
+ fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
+ for (j=1; j<=i;j++){
+ fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
+ fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
+ }
+ }
+ }/* end of loop for state */
+ } /* end of loop for age */
+
+ /* Confidence intervalle of pij */
+ /*
+ fprintf(ficgp,"\nset noparametric;unset label");
+ fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+ fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
+ fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
+ fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
+ fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
+ */
+
+ /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
+ first1=1;
+ for (k2=1; k2<=(nlstate);k2++){
+ for (l2=1; l2<=(nlstate+ndeath);l2++){
+ if(l2==k2) continue;
+ j=(k2-1)*(nlstate+ndeath)+l2;
+ for (k1=1; k1<=(nlstate);k1++){
+ for (l1=1; l1<=(nlstate+ndeath);l1++){
+ if(l1==k1) continue;
+ i=(k1-1)*(nlstate+ndeath)+l1;
+ if(i<=j) continue;
+ for (age=bage; age<=fage; age ++){
+ if ((int)age %5==0){
+ v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
+ v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
+ cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
+ mu1=mu[i][(int) age]/stepm*YEARM ;
+ mu2=mu[j][(int) age]/stepm*YEARM;
+ c12=cv12/sqrt(v1*v2);
+ /* Computing eigen value of matrix of covariance */
+ lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
+ /* Eigen vectors */
+ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
+ /*v21=sqrt(1.-v11*v11); *//* error */
+ v21=(lc1-v1)/cv12*v11;
+ v12=-v21;
+ v22=v11;
+ tnalp=v21/v11;
+ if(first1==1){
+ first1=0;
+ printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+ }
+ fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
+ /*printf(fignu*/
+ /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
+ /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
+ if(first==1){
+ first=0;
+ fprintf(ficgp,"\nset parametric;unset label");
+ fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
+ fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
+ fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
+ fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
+ fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
+ 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(lc2),\
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ }else{
+ first=0;
+ fprintf(fichtm," %d (%.3f),",(int) age, c12);
+ fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
+ fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
+ fprintf(ficgp,"\nreplot %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(lc2),\
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
+ }/* if first */
+ } /* age mod 5 */
+ } /* end loop age */
+ fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
+ first=1;
+ } /*l12 */
+ } /* k12 */
+ } /*l1 */
+ }/* k1 */
+ } /* loop covariates */
+ free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
+ free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
+ free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+ free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+ free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
+ }
+ free_vector(xp,1,npar);
+ fclose(ficresprob);
+ fclose(ficresprobcov);
+ fclose(ficresprobcor);
+ fclose(ficgp);
+ fclose(fichtm);
+}
+
+
+/******************* Printing html file ***********/
+void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
+ int lastpass, int stepm, int weightopt, char model[],\
+ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
+ int popforecast, int estepm ,\
+ double jprev1, double mprev1,double anprev1, \
+ double jprev2, double mprev2,double anprev2){
+ int jj1, k1, i1, cpt;
+ /*char optionfilehtm[FILENAMELENGTH];*/
+ if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
+ printf("Problem with %s \n",optionfilehtm), exit(0);
+ fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
+ }
+
+ fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
+ - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
+ - Life expectancies by age and initial health status (estepm=%2d months):
+ <a href=\"e%s\">e%s</a> <br>\n</li>", \
+ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
+
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
+
+ m=cptcoveff;
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+ for(i1=1; i1<=ncodemax[k1];i1++){
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++)
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+ }
+ /* Pij */
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
+<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ /* Quasi-incidences */
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
+<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ /* Stable prevalence in each health state */
+ for(cpt=1; cpt<nlstate;cpt++){
+ fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
+<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ }
+ for(cpt=1; cpt<=nlstate;cpt++) {
+ fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
+<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ }
+ fprintf(fichtm,"\n<br>- Total life expectancy by age and
+health expectancies in states (1) and (2): e%s%d.png<br>
+<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
+ } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+
+
+ fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
+ - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
+ - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
+ - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
+ - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
+ - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
+ - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
+
+ if(popforecast==1) fprintf(fichtm,"\n
+ - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
+ - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
+ <br>",fileres,fileres,fileres,fileres);
+ else
+ fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);
+fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
+
+ m=cptcoveff;
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}
+
+ jj1=0;
+ for(k1=1; k1<=m;k1++){
+ for(i1=1; i1<=ncodemax[k1];i1++){
+ jj1++;
+ if (cptcovn > 0) {
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
+ for (cpt=1; cpt<=cptcoveff;cpt++)
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
+ }
+ for(cpt=1; cpt<=nlstate;cpt++) {
+ fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
+interval) in state (%d): v%s%d%d.png <br>
+<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
+ }
+ } /* end i1 */
+ }/* End k1 */
+ fprintf(fichtm,"</ul>");
+fclose(fichtm);
+}
+
+/******************* Gnuplot file **************/
+void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
+
+ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
+ int ng;
+ if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
+ printf("Problem with file %s",optionfilegnuplot);
+ fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
+ }
+
+#ifdef windows
+ fprintf(ficgp,"cd \"%s\" \n",pathc);
+#endif
+m=pow(2,cptcoveff);
+
+ /* 1eme*/
+ for (cpt=1; cpt<= nlstate ; cpt ++) {
+ for (k1=1; k1<= m ; k1 ++) {
+ fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
+
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);
+ for (i=1; i<= nlstate ; i ++) {
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
+ }
+ }
+ /*2 eme*/
+
+ for (k1=1; k1<= m ; k1 ++) {
+ fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
+ fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
+
+ for (i=1; i<= nlstate+1 ; i ++) {
+ k=2*i;
+ fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
+ else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
+ fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ fprintf(ficgp,"\" t\"\" w l 0,");
+ fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
+ for (j=1; j<= nlstate+1 ; j ++) {
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
+ else fprintf(ficgp," \%%*lf (\%%*lf)");
+ }
+ if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
+ else fprintf(ficgp,"\" t\"\" w l 0,");
+ }
+ }
+
+ /*3eme*/
+
+ for (k1=1; k1<= m ; k1 ++) {
+ for (cpt=1; cpt<= nlstate ; cpt ++) {
+ k=2+nlstate*(2*cpt-2);
+ fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+ fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
+ /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+ fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
+
+ */
+ for (i=1; i< nlstate ; i ++) {
+ fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
+
+ }
+ }
+ }
+
+ /* CV preval stat */
+ for (k1=1; k1<= m ; k1 ++) {
+ for (cpt=1; cpt<nlstate ; cpt ++) {
+ k=3;
+ fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
+
+ for (i=1; i< nlstate ; i ++)
+ fprintf(ficgp,"+$%d",k+i+1);
+ fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
+
+ l=3+(nlstate+ndeath)*cpt;
+ fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
+ for (i=1; i< nlstate ; i ++) {
+ l=3+(nlstate+ndeath)*cpt;
+ fprintf(ficgp,"+$%d",l+i+1);
+ }
+ fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
+ }
+ }
+
+ /* proba elementaires */
+ for(i=1,jk=1; i <=nlstate; i++){
+ for(k=1; k <=(nlstate+ndeath); k++){
+ if (k != i) {
+ for(j=1; j <=ncovmodel; j++){
+ fprintf(ficgp,"p%d=%f ",jk,p[jk]);
+ jk++;
+ fprintf(ficgp,"\n");
+ }
+ }
+ }
+ }
+
+ for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
+ for(jk=1; jk <=m; jk++) {
+ fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
+ if (ng==2)
+ fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
+ else
+ fprintf(ficgp,"\nset title \"Probability\"\n");
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
+ i=1;
+ for(k2=1; k2<=nlstate; k2++) {
+ k3=i;
+ for(k=1; k<=(nlstate+ndeath); k++) {
+ if (k != k2){
+ if(ng==2)
+ fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
+ else
+ fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
+ ij=1;
+ for(j=3; j <=ncovmodel; j++) {
+ if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+ fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+ ij++;
+ }
+ else
+ fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+ }
+ fprintf(ficgp,")/(1");
+
+ for(k1=1; k1 <=nlstate; k1++){
+ fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
+ ij=1;
+ for(j=3; j <=ncovmodel; j++){
+ if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
+ fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
+ ij++;
+ }
+ else
+ fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
+ }
+ fprintf(ficgp,")");
+ }
+ fprintf(ficgp,") t \"p%d%d\" ", k2,k);
+ if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
+ i=i+ncovmodel;
+ }
+ } /* end k */
+ } /* end k2 */
+ } /* end jk */
+ } /* end ng */
+ fclose(ficgp);
+} /* end gnuplot */
+
+
+/*************** Moving average **************/
+void movingaverage(double ***probs, double bage,double fage, double ***mobaverage){
+
+ int i, cpt, cptcod;
+ double age;
+ for (age=bage; age<=fage; age++)
+ for (i=1; i<=nlstate;i++)
+ for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
+ mobaverage[(int)age][i][cptcod]=0.;
+
+ for (age=bage+4; age<=fage; age++){
+ for (i=1; i<=nlstate;i++){
+ for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ for (cpt=0;cpt<=4;cpt++){
+ mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]+probs[(int)age-cpt][i][cptcod];
+ }
+ mobaverage[(int)age-2][i][cptcod]=mobaverage[(int)age-2][i][cptcod]/5;
+ }
+ }
+ }
+
+}
+
+
+/************** Forecasting ******************/
+prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
+
+ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+ int *popage;
+ double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ double *popeffectif,*popcount;
+ double ***p3mat;
+ char fileresf[FILENAMELENGTH];
+
+ agelim=AGESUP;
+calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
+
+ prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+
+
+ strcpy(fileresf,"f");
+ strcat(fileresf,fileres);
+ if((ficresf=fopen(fileresf,"w"))==NULL) {
+ printf("Problem with forecast resultfile: %s\n", fileresf);
+ fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
+ }
+ printf("Computing forecasting: result on file '%s' \n", fileresf);
+ fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
+
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;
+
+ if (mobilav==1) {
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ movingaverage(probs, ageminpar,fage, mobaverage);
+ }
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ if (stepm<=12) stepsize=1;
+
+ agelim=AGESUP;
+
+ hstepm=1;
+ hstepm=hstepm/stepm;
+ yp1=modf(dateintmean,&yp);
+ anprojmean=yp;
+ yp2=modf((yp1*12),&yp);
+ mprojmean=yp;
+ yp1=modf((yp2*30.5),&yp);
+ jprojmean=yp;
+ if(jprojmean==0) jprojmean=1;
+ if(mprojmean==0) jprojmean=1;
+
+ fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);
+
+ for(cptcov=1;cptcov<=i2;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ k=k+1;
+ fprintf(ficresf,"\n#******");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficresf,"******\n");
+ fprintf(ficresf,"# StartingAge FinalAge");
+ for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
+
+
+ for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
+ fprintf(ficresf,"\n");
+ fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);
+
+ for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ nhstepm = nhstepm/hstepm;
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+
+ for (h=0; h<=nhstepm; h++){
+ if (h==(int) (calagedate+YEARM*cpt)) {
+ fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);
+ }
+ for(j=1; j<=nlstate+ndeath;j++) {
+ kk1=0.;kk2=0;
+ for(i=1; i<=nlstate;i++) {
+ if (mobilav==1)
+ kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+ else {
+ kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+ }
+
+ }
+ if (h==(int)(calagedate+12*cpt)){
+ fprintf(ficresf," %.3f", kk1);
+
+ }
+ }
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ }
+ }
+ }
+ }
+
+ if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+ fclose(ficresf);
+}
+/************** Forecasting ******************/
+populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
+
+ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
+ int *popage;
+ double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
+ double *popeffectif,*popcount;
+ double ***p3mat,***tabpop,***tabpopprev;
+ char filerespop[FILENAMELENGTH];
+
+ tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ agelim=AGESUP;
+ calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
+
+ prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+
+
+ strcpy(filerespop,"pop");
+ strcat(filerespop,fileres);
+ if((ficrespop=fopen(filerespop,"w"))==NULL) {
+ printf("Problem with forecast resultfile: %s\n", filerespop);
+ fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
+ }
+ printf("Computing forecasting: result on file '%s' \n", filerespop);
+ fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
+
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;
+
+ if (mobilav==1) {
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ movingaverage(probs, ageminpar, fage, mobaverage);
+ }
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ if (stepm<=12) stepsize=1;
+
+ agelim=AGESUP;
+
+ hstepm=1;
+ hstepm=hstepm/stepm;
+
+ if (popforecast==1) {
+ if((ficpop=fopen(popfile,"r"))==NULL) {
+ printf("Problem with population file : %s\n",popfile);exit(0);
+ fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
+ }
+ popage=ivector(0,AGESUP);
+ popeffectif=vector(0,AGESUP);
+ popcount=vector(0,AGESUP);
+
+ i=1;
+ while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
+
+ imx=i;
+ for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
+ }
+
+ for(cptcov=1;cptcov<=i2;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
+ k=k+1;
+ fprintf(ficrespop,"\n#******");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficrespop,"******\n");
+ fprintf(ficrespop,"# Age");
+ for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
+ if (popforecast==1) fprintf(ficrespop," [Population]");
+
+ for (cpt=0; cpt<=0;cpt++) {
+ fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+
+ for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ nhstepm = nhstepm/hstepm;
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+
+ for (h=0; h<=nhstepm; h++){
+ if (h==(int) (calagedate+YEARM*cpt)) {
+ fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ }
+ for(j=1; j<=nlstate+ndeath;j++) {
+ kk1=0.;kk2=0;
+ for(i=1; i<=nlstate;i++) {
+ if (mobilav==1)
+ kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
+ else {
+ kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
+ }
+ }
+ if (h==(int)(calagedate+12*cpt)){
+ tabpop[(int)(agedeb)][j][cptcod]=kk1;
+ /*fprintf(ficrespop," %.3f", kk1);
+ if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
+ }
+ }
+ for(i=1; i<=nlstate;i++){
+ kk1=0.;
+ for(j=1; j<=nlstate;j++){
+ kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
+ }
+ tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
+ }
+
+ if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
+ fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ }
+ }
+
+ /******/
+
+ for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
+ fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
+ for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
+ nhstepm = nhstepm/hstepm;
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ for (h=0; h<=nhstepm; h++){
+ if (h==(int) (calagedate+YEARM*cpt)) {
+ fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
+ }
+ for(j=1; j<=nlstate+ndeath;j++) {
+ kk1=0.;kk2=0;
+ for(i=1; i<=nlstate;i++) {
+ kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
+ }
+ if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
+ }
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ }
+ }
+ }
+ }
+
+ if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+ if (popforecast==1) {
+ free_ivector(popage,0,AGESUP);
+ free_vector(popeffectif,0,AGESUP);
+ free_vector(popcount,0,AGESUP);
+ }
+ free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ fclose(ficrespop);
+}
+
+/***********************************************/
+/**************** Main Program *****************/
+/***********************************************/
+
+int main(int argc, char *argv[])
+{
+
+ int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
+ double agedeb, agefin,hf;
+ double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
+
+ double fret;
+ double **xi,tmp,delta;
+
+ double dum; /* Dummy variable */
+ double ***p3mat;
+ double ***mobaverage;
+ int *indx;
+ char line[MAXLINE], linepar[MAXLINE];
+ char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
+ int firstobs=1, lastobs=10;
+ int sdeb, sfin; /* Status at beginning and end */
+ int c, h , cpt,l;
+ int ju,jl, mi;
+ int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
+ int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;
+ int mobilav=0,popforecast=0;
+ int hstepm, nhstepm;
+ double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
+
+ double bage, fage, age, agelim, agebase;
+ double ftolpl=FTOL;
+ double **prlim;
+ double *severity;
+ double ***param; /* Matrix of parameters */
+ double *p;
+ double **matcov; /* Matrix of covariance */
+ double ***delti3; /* Scale */
+ double *delti; /* Scale */
+ double ***eij, ***vareij;
+ double **varpl; /* Variances of prevalence limits by age */
+ double *epj, vepp;
+ double kk1, kk2;
+ double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;
+
+
+ char *alph[]={"a","a","b","c","d","e"}, str[4];
+
+
+ char z[1]="c", occ;
+#include <sys/time.h>
+#include <time.h>
+ char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
+
+ /* long total_usecs;
+ struct timeval start_time, end_time;
+
+ gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
+ getcwd(pathcd, size);
+
+ printf("\n%s",version);
+ if(argc <=1){
+ printf("\nEnter the parameter file name: ");
+ scanf("%s",pathtot);
+ }
+ else{
+ strcpy(pathtot,argv[1]);
+ }
+ /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
+ /*cygwin_split_path(pathtot,path,optionfile);
+ printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
+ /* cutv(path,optionfile,pathtot,'\\');*/
+
+ split(pathtot,path,optionfile,optionfilext,optionfilefiname);
+ printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ chdir(path);
+ replace(pathc,path);
+
+/*-------- arguments in the command line --------*/
+
+ /* Log file */
+ strcat(filelog, optionfilefiname);
+ strcat(filelog,".log"); /* */
+ if((ficlog=fopen(filelog,"w"))==NULL) {
+ printf("Problem with logfile %s\n",filelog);
+ goto end;
+ }
+ fprintf(ficlog,"Log filename:%s\n",filelog);
+ fprintf(ficlog,"\n%s",version);
+ fprintf(ficlog,"\nEnter the parameter file name: ");
+ fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ fflush(ficlog);
+
+ /* */
+ strcpy(fileres,"r");
+ strcat(fileres, optionfilefiname);
+ strcat(fileres,".txt"); /* Other files have txt extension */
+
+ /*---------arguments file --------*/
+
+ if((ficpar=fopen(optionfile,"r"))==NULL) {
+ printf("Problem with optionfile %s\n",optionfile);
+ fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
+ goto end;
+ }
+
+ strcpy(filereso,"o");
+ strcat(filereso,fileres);
+ if((ficparo=fopen(filereso,"w"))==NULL) {
+ printf("Problem with Output resultfile: %s\n", filereso);
+ fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
+ goto end;
+ }
+
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
+ printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
+ fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
+while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+
+ covar=matrix(0,NCOVMAX,1,n);
+ cptcovn=0;
+ if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
+
+ ncovmodel=2+cptcovn;
+ nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
+
+ /* Read guess parameters */
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ for(i=1; i <=nlstate; i++)
+ for(j=1; j <=nlstate+ndeath-1; j++){
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ if(mle==1)
+ printf("%1d%1d",i,j);
+ fprintf(ficlog,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar," %lf",¶m[i][j][k]);
+ if(mle==1){
+ printf(" %lf",param[i][j][k]);
+ fprintf(ficlog," %lf",param[i][j][k]);
+ }
+ else
+ fprintf(ficlog," %lf",param[i][j][k]);
+ fprintf(ficparo," %lf",param[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficparo,"\n");
+ }
+
+ npar= (nlstate+ndeath-1)*nlstate*ncovmodel;
+
+ p=param[1][1];
+
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
+ delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */
+ for(i=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath-1; j++){
+ fscanf(ficpar,"%1d%1d",&i1,&j1);
+ printf("%1d%1d",i,j);
+ fprintf(ficparo,"%1d%1d",i1,j1);
+ for(k=1; k<=ncovmodel;k++){
+ fscanf(ficpar,"%le",&delti3[i][j][k]);
+ printf(" %le",delti3[i][j][k]);
+ fprintf(ficparo," %le",delti3[i][j][k]);
+ }
+ fscanf(ficpar,"\n");
+ printf("\n");
+ fprintf(ficparo,"\n");
+ }
+ }
+ delti=delti3[1][1];
+
+ /* Reads comments: lines beginning with '#' */
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ matcov=matrix(1,npar,1,npar);
+ for(i=1; i <=npar; i++){
+ fscanf(ficpar,"%s",&str);
+ if(mle==1)
+ printf("%s",str);
+ fprintf(ficlog,"%s",str);
+ fprintf(ficparo,"%s",str);
+ for(j=1; j <=i; j++){
+ fscanf(ficpar," %le",&matcov[i][j]);
+ if(mle==1){
+ printf(" %.5le",matcov[i][j]);
+ fprintf(ficlog," %.5le",matcov[i][j]);
+ }
+ else
+ fprintf(ficlog," %.5le",matcov[i][j]);
+ fprintf(ficparo," %.5le",matcov[i][j]);
+ }
+ fscanf(ficpar,"\n");
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficparo,"\n");
+ }
+ for(i=1; i <=npar; i++)
+ for(j=i+1;j<=npar;j++)
+ matcov[i][j]=matcov[j][i];
+
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+
+ /*-------- Rewriting paramater file ----------*/
+ strcpy(rfileres,"r"); /* "Rparameterfile */
+ strcat(rfileres,optionfilefiname); /* Parameter file first name*/
+ strcat(rfileres,"."); /* */
+ strcat(rfileres,optionfilext); /* Other files have txt extension */
+ if((ficres =fopen(rfileres,"w"))==NULL) {
+ printf("Problem writing new parameter file: %s\n", fileres);goto end;
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
+ }
+ fprintf(ficres,"#%s\n",version);
+
+ /*-------- data file ----------*/
+ if((fic=fopen(datafile,"r"))==NULL) {
+ printf("Problem with datafile: %s\n", datafile);goto end;
+ fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+ }
+
+ n= lastobs;
+ severity = vector(1,maxwav);
+ outcome=imatrix(1,maxwav+1,1,n);
+ num=ivector(1,n);
+ moisnais=vector(1,n);
+ annais=vector(1,n);
+ moisdc=vector(1,n);
+ andc=vector(1,n);
+ agedc=vector(1,n);
+ cod=ivector(1,n);
+ weight=vector(1,n);
+ for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
+ mint=matrix(1,maxwav,1,n);
+ anint=matrix(1,maxwav,1,n);
+ s=imatrix(1,maxwav+1,1,n);
+ adl=imatrix(1,maxwav+1,1,n);
+ tab=ivector(1,NCOVMAX);
+ ncodemax=ivector(1,8);
+
+ i=1;
+ while (fgets(line, MAXLINE, fic) != NULL) {
+ if ((i >= firstobs) && (i <=lastobs)) {
+
+ for (j=maxwav;j>=1;j--){
+ cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
+ strcpy(line,stra);
+ cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+ cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+ }
+
+ cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
+ cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
+
+ cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
+ cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
+
+ cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
+ for (j=ncovcol;j>=1;j--){
+ cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+ }
+ num[i]=atol(stra);
+
+ /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+ printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+
+ i=i+1;
+ }
+ }
+ /* printf("ii=%d", ij);
+ scanf("%d",i);*/
+ imx=i-1; /* Number of individuals */
+
+ /* for (i=1; i<=imx; i++){
+ if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
+ if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
+ if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
+ }*/
+ /* for (i=1; i<=imx; i++){
+ if (s[4][i]==9) s[4][i]=-1;
+ printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
+
+
+ /* Calculation of the number of parameter from char model*/
+ Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
+ Tprod=ivector(1,15);
+ Tvaraff=ivector(1,15);
+ Tvard=imatrix(1,15,1,2);
+ Tage=ivector(1,15);
+
+ if (strlen(model) >1){
+ j=0, j1=0, k1=1, k2=1;
+ j=nbocc(model,'+');
+ j1=nbocc(model,'*');
+ cptcovn=j+1;
+ cptcovprod=j1;
+
+ strcpy(modelsav,model);
+ if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
+ printf("Error. Non available option model=%s ",model);
+ fprintf(ficlog,"Error. Non available option model=%s ",model);
+ goto end;
+ }
+
+ for(i=(j+1); i>=1;i--){
+ cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
+ if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */
+ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
+ /*scanf("%d",i);*/
+ if (strchr(strb,'*')) { /* Model includes a product */
+ cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
+ if (strcmp(strc,"age")==0) { /* Vn*age */
+ cptcovprod--;
+ cutv(strb,stre,strd,'V');
+ Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
+ cptcovage++;
+ Tage[cptcovage]=i;
+ /*printf("stre=%s ", stre);*/
+ }
+ else if (strcmp(strd,"age")==0) { /* or age*Vn */
+ cptcovprod--;
+ cutv(strb,stre,strc,'V');
+ Tvar[i]=atoi(stre);
+ cptcovage++;
+ Tage[cptcovage]=i;
+ }
+ else { /* Age is not in the model */
+ cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
+ Tvar[i]=ncovcol+k1;
+ cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
+ Tprod[k1]=i;
+ Tvard[k1][1]=atoi(strc); /* m*/
+ Tvard[k1][2]=atoi(stre); /* n */
+ Tvar[cptcovn+k2]=Tvard[k1][1];
+ Tvar[cptcovn+k2+1]=Tvard[k1][2];
+ for (k=1; k<=lastobs;k++)
+ covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
+ k1++;
+ k2=k2+2;
+ }
+ }
+ else { /* no more sum */
+ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
+ /* scanf("%d",i);*/
+ cutv(strd,strc,strb,'V');
+ Tvar[i]=atoi(strc);
+ }
+ strcpy(modelsav,stra);
+ /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
+ scanf("%d",i);*/
+ } /* end of loop + */
+ } /* end model */
+
+ /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
+ printf("cptcovprod=%d ", cptcovprod);
+ fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
+ scanf("%d ",i);*/
+ fclose(fic);
+
+ /* if(mle==1){*/
+ if (weightopt != 1) { /* Maximisation without weights*/
+ for(i=1;i<=n;i++) weight[i]=1.0;
+ }
+ /*-calculation of age at interview from date of interview and age at death -*/
+ agev=matrix(1,maxwav,1,imx);
+
+ for (i=1; i<=imx; i++) {
+ for(m=2; (m<= maxwav); m++) {
+ if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
+ anint[m][i]=9999;
+ s[m][i]=-1;
+ }
+ if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
+ }
+ }
+
+ for (i=1; i<=imx; i++) {
+ agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
+ for(m=1; (m<= maxwav); m++){
+ if(s[m][i] >0){
+ if (s[m][i] >= nlstate+1) {
+ if(agedc[i]>0)
+ if(moisdc[i]!=99 && andc[i]!=9999)
+ agev[m][i]=agedc[i];
+ /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
+ else {
+ if (andc[i]!=9999){
+ printf("Warning negative age at death: %d line:%d\n",num[i],i);
+ fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
+ agev[m][i]=-1;
+ }
+ }
+ }
+ else if(s[m][i] !=9){ /* Should no more exist */
+ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
+ if(mint[m][i]==99 || anint[m][i]==9999)
+ agev[m][i]=1;
+ else if(agev[m][i] <agemin){
+ agemin=agev[m][i];
+ /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
+ }
+ else if(agev[m][i] >agemax){
+ agemax=agev[m][i];
+ /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
+ }
+ /*agev[m][i]=anint[m][i]-annais[i];*/
+ /* agev[m][i] = age[i]+2*m;*/
+ }
+ else { /* =9 */
+ agev[m][i]=1;
+ s[m][i]=-1;
+ }
+ }
+ else /*= 0 Unknown */
+ agev[m][i]=1;
+ }
+
+ }
+ for (i=1; i<=imx; i++) {
+ for(m=1; (m<= maxwav); m++){
+ if (s[m][i] > (nlstate+ndeath)) {
+ printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+ fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
+ goto end;
+ }
+ }
+ }
+
+printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
+
+ free_vector(severity,1,maxwav);
+ free_imatrix(outcome,1,maxwav+1,1,n);
+ free_vector(moisnais,1,n);
+ free_vector(annais,1,n);
+ /* free_matrix(mint,1,maxwav,1,n);
+ free_matrix(anint,1,maxwav,1,n);*/
+ free_vector(moisdc,1,n);
+ free_vector(andc,1,n);
+
+
+ wav=ivector(1,imx);
+ dh=imatrix(1,lastpass-firstpass+1,1,imx);
+ mw=imatrix(1,lastpass-firstpass+1,1,imx);
+
+ /* Concatenates waves */
+ concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
+
+
+ Tcode=ivector(1,100);
+ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
+ ncodemax[1]=1;
+ if (cptcovn > 0) tricode(Tvar,nbcode,imx);
+
+ codtab=imatrix(1,100,1,10);
+ h=0;
+ m=pow(2,cptcoveff);
+
+ for(k=1;k<=cptcoveff; k++){
+ for(i=1; i <=(m/pow(2,k));i++){
+ for(j=1; j <= ncodemax[k]; j++){
+ for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
+ h++;
+ if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
+ /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
+ }
+ }
+ }
+ }
+ /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
+ codtab[1][2]=1;codtab[2][2]=2; */
+ /* for(i=1; i <=m ;i++){
+ for(k=1; k <=cptcovn; k++){
+ printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
+ }
+ printf("\n");
+ }
+ scanf("%d",i);*/
+
+ /* Calculates basic frequencies. Computes observed prevalence at single age
+ and prints on file fileres'p'. */
+
+
+
+ pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+
+ /* For Powell, parameters are in a vector p[] starting at p[1]
+ so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
+ p=param[1][1]; /* *(*(*(param +1)+1)+0) */
+
+ if(mle==1){
+ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
+ }
+
+ /*--------- results files --------------*/
+ fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
+
+
+ jk=1;
+ fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
+ for(i=1,jk=1; i <=nlstate; i++){
+ for(k=1; k <=(nlstate+ndeath); k++){
+ if (k != i)
+ {
+ printf("%d%d ",i,k);
+ fprintf(ficlog,"%d%d ",i,k);
+ fprintf(ficres,"%1d%1d ",i,k);
+ for(j=1; j <=ncovmodel; j++){
+ printf("%f ",p[jk]);
+ fprintf(ficlog,"%f ",p[jk]);
+ fprintf(ficres,"%f ",p[jk]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
+ }
+ }
+ if(mle==1){
+ /* Computing hessian and covariance matrix */
+ ftolhess=ftol; /* Usually correct */
+ hesscov(matcov, p, npar, delti, ftolhess, func);
+ }
+ fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
+ printf("# Scales (for hessian or gradient estimation)\n");
+ fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
+ for(i=1,jk=1; i <=nlstate; i++){
+ for(j=1; j <=nlstate+ndeath; j++){
+ if (j!=i) {
+ fprintf(ficres,"%1d%1d",i,j);
+ printf("%1d%1d",i,j);
+ fprintf(ficlog,"%1d%1d",i,j);
+ for(k=1; k<=ncovmodel;k++){
+ printf(" %.5e",delti[jk]);
+ fprintf(ficlog," %.5e",delti[jk]);
+ fprintf(ficres," %.5e",delti[jk]);
+ jk++;
+ }
+ printf("\n");
+ fprintf(ficlog,"\n");
+ fprintf(ficres,"\n");
+ }
+ }
+ }
+
+ k=1;
+ fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
+ if(mle==1)
+ printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
+ fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
+ for(i=1;i<=npar;i++){
+ /* if (k>nlstate) k=1;
+ i1=(i-1)/(ncovmodel*nlstate)+1;
+ fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
+ printf("%s%d%d",alph[k],i1,tab[i]);*/
+ fprintf(ficres,"%3d",i);
+ if(mle==1)
+ printf("%3d",i);
+ fprintf(ficlog,"%3d",i);
+ for(j=1; j<=i;j++){
+ fprintf(ficres," %.5e",matcov[i][j]);
+ if(mle==1)
+ printf(" %.5e",matcov[i][j]);
+ fprintf(ficlog," %.5e",matcov[i][j]);
+ }
+ fprintf(ficres,"\n");
+ if(mle==1)
+ printf("\n");
+ fprintf(ficlog,"\n");
+ k++;
+ }
+
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+ estepm=0;
+ fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
+ if (estepm==0 || estepm < stepm) estepm=stepm;
+ if (fage <= 2) {
+ bage = ageminpar;
+ fage = agemaxpar;
+ }
+
+ fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
+ fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+ fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
+
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
+ fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav);
+ fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,&mobilav);
+
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+
+ dateprev1=anprev1+mprev1/12.+jprev1/365.;
+ dateprev2=anprev2+mprev2/12.+jprev2/365.;
+
+ fscanf(ficpar,"pop_based=%d\n",&popbased);
+ fprintf(ficparo,"pop_based=%d\n",popbased);
+ fprintf(ficres,"pop_based=%d\n",popbased);
+
+ while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
+fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
+fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
+
+
+while((c=getc(ficpar))=='#' && c!= EOF){
+ ungetc(c,ficpar);
+ fgets(line, MAXLINE, ficpar);
+ puts(line);
+ fputs(line,ficparo);
+ }
+ ungetc(c,ficpar);
+
+ fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
+ fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+ fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
+
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
+/*------------ gnuplot -------------*/
+ strcpy(optionfilegnuplot,optionfilefiname);
+ strcat(optionfilegnuplot,".gp");
+ if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
+ printf("Problem with file %s",optionfilegnuplot);
+ }
+ fclose(ficgp);
+ printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
+/*--------- index.htm --------*/
+
+ strcpy(optionfilehtm,optionfile);
+ strcat(optionfilehtm,".htm");
+ if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
+ printf("Problem with %s \n",optionfilehtm), exit(0);
+ }
+
+ fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
+\n
+Total number of observations=%d <br>\n
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
+<hr size=\"2\" color=\"#EC5E5E\">
+ <ul><li><h4>Parameter files</h4>\n
+ - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
+ - Log file of the run: <a href=\"%s\">%s</a><br>\n
+ - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
+ fclose(fichtm);
+
+ printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
+
+/*------------ free_vector -------------*/
+ chdir(path);
+
+ free_ivector(wav,1,imx);
+ free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
+ free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
+ free_ivector(num,1,n);
+ free_vector(agedc,1,n);
+ /*free_matrix(covar,1,NCOVMAX,1,n);*/
+ fclose(ficparo);
+ fclose(ficres);
+
+
+ /*--------------- Prevalence limit --------------*/
+
+ strcpy(filerespl,"pl");
+ strcat(filerespl,fileres);
+ if((ficrespl=fopen(filerespl,"w"))==NULL) {
+ printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+ fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
+ }
+ printf("Computing prevalence limit: result on file '%s' \n", filerespl);
+ fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
+ fprintf(ficrespl,"#Prevalence limit\n");
+ fprintf(ficrespl,"#Age ");
+ for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
+ fprintf(ficrespl,"\n");
+
+ prlim=matrix(1,nlstate,1,nlstate);
+ pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
+ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
+ k=0;
+ agebase=ageminpar;
+ agelim=agemaxpar;
+ ftolpl=1.e-10;
+ i1=cptcoveff;
+ if (cptcovn < 1){i1=1;}
+
+ for(cptcov=1;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ k=k+1;
+ /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
+ fprintf(ficrespl,"\n#******");
+ printf("\n#******");
+ fprintf(ficlog,"\n#******");
+ for(j=1;j<=cptcoveff;j++) {
+ fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
+ fprintf(ficrespl,"******\n");
+ printf("******\n");
+ fprintf(ficlog,"******\n");
+
+ for (age=agebase; age<=agelim; age++){
+ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+ fprintf(ficrespl,"%.0f",age );
+ for(i=1; i<=nlstate;i++)
+ fprintf(ficrespl," %.5f", prlim[i][i]);
+ fprintf(ficrespl,"\n");
+ }
+ }
+ }
+ fclose(ficrespl);
+
+ /*------------- h Pij x at various ages ------------*/
+
+ strcpy(filerespij,"pij"); strcat(filerespij,fileres);
+ if((ficrespij=fopen(filerespij,"w"))==NULL) {
+ printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
+ fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
+ }
+ printf("Computing pij: result on file '%s' \n", filerespij);
+ fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
+
+ stepsize=(int) (stepm+YEARM-1)/YEARM;
+ /*if (stepm<=24) stepsize=2;*/
+
+ agelim=AGESUP;
+ hstepm=stepsize*YEARM; /* Every year of age */
+ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
+
+ /* hstepm=1; aff par mois*/
+
+ k=0;
+ for(cptcov=1;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ k=k+1;
+ fprintf(ficrespij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficrespij,"******\n");
+
+ for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
+
+ /* nhstepm=nhstepm*YEARM; aff par mois*/
+
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ oldm=oldms;savm=savms;
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
+ fprintf(ficrespij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespij," %1d-%1d",i,j);
+ fprintf(ficrespij,"\n");
+ for (h=0; h<=nhstepm; h++){
+ fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate+ndeath;j++)
+ fprintf(ficrespij," %.5f", p3mat[i][j][h]);
+ fprintf(ficrespij,"\n");
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ fprintf(ficrespij,"\n");
+ }
+ }
+ }
+
+ varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
+
+ fclose(ficrespij);
+
+
+ /*---------- Forecasting ------------------*/
+ if((stepm == 1) && (strcmp(model,".")==0)){
+ prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
+ if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
+ }
+ else{
+ erreur=108;
+ printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+ fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
+ }
+
+
+ /*---------- Health expectancies and variances ------------*/
+
+ strcpy(filerest,"t");
+ strcat(filerest,fileres);
+ if((ficrest=fopen(filerest,"w"))==NULL) {
+ printf("Problem with total LE resultfile: %s\n", filerest);goto end;
+ fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
+ }
+ printf("Computing Total LEs with variances: file '%s' \n", filerest);
+ fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+
+
+ strcpy(filerese,"e");
+ strcat(filerese,fileres);
+ if((ficreseij=fopen(filerese,"w"))==NULL) {
+ printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+ fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
+ }
+ printf("Computing Health Expectancies: result on file '%s' \n", filerese);
+ fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+
+ strcpy(fileresv,"v");
+ strcat(fileresv,fileres);
+ if((ficresvij=fopen(fileresv,"w"))==NULL) {
+ printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
+ fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
+ }
+ printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
+ calagedate=-1;
+ prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
+ if (mobilav==1) {
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+ movingaverage(probs, ageminpar, fage, mobaverage);
+ }
+
+ k=0;
+ for(cptcov=1;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ k=k+1;
+ fprintf(ficrest,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficrest,"******\n");
+
+ fprintf(ficreseij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficreseij,"******\n");
+
+ fprintf(ficresvij,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficresvij,"******\n");
+
+ eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
+
+ vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
+ if(popbased==1){
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
+ }
+
+
+ fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+ for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
+ fprintf(ficrest,"\n");
+
+ epj=vector(1,nlstate+1);
+ for(age=bage; age <=fage ;age++){
+ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
+ if (popbased==1) {
+ if(mobilav !=1){
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=probs[(int)age][i][k];
+ }else{ /* mobilav=1 */
+ for(i=1; i<=nlstate;i++)
+ prlim[i][i]=mobaverage[(int)age][i][k];
+ }
+ }
+
+ fprintf(ficrest," %4.0f",age);
+ for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
+ for(i=1, epj[j]=0.;i <=nlstate;i++) {
+ epj[j] += prlim[i][i]*eij[i][j][(int)age];
+ /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
+ }
+ epj[nlstate+1] +=epj[j];
+ }
+
+ for(i=1, vepp=0.;i <=nlstate;i++)
+ for(j=1;j <=nlstate;j++)
+ vepp += vareij[i][j][(int)age];
+ fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
+ for(j=1;j <=nlstate;j++){
+ fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
+ }
+ fprintf(ficrest,"\n");
+ }
+ }
+ }
+free_matrix(mint,1,maxwav,1,n);
+ free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
+ free_vector(weight,1,n);
+ fclose(ficreseij);
+ fclose(ficresvij);
+ fclose(ficrest);
+ fclose(ficpar);
+ free_vector(epj,1,nlstate+1);
+
+ /*------- Variance limit prevalence------*/
+
+ strcpy(fileresvpl,"vpl");
+ strcat(fileresvpl,fileres);
+ if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
+ printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);
+ exit(0);
+ }
+ printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);
+
+ k=0;
+ for(cptcov=1;cptcov<=i1;cptcov++){
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
+ k=k+1;
+ fprintf(ficresvpl,"\n#****** ");
+ for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ fprintf(ficresvpl,"******\n");
+
+ varpl=matrix(1,nlstate,(int) bage, (int) fage);
+ oldm=oldms;savm=savms;
+ varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
+ }
+ }
+
+ fclose(ficresvpl);
+
+ /*---------- End : free ----------------*/
+ free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
+
+ free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
+
+
+ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
+ free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
+ free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
+ free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
+
+ free_matrix(matcov,1,npar,1,npar);
+ free_vector(delti,1,npar);
+ free_matrix(agev,1,maxwav,1,imx);
+ free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
+ if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
+
+ fprintf(fichtm,"\n</body>");
+ fclose(fichtm);
+ fclose(ficgp);
+
+
+ if(erreur >0){
+ printf("End of Imach with error or warning %d\n",erreur);
+ fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
+ }else{
+ printf("End of Imach\n");
+ fprintf(ficlog,"End of Imach\n");
+ }
+ printf("See log file on %s\n",filelog);
+ fclose(ficlog);
+ /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
+
+ /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
+ /*printf("Total time was %d uSec.\n", total_usecs);*/
+ /*------ End -----------*/
+
+
+ end:
+#ifdef windows
+ /* chdir(pathcd);*/
+#endif
+ /*system("wgnuplot graph.plt");*/
+ /*system("../gp37mgw/wgnuplot graph.plt");*/
+ /*system("cd ../gp37mgw");*/
+ /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
+ strcpy(plotcmd,GNUPLOTPROGRAM);
+ strcat(plotcmd," ");
+ strcat(plotcmd,optionfilegnuplot);
+ system(plotcmd);
+
+#ifdef windows
+ while (z[0] != 'q') {
+ /* chdir(path); */
+ printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
+ scanf("%s",z);
+ if (z[0] == 'c') system("./imach");
+ else if (z[0] == 'e') system(optionfilehtm);
+ else if (z[0] == 'g') system(plotcmd);
+ else if (z[0] == 'q') exit(0);
+ }
+#endif
+}
+
+
git://henry.ined.fr / .git / commitdiff