1: /* $Id: imach.c,v 1.74 2003/05/02 18:51:41 brouard Exp $
2: Interpolated Markov Chain
3:
4: Short summary of the programme:
5:
6: This program computes Healthy Life Expectancies from
7: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
8: first survey ("cross") where individuals from different ages are
9: interviewed on their health status or degree of disability (in the
10: case of a health survey which is our main interest) -2- at least a
11: second wave of interviews ("longitudinal") which measure each change
12: (if any) in individual health status. Health expectancies are
13: computed from the time spent in each health state according to a
14: model. More health states you consider, more time is necessary to reach the
15: Maximum Likelihood of the parameters involved in the model. The
16: simplest model is the multinomial logistic model where pij is the
17: probability to be observed in state j at the second wave
18: conditional to be observed in state i at the first wave. Therefore
19: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
20: 'age' is age and 'sex' is a covariate. If you want to have a more
21: complex model than "constant and age", you should modify the program
22: where the markup *Covariates have to be included here again* invites
23: you to do it. More covariates you add, slower the
24: convergence.
25:
26: The advantage of this computer programme, compared to a simple
27: multinomial logistic model, is clear when the delay between waves is not
28: identical for each individual. Also, if a individual missed an
29: intermediate interview, the information is lost, but taken into
30: account using an interpolation or extrapolation.
31:
32: hPijx is the probability to be observed in state i at age x+h
33: conditional to the observed state i at age x. The delay 'h' can be
34: split into an exact number (nh*stepm) of unobserved intermediate
35: states. This elementary transition (by month, quarter,
36: semester or year) is modelled as a multinomial logistic. The hPx
37: matrix is simply the matrix product of nh*stepm elementary matrices
38: and the contribution of each individual to the likelihood is simply
39: hPijx.
40:
41: Also this programme outputs the covariance matrix of the parameters but also
42: of the life expectancies. It also computes the stable prevalence.
43:
44: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
45: Institut national d'études démographiques, Paris.
46: This software have been partly granted by Euro-REVES, a concerted action
47: from the European Union.
48: It is copyrighted identically to a GNU software product, ie programme and
49: software can be distributed freely for non commercial use. Latest version
50: can be accessed at http://euroreves.ined.fr/imach .
51:
52: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
53: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
54:
55: **********************************************************************/
56: /*
57: main
58: read parameterfile
59: read datafile
60: concatwav
61: if (mle >= 1)
62: mlikeli
63: print results files
64: if mle==1
65: computes hessian
66: read end of parameter file: agemin, agemax, bage, fage, estepm
67: begin-prev-date,...
68: open gnuplot file
69: open html file
70: stable prevalence
71: for age prevalim()
72: h Pij x
73: variance of p varprob
74: forecasting if prevfcast==1 prevforecast call prevalence()
75: health expectancies
76: Variance-covariance of DFLE
77: prevalence()
78: movingaverage()
79: varevsij()
80: if popbased==1 varevsij(,popbased)
81: total life expectancies
82: Variance of stable prevalence
83: end
84: */
85:
86:
87:
88:
89: #include <math.h>
90: #include <stdio.h>
91: #include <stdlib.h>
92: #include <unistd.h>
93:
94: #define MAXLINE 256
95: #define GNUPLOTPROGRAM "gnuplot"
96: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
97: #define FILENAMELENGTH 80
98: /*#define DEBUG*/
99: #define windows
100: #define GLOCK_ERROR_NOPATH -1 /* empty path */
101: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
102:
103: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
104: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
105:
106: #define NINTERVMAX 8
107: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
108: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
109: #define NCOVMAX 8 /* Maximum number of covariates */
110: #define MAXN 20000
111: #define YEARM 12. /* Number of months per year */
112: #define AGESUP 130
113: #define AGEBASE 40
114: #ifdef windows
115: #define DIRSEPARATOR '\\'
116: #define ODIRSEPARATOR '/'
117: #else
118: #define DIRSEPARATOR '/'
119: #define ODIRSEPARATOR '\\'
120: #endif
121:
122: char version[80]="Imach version 0.95, February 2003, INED-EUROREVES ";
123: int erreur; /* Error number */
124: int nvar;
125: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
126: int npar=NPARMAX;
127: int nlstate=2; /* Number of live states */
128: int ndeath=1; /* Number of dead states */
129: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
130: int popbased=0;
131:
132: int *wav; /* Number of waves for this individuual 0 is possible */
133: int maxwav; /* Maxim number of waves */
134: int jmin, jmax; /* min, max spacing between 2 waves */
135: int mle, weightopt;
136: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
137: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
138: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
139: * wave mi and wave mi+1 is not an exact multiple of stepm. */
140: double jmean; /* Mean space between 2 waves */
141: double **oldm, **newm, **savm; /* Working pointers to matrices */
142: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
143: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
144: FILE *ficlog;
145: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
146: FILE *ficresprobmorprev;
147: FILE *fichtm; /* Html File */
148: FILE *ficreseij;
149: char filerese[FILENAMELENGTH];
150: FILE *ficresvij;
151: char fileresv[FILENAMELENGTH];
152: FILE *ficresvpl;
153: char fileresvpl[FILENAMELENGTH];
154: char title[MAXLINE];
155: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
156: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
157:
158: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
159: char filelog[FILENAMELENGTH]; /* Log file */
160: char filerest[FILENAMELENGTH];
161: char fileregp[FILENAMELENGTH];
162: char popfile[FILENAMELENGTH];
163:
164: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
165:
166: #define NR_END 1
167: #define FREE_ARG char*
168: #define FTOL 1.0e-10
169:
170: #define NRANSI
171: #define ITMAX 200
172:
173: #define TOL 2.0e-4
174:
175: #define CGOLD 0.3819660
176: #define ZEPS 1.0e-10
177: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
178:
179: #define GOLD 1.618034
180: #define GLIMIT 100.0
181: #define TINY 1.0e-20
182:
183: static double maxarg1,maxarg2;
184: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
185: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
186:
187: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
188: #define rint(a) floor(a+0.5)
189:
190: static double sqrarg;
191: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
192: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
193:
194: int imx;
195: int stepm;
196: /* Stepm, step in month: minimum step interpolation*/
197:
198: int estepm;
199: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
200:
201: int m,nb;
202: int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
203: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
204: double **pmmij, ***probs;
205: double dateintmean=0;
206:
207: double *weight;
208: int **s; /* Status */
209: double *agedc, **covar, idx;
210: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
211:
212: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
213: double ftolhess; /* Tolerance for computing hessian */
214:
215: /**************** split *************************/
216: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
217: {
218: char *ss; /* pointer */
219: int l1, l2; /* length counters */
220:
221: l1 = strlen(path ); /* length of path */
222: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
223: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
224: if ( ss == NULL ) { /* no directory, so use current */
225: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
226: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
227: /* get current working directory */
228: /* extern char* getcwd ( char *buf , int len);*/
229: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
230: return( GLOCK_ERROR_GETCWD );
231: }
232: strcpy( name, path ); /* we've got it */
233: } else { /* strip direcotry from path */
234: ss++; /* after this, the filename */
235: l2 = strlen( ss ); /* length of filename */
236: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
237: strcpy( name, ss ); /* save file name */
238: strncpy( dirc, path, l1 - l2 ); /* now the directory */
239: dirc[l1-l2] = 0; /* add zero */
240: }
241: l1 = strlen( dirc ); /* length of directory */
242: #ifdef windows
243: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
244: #else
245: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
246: #endif
247: ss = strrchr( name, '.' ); /* find last / */
248: ss++;
249: strcpy(ext,ss); /* save extension */
250: l1= strlen( name);
251: l2= strlen(ss)+1;
252: strncpy( finame, name, l1-l2);
253: finame[l1-l2]= 0;
254: return( 0 ); /* we're done */
255: }
256:
257:
258: /******************************************/
259:
260: void replace(char *s, char*t)
261: {
262: int i;
263: int lg=20;
264: i=0;
265: lg=strlen(t);
266: for(i=0; i<= lg; i++) {
267: (s[i] = t[i]);
268: if (t[i]== '\\') s[i]='/';
269: }
270: }
271:
272: int nbocc(char *s, char occ)
273: {
274: int i,j=0;
275: int lg=20;
276: i=0;
277: lg=strlen(s);
278: for(i=0; i<= lg; i++) {
279: if (s[i] == occ ) j++;
280: }
281: return j;
282: }
283:
284: void cutv(char *u,char *v, char*t, char occ)
285: {
286: /* cuts string t into u and v where u is ended by char occ excluding it
287: and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
288: gives u="abcedf" and v="ghi2j" */
289: int i,lg,j,p=0;
290: i=0;
291: for(j=0; j<=strlen(t)-1; j++) {
292: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
293: }
294:
295: lg=strlen(t);
296: for(j=0; j<p; j++) {
297: (u[j] = t[j]);
298: }
299: u[p]='\0';
300:
301: for(j=0; j<= lg; j++) {
302: if (j>=(p+1))(v[j-p-1] = t[j]);
303: }
304: }
305:
306: /********************** nrerror ********************/
307:
308: void nrerror(char error_text[])
309: {
310: fprintf(stderr,"ERREUR ...\n");
311: fprintf(stderr,"%s\n",error_text);
312: exit(EXIT_FAILURE);
313: }
314: /*********************** vector *******************/
315: double *vector(int nl, int nh)
316: {
317: double *v;
318: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
319: if (!v) nrerror("allocation failure in vector");
320: return v-nl+NR_END;
321: }
322:
323: /************************ free vector ******************/
324: void free_vector(double*v, int nl, int nh)
325: {
326: free((FREE_ARG)(v+nl-NR_END));
327: }
328:
329: /************************ivector *******************************/
330: int *ivector(long nl,long nh)
331: {
332: int *v;
333: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
334: if (!v) nrerror("allocation failure in ivector");
335: return v-nl+NR_END;
336: }
337:
338: /******************free ivector **************************/
339: void free_ivector(int *v, long nl, long nh)
340: {
341: free((FREE_ARG)(v+nl-NR_END));
342: }
343:
344: /******************* imatrix *******************************/
345: int **imatrix(long nrl, long nrh, long ncl, long nch)
346: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
347: {
348: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
349: int **m;
350:
351: /* allocate pointers to rows */
352: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
353: if (!m) nrerror("allocation failure 1 in matrix()");
354: m += NR_END;
355: m -= nrl;
356:
357:
358: /* allocate rows and set pointers to them */
359: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
360: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
361: m[nrl] += NR_END;
362: m[nrl] -= ncl;
363:
364: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
365:
366: /* return pointer to array of pointers to rows */
367: return m;
368: }
369:
370: /****************** free_imatrix *************************/
371: void free_imatrix(m,nrl,nrh,ncl,nch)
372: int **m;
373: long nch,ncl,nrh,nrl;
374: /* free an int matrix allocated by imatrix() */
375: {
376: free((FREE_ARG) (m[nrl]+ncl-NR_END));
377: free((FREE_ARG) (m+nrl-NR_END));
378: }
379:
380: /******************* matrix *******************************/
381: double **matrix(long nrl, long nrh, long ncl, long nch)
382: {
383: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
384: double **m;
385:
386: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
387: if (!m) nrerror("allocation failure 1 in matrix()");
388: m += NR_END;
389: m -= nrl;
390:
391: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
392: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
393: m[nrl] += NR_END;
394: m[nrl] -= ncl;
395:
396: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
397: return m;
398: /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])
399: */
400: }
401:
402: /*************************free matrix ************************/
403: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
404: {
405: free((FREE_ARG)(m[nrl]+ncl-NR_END));
406: free((FREE_ARG)(m+nrl-NR_END));
407: }
408:
409: /******************* ma3x *******************************/
410: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
411: {
412: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
413: double ***m;
414:
415: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
416: if (!m) nrerror("allocation failure 1 in matrix()");
417: m += NR_END;
418: m -= nrl;
419:
420: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
421: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
422: m[nrl] += NR_END;
423: m[nrl] -= ncl;
424:
425: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
426:
427: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
428: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
429: m[nrl][ncl] += NR_END;
430: m[nrl][ncl] -= nll;
431: for (j=ncl+1; j<=nch; j++)
432: m[nrl][j]=m[nrl][j-1]+nlay;
433:
434: for (i=nrl+1; i<=nrh; i++) {
435: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
436: for (j=ncl+1; j<=nch; j++)
437: m[i][j]=m[i][j-1]+nlay;
438: }
439: return m;
440: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
441: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
442: */
443: }
444:
445: /*************************free ma3x ************************/
446: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
447: {
448: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
449: free((FREE_ARG)(m[nrl]+ncl-NR_END));
450: free((FREE_ARG)(m+nrl-NR_END));
451: }
452:
453: /***************** f1dim *************************/
454: extern int ncom;
455: extern double *pcom,*xicom;
456: extern double (*nrfunc)(double []);
457:
458: double f1dim(double x)
459: {
460: int j;
461: double f;
462: double *xt;
463:
464: xt=vector(1,ncom);
465: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
466: f=(*nrfunc)(xt);
467: free_vector(xt,1,ncom);
468: return f;
469: }
470:
471: /*****************brent *************************/
472: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
473: {
474: int iter;
475: double a,b,d,etemp;
476: double fu,fv,fw,fx;
477: double ftemp;
478: double p,q,r,tol1,tol2,u,v,w,x,xm;
479: double e=0.0;
480:
481: a=(ax < cx ? ax : cx);
482: b=(ax > cx ? ax : cx);
483: x=w=v=bx;
484: fw=fv=fx=(*f)(x);
485: for (iter=1;iter<=ITMAX;iter++) {
486: xm=0.5*(a+b);
487: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
488: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
489: printf(".");fflush(stdout);
490: fprintf(ficlog,".");fflush(ficlog);
491: #ifdef DEBUG
492: 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);
493: 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);
494: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
495: #endif
496: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
497: *xmin=x;
498: return fx;
499: }
500: ftemp=fu;
501: if (fabs(e) > tol1) {
502: r=(x-w)*(fx-fv);
503: q=(x-v)*(fx-fw);
504: p=(x-v)*q-(x-w)*r;
505: q=2.0*(q-r);
506: if (q > 0.0) p = -p;
507: q=fabs(q);
508: etemp=e;
509: e=d;
510: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
511: d=CGOLD*(e=(x >= xm ? a-x : b-x));
512: else {
513: d=p/q;
514: u=x+d;
515: if (u-a < tol2 || b-u < tol2)
516: d=SIGN(tol1,xm-x);
517: }
518: } else {
519: d=CGOLD*(e=(x >= xm ? a-x : b-x));
520: }
521: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
522: fu=(*f)(u);
523: if (fu <= fx) {
524: if (u >= x) a=x; else b=x;
525: SHFT(v,w,x,u)
526: SHFT(fv,fw,fx,fu)
527: } else {
528: if (u < x) a=u; else b=u;
529: if (fu <= fw || w == x) {
530: v=w;
531: w=u;
532: fv=fw;
533: fw=fu;
534: } else if (fu <= fv || v == x || v == w) {
535: v=u;
536: fv=fu;
537: }
538: }
539: }
540: nrerror("Too many iterations in brent");
541: *xmin=x;
542: return fx;
543: }
544:
545: /****************** mnbrak ***********************/
546:
547: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
548: double (*func)(double))
549: {
550: double ulim,u,r,q, dum;
551: double fu;
552:
553: *fa=(*func)(*ax);
554: *fb=(*func)(*bx);
555: if (*fb > *fa) {
556: SHFT(dum,*ax,*bx,dum)
557: SHFT(dum,*fb,*fa,dum)
558: }
559: *cx=(*bx)+GOLD*(*bx-*ax);
560: *fc=(*func)(*cx);
561: while (*fb > *fc) {
562: r=(*bx-*ax)*(*fb-*fc);
563: q=(*bx-*cx)*(*fb-*fa);
564: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
565: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
566: ulim=(*bx)+GLIMIT*(*cx-*bx);
567: if ((*bx-u)*(u-*cx) > 0.0) {
568: fu=(*func)(u);
569: } else if ((*cx-u)*(u-ulim) > 0.0) {
570: fu=(*func)(u);
571: if (fu < *fc) {
572: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
573: SHFT(*fb,*fc,fu,(*func)(u))
574: }
575: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
576: u=ulim;
577: fu=(*func)(u);
578: } else {
579: u=(*cx)+GOLD*(*cx-*bx);
580: fu=(*func)(u);
581: }
582: SHFT(*ax,*bx,*cx,u)
583: SHFT(*fa,*fb,*fc,fu)
584: }
585: }
586:
587: /*************** linmin ************************/
588:
589: int ncom;
590: double *pcom,*xicom;
591: double (*nrfunc)(double []);
592:
593: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
594: {
595: double brent(double ax, double bx, double cx,
596: double (*f)(double), double tol, double *xmin);
597: double f1dim(double x);
598: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
599: double *fc, double (*func)(double));
600: int j;
601: double xx,xmin,bx,ax;
602: double fx,fb,fa;
603:
604: ncom=n;
605: pcom=vector(1,n);
606: xicom=vector(1,n);
607: nrfunc=func;
608: for (j=1;j<=n;j++) {
609: pcom[j]=p[j];
610: xicom[j]=xi[j];
611: }
612: ax=0.0;
613: xx=1.0;
614: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
615: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
616: #ifdef DEBUG
617: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
618: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
619: #endif
620: for (j=1;j<=n;j++) {
621: xi[j] *= xmin;
622: p[j] += xi[j];
623: }
624: free_vector(xicom,1,n);
625: free_vector(pcom,1,n);
626: }
627:
628: /*************** powell ************************/
629: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
630: double (*func)(double []))
631: {
632: void linmin(double p[], double xi[], int n, double *fret,
633: double (*func)(double []));
634: int i,ibig,j;
635: double del,t,*pt,*ptt,*xit;
636: double fp,fptt;
637: double *xits;
638: pt=vector(1,n);
639: ptt=vector(1,n);
640: xit=vector(1,n);
641: xits=vector(1,n);
642: *fret=(*func)(p);
643: for (j=1;j<=n;j++) pt[j]=p[j];
644: for (*iter=1;;++(*iter)) {
645: fp=(*fret);
646: ibig=0;
647: del=0.0;
648: printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
649: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
650: for (i=1;i<=n;i++)
651: printf(" %d %.12f",i, p[i]);
652: fprintf(ficlog," %d %.12f",i, p[i]);
653: printf("\n");
654: fprintf(ficlog,"\n");
655: for (i=1;i<=n;i++) {
656: for (j=1;j<=n;j++) xit[j]=xi[j][i];
657: fptt=(*fret);
658: #ifdef DEBUG
659: printf("fret=%lf \n",*fret);
660: fprintf(ficlog,"fret=%lf \n",*fret);
661: #endif
662: printf("%d",i);fflush(stdout);
663: fprintf(ficlog,"%d",i);fflush(ficlog);
664: linmin(p,xit,n,fret,func);
665: if (fabs(fptt-(*fret)) > del) {
666: del=fabs(fptt-(*fret));
667: ibig=i;
668: }
669: #ifdef DEBUG
670: printf("%d %.12e",i,(*fret));
671: fprintf(ficlog,"%d %.12e",i,(*fret));
672: for (j=1;j<=n;j++) {
673: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
674: printf(" x(%d)=%.12e",j,xit[j]);
675: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
676: }
677: for(j=1;j<=n;j++) {
678: printf(" p=%.12e",p[j]);
679: fprintf(ficlog," p=%.12e",p[j]);
680: }
681: printf("\n");
682: fprintf(ficlog,"\n");
683: #endif
684: }
685: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
686: #ifdef DEBUG
687: int k[2],l;
688: k[0]=1;
689: k[1]=-1;
690: printf("Max: %.12e",(*func)(p));
691: fprintf(ficlog,"Max: %.12e",(*func)(p));
692: for (j=1;j<=n;j++) {
693: printf(" %.12e",p[j]);
694: fprintf(ficlog," %.12e",p[j]);
695: }
696: printf("\n");
697: fprintf(ficlog,"\n");
698: for(l=0;l<=1;l++) {
699: for (j=1;j<=n;j++) {
700: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
701: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
702: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
703: }
704: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
705: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
706: }
707: #endif
708:
709:
710: free_vector(xit,1,n);
711: free_vector(xits,1,n);
712: free_vector(ptt,1,n);
713: free_vector(pt,1,n);
714: return;
715: }
716: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
717: for (j=1;j<=n;j++) {
718: ptt[j]=2.0*p[j]-pt[j];
719: xit[j]=p[j]-pt[j];
720: pt[j]=p[j];
721: }
722: fptt=(*func)(ptt);
723: if (fptt < fp) {
724: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
725: if (t < 0.0) {
726: linmin(p,xit,n,fret,func);
727: for (j=1;j<=n;j++) {
728: xi[j][ibig]=xi[j][n];
729: xi[j][n]=xit[j];
730: }
731: #ifdef DEBUG
732: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
733: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
734: for(j=1;j<=n;j++){
735: printf(" %.12e",xit[j]);
736: fprintf(ficlog," %.12e",xit[j]);
737: }
738: printf("\n");
739: fprintf(ficlog,"\n");
740: #endif
741: }
742: }
743: }
744: }
745:
746: /**** Prevalence limit (stable prevalence) ****************/
747:
748: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
749: {
750: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
751: matrix by transitions matrix until convergence is reached */
752:
753: int i, ii,j,k;
754: double min, max, maxmin, maxmax,sumnew=0.;
755: double **matprod2();
756: double **out, cov[NCOVMAX], **pmij();
757: double **newm;
758: double agefin, delaymax=50 ; /* Max number of years to converge */
759:
760: for (ii=1;ii<=nlstate+ndeath;ii++)
761: for (j=1;j<=nlstate+ndeath;j++){
762: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
763: }
764:
765: cov[1]=1.;
766:
767: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
768: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
769: newm=savm;
770: /* Covariates have to be included here again */
771: cov[2]=agefin;
772:
773: for (k=1; k<=cptcovn;k++) {
774: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
775: /* 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]]);*/
776: }
777: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
778: for (k=1; k<=cptcovprod;k++)
779: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
780:
781: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
782: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
783: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
784: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
785:
786: savm=oldm;
787: oldm=newm;
788: maxmax=0.;
789: for(j=1;j<=nlstate;j++){
790: min=1.;
791: max=0.;
792: for(i=1; i<=nlstate; i++) {
793: sumnew=0;
794: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
795: prlim[i][j]= newm[i][j]/(1-sumnew);
796: max=FMAX(max,prlim[i][j]);
797: min=FMIN(min,prlim[i][j]);
798: }
799: maxmin=max-min;
800: maxmax=FMAX(maxmax,maxmin);
801: }
802: if(maxmax < ftolpl){
803: return prlim;
804: }
805: }
806: }
807:
808: /*************** transition probabilities ***************/
809:
810: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
811: {
812: double s1, s2;
813: /*double t34;*/
814: int i,j,j1, nc, ii, jj;
815:
816: for(i=1; i<= nlstate; i++){
817: for(j=1; j<i;j++){
818: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
819: /*s2 += param[i][j][nc]*cov[nc];*/
820: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
821: /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
822: }
823: ps[i][j]=s2;
824: /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
825: }
826: for(j=i+1; j<=nlstate+ndeath;j++){
827: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
828: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
829: /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
830: }
831: ps[i][j]=s2;
832: }
833: }
834: /*ps[3][2]=1;*/
835:
836: for(i=1; i<= nlstate; i++){
837: s1=0;
838: for(j=1; j<i; j++)
839: s1+=exp(ps[i][j]);
840: for(j=i+1; j<=nlstate+ndeath; j++)
841: s1+=exp(ps[i][j]);
842: ps[i][i]=1./(s1+1.);
843: for(j=1; j<i; j++)
844: ps[i][j]= exp(ps[i][j])*ps[i][i];
845: for(j=i+1; j<=nlstate+ndeath; j++)
846: ps[i][j]= exp(ps[i][j])*ps[i][i];
847: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
848: } /* end i */
849:
850: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
851: for(jj=1; jj<= nlstate+ndeath; jj++){
852: ps[ii][jj]=0;
853: ps[ii][ii]=1;
854: }
855: }
856:
857:
858: /* for(ii=1; ii<= nlstate+ndeath; ii++){
859: for(jj=1; jj<= nlstate+ndeath; jj++){
860: printf("%lf ",ps[ii][jj]);
861: }
862: printf("\n ");
863: }
864: printf("\n ");printf("%lf ",cov[2]);*/
865: /*
866: for(i=1; i<= npar; i++) printf("%f ",x[i]);
867: goto end;*/
868: return ps;
869: }
870:
871: /**************** Product of 2 matrices ******************/
872:
873: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
874: {
875: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
876: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
877: /* in, b, out are matrice of pointers which should have been initialized
878: before: only the contents of out is modified. The function returns
879: a pointer to pointers identical to out */
880: long i, j, k;
881: for(i=nrl; i<= nrh; i++)
882: for(k=ncolol; k<=ncoloh; k++)
883: for(j=ncl,out[i][k]=0.; j<=nch; j++)
884: out[i][k] +=in[i][j]*b[j][k];
885:
886: return out;
887: }
888:
889:
890: /************* Higher Matrix Product ***************/
891:
892: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
893: {
894: /* Computes the transition matrix starting at age 'age' over
895: 'nhstepm*hstepm*stepm' months (i.e. until
896: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
897: nhstepm*hstepm matrices.
898: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
899: (typically every 2 years instead of every month which is too big
900: for the memory).
901: Model is determined by parameters x and covariates have to be
902: included manually here.
903:
904: */
905:
906: int i, j, d, h, k;
907: double **out, cov[NCOVMAX];
908: double **newm;
909:
910: /* Hstepm could be zero and should return the unit matrix */
911: for (i=1;i<=nlstate+ndeath;i++)
912: for (j=1;j<=nlstate+ndeath;j++){
913: oldm[i][j]=(i==j ? 1.0 : 0.0);
914: po[i][j][0]=(i==j ? 1.0 : 0.0);
915: }
916: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
917: for(h=1; h <=nhstepm; h++){
918: for(d=1; d <=hstepm; d++){
919: newm=savm;
920: /* Covariates have to be included here again */
921: cov[1]=1.;
922: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
923: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
924: for (k=1; k<=cptcovage;k++)
925: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
926: for (k=1; k<=cptcovprod;k++)
927: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
928:
929:
930: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
931: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
932: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
933: pmij(pmmij,cov,ncovmodel,x,nlstate));
934: savm=oldm;
935: oldm=newm;
936: }
937: for(i=1; i<=nlstate+ndeath; i++)
938: for(j=1;j<=nlstate+ndeath;j++) {
939: po[i][j][h]=newm[i][j];
940: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
941: */
942: }
943: } /* end h */
944: return po;
945: }
946:
947:
948: /*************** log-likelihood *************/
949: double func( double *x)
950: {
951: int i, ii, j, k, mi, d, kk;
952: double l, ll[NLSTATEMAX], cov[NCOVMAX];
953: double **out;
954: double sw; /* Sum of weights */
955: double lli; /* Individual log likelihood */
956: int s1, s2;
957: double bbh, survp;
958: long ipmx;
959: /*extern weight */
960: /* We are differentiating ll according to initial status */
961: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
962: /*for(i=1;i<imx;i++)
963: printf(" %d\n",s[4][i]);
964: */
965: cov[1]=1.;
966:
967: for(k=1; k<=nlstate; k++) ll[k]=0.;
968:
969: if(mle==1){
970: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
971: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
972: for(mi=1; mi<= wav[i]-1; mi++){
973: for (ii=1;ii<=nlstate+ndeath;ii++)
974: for (j=1;j<=nlstate+ndeath;j++){
975: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
976: savm[ii][j]=(ii==j ? 1.0 : 0.0);
977: }
978: for(d=0; d<dh[mi][i]; d++){
979: newm=savm;
980: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
981: for (kk=1; kk<=cptcovage;kk++) {
982: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
983: }
984: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
985: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
986: savm=oldm;
987: oldm=newm;
988: } /* end mult */
989:
990: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
991: /* But now since version 0.9 we anticipate for bias and large stepm.
992: * If stepm is larger than one month (smallest stepm) and if the exact delay
993: * (in months) between two waves is not a multiple of stepm, we rounded to
994: * the nearest (and in case of equal distance, to the lowest) interval but now
995: * we keep into memory the bias bh[mi][i] and also the previous matrix product
996: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
997: * probability in order to take into account the bias as a fraction of the way
998: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
999: * -stepm/2 to stepm/2 .
1000: * For stepm=1 the results are the same as for previous versions of Imach.
1001: * For stepm > 1 the results are less biased than in previous versions.
1002: */
1003: s1=s[mw[mi][i]][i];
1004: s2=s[mw[mi+1][i]][i];
1005: bbh=(double)bh[mi][i]/(double)stepm;
1006: /* bias is positive if real duration
1007: * is higher than the multiple of stepm and negative otherwise.
1008: */
1009: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1010: if( s2 > nlstate){
1011: /* i.e. if s2 is a death state and if the date of death is known then the contribution
1012: to the likelihood is the probability to die between last step unit time and current
1013: step unit time, which is also the differences between probability to die before dh
1014: and probability to die before dh-stepm .
1015: In version up to 0.92 likelihood was computed
1016: as if date of death was unknown. Death was treated as any other
1017: health state: the date of the interview describes the actual state
1018: and not the date of a change in health state. The former idea was
1019: to consider that at each interview the state was recorded
1020: (healthy, disable or death) and IMaCh was corrected; but when we
1021: introduced the exact date of death then we should have modified
1022: the contribution of an exact death to the likelihood. This new
1023: contribution is smaller and very dependent of the step unit
1024: stepm. It is no more the probability to die between last interview
1025: and month of death but the probability to survive from last
1026: interview up to one month before death multiplied by the
1027: probability to die within a month. Thanks to Chris
1028: Jackson for correcting this bug. Former versions increased
1029: mortality artificially. The bad side is that we add another loop
1030: which slows down the processing. The difference can be up to 10%
1031: lower mortality.
1032: */
1033: lli=log(out[s1][s2] - savm[s1][s2]);
1034: }else{
1035: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1036: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
1037: }
1038: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1039: /*if(lli ==000.0)*/
1040: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1041: ipmx +=1;
1042: sw += weight[i];
1043: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1044: } /* end of wave */
1045: } /* end of individual */
1046: } else if(mle==2){
1047: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1048: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1049: for(mi=1; mi<= wav[i]-1; mi++){
1050: for (ii=1;ii<=nlstate+ndeath;ii++)
1051: for (j=1;j<=nlstate+ndeath;j++){
1052: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1053: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1054: }
1055: for(d=0; d<=dh[mi][i]; d++){
1056: newm=savm;
1057: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1058: for (kk=1; kk<=cptcovage;kk++) {
1059: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1060: }
1061: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1062: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1063: savm=oldm;
1064: oldm=newm;
1065: } /* end mult */
1066:
1067: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1068: /* But now since version 0.9 we anticipate for bias and large stepm.
1069: * If stepm is larger than one month (smallest stepm) and if the exact delay
1070: * (in months) between two waves is not a multiple of stepm, we rounded to
1071: * the nearest (and in case of equal distance, to the lowest) interval but now
1072: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1073: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1074: * probability in order to take into account the bias as a fraction of the way
1075: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1076: * -stepm/2 to stepm/2 .
1077: * For stepm=1 the results are the same as for previous versions of Imach.
1078: * For stepm > 1 the results are less biased than in previous versions.
1079: */
1080: s1=s[mw[mi][i]][i];
1081: s2=s[mw[mi+1][i]][i];
1082: bbh=(double)bh[mi][i]/(double)stepm;
1083: /* bias is positive if real duration
1084: * is higher than the multiple of stepm and negative otherwise.
1085: */
1086: lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
1087: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1088: /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
1089: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1090: /*if(lli ==000.0)*/
1091: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1092: ipmx +=1;
1093: sw += weight[i];
1094: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1095: } /* end of wave */
1096: } /* end of individual */
1097: } else if(mle==3){ /* exponential inter-extrapolation */
1098: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1099: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1100: for(mi=1; mi<= wav[i]-1; mi++){
1101: for (ii=1;ii<=nlstate+ndeath;ii++)
1102: for (j=1;j<=nlstate+ndeath;j++){
1103: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1104: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1105: }
1106: for(d=0; d<dh[mi][i]; d++){
1107: newm=savm;
1108: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1109: for (kk=1; kk<=cptcovage;kk++) {
1110: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1111: }
1112: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1113: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1114: savm=oldm;
1115: oldm=newm;
1116: } /* end mult */
1117:
1118: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1119: /* But now since version 0.9 we anticipate for bias and large stepm.
1120: * If stepm is larger than one month (smallest stepm) and if the exact delay
1121: * (in months) between two waves is not a multiple of stepm, we rounded to
1122: * the nearest (and in case of equal distance, to the lowest) interval but now
1123: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1124: * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
1125: * probability in order to take into account the bias as a fraction of the way
1126: * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
1127: * -stepm/2 to stepm/2 .
1128: * For stepm=1 the results are the same as for previous versions of Imach.
1129: * For stepm > 1 the results are less biased than in previous versions.
1130: */
1131: s1=s[mw[mi][i]][i];
1132: s2=s[mw[mi+1][i]][i];
1133: bbh=(double)bh[mi][i]/(double)stepm;
1134: /* bias is positive if real duration
1135: * is higher than the multiple of stepm and negative otherwise.
1136: */
1137: /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
1138: lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1139: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1140: /*if(lli ==000.0)*/
1141: /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
1142: ipmx +=1;
1143: sw += weight[i];
1144: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1145: } /* end of wave */
1146: } /* end of individual */
1147: }else{ /* ml=4 no inter-extrapolation */
1148: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1149: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1150: for(mi=1; mi<= wav[i]-1; mi++){
1151: for (ii=1;ii<=nlstate+ndeath;ii++)
1152: for (j=1;j<=nlstate+ndeath;j++){
1153: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1154: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1155: }
1156: for(d=0; d<dh[mi][i]; d++){
1157: newm=savm;
1158: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1159: for (kk=1; kk<=cptcovage;kk++) {
1160: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1161: }
1162:
1163: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1164: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1165: savm=oldm;
1166: oldm=newm;
1167: } /* end mult */
1168:
1169: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1170: ipmx +=1;
1171: sw += weight[i];
1172: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1173: } /* end of wave */
1174: } /* end of individual */
1175: } /* End of if */
1176: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1177: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1178: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1179: return -l;
1180: }
1181:
1182:
1183: /*********** Maximum Likelihood Estimation ***************/
1184:
1185: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1186: {
1187: int i,j, iter;
1188: double **xi;
1189: double fret;
1190: xi=matrix(1,npar,1,npar);
1191: for (i=1;i<=npar;i++)
1192: for (j=1;j<=npar;j++)
1193: xi[i][j]=(i==j ? 1.0 : 0.0);
1194: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1195: powell(p,xi,npar,ftol,&iter,&fret,func);
1196:
1197: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1198: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1199: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1200:
1201: }
1202:
1203: /**** Computes Hessian and covariance matrix ***/
1204: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1205: {
1206: double **a,**y,*x,pd;
1207: double **hess;
1208: int i, j,jk;
1209: int *indx;
1210:
1211: double hessii(double p[], double delta, int theta, double delti[]);
1212: double hessij(double p[], double delti[], int i, int j);
1213: void lubksb(double **a, int npar, int *indx, double b[]) ;
1214: void ludcmp(double **a, int npar, int *indx, double *d) ;
1215:
1216: hess=matrix(1,npar,1,npar);
1217:
1218: printf("\nCalculation of the hessian matrix. Wait...\n");
1219: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1220: for (i=1;i<=npar;i++){
1221: printf("%d",i);fflush(stdout);
1222: fprintf(ficlog,"%d",i);fflush(ficlog);
1223: hess[i][i]=hessii(p,ftolhess,i,delti);
1224: /*printf(" %f ",p[i]);*/
1225: /*printf(" %lf ",hess[i][i]);*/
1226: }
1227:
1228: for (i=1;i<=npar;i++) {
1229: for (j=1;j<=npar;j++) {
1230: if (j>i) {
1231: printf(".%d%d",i,j);fflush(stdout);
1232: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1233: hess[i][j]=hessij(p,delti,i,j);
1234: hess[j][i]=hess[i][j];
1235: /*printf(" %lf ",hess[i][j]);*/
1236: }
1237: }
1238: }
1239: printf("\n");
1240: fprintf(ficlog,"\n");
1241:
1242: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1243: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1244:
1245: a=matrix(1,npar,1,npar);
1246: y=matrix(1,npar,1,npar);
1247: x=vector(1,npar);
1248: indx=ivector(1,npar);
1249: for (i=1;i<=npar;i++)
1250: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1251: ludcmp(a,npar,indx,&pd);
1252:
1253: for (j=1;j<=npar;j++) {
1254: for (i=1;i<=npar;i++) x[i]=0;
1255: x[j]=1;
1256: lubksb(a,npar,indx,x);
1257: for (i=1;i<=npar;i++){
1258: matcov[i][j]=x[i];
1259: }
1260: }
1261:
1262: printf("\n#Hessian matrix#\n");
1263: fprintf(ficlog,"\n#Hessian matrix#\n");
1264: for (i=1;i<=npar;i++) {
1265: for (j=1;j<=npar;j++) {
1266: printf("%.3e ",hess[i][j]);
1267: fprintf(ficlog,"%.3e ",hess[i][j]);
1268: }
1269: printf("\n");
1270: fprintf(ficlog,"\n");
1271: }
1272:
1273: /* Recompute Inverse */
1274: for (i=1;i<=npar;i++)
1275: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1276: ludcmp(a,npar,indx,&pd);
1277:
1278: /* printf("\n#Hessian matrix recomputed#\n");
1279:
1280: for (j=1;j<=npar;j++) {
1281: for (i=1;i<=npar;i++) x[i]=0;
1282: x[j]=1;
1283: lubksb(a,npar,indx,x);
1284: for (i=1;i<=npar;i++){
1285: y[i][j]=x[i];
1286: printf("%.3e ",y[i][j]);
1287: fprintf(ficlog,"%.3e ",y[i][j]);
1288: }
1289: printf("\n");
1290: fprintf(ficlog,"\n");
1291: }
1292: */
1293:
1294: free_matrix(a,1,npar,1,npar);
1295: free_matrix(y,1,npar,1,npar);
1296: free_vector(x,1,npar);
1297: free_ivector(indx,1,npar);
1298: free_matrix(hess,1,npar,1,npar);
1299:
1300:
1301: }
1302:
1303: /*************** hessian matrix ****************/
1304: double hessii( double x[], double delta, int theta, double delti[])
1305: {
1306: int i;
1307: int l=1, lmax=20;
1308: double k1,k2;
1309: double p2[NPARMAX+1];
1310: double res;
1311: double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1312: double fx;
1313: int k=0,kmax=10;
1314: double l1;
1315:
1316: fx=func(x);
1317: for (i=1;i<=npar;i++) p2[i]=x[i];
1318: for(l=0 ; l <=lmax; l++){
1319: l1=pow(10,l);
1320: delts=delt;
1321: for(k=1 ; k <kmax; k=k+1){
1322: delt = delta*(l1*k);
1323: p2[theta]=x[theta] +delt;
1324: k1=func(p2)-fx;
1325: p2[theta]=x[theta]-delt;
1326: k2=func(p2)-fx;
1327: /*res= (k1-2.0*fx+k2)/delt/delt; */
1328: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1329:
1330: #ifdef DEBUG
1331: 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);
1332: 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);
1333: #endif
1334: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1335: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1336: k=kmax;
1337: }
1338: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1339: k=kmax; l=lmax*10.;
1340: }
1341: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1342: delts=delt;
1343: }
1344: }
1345: }
1346: delti[theta]=delts;
1347: return res;
1348:
1349: }
1350:
1351: double hessij( double x[], double delti[], int thetai,int thetaj)
1352: {
1353: int i;
1354: int l=1, l1, lmax=20;
1355: double k1,k2,k3,k4,res,fx;
1356: double p2[NPARMAX+1];
1357: int k;
1358:
1359: fx=func(x);
1360: for (k=1; k<=2; k++) {
1361: for (i=1;i<=npar;i++) p2[i]=x[i];
1362: p2[thetai]=x[thetai]+delti[thetai]/k;
1363: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1364: k1=func(p2)-fx;
1365:
1366: p2[thetai]=x[thetai]+delti[thetai]/k;
1367: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1368: k2=func(p2)-fx;
1369:
1370: p2[thetai]=x[thetai]-delti[thetai]/k;
1371: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1372: k3=func(p2)-fx;
1373:
1374: p2[thetai]=x[thetai]-delti[thetai]/k;
1375: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1376: k4=func(p2)-fx;
1377: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1378: #ifdef DEBUG
1379: 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);
1380: 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);
1381: #endif
1382: }
1383: return res;
1384: }
1385:
1386: /************** Inverse of matrix **************/
1387: void ludcmp(double **a, int n, int *indx, double *d)
1388: {
1389: int i,imax,j,k;
1390: double big,dum,sum,temp;
1391: double *vv;
1392:
1393: vv=vector(1,n);
1394: *d=1.0;
1395: for (i=1;i<=n;i++) {
1396: big=0.0;
1397: for (j=1;j<=n;j++)
1398: if ((temp=fabs(a[i][j])) > big) big=temp;
1399: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1400: vv[i]=1.0/big;
1401: }
1402: for (j=1;j<=n;j++) {
1403: for (i=1;i<j;i++) {
1404: sum=a[i][j];
1405: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1406: a[i][j]=sum;
1407: }
1408: big=0.0;
1409: for (i=j;i<=n;i++) {
1410: sum=a[i][j];
1411: for (k=1;k<j;k++)
1412: sum -= a[i][k]*a[k][j];
1413: a[i][j]=sum;
1414: if ( (dum=vv[i]*fabs(sum)) >= big) {
1415: big=dum;
1416: imax=i;
1417: }
1418: }
1419: if (j != imax) {
1420: for (k=1;k<=n;k++) {
1421: dum=a[imax][k];
1422: a[imax][k]=a[j][k];
1423: a[j][k]=dum;
1424: }
1425: *d = -(*d);
1426: vv[imax]=vv[j];
1427: }
1428: indx[j]=imax;
1429: if (a[j][j] == 0.0) a[j][j]=TINY;
1430: if (j != n) {
1431: dum=1.0/(a[j][j]);
1432: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1433: }
1434: }
1435: free_vector(vv,1,n); /* Doesn't work */
1436: ;
1437: }
1438:
1439: void lubksb(double **a, int n, int *indx, double b[])
1440: {
1441: int i,ii=0,ip,j;
1442: double sum;
1443:
1444: for (i=1;i<=n;i++) {
1445: ip=indx[i];
1446: sum=b[ip];
1447: b[ip]=b[i];
1448: if (ii)
1449: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1450: else if (sum) ii=i;
1451: b[i]=sum;
1452: }
1453: for (i=n;i>=1;i--) {
1454: sum=b[i];
1455: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1456: b[i]=sum/a[i][i];
1457: }
1458: }
1459:
1460: /************ Frequencies ********************/
1461: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
1462: { /* Some frequencies */
1463:
1464: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1465: int first;
1466: double ***freq; /* Frequencies */
1467: double *pp, **prop;
1468: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1469: FILE *ficresp;
1470: char fileresp[FILENAMELENGTH];
1471:
1472: pp=vector(1,nlstate);
1473: prop=matrix(1,nlstate,iagemin,iagemax+3);
1474: strcpy(fileresp,"p");
1475: strcat(fileresp,fileres);
1476: if((ficresp=fopen(fileresp,"w"))==NULL) {
1477: printf("Problem with prevalence resultfile: %s\n", fileresp);
1478: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1479: exit(0);
1480: }
1481: freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
1482: j1=0;
1483:
1484: j=cptcoveff;
1485: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1486:
1487: first=1;
1488:
1489: for(k1=1; k1<=j;k1++){
1490: for(i1=1; i1<=ncodemax[k1];i1++){
1491: j1++;
1492: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1493: scanf("%d", i);*/
1494: for (i=-1; i<=nlstate+ndeath; i++)
1495: for (jk=-1; jk<=nlstate+ndeath; jk++)
1496: for(m=iagemin; m <= iagemax+3; m++)
1497: freq[i][jk][m]=0;
1498:
1499: for (i=1; i<=nlstate; i++)
1500: for(m=iagemin; m <= iagemax+3; m++)
1501: prop[i][m]=0;
1502:
1503: dateintsum=0;
1504: k2cpt=0;
1505: for (i=1; i<=imx; i++) {
1506: bool=1;
1507: if (cptcovn>0) {
1508: for (z1=1; z1<=cptcoveff; z1++)
1509: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1510: bool=0;
1511: }
1512: if (bool==1){
1513: for(m=firstpass; m<=lastpass; m++){
1514: k2=anint[m][i]+(mint[m][i]/12.);
1515: if ((k2>=dateprev1) && (k2<=dateprev2)) {
1516: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1517: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1518: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1519: if (m<lastpass) {
1520: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1521: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1522: }
1523:
1524: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1525: dateintsum=dateintsum+k2;
1526: k2cpt++;
1527: }
1528: }
1529: }
1530: }
1531: }
1532:
1533: fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
1534:
1535: if (cptcovn>0) {
1536: fprintf(ficresp, "\n#********** Variable ");
1537: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1538: fprintf(ficresp, "**********\n#");
1539: }
1540: for(i=1; i<=nlstate;i++)
1541: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1542: fprintf(ficresp, "\n");
1543:
1544: for(i=iagemin; i <= iagemax+3; i++){
1545: if(i==iagemax+3){
1546: fprintf(ficlog,"Total");
1547: }else{
1548: if(first==1){
1549: first=0;
1550: printf("See log file for details...\n");
1551: }
1552: fprintf(ficlog,"Age %d", i);
1553: }
1554: for(jk=1; jk <=nlstate ; jk++){
1555: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1556: pp[jk] += freq[jk][m][i];
1557: }
1558: for(jk=1; jk <=nlstate ; jk++){
1559: for(m=-1, pos=0; m <=0 ; m++)
1560: pos += freq[jk][m][i];
1561: if(pp[jk]>=1.e-10){
1562: if(first==1){
1563: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1564: }
1565: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1566: }else{
1567: if(first==1)
1568: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1569: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1570: }
1571: }
1572:
1573: for(jk=1; jk <=nlstate ; jk++){
1574: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
1575: pp[jk] += freq[jk][m][i];
1576: }
1577: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
1578: pos += pp[jk];
1579: posprop += prop[jk][i];
1580: }
1581: for(jk=1; jk <=nlstate ; jk++){
1582: if(pos>=1.e-5){
1583: if(first==1)
1584: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1585: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
1586: }else{
1587: if(first==1)
1588: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1589: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
1590: }
1591: if( i <= iagemax){
1592: if(pos>=1.e-5){
1593: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1594: probs[i][jk][j1]= pp[jk]/pos;
1595: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
1596: }
1597: else
1598: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1599: }
1600: }
1601:
1602: for(jk=-1; jk <=nlstate+ndeath; jk++)
1603: for(m=-1; m <=nlstate+ndeath; m++)
1604: if(freq[jk][m][i] !=0 ) {
1605: if(first==1)
1606: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
1607: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
1608: }
1609: if(i <= iagemax)
1610: fprintf(ficresp,"\n");
1611: if(first==1)
1612: printf("Others in log...\n");
1613: fprintf(ficlog,"\n");
1614: }
1615: }
1616: }
1617: dateintmean=dateintsum/k2cpt;
1618:
1619: fclose(ficresp);
1620: free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
1621: free_vector(pp,1,nlstate);
1622: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
1623: /* End of Freq */
1624: }
1625:
1626: /************ Prevalence ********************/
1627: void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
1628: {
1629: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
1630: in each health status at the date of interview (if between dateprev1 and dateprev2).
1631: We still use firstpass and lastpass as another selection.
1632: */
1633:
1634: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
1635: double ***freq; /* Frequencies */
1636: double *pp, **prop;
1637: double pos,posprop;
1638: double y2; /* in fractional years */
1639: int iagemin, iagemax;
1640:
1641: iagemin= (int) agemin;
1642: iagemax= (int) agemax;
1643: /*pp=vector(1,nlstate);*/
1644: prop=matrix(1,nlstate,iagemin,iagemax+3);
1645: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
1646: j1=0;
1647:
1648: j=cptcoveff;
1649: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1650:
1651: for(k1=1; k1<=j;k1++){
1652: for(i1=1; i1<=ncodemax[k1];i1++){
1653: j1++;
1654:
1655: for (i=1; i<=nlstate; i++)
1656: for(m=iagemin; m <= iagemax+3; m++)
1657: prop[i][m]=0.0;
1658:
1659: for (i=1; i<=imx; i++) { /* Each individual */
1660: bool=1;
1661: if (cptcovn>0) {
1662: for (z1=1; z1<=cptcoveff; z1++)
1663: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1664: bool=0;
1665: }
1666: if (bool==1) {
1667: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
1668: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
1669: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
1670: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1671: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1672: if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
1673: if (s[m][i]>0 && s[m][i]<=nlstate) {
1674: /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
1675: prop[s[m][i]][(int)agev[m][i]] += weight[i];
1676: prop[s[m][i]][iagemax+3] += weight[i];
1677: }
1678: }
1679: } /* end selection of waves */
1680: }
1681: }
1682: for(i=iagemin; i <= iagemax+3; i++){
1683:
1684: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
1685: posprop += prop[jk][i];
1686: }
1687:
1688: for(jk=1; jk <=nlstate ; jk++){
1689: if( i <= iagemax){
1690: if(posprop>=1.e-5){
1691: probs[i][jk][j1]= prop[jk][i]/posprop;
1692: }
1693: }
1694: }/* end jk */
1695: }/* end i */
1696: } /* end i1 */
1697: } /* end k1 */
1698:
1699: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
1700: /*free_vector(pp,1,nlstate);*/
1701: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
1702: } /* End of prevalence */
1703:
1704: /************* Waves Concatenation ***************/
1705:
1706: void concatwav(int wav[], int **dh, int **bh, int **mw, int **s, double *agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
1707: {
1708: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
1709: Death is a valid wave (if date is known).
1710: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
1711: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
1712: and mw[mi+1][i]. dh depends on stepm.
1713: */
1714:
1715: int i, mi, m;
1716: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
1717: double sum=0., jmean=0.;*/
1718: int first;
1719: int j, k=0,jk, ju, jl;
1720: double sum=0.;
1721: first=0;
1722: jmin=1e+5;
1723: jmax=-1;
1724: jmean=0.;
1725: for(i=1; i<=imx; i++){
1726: mi=0;
1727: m=firstpass;
1728: while(s[m][i] <= nlstate){
1729: if(s[m][i]>=1)
1730: mw[++mi][i]=m;
1731: if(m >=lastpass)
1732: break;
1733: else
1734: m++;
1735: }/* end while */
1736: if (s[m][i] > nlstate){
1737: mi++; /* Death is another wave */
1738: /* if(mi==0) never been interviewed correctly before death */
1739: /* Only death is a correct wave */
1740: mw[mi][i]=m;
1741: }
1742:
1743: wav[i]=mi;
1744: if(mi==0){
1745: if(first==0){
1746: printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
1747: first=1;
1748: }
1749: if(first==1){
1750: fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
1751: }
1752: } /* end mi==0 */
1753: }
1754:
1755: for(i=1; i<=imx; i++){
1756: for(mi=1; mi<wav[i];mi++){
1757: if (stepm <=0)
1758: dh[mi][i]=1;
1759: else{
1760: if (s[mw[mi+1][i]][i] > nlstate) {
1761: if (agedc[i] < 2*AGESUP) {
1762: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
1763: if(j==0) j=1; /* Survives at least one month after exam */
1764: k=k+1;
1765: if (j >= jmax) jmax=j;
1766: if (j <= jmin) jmin=j;
1767: sum=sum+j;
1768: /*if (j<0) printf("j=%d num=%d \n",j,i); */
1769: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1770: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1771: }
1772: }
1773: else{
1774: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
1775: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
1776: k=k+1;
1777: if (j >= jmax) jmax=j;
1778: else if (j <= jmin)jmin=j;
1779: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
1780: /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
1781: sum=sum+j;
1782: }
1783: jk= j/stepm;
1784: jl= j -jk*stepm;
1785: ju= j -(jk+1)*stepm;
1786: if(mle <=1){
1787: if(jl==0){
1788: dh[mi][i]=jk;
1789: bh[mi][i]=0;
1790: }else{ /* We want a negative bias in order to only have interpolation ie
1791: * at the price of an extra matrix product in likelihood */
1792: dh[mi][i]=jk+1;
1793: bh[mi][i]=ju;
1794: }
1795: }else{
1796: if(jl <= -ju){
1797: dh[mi][i]=jk;
1798: bh[mi][i]=jl; /* bias is positive if real duration
1799: * is higher than the multiple of stepm and negative otherwise.
1800: */
1801: }
1802: else{
1803: dh[mi][i]=jk+1;
1804: bh[mi][i]=ju;
1805: }
1806: if(dh[mi][i]==0){
1807: dh[mi][i]=1; /* At least one step */
1808: bh[mi][i]=ju; /* At least one step */
1809: /* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
1810: }
1811: }
1812: } /* end if mle */
1813: } /* end wave */
1814: }
1815: jmean=sum/k;
1816: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1817: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
1818: }
1819:
1820: /*********** Tricode ****************************/
1821: void tricode(int *Tvar, int **nbcode, int imx)
1822: {
1823:
1824: int Ndum[20],ij=1, k, j, i, maxncov=19;
1825: int cptcode=0;
1826: cptcoveff=0;
1827:
1828: for (k=0; k<maxncov; k++) Ndum[k]=0;
1829: for (k=1; k<=7; k++) ncodemax[k]=0;
1830:
1831: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
1832: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
1833: modality*/
1834: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
1835: Ndum[ij]++; /*store the modality */
1836: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1837: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
1838: Tvar[j]. If V=sex and male is 0 and
1839: female is 1, then cptcode=1.*/
1840: }
1841:
1842: for (i=0; i<=cptcode; i++) {
1843: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
1844: }
1845:
1846: ij=1;
1847: for (i=1; i<=ncodemax[j]; i++) {
1848: for (k=0; k<= maxncov; k++) {
1849: if (Ndum[k] != 0) {
1850: nbcode[Tvar[j]][ij]=k;
1851: /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1852:
1853: ij++;
1854: }
1855: if (ij > ncodemax[j]) break;
1856: }
1857: }
1858: }
1859:
1860: for (k=0; k< maxncov; k++) Ndum[k]=0;
1861:
1862: for (i=1; i<=ncovmodel-2; i++) {
1863: /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1864: ij=Tvar[i];
1865: Ndum[ij]++;
1866: }
1867:
1868: ij=1;
1869: for (i=1; i<= maxncov; i++) {
1870: if((Ndum[i]!=0) && (i<=ncovcol)){
1871: Tvaraff[ij]=i; /*For printing */
1872: ij++;
1873: }
1874: }
1875:
1876: cptcoveff=ij-1; /*Number of simple covariates*/
1877: }
1878:
1879: /*********** Health Expectancies ****************/
1880:
1881: 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 )
1882:
1883: {
1884: /* Health expectancies */
1885: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
1886: double age, agelim, hf;
1887: double ***p3mat,***varhe;
1888: double **dnewm,**doldm;
1889: double *xp;
1890: double **gp, **gm;
1891: double ***gradg, ***trgradg;
1892: int theta;
1893:
1894: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
1895: xp=vector(1,npar);
1896: dnewm=matrix(1,nlstate*nlstate,1,npar);
1897: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
1898:
1899: fprintf(ficreseij,"# Health expectancies\n");
1900: fprintf(ficreseij,"# Age");
1901: for(i=1; i<=nlstate;i++)
1902: for(j=1; j<=nlstate;j++)
1903: fprintf(ficreseij," %1d-%1d (SE)",i,j);
1904: fprintf(ficreseij,"\n");
1905:
1906: if(estepm < stepm){
1907: printf ("Problem %d lower than %d\n",estepm, stepm);
1908: }
1909: else hstepm=estepm;
1910: /* We compute the life expectancy from trapezoids spaced every estepm months
1911: * This is mainly to measure the difference between two models: for example
1912: * if stepm=24 months pijx are given only every 2 years and by summing them
1913: * we are calculating an estimate of the Life Expectancy assuming a linear
1914: * progression in between and thus overestimating or underestimating according
1915: * to the curvature of the survival function. If, for the same date, we
1916: * estimate the model with stepm=1 month, we can keep estepm to 24 months
1917: * to compare the new estimate of Life expectancy with the same linear
1918: * hypothesis. A more precise result, taking into account a more precise
1919: * curvature will be obtained if estepm is as small as stepm. */
1920:
1921: /* For example we decided to compute the life expectancy with the smallest unit */
1922: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
1923: nhstepm is the number of hstepm from age to agelim
1924: nstepm is the number of stepm from age to agelin.
1925: Look at hpijx to understand the reason of that which relies in memory size
1926: and note for a fixed period like estepm months */
1927: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
1928: survival function given by stepm (the optimization length). Unfortunately it
1929: means that if the survival funtion is printed only each two years of age and if
1930: you sum them up and add 1 year (area under the trapezoids) you won't get the same
1931: results. So we changed our mind and took the option of the best precision.
1932: */
1933: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
1934:
1935: agelim=AGESUP;
1936: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
1937: /* nhstepm age range expressed in number of stepm */
1938: nstepm=(int) rint((agelim-age)*YEARM/stepm);
1939: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
1940: /* if (stepm >= YEARM) hstepm=1;*/
1941: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
1942: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
1943: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
1944: gp=matrix(0,nhstepm,1,nlstate*nlstate);
1945: gm=matrix(0,nhstepm,1,nlstate*nlstate);
1946:
1947: /* Computed by stepm unit matrices, product of hstepm matrices, stored
1948: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
1949: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
1950:
1951:
1952: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
1953:
1954: /* Computing Variances of health expectancies */
1955:
1956: for(theta=1; theta <=npar; theta++){
1957: for(i=1; i<=npar; i++){
1958: xp[i] = x[i] + (i==theta ?delti[theta]:0);
1959: }
1960: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1961:
1962: cptj=0;
1963: for(j=1; j<= nlstate; j++){
1964: for(i=1; i<=nlstate; i++){
1965: cptj=cptj+1;
1966: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
1967: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1968: }
1969: }
1970: }
1971:
1972:
1973: for(i=1; i<=npar; i++)
1974: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1975: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1976:
1977: cptj=0;
1978: for(j=1; j<= nlstate; j++){
1979: for(i=1;i<=nlstate;i++){
1980: cptj=cptj+1;
1981: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
1982: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
1983: }
1984: }
1985: }
1986: for(j=1; j<= nlstate*nlstate; j++)
1987: for(h=0; h<=nhstepm-1; h++){
1988: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
1989: }
1990: }
1991:
1992: /* End theta */
1993:
1994: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
1995:
1996: for(h=0; h<=nhstepm-1; h++)
1997: for(j=1; j<=nlstate*nlstate;j++)
1998: for(theta=1; theta <=npar; theta++)
1999: trgradg[h][j][theta]=gradg[h][theta][j];
2000:
2001:
2002: for(i=1;i<=nlstate*nlstate;i++)
2003: for(j=1;j<=nlstate*nlstate;j++)
2004: varhe[i][j][(int)age] =0.;
2005:
2006: printf("%d|",(int)age);fflush(stdout);
2007: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2008: for(h=0;h<=nhstepm-1;h++){
2009: for(k=0;k<=nhstepm-1;k++){
2010: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2011: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2012: for(i=1;i<=nlstate*nlstate;i++)
2013: for(j=1;j<=nlstate*nlstate;j++)
2014: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2015: }
2016: }
2017: /* Computing expectancies */
2018: for(i=1; i<=nlstate;i++)
2019: for(j=1; j<=nlstate;j++)
2020: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2021: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2022:
2023: /* 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]);*/
2024:
2025: }
2026:
2027: fprintf(ficreseij,"%3.0f",age );
2028: cptj=0;
2029: for(i=1; i<=nlstate;i++)
2030: for(j=1; j<=nlstate;j++){
2031: cptj++;
2032: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2033: }
2034: fprintf(ficreseij,"\n");
2035:
2036: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2037: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2038: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2039: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2040: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2041: }
2042: printf("\n");
2043: fprintf(ficlog,"\n");
2044:
2045: free_vector(xp,1,npar);
2046: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2047: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2048: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2049: }
2050:
2051: /************ Variance ******************/
2052: 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)
2053: {
2054: /* Variance of health expectancies */
2055: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2056: /* double **newm;*/
2057: double **dnewm,**doldm;
2058: double **dnewmp,**doldmp;
2059: int i, j, nhstepm, hstepm, h, nstepm ;
2060: int k, cptcode;
2061: double *xp;
2062: double **gp, **gm; /* for var eij */
2063: double ***gradg, ***trgradg; /*for var eij */
2064: double **gradgp, **trgradgp; /* for var p point j */
2065: double *gpp, *gmp; /* for var p point j */
2066: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2067: double ***p3mat;
2068: double age,agelim, hf;
2069: double ***mobaverage;
2070: int theta;
2071: char digit[4];
2072: char digitp[25];
2073:
2074: char fileresprobmorprev[FILENAMELENGTH];
2075:
2076: if(popbased==1){
2077: if(mobilav!=0)
2078: strcpy(digitp,"-populbased-mobilav-");
2079: else strcpy(digitp,"-populbased-nomobil-");
2080: }
2081: else
2082: strcpy(digitp,"-stablbased-");
2083:
2084: if (mobilav!=0) {
2085: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2086: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2087: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2088: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2089: }
2090: }
2091:
2092: strcpy(fileresprobmorprev,"prmorprev");
2093: sprintf(digit,"%-d",ij);
2094: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2095: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2096: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2097: strcat(fileresprobmorprev,fileres);
2098: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2099: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2100: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2101: }
2102: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2103: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2104: fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
2105: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2106: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2107: fprintf(ficresprobmorprev," p.%-d SE",j);
2108: for(i=1; i<=nlstate;i++)
2109: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2110: }
2111: fprintf(ficresprobmorprev,"\n");
2112: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2113: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2114: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2115: exit(0);
2116: }
2117: else{
2118: fprintf(ficgp,"\n# Routine varevsij");
2119: }
2120: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2121: printf("Problem with html file: %s\n", optionfilehtm);
2122: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2123: exit(0);
2124: }
2125: else{
2126: fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
2127: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2128: }
2129: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2130:
2131: 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");
2132: fprintf(ficresvij,"# Age");
2133: for(i=1; i<=nlstate;i++)
2134: for(j=1; j<=nlstate;j++)
2135: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2136: fprintf(ficresvij,"\n");
2137:
2138: xp=vector(1,npar);
2139: dnewm=matrix(1,nlstate,1,npar);
2140: doldm=matrix(1,nlstate,1,nlstate);
2141: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2142: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2143:
2144: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2145: gpp=vector(nlstate+1,nlstate+ndeath);
2146: gmp=vector(nlstate+1,nlstate+ndeath);
2147: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2148:
2149: if(estepm < stepm){
2150: printf ("Problem %d lower than %d\n",estepm, stepm);
2151: }
2152: else hstepm=estepm;
2153: /* For example we decided to compute the life expectancy with the smallest unit */
2154: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2155: nhstepm is the number of hstepm from age to agelim
2156: nstepm is the number of stepm from age to agelin.
2157: Look at hpijx to understand the reason of that which relies in memory size
2158: and note for a fixed period like k years */
2159: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2160: survival function given by stepm (the optimization length). Unfortunately it
2161: means that if the survival funtion is printed every two years of age and if
2162: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2163: results. So we changed our mind and took the option of the best precision.
2164: */
2165: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2166: agelim = AGESUP;
2167: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2168: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2169: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2170: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2171: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2172: gp=matrix(0,nhstepm,1,nlstate);
2173: gm=matrix(0,nhstepm,1,nlstate);
2174:
2175:
2176: for(theta=1; theta <=npar; theta++){
2177: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2178: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2179: }
2180: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2181: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2182:
2183: if (popbased==1) {
2184: if(mobilav ==0){
2185: for(i=1; i<=nlstate;i++)
2186: prlim[i][i]=probs[(int)age][i][ij];
2187: }else{ /* mobilav */
2188: for(i=1; i<=nlstate;i++)
2189: prlim[i][i]=mobaverage[(int)age][i][ij];
2190: }
2191: }
2192:
2193: for(j=1; j<= nlstate; j++){
2194: for(h=0; h<=nhstepm; h++){
2195: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2196: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2197: }
2198: }
2199: /* This for computing probability of death (h=1 means
2200: computed over hstepm matrices product = hstepm*stepm months)
2201: as a weighted average of prlim.
2202: */
2203: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2204: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2205: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2206: }
2207: /* end probability of death */
2208:
2209: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2210: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2211: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2212: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2213:
2214: if (popbased==1) {
2215: if(mobilav ==0){
2216: for(i=1; i<=nlstate;i++)
2217: prlim[i][i]=probs[(int)age][i][ij];
2218: }else{ /* mobilav */
2219: for(i=1; i<=nlstate;i++)
2220: prlim[i][i]=mobaverage[(int)age][i][ij];
2221: }
2222: }
2223:
2224: for(j=1; j<= nlstate; j++){
2225: for(h=0; h<=nhstepm; h++){
2226: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2227: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2228: }
2229: }
2230: /* This for computing probability of death (h=1 means
2231: computed over hstepm matrices product = hstepm*stepm months)
2232: as a weighted average of prlim.
2233: */
2234: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2235: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2236: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2237: }
2238: /* end probability of death */
2239:
2240: for(j=1; j<= nlstate; j++) /* vareij */
2241: for(h=0; h<=nhstepm; h++){
2242: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2243: }
2244:
2245: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2246: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2247: }
2248:
2249: } /* End theta */
2250:
2251: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2252:
2253: for(h=0; h<=nhstepm; h++) /* veij */
2254: for(j=1; j<=nlstate;j++)
2255: for(theta=1; theta <=npar; theta++)
2256: trgradg[h][j][theta]=gradg[h][theta][j];
2257:
2258: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2259: for(theta=1; theta <=npar; theta++)
2260: trgradgp[j][theta]=gradgp[theta][j];
2261:
2262:
2263: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2264: for(i=1;i<=nlstate;i++)
2265: for(j=1;j<=nlstate;j++)
2266: vareij[i][j][(int)age] =0.;
2267:
2268: for(h=0;h<=nhstepm;h++){
2269: for(k=0;k<=nhstepm;k++){
2270: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2271: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2272: for(i=1;i<=nlstate;i++)
2273: for(j=1;j<=nlstate;j++)
2274: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2275: }
2276: }
2277:
2278: /* pptj */
2279: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2280: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2281: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2282: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2283: varppt[j][i]=doldmp[j][i];
2284: /* end ppptj */
2285: /* x centered again */
2286: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2287: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2288:
2289: if (popbased==1) {
2290: if(mobilav ==0){
2291: for(i=1; i<=nlstate;i++)
2292: prlim[i][i]=probs[(int)age][i][ij];
2293: }else{ /* mobilav */
2294: for(i=1; i<=nlstate;i++)
2295: prlim[i][i]=mobaverage[(int)age][i][ij];
2296: }
2297: }
2298:
2299: /* This for computing probability of death (h=1 means
2300: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2301: as a weighted average of prlim.
2302: */
2303: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2304: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2305: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2306: }
2307: /* end probability of death */
2308:
2309: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2310: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2311: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2312: for(i=1; i<=nlstate;i++){
2313: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2314: }
2315: }
2316: fprintf(ficresprobmorprev,"\n");
2317:
2318: fprintf(ficresvij,"%.0f ",age );
2319: for(i=1; i<=nlstate;i++)
2320: for(j=1; j<=nlstate;j++){
2321: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2322: }
2323: fprintf(ficresvij,"\n");
2324: free_matrix(gp,0,nhstepm,1,nlstate);
2325: free_matrix(gm,0,nhstepm,1,nlstate);
2326: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2327: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2328: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2329: } /* End age */
2330: free_vector(gpp,nlstate+1,nlstate+ndeath);
2331: free_vector(gmp,nlstate+1,nlstate+ndeath);
2332: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2333: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2334: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2335: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2336: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2337: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2338: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2339: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2340: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
2341: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
2342: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
2343: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
2344: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
2345: /* 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);
2346: */
2347: fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
2348:
2349: free_vector(xp,1,npar);
2350: free_matrix(doldm,1,nlstate,1,nlstate);
2351: free_matrix(dnewm,1,nlstate,1,npar);
2352: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2353: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2354: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2355: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2356: fclose(ficresprobmorprev);
2357: fclose(ficgp);
2358: fclose(fichtm);
2359: }
2360:
2361: /************ Variance of prevlim ******************/
2362: 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)
2363: {
2364: /* Variance of prevalence limit */
2365: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2366: double **newm;
2367: double **dnewm,**doldm;
2368: int i, j, nhstepm, hstepm;
2369: int k, cptcode;
2370: double *xp;
2371: double *gp, *gm;
2372: double **gradg, **trgradg;
2373: double age,agelim;
2374: int theta;
2375:
2376: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2377: fprintf(ficresvpl,"# Age");
2378: for(i=1; i<=nlstate;i++)
2379: fprintf(ficresvpl," %1d-%1d",i,i);
2380: fprintf(ficresvpl,"\n");
2381:
2382: xp=vector(1,npar);
2383: dnewm=matrix(1,nlstate,1,npar);
2384: doldm=matrix(1,nlstate,1,nlstate);
2385:
2386: hstepm=1*YEARM; /* Every year of age */
2387: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2388: agelim = AGESUP;
2389: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2390: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2391: if (stepm >= YEARM) hstepm=1;
2392: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2393: gradg=matrix(1,npar,1,nlstate);
2394: gp=vector(1,nlstate);
2395: gm=vector(1,nlstate);
2396:
2397: for(theta=1; theta <=npar; theta++){
2398: for(i=1; i<=npar; i++){ /* Computes gradient */
2399: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2400: }
2401: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2402: for(i=1;i<=nlstate;i++)
2403: gp[i] = prlim[i][i];
2404:
2405: for(i=1; i<=npar; i++) /* Computes gradient */
2406: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2407: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2408: for(i=1;i<=nlstate;i++)
2409: gm[i] = prlim[i][i];
2410:
2411: for(i=1;i<=nlstate;i++)
2412: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2413: } /* End theta */
2414:
2415: trgradg =matrix(1,nlstate,1,npar);
2416:
2417: for(j=1; j<=nlstate;j++)
2418: for(theta=1; theta <=npar; theta++)
2419: trgradg[j][theta]=gradg[theta][j];
2420:
2421: for(i=1;i<=nlstate;i++)
2422: varpl[i][(int)age] =0.;
2423: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2424: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2425: for(i=1;i<=nlstate;i++)
2426: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2427:
2428: fprintf(ficresvpl,"%.0f ",age );
2429: for(i=1; i<=nlstate;i++)
2430: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2431: fprintf(ficresvpl,"\n");
2432: free_vector(gp,1,nlstate);
2433: free_vector(gm,1,nlstate);
2434: free_matrix(gradg,1,npar,1,nlstate);
2435: free_matrix(trgradg,1,nlstate,1,npar);
2436: } /* End age */
2437:
2438: free_vector(xp,1,npar);
2439: free_matrix(doldm,1,nlstate,1,npar);
2440: free_matrix(dnewm,1,nlstate,1,nlstate);
2441:
2442: }
2443:
2444: /************ Variance of one-step probabilities ******************/
2445: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
2446: {
2447: int i, j=0, i1, k1, l1, t, tj;
2448: int k2, l2, j1, z1;
2449: int k=0,l, cptcode;
2450: int first=1, first1;
2451: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2452: double **dnewm,**doldm;
2453: double *xp;
2454: double *gp, *gm;
2455: double **gradg, **trgradg;
2456: double **mu;
2457: double age,agelim, cov[NCOVMAX];
2458: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2459: int theta;
2460: char fileresprob[FILENAMELENGTH];
2461: char fileresprobcov[FILENAMELENGTH];
2462: char fileresprobcor[FILENAMELENGTH];
2463:
2464: double ***varpij;
2465:
2466: strcpy(fileresprob,"prob");
2467: strcat(fileresprob,fileres);
2468: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2469: printf("Problem with resultfile: %s\n", fileresprob);
2470: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2471: }
2472: strcpy(fileresprobcov,"probcov");
2473: strcat(fileresprobcov,fileres);
2474: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2475: printf("Problem with resultfile: %s\n", fileresprobcov);
2476: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2477: }
2478: strcpy(fileresprobcor,"probcor");
2479: strcat(fileresprobcor,fileres);
2480: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2481: printf("Problem with resultfile: %s\n", fileresprobcor);
2482: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2483: }
2484: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2485: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2486: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2487: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2488: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2489: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2490:
2491: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2492: fprintf(ficresprob,"# Age");
2493: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2494: fprintf(ficresprobcov,"# Age");
2495: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2496: fprintf(ficresprobcov,"# Age");
2497:
2498:
2499: for(i=1; i<=nlstate;i++)
2500: for(j=1; j<=(nlstate+ndeath);j++){
2501: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2502: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2503: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2504: }
2505: /* fprintf(ficresprob,"\n");
2506: fprintf(ficresprobcov,"\n");
2507: fprintf(ficresprobcor,"\n");
2508: */
2509: xp=vector(1,npar);
2510: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2511: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2512: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2513: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2514: first=1;
2515: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2516: printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
2517: fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
2518: exit(0);
2519: }
2520: else{
2521: fprintf(ficgp,"\n# Routine varprob");
2522: }
2523: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2524: printf("Problem with html file: %s\n", optionfilehtm);
2525: fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
2526: exit(0);
2527: }
2528: else{
2529: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2530: fprintf(fichtm,"\n");
2531:
2532: fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
2533: 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");
2534: 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");
2535:
2536: }
2537:
2538: cov[1]=1;
2539: tj=cptcoveff;
2540: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2541: j1=0;
2542: for(t=1; t<=tj;t++){
2543: for(i1=1; i1<=ncodemax[t];i1++){
2544: j1++;
2545: if (cptcovn>0) {
2546: fprintf(ficresprob, "\n#********** Variable ");
2547: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2548: fprintf(ficresprob, "**********\n#\n");
2549: fprintf(ficresprobcov, "\n#********** Variable ");
2550: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2551: fprintf(ficresprobcov, "**********\n#\n");
2552:
2553: fprintf(ficgp, "\n#********** Variable ");
2554: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2555: fprintf(ficgp, "**********\n#\n");
2556:
2557:
2558: fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2559: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2560: fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2561:
2562: fprintf(ficresprobcor, "\n#********** Variable ");
2563: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2564: fprintf(ficresprobcor, "**********\n#");
2565: }
2566:
2567: for (age=bage; age<=fage; age ++){
2568: cov[2]=age;
2569: for (k=1; k<=cptcovn;k++) {
2570: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
2571: }
2572: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
2573: for (k=1; k<=cptcovprod;k++)
2574: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2575:
2576: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
2577: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2578: gp=vector(1,(nlstate)*(nlstate+ndeath));
2579: gm=vector(1,(nlstate)*(nlstate+ndeath));
2580:
2581: for(theta=1; theta <=npar; theta++){
2582: for(i=1; i<=npar; i++)
2583: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
2584:
2585: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2586:
2587: k=0;
2588: for(i=1; i<= (nlstate); i++){
2589: for(j=1; j<=(nlstate+ndeath);j++){
2590: k=k+1;
2591: gp[k]=pmmij[i][j];
2592: }
2593: }
2594:
2595: for(i=1; i<=npar; i++)
2596: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
2597:
2598: pmij(pmmij,cov,ncovmodel,xp,nlstate);
2599: k=0;
2600: for(i=1; i<=(nlstate); i++){
2601: for(j=1; j<=(nlstate+ndeath);j++){
2602: k=k+1;
2603: gm[k]=pmmij[i][j];
2604: }
2605: }
2606:
2607: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
2608: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
2609: }
2610:
2611: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
2612: for(theta=1; theta <=npar; theta++)
2613: trgradg[j][theta]=gradg[theta][j];
2614:
2615: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
2616: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
2617: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
2618: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
2619: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2620: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
2621:
2622: pmij(pmmij,cov,ncovmodel,x,nlstate);
2623:
2624: k=0;
2625: for(i=1; i<=(nlstate); i++){
2626: for(j=1; j<=(nlstate+ndeath);j++){
2627: k=k+1;
2628: mu[k][(int) age]=pmmij[i][j];
2629: }
2630: }
2631: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
2632: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
2633: varpij[i][j][(int)age] = doldm[i][j];
2634:
2635: /*printf("\n%d ",(int)age);
2636: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2637: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2638: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
2639: }*/
2640:
2641: fprintf(ficresprob,"\n%d ",(int)age);
2642: fprintf(ficresprobcov,"\n%d ",(int)age);
2643: fprintf(ficresprobcor,"\n%d ",(int)age);
2644:
2645: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
2646: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
2647: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
2648: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
2649: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
2650: }
2651: i=0;
2652: for (k=1; k<=(nlstate);k++){
2653: for (l=1; l<=(nlstate+ndeath);l++){
2654: i=i++;
2655: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
2656: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
2657: for (j=1; j<=i;j++){
2658: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
2659: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
2660: }
2661: }
2662: }/* end of loop for state */
2663: } /* end of loop for age */
2664:
2665: /* Confidence intervalle of pij */
2666: /*
2667: fprintf(ficgp,"\nset noparametric;unset label");
2668: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
2669: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2670: 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);
2671: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
2672: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
2673: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
2674: */
2675:
2676: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
2677: first1=1;
2678: for (k2=1; k2<=(nlstate);k2++){
2679: for (l2=1; l2<=(nlstate+ndeath);l2++){
2680: if(l2==k2) continue;
2681: j=(k2-1)*(nlstate+ndeath)+l2;
2682: for (k1=1; k1<=(nlstate);k1++){
2683: for (l1=1; l1<=(nlstate+ndeath);l1++){
2684: if(l1==k1) continue;
2685: i=(k1-1)*(nlstate+ndeath)+l1;
2686: if(i<=j) continue;
2687: for (age=bage; age<=fage; age ++){
2688: if ((int)age %5==0){
2689: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
2690: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
2691: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
2692: mu1=mu[i][(int) age]/stepm*YEARM ;
2693: mu2=mu[j][(int) age]/stepm*YEARM;
2694: c12=cv12/sqrt(v1*v2);
2695: /* Computing eigen value of matrix of covariance */
2696: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2697: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2698: /* Eigen vectors */
2699: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
2700: /*v21=sqrt(1.-v11*v11); *//* error */
2701: v21=(lc1-v1)/cv12*v11;
2702: v12=-v21;
2703: v22=v11;
2704: tnalp=v21/v11;
2705: if(first1==1){
2706: first1=0;
2707: 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);
2708: }
2709: 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);
2710: /*printf(fignu*/
2711: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
2712: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
2713: if(first==1){
2714: first=0;
2715: fprintf(ficgp,"\nset parametric;unset label");
2716: 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);
2717: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
2718: 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);
2719: fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
2720: fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
2721: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
2722: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2723: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2724: 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",\
2725: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2726: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2727: }else{
2728: first=0;
2729: fprintf(fichtm," %d (%.3f),",(int) age, c12);
2730: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
2731: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
2732: 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",\
2733: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
2734: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
2735: }/* if first */
2736: } /* age mod 5 */
2737: } /* end loop age */
2738: fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
2739: first=1;
2740: } /*l12 */
2741: } /* k12 */
2742: } /*l1 */
2743: }/* k1 */
2744: } /* loop covariates */
2745: }
2746: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
2747: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
2748: free_vector(xp,1,npar);
2749: fclose(ficresprob);
2750: fclose(ficresprobcov);
2751: fclose(ficresprobcor);
2752: fclose(ficgp);
2753: fclose(fichtm);
2754: }
2755:
2756:
2757: /******************* Printing html file ***********/
2758: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
2759: int lastpass, int stepm, int weightopt, char model[],\
2760: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
2761: int popforecast, int estepm ,\
2762: double jprev1, double mprev1,double anprev1, \
2763: double jprev2, double mprev2,double anprev2){
2764: int jj1, k1, i1, cpt;
2765: /*char optionfilehtm[FILENAMELENGTH];*/
2766: if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
2767: printf("Problem with %s \n",optionfilehtm), exit(0);
2768: fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
2769: }
2770:
2771: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
2772: - 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
2773: - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
2774: - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
2775: - Life expectancies by age and initial health status (estepm=%2d months):
2776: <a href=\"e%s\">e%s</a> <br>\n</li>", \
2777: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
2778:
2779: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
2780:
2781: m=cptcoveff;
2782: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2783:
2784: jj1=0;
2785: for(k1=1; k1<=m;k1++){
2786: for(i1=1; i1<=ncodemax[k1];i1++){
2787: jj1++;
2788: if (cptcovn > 0) {
2789: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2790: for (cpt=1; cpt<=cptcoveff;cpt++)
2791: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2792: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2793: }
2794: /* Pij */
2795: 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>
2796: <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2797: /* Quasi-incidences */
2798: 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>
2799: <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2800: /* Stable prevalence in each health state */
2801: for(cpt=1; cpt<nlstate;cpt++){
2802: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
2803: <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2804: }
2805: for(cpt=1; cpt<=nlstate;cpt++) {
2806: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
2807: <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2808: }
2809: fprintf(fichtm,"\n<br>- Total life expectancy by age and
2810: health expectancies in states (1) and (2): e%s%d.png<br>
2811: <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
2812: } /* end i1 */
2813: }/* End k1 */
2814: fprintf(fichtm,"</ul>");
2815:
2816:
2817: fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
2818: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
2819: - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
2820: - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
2821: - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
2822: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
2823: - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
2824: - 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);
2825:
2826: if(popforecast==1) fprintf(fichtm,"\n
2827: - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n
2828: - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n
2829: <br>",fileres,fileres,fileres,fileres);
2830: else
2831: 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);
2832: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
2833:
2834: m=cptcoveff;
2835: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
2836:
2837: jj1=0;
2838: for(k1=1; k1<=m;k1++){
2839: for(i1=1; i1<=ncodemax[k1];i1++){
2840: jj1++;
2841: if (cptcovn > 0) {
2842: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
2843: for (cpt=1; cpt<=cptcoveff;cpt++)
2844: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
2845: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
2846: }
2847: for(cpt=1; cpt<=nlstate;cpt++) {
2848: fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
2849: interval) in state (%d): v%s%d%d.png <br>
2850: <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
2851: }
2852: } /* end i1 */
2853: }/* End k1 */
2854: fprintf(fichtm,"</ul>");
2855: fclose(fichtm);
2856: }
2857:
2858: /******************* Gnuplot file **************/
2859: void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
2860:
2861: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
2862: int ng;
2863: if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
2864: printf("Problem with file %s",optionfilegnuplot);
2865: fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
2866: }
2867:
2868: /*#ifdef windows */
2869: fprintf(ficgp,"cd \"%s\" \n",pathc);
2870: /*#endif */
2871: m=pow(2,cptcoveff);
2872:
2873: /* 1eme*/
2874: for (cpt=1; cpt<= nlstate ; cpt ++) {
2875: for (k1=1; k1<= m ; k1 ++) {
2876: fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2877: 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);
2878:
2879: for (i=1; i<= nlstate ; i ++) {
2880: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2881: else fprintf(ficgp," \%%*lf (\%%*lf)");
2882: }
2883: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
2884: for (i=1; i<= nlstate ; i ++) {
2885: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2886: else fprintf(ficgp," \%%*lf (\%%*lf)");
2887: }
2888: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
2889: for (i=1; i<= nlstate ; i ++) {
2890: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
2891: else fprintf(ficgp," \%%*lf (\%%*lf)");
2892: }
2893: fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
2894: }
2895: }
2896: /*2 eme*/
2897:
2898: for (k1=1; k1<= m ; k1 ++) {
2899: fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
2900: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
2901:
2902: for (i=1; i<= nlstate+1 ; i ++) {
2903: k=2*i;
2904: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
2905: for (j=1; j<= nlstate+1 ; j ++) {
2906: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2907: else fprintf(ficgp," \%%*lf (\%%*lf)");
2908: }
2909: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
2910: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
2911: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
2912: for (j=1; j<= nlstate+1 ; j ++) {
2913: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2914: else fprintf(ficgp," \%%*lf (\%%*lf)");
2915: }
2916: fprintf(ficgp,"\" t\"\" w l 0,");
2917: fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
2918: for (j=1; j<= nlstate+1 ; j ++) {
2919: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
2920: else fprintf(ficgp," \%%*lf (\%%*lf)");
2921: }
2922: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
2923: else fprintf(ficgp,"\" t\"\" w l 0,");
2924: }
2925: }
2926:
2927: /*3eme*/
2928:
2929: for (k1=1; k1<= m ; k1 ++) {
2930: for (cpt=1; cpt<= nlstate ; cpt ++) {
2931: k=2+nlstate*(2*cpt-2);
2932: fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2933: fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
2934: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2935: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2936: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2937: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
2938: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
2939: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
2940:
2941: */
2942: for (i=1; i< nlstate ; i ++) {
2943: 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);
2944:
2945: }
2946: }
2947: }
2948:
2949: /* CV preval stat */
2950: for (k1=1; k1<= m ; k1 ++) {
2951: for (cpt=1; cpt<nlstate ; cpt ++) {
2952: k=3;
2953: fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
2954: 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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
2955:
2956: for (i=1; i< nlstate ; i ++)
2957: fprintf(ficgp,"+$%d",k+i+1);
2958: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
2959:
2960: l=3+(nlstate+ndeath)*cpt;
2961: fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
2962: for (i=1; i< nlstate ; i ++) {
2963: l=3+(nlstate+ndeath)*cpt;
2964: fprintf(ficgp,"+$%d",l+i+1);
2965: }
2966: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
2967: }
2968: }
2969:
2970: /* proba elementaires */
2971: for(i=1,jk=1; i <=nlstate; i++){
2972: for(k=1; k <=(nlstate+ndeath); k++){
2973: if (k != i) {
2974: for(j=1; j <=ncovmodel; j++){
2975: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
2976: jk++;
2977: fprintf(ficgp,"\n");
2978: }
2979: }
2980: }
2981: }
2982:
2983: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
2984: for(jk=1; jk <=m; jk++) {
2985: fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
2986: if (ng==2)
2987: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
2988: else
2989: fprintf(ficgp,"\nset title \"Probability\"\n");
2990: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
2991: i=1;
2992: for(k2=1; k2<=nlstate; k2++) {
2993: k3=i;
2994: for(k=1; k<=(nlstate+ndeath); k++) {
2995: if (k != k2){
2996: if(ng==2)
2997: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
2998: else
2999: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3000: ij=1;
3001: for(j=3; j <=ncovmodel; j++) {
3002: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3003: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3004: ij++;
3005: }
3006: else
3007: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3008: }
3009: fprintf(ficgp,")/(1");
3010:
3011: for(k1=1; k1 <=nlstate; k1++){
3012: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3013: ij=1;
3014: for(j=3; j <=ncovmodel; j++){
3015: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3016: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3017: ij++;
3018: }
3019: else
3020: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3021: }
3022: fprintf(ficgp,")");
3023: }
3024: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3025: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3026: i=i+ncovmodel;
3027: }
3028: } /* end k */
3029: } /* end k2 */
3030: } /* end jk */
3031: } /* end ng */
3032: fclose(ficgp);
3033: } /* end gnuplot */
3034:
3035:
3036: /*************** Moving average **************/
3037: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3038:
3039: int i, cpt, cptcod;
3040: int modcovmax =1;
3041: int mobilavrange, mob;
3042: double age;
3043:
3044: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3045: a covariate has 2 modalities */
3046: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3047:
3048: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3049: if(mobilav==1) mobilavrange=5; /* default */
3050: else mobilavrange=mobilav;
3051: for (age=bage; age<=fage; age++)
3052: for (i=1; i<=nlstate;i++)
3053: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3054: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3055: /* We keep the original values on the extreme ages bage, fage and for
3056: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3057: we use a 5 terms etc. until the borders are no more concerned.
3058: */
3059: for (mob=3;mob <=mobilavrange;mob=mob+2){
3060: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3061: for (i=1; i<=nlstate;i++){
3062: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3063: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3064: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3065: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3066: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3067: }
3068: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3069: }
3070: }
3071: }/* end age */
3072: }/* end mob */
3073: }else return -1;
3074: return 0;
3075: }/* End movingaverage */
3076:
3077:
3078: /************** Forecasting ******************/
3079: prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
3080: /* proj1, year, month, day of starting projection
3081: agemin, agemax range of age
3082: dateprev1 dateprev2 range of dates during which prevalence is computed
3083: anproj2 year of en of projection (same day and month as proj1).
3084: */
3085: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3086: int *popage;
3087: double agec; /* generic age */
3088: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3089: double *popeffectif,*popcount;
3090: double ***p3mat;
3091: double ***mobaverage;
3092: char fileresf[FILENAMELENGTH];
3093:
3094: agelim=AGESUP;
3095: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3096:
3097: strcpy(fileresf,"f");
3098: strcat(fileresf,fileres);
3099: if((ficresf=fopen(fileresf,"w"))==NULL) {
3100: printf("Problem with forecast resultfile: %s\n", fileresf);
3101: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3102: }
3103: printf("Computing forecasting: result on file '%s' \n", fileresf);
3104: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3105:
3106: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3107:
3108: if (mobilav!=0) {
3109: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3110: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3111: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3112: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3113: }
3114: }
3115:
3116: stepsize=(int) (stepm+YEARM-1)/YEARM;
3117: if (stepm<=12) stepsize=1;
3118: if(estepm < stepm){
3119: printf ("Problem %d lower than %d\n",estepm, stepm);
3120: }
3121: else hstepm=estepm;
3122:
3123: hstepm=hstepm/stepm;
3124: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3125: fractional in yp1 */
3126: anprojmean=yp;
3127: yp2=modf((yp1*12),&yp);
3128: mprojmean=yp;
3129: yp1=modf((yp2*30.5),&yp);
3130: jprojmean=yp;
3131: if(jprojmean==0) jprojmean=1;
3132: if(mprojmean==0) jprojmean=1;
3133:
3134: i1=cptcoveff;
3135: if (cptcovn < 1){i1=1;}
3136:
3137: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3138:
3139: fprintf(ficresf,"#****** Routine prevforecast **\n");
3140:
3141: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3142: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3143: k=k+1;
3144: fprintf(ficresf,"\n#******");
3145: for(j=1;j<=cptcoveff;j++) {
3146: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3147: }
3148: fprintf(ficresf,"******\n");
3149: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3150: for(j=1; j<=nlstate+ndeath;j++){
3151: for(i=1; i<=nlstate;i++)
3152: fprintf(ficresf," p%d%d",i,j);
3153: fprintf(ficresf," p.%d",j);
3154: }
3155: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3156: fprintf(ficresf,"\n");
3157: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3158:
3159: for (agec=fage; agec>=(ageminpar-1); agec--){
3160: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3161: nhstepm = nhstepm/hstepm;
3162: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3163: oldm=oldms;savm=savms;
3164: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3165:
3166: for (h=0; h<=nhstepm; h++){
3167: if (h==(int) (YEARM*yearp)) {
3168: fprintf(ficresf,"\n");
3169: for(j=1;j<=cptcoveff;j++)
3170: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3171: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3172: }
3173: for(j=1; j<=nlstate+ndeath;j++) {
3174: ppij=0.;
3175: for(i=1; i<=nlstate;i++) {
3176: if (mobilav==1)
3177: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3178: else {
3179: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3180: }
3181: if (h==(int)(YEARM*yearp))
3182: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3183: }
3184: if (h==(int)(YEARM*yearp)){
3185: fprintf(ficresf," %.3f", ppij);
3186: }
3187: }
3188: }
3189: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3190: }
3191: }
3192: }
3193: }
3194:
3195: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3196:
3197: fclose(ficresf);
3198: }
3199:
3200: /************** Forecasting *****not tested NB*************/
3201: 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){
3202:
3203: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3204: int *popage;
3205: double calagedatem, agelim, kk1, kk2;
3206: double *popeffectif,*popcount;
3207: double ***p3mat,***tabpop,***tabpopprev;
3208: double ***mobaverage;
3209: char filerespop[FILENAMELENGTH];
3210:
3211: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3212: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3213: agelim=AGESUP;
3214: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3215:
3216: prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3217:
3218:
3219: strcpy(filerespop,"pop");
3220: strcat(filerespop,fileres);
3221: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3222: printf("Problem with forecast resultfile: %s\n", filerespop);
3223: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3224: }
3225: printf("Computing forecasting: result on file '%s' \n", filerespop);
3226: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3227:
3228: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3229:
3230: if (mobilav!=0) {
3231: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3232: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3233: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3234: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3235: }
3236: }
3237:
3238: stepsize=(int) (stepm+YEARM-1)/YEARM;
3239: if (stepm<=12) stepsize=1;
3240:
3241: agelim=AGESUP;
3242:
3243: hstepm=1;
3244: hstepm=hstepm/stepm;
3245:
3246: if (popforecast==1) {
3247: if((ficpop=fopen(popfile,"r"))==NULL) {
3248: printf("Problem with population file : %s\n",popfile);exit(0);
3249: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3250: }
3251: popage=ivector(0,AGESUP);
3252: popeffectif=vector(0,AGESUP);
3253: popcount=vector(0,AGESUP);
3254:
3255: i=1;
3256: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3257:
3258: imx=i;
3259: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3260: }
3261:
3262: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3263: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3264: k=k+1;
3265: fprintf(ficrespop,"\n#******");
3266: for(j=1;j<=cptcoveff;j++) {
3267: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3268: }
3269: fprintf(ficrespop,"******\n");
3270: fprintf(ficrespop,"# Age");
3271: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3272: if (popforecast==1) fprintf(ficrespop," [Population]");
3273:
3274: for (cpt=0; cpt<=0;cpt++) {
3275: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3276:
3277: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3278: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3279: nhstepm = nhstepm/hstepm;
3280:
3281: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3282: oldm=oldms;savm=savms;
3283: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3284:
3285: for (h=0; h<=nhstepm; h++){
3286: if (h==(int) (calagedatem+YEARM*cpt)) {
3287: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3288: }
3289: for(j=1; j<=nlstate+ndeath;j++) {
3290: kk1=0.;kk2=0;
3291: for(i=1; i<=nlstate;i++) {
3292: if (mobilav==1)
3293: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3294: else {
3295: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3296: }
3297: }
3298: if (h==(int)(calagedatem+12*cpt)){
3299: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3300: /*fprintf(ficrespop," %.3f", kk1);
3301: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3302: }
3303: }
3304: for(i=1; i<=nlstate;i++){
3305: kk1=0.;
3306: for(j=1; j<=nlstate;j++){
3307: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3308: }
3309: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3310: }
3311:
3312: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3313: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3314: }
3315: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3316: }
3317: }
3318:
3319: /******/
3320:
3321: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3322: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3323: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3324: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3325: nhstepm = nhstepm/hstepm;
3326:
3327: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3328: oldm=oldms;savm=savms;
3329: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3330: for (h=0; h<=nhstepm; h++){
3331: if (h==(int) (calagedatem+YEARM*cpt)) {
3332: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3333: }
3334: for(j=1; j<=nlstate+ndeath;j++) {
3335: kk1=0.;kk2=0;
3336: for(i=1; i<=nlstate;i++) {
3337: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3338: }
3339: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3340: }
3341: }
3342: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3343: }
3344: }
3345: }
3346: }
3347:
3348: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3349:
3350: if (popforecast==1) {
3351: free_ivector(popage,0,AGESUP);
3352: free_vector(popeffectif,0,AGESUP);
3353: free_vector(popcount,0,AGESUP);
3354: }
3355: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3356: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3357: fclose(ficrespop);
3358: }
3359:
3360: /***********************************************/
3361: /**************** Main Program *****************/
3362: /***********************************************/
3363:
3364: int main(int argc, char *argv[])
3365: {
3366: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
3367: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
3368: double agedeb, agefin,hf;
3369: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
3370:
3371: double fret;
3372: double **xi,tmp,delta;
3373:
3374: double dum; /* Dummy variable */
3375: double ***p3mat;
3376: double ***mobaverage;
3377: int *indx;
3378: char line[MAXLINE], linepar[MAXLINE];
3379: char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
3380: int firstobs=1, lastobs=10;
3381: int sdeb, sfin; /* Status at beginning and end */
3382: int c, h , cpt,l;
3383: int ju,jl, mi;
3384: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
3385: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
3386: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
3387: int mobilav=0,popforecast=0;
3388: int hstepm, nhstepm;
3389: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
3390: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
3391:
3392: double bage, fage, age, agelim, agebase;
3393: double ftolpl=FTOL;
3394: double **prlim;
3395: double *severity;
3396: double ***param; /* Matrix of parameters */
3397: double *p;
3398: double **matcov; /* Matrix of covariance */
3399: double ***delti3; /* Scale */
3400: double *delti; /* Scale */
3401: double ***eij, ***vareij;
3402: double **varpl; /* Variances of prevalence limits by age */
3403: double *epj, vepp;
3404: double kk1, kk2;
3405: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
3406:
3407: char *alph[]={"a","a","b","c","d","e"}, str[4];
3408:
3409:
3410: char z[1]="c", occ;
3411: #include <sys/time.h>
3412: #include <time.h>
3413: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
3414:
3415: /* long total_usecs;
3416: struct timeval start_time, end_time;
3417:
3418: gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
3419: getcwd(pathcd, size);
3420:
3421: printf("\n%s",version);
3422: if(argc <=1){
3423: printf("\nEnter the parameter file name: ");
3424: scanf("%s",pathtot);
3425: }
3426: else{
3427: strcpy(pathtot,argv[1]);
3428: }
3429: /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
3430: /*cygwin_split_path(pathtot,path,optionfile);
3431: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
3432: /* cutv(path,optionfile,pathtot,'\\');*/
3433:
3434: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
3435: printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3436: chdir(path);
3437: replace(pathc,path);
3438:
3439: /*-------- arguments in the command line --------*/
3440:
3441: /* Log file */
3442: strcat(filelog, optionfilefiname);
3443: strcat(filelog,".log"); /* */
3444: if((ficlog=fopen(filelog,"w"))==NULL) {
3445: printf("Problem with logfile %s\n",filelog);
3446: goto end;
3447: }
3448: fprintf(ficlog,"Log filename:%s\n",filelog);
3449: fprintf(ficlog,"\n%s",version);
3450: fprintf(ficlog,"\nEnter the parameter file name: ");
3451: fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
3452: fflush(ficlog);
3453:
3454: /* */
3455: strcpy(fileres,"r");
3456: strcat(fileres, optionfilefiname);
3457: strcat(fileres,".txt"); /* Other files have txt extension */
3458:
3459: /*---------arguments file --------*/
3460:
3461: if((ficpar=fopen(optionfile,"r"))==NULL) {
3462: printf("Problem with optionfile %s\n",optionfile);
3463: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
3464: goto end;
3465: }
3466:
3467: strcpy(filereso,"o");
3468: strcat(filereso,fileres);
3469: if((ficparo=fopen(filereso,"w"))==NULL) {
3470: printf("Problem with Output resultfile: %s\n", filereso);
3471: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
3472: goto end;
3473: }
3474:
3475: /* Reads comments: lines beginning with '#' */
3476: while((c=getc(ficpar))=='#' && c!= EOF){
3477: ungetc(c,ficpar);
3478: fgets(line, MAXLINE, ficpar);
3479: puts(line);
3480: fputs(line,ficparo);
3481: }
3482: ungetc(c,ficpar);
3483:
3484: 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);
3485: 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);
3486: 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);
3487: while((c=getc(ficpar))=='#' && c!= EOF){
3488: ungetc(c,ficpar);
3489: fgets(line, MAXLINE, ficpar);
3490: puts(line);
3491: fputs(line,ficparo);
3492: }
3493: ungetc(c,ficpar);
3494:
3495:
3496: covar=matrix(0,NCOVMAX,1,n);
3497: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
3498: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
3499:
3500: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
3501: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
3502:
3503: /* Read guess parameters */
3504: /* Reads comments: lines beginning with '#' */
3505: while((c=getc(ficpar))=='#' && c!= EOF){
3506: ungetc(c,ficpar);
3507: fgets(line, MAXLINE, ficpar);
3508: puts(line);
3509: fputs(line,ficparo);
3510: }
3511: ungetc(c,ficpar);
3512:
3513: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3514: for(i=1; i <=nlstate; i++)
3515: for(j=1; j <=nlstate+ndeath-1; j++){
3516: fscanf(ficpar,"%1d%1d",&i1,&j1);
3517: fprintf(ficparo,"%1d%1d",i1,j1);
3518: if(mle==1)
3519: printf("%1d%1d",i,j);
3520: fprintf(ficlog,"%1d%1d",i,j);
3521: for(k=1; k<=ncovmodel;k++){
3522: fscanf(ficpar," %lf",¶m[i][j][k]);
3523: if(mle==1){
3524: printf(" %lf",param[i][j][k]);
3525: fprintf(ficlog," %lf",param[i][j][k]);
3526: }
3527: else
3528: fprintf(ficlog," %lf",param[i][j][k]);
3529: fprintf(ficparo," %lf",param[i][j][k]);
3530: }
3531: fscanf(ficpar,"\n");
3532: if(mle==1)
3533: printf("\n");
3534: fprintf(ficlog,"\n");
3535: fprintf(ficparo,"\n");
3536: }
3537:
3538: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3539:
3540: p=param[1][1];
3541:
3542: /* Reads comments: lines beginning with '#' */
3543: while((c=getc(ficpar))=='#' && c!= EOF){
3544: ungetc(c,ficpar);
3545: fgets(line, MAXLINE, ficpar);
3546: puts(line);
3547: fputs(line,ficparo);
3548: }
3549: ungetc(c,ficpar);
3550:
3551: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
3552: /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
3553: for(i=1; i <=nlstate; i++){
3554: for(j=1; j <=nlstate+ndeath-1; j++){
3555: fscanf(ficpar,"%1d%1d",&i1,&j1);
3556: printf("%1d%1d",i,j);
3557: fprintf(ficparo,"%1d%1d",i1,j1);
3558: for(k=1; k<=ncovmodel;k++){
3559: fscanf(ficpar,"%le",&delti3[i][j][k]);
3560: printf(" %le",delti3[i][j][k]);
3561: fprintf(ficparo," %le",delti3[i][j][k]);
3562: }
3563: fscanf(ficpar,"\n");
3564: printf("\n");
3565: fprintf(ficparo,"\n");
3566: }
3567: }
3568: delti=delti3[1][1];
3569:
3570:
3571: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
3572:
3573: /* Reads comments: lines beginning with '#' */
3574: while((c=getc(ficpar))=='#' && c!= EOF){
3575: ungetc(c,ficpar);
3576: fgets(line, MAXLINE, ficpar);
3577: puts(line);
3578: fputs(line,ficparo);
3579: }
3580: ungetc(c,ficpar);
3581:
3582: matcov=matrix(1,npar,1,npar);
3583: for(i=1; i <=npar; i++){
3584: fscanf(ficpar,"%s",&str);
3585: if(mle==1)
3586: printf("%s",str);
3587: fprintf(ficlog,"%s",str);
3588: fprintf(ficparo,"%s",str);
3589: for(j=1; j <=i; j++){
3590: fscanf(ficpar," %le",&matcov[i][j]);
3591: if(mle==1){
3592: printf(" %.5le",matcov[i][j]);
3593: fprintf(ficlog," %.5le",matcov[i][j]);
3594: }
3595: else
3596: fprintf(ficlog," %.5le",matcov[i][j]);
3597: fprintf(ficparo," %.5le",matcov[i][j]);
3598: }
3599: fscanf(ficpar,"\n");
3600: if(mle==1)
3601: printf("\n");
3602: fprintf(ficlog,"\n");
3603: fprintf(ficparo,"\n");
3604: }
3605: for(i=1; i <=npar; i++)
3606: for(j=i+1;j<=npar;j++)
3607: matcov[i][j]=matcov[j][i];
3608:
3609: if(mle==1)
3610: printf("\n");
3611: fprintf(ficlog,"\n");
3612:
3613:
3614: /*-------- Rewriting paramater file ----------*/
3615: strcpy(rfileres,"r"); /* "Rparameterfile */
3616: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
3617: strcat(rfileres,"."); /* */
3618: strcat(rfileres,optionfilext); /* Other files have txt extension */
3619: if((ficres =fopen(rfileres,"w"))==NULL) {
3620: printf("Problem writing new parameter file: %s\n", fileres);goto end;
3621: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
3622: }
3623: fprintf(ficres,"#%s\n",version);
3624:
3625: /*-------- data file ----------*/
3626: if((fic=fopen(datafile,"r"))==NULL) {
3627: printf("Problem with datafile: %s\n", datafile);goto end;
3628: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
3629: }
3630:
3631: n= lastobs;
3632: severity = vector(1,maxwav);
3633: outcome=imatrix(1,maxwav+1,1,n);
3634: num=ivector(1,n);
3635: moisnais=vector(1,n);
3636: annais=vector(1,n);
3637: moisdc=vector(1,n);
3638: andc=vector(1,n);
3639: agedc=vector(1,n);
3640: cod=ivector(1,n);
3641: weight=vector(1,n);
3642: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
3643: mint=matrix(1,maxwav,1,n);
3644: anint=matrix(1,maxwav,1,n);
3645: s=imatrix(1,maxwav+1,1,n);
3646: tab=ivector(1,NCOVMAX);
3647: ncodemax=ivector(1,8);
3648:
3649: i=1;
3650: while (fgets(line, MAXLINE, fic) != NULL) {
3651: if ((i >= firstobs) && (i <=lastobs)) {
3652:
3653: for (j=maxwav;j>=1;j--){
3654: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
3655: strcpy(line,stra);
3656: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3657: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3658: }
3659:
3660: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
3661: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
3662:
3663: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
3664: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
3665:
3666: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
3667: for (j=ncovcol;j>=1;j--){
3668: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
3669: }
3670: num[i]=atol(stra);
3671:
3672: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
3673: 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;}*/
3674:
3675: i=i+1;
3676: }
3677: }
3678: /* printf("ii=%d", ij);
3679: scanf("%d",i);*/
3680: imx=i-1; /* Number of individuals */
3681:
3682: /* for (i=1; i<=imx; i++){
3683: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
3684: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
3685: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
3686: }*/
3687: /* for (i=1; i<=imx; i++){
3688: if (s[4][i]==9) s[4][i]=-1;
3689: 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]));}*/
3690:
3691: for (i=1; i<=imx; i++)
3692:
3693: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
3694: else weight[i]=1;*/
3695:
3696: /* Calculation of the number of parameter from char model*/
3697: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
3698: Tprod=ivector(1,15);
3699: Tvaraff=ivector(1,15);
3700: Tvard=imatrix(1,15,1,2);
3701: Tage=ivector(1,15);
3702:
3703: if (strlen(model) >1){ /* If there is at least 1 covariate */
3704: j=0, j1=0, k1=1, k2=1;
3705: j=nbocc(model,'+'); /* j=Number of '+' */
3706: j1=nbocc(model,'*'); /* j1=Number of '*' */
3707: cptcovn=j+1;
3708: cptcovprod=j1; /*Number of products */
3709:
3710: strcpy(modelsav,model);
3711: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
3712: printf("Error. Non available option model=%s ",model);
3713: fprintf(ficlog,"Error. Non available option model=%s ",model);
3714: goto end;
3715: }
3716:
3717: /* This loop fills the array Tvar from the string 'model'.*/
3718:
3719: for(i=(j+1); i>=1;i--){
3720: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
3721: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
3722: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
3723: /*scanf("%d",i);*/
3724: if (strchr(strb,'*')) { /* Model includes a product */
3725: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
3726: if (strcmp(strc,"age")==0) { /* Vn*age */
3727: cptcovprod--;
3728: cutv(strb,stre,strd,'V');
3729: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
3730: cptcovage++;
3731: Tage[cptcovage]=i;
3732: /*printf("stre=%s ", stre);*/
3733: }
3734: else if (strcmp(strd,"age")==0) { /* or age*Vn */
3735: cptcovprod--;
3736: cutv(strb,stre,strc,'V');
3737: Tvar[i]=atoi(stre);
3738: cptcovage++;
3739: Tage[cptcovage]=i;
3740: }
3741: else { /* Age is not in the model */
3742: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
3743: Tvar[i]=ncovcol+k1;
3744: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
3745: Tprod[k1]=i;
3746: Tvard[k1][1]=atoi(strc); /* m*/
3747: Tvard[k1][2]=atoi(stre); /* n */
3748: Tvar[cptcovn+k2]=Tvard[k1][1];
3749: Tvar[cptcovn+k2+1]=Tvard[k1][2];
3750: for (k=1; k<=lastobs;k++)
3751: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
3752: k1++;
3753: k2=k2+2;
3754: }
3755: }
3756: else { /* no more sum */
3757: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
3758: /* scanf("%d",i);*/
3759: cutv(strd,strc,strb,'V');
3760: Tvar[i]=atoi(strc);
3761: }
3762: strcpy(modelsav,stra);
3763: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
3764: scanf("%d",i);*/
3765: } /* end of loop + */
3766: } /* end model */
3767:
3768: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
3769: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
3770:
3771: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
3772: printf("cptcovprod=%d ", cptcovprod);
3773: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
3774:
3775: scanf("%d ",i);
3776: fclose(fic);*/
3777:
3778: /* if(mle==1){*/
3779: if (weightopt != 1) { /* Maximisation without weights*/
3780: for(i=1;i<=n;i++) weight[i]=1.0;
3781: }
3782: /*-calculation of age at interview from date of interview and age at death -*/
3783: agev=matrix(1,maxwav,1,imx);
3784:
3785: for (i=1; i<=imx; i++) {
3786: for(m=2; (m<= maxwav); m++) {
3787: if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
3788: anint[m][i]=9999;
3789: s[m][i]=-1;
3790: }
3791: if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
3792: }
3793: }
3794:
3795: for (i=1; i<=imx; i++) {
3796: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
3797: for(m=firstpass; (m<= lastpass); m++){
3798: if(s[m][i] >0){
3799: if (s[m][i] >= nlstate+1) {
3800: if(agedc[i]>0)
3801: if(moisdc[i]!=99 && andc[i]!=9999)
3802: agev[m][i]=agedc[i];
3803: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
3804: else {
3805: if (andc[i]!=9999){
3806: printf("Warning negative age at death: %d line:%d\n",num[i],i);
3807: fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
3808: agev[m][i]=-1;
3809: }
3810: }
3811: }
3812: else if(s[m][i] !=9){ /* Standard case, age in fractional
3813: years but with the precision of a
3814: month */
3815: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
3816: if(mint[m][i]==99 || anint[m][i]==9999)
3817: agev[m][i]=1;
3818: else if(agev[m][i] <agemin){
3819: agemin=agev[m][i];
3820: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
3821: }
3822: else if(agev[m][i] >agemax){
3823: agemax=agev[m][i];
3824: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
3825: }
3826: /*agev[m][i]=anint[m][i]-annais[i];*/
3827: /* agev[m][i] = age[i]+2*m;*/
3828: }
3829: else { /* =9 */
3830: agev[m][i]=1;
3831: s[m][i]=-1;
3832: }
3833: }
3834: else /*= 0 Unknown */
3835: agev[m][i]=1;
3836: }
3837:
3838: }
3839: for (i=1; i<=imx; i++) {
3840: for(m=firstpass; (m<=lastpass); m++){
3841: if (s[m][i] > (nlstate+ndeath)) {
3842: 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);
3843: 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);
3844: goto end;
3845: }
3846: }
3847: }
3848:
3849: /*for (i=1; i<=imx; i++){
3850: for (m=firstpass; (m<lastpass); m++){
3851: printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
3852: }
3853:
3854: }*/
3855:
3856: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3857: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
3858:
3859: free_vector(severity,1,maxwav);
3860: free_imatrix(outcome,1,maxwav+1,1,n);
3861: free_vector(moisnais,1,n);
3862: free_vector(annais,1,n);
3863: /* free_matrix(mint,1,maxwav,1,n);
3864: free_matrix(anint,1,maxwav,1,n);*/
3865: free_vector(moisdc,1,n);
3866: free_vector(andc,1,n);
3867:
3868:
3869: wav=ivector(1,imx);
3870: dh=imatrix(1,lastpass-firstpass+1,1,imx);
3871: bh=imatrix(1,lastpass-firstpass+1,1,imx);
3872: mw=imatrix(1,lastpass-firstpass+1,1,imx);
3873:
3874: /* Concatenates waves */
3875: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
3876:
3877: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
3878:
3879: Tcode=ivector(1,100);
3880: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
3881: ncodemax[1]=1;
3882: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
3883:
3884: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
3885: the estimations*/
3886: h=0;
3887: m=pow(2,cptcoveff);
3888:
3889: for(k=1;k<=cptcoveff; k++){
3890: for(i=1; i <=(m/pow(2,k));i++){
3891: for(j=1; j <= ncodemax[k]; j++){
3892: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
3893: h++;
3894: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
3895: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
3896: }
3897: }
3898: }
3899: }
3900: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
3901: codtab[1][2]=1;codtab[2][2]=2; */
3902: /* for(i=1; i <=m ;i++){
3903: for(k=1; k <=cptcovn; k++){
3904: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
3905: }
3906: printf("\n");
3907: }
3908: scanf("%d",i);*/
3909:
3910: /* Calculates basic frequencies. Computes observed prevalence at single age
3911: and prints on file fileres'p'. */
3912:
3913: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3914: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3915: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3916: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
3917: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
3918:
3919:
3920: /* For Powell, parameters are in a vector p[] starting at p[1]
3921: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
3922: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
3923:
3924: if(mle>=1){ /* Could be 1 or 2 */
3925: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
3926: }
3927:
3928: /*--------- results files --------------*/
3929: 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);
3930:
3931:
3932: jk=1;
3933: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3934: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3935: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3936: for(i=1,jk=1; i <=nlstate; i++){
3937: for(k=1; k <=(nlstate+ndeath); k++){
3938: if (k != i)
3939: {
3940: printf("%d%d ",i,k);
3941: fprintf(ficlog,"%d%d ",i,k);
3942: fprintf(ficres,"%1d%1d ",i,k);
3943: for(j=1; j <=ncovmodel; j++){
3944: printf("%f ",p[jk]);
3945: fprintf(ficlog,"%f ",p[jk]);
3946: fprintf(ficres,"%f ",p[jk]);
3947: jk++;
3948: }
3949: printf("\n");
3950: fprintf(ficlog,"\n");
3951: fprintf(ficres,"\n");
3952: }
3953: }
3954: }
3955: if(mle==1){
3956: /* Computing hessian and covariance matrix */
3957: ftolhess=ftol; /* Usually correct */
3958: hesscov(matcov, p, npar, delti, ftolhess, func);
3959: }
3960: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
3961: printf("# Scales (for hessian or gradient estimation)\n");
3962: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
3963: for(i=1,jk=1; i <=nlstate; i++){
3964: for(j=1; j <=nlstate+ndeath; j++){
3965: if (j!=i) {
3966: fprintf(ficres,"%1d%1d",i,j);
3967: printf("%1d%1d",i,j);
3968: fprintf(ficlog,"%1d%1d",i,j);
3969: for(k=1; k<=ncovmodel;k++){
3970: printf(" %.5e",delti[jk]);
3971: fprintf(ficlog," %.5e",delti[jk]);
3972: fprintf(ficres," %.5e",delti[jk]);
3973: jk++;
3974: }
3975: printf("\n");
3976: fprintf(ficlog,"\n");
3977: fprintf(ficres,"\n");
3978: }
3979: }
3980: }
3981:
3982: 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");
3983: if(mle==1)
3984: 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");
3985: 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");
3986: for(i=1,k=1;i<=npar;i++){
3987: /* if (k>nlstate) k=1;
3988: i1=(i-1)/(ncovmodel*nlstate)+1;
3989: fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
3990: printf("%s%d%d",alph[k],i1,tab[i]);
3991: */
3992: fprintf(ficres,"%3d",i);
3993: if(mle==1)
3994: printf("%3d",i);
3995: fprintf(ficlog,"%3d",i);
3996: for(j=1; j<=i;j++){
3997: fprintf(ficres," %.5e",matcov[i][j]);
3998: if(mle==1)
3999: printf(" %.5e",matcov[i][j]);
4000: fprintf(ficlog," %.5e",matcov[i][j]);
4001: }
4002: fprintf(ficres,"\n");
4003: if(mle==1)
4004: printf("\n");
4005: fprintf(ficlog,"\n");
4006: k++;
4007: }
4008:
4009: while((c=getc(ficpar))=='#' && c!= EOF){
4010: ungetc(c,ficpar);
4011: fgets(line, MAXLINE, ficpar);
4012: puts(line);
4013: fputs(line,ficparo);
4014: }
4015: ungetc(c,ficpar);
4016:
4017: estepm=0;
4018: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
4019: if (estepm==0 || estepm < stepm) estepm=stepm;
4020: if (fage <= 2) {
4021: bage = ageminpar;
4022: fage = agemaxpar;
4023: }
4024:
4025: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
4026: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4027: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
4028:
4029: while((c=getc(ficpar))=='#' && c!= EOF){
4030: ungetc(c,ficpar);
4031: fgets(line, MAXLINE, ficpar);
4032: puts(line);
4033: fputs(line,ficparo);
4034: }
4035: ungetc(c,ficpar);
4036:
4037: 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);
4038: 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);
4039: 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);
4040: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4041: fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
4042:
4043: while((c=getc(ficpar))=='#' && c!= EOF){
4044: ungetc(c,ficpar);
4045: fgets(line, MAXLINE, ficpar);
4046: puts(line);
4047: fputs(line,ficparo);
4048: }
4049: ungetc(c,ficpar);
4050:
4051:
4052: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
4053: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
4054:
4055: fscanf(ficpar,"pop_based=%d\n",&popbased);
4056: fprintf(ficparo,"pop_based=%d\n",popbased);
4057: fprintf(ficres,"pop_based=%d\n",popbased);
4058:
4059: while((c=getc(ficpar))=='#' && c!= EOF){
4060: ungetc(c,ficpar);
4061: fgets(line, MAXLINE, ficpar);
4062: puts(line);
4063: fputs(line,ficparo);
4064: }
4065: ungetc(c,ficpar);
4066:
4067: fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
4068: fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4069: printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4070: fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4071: fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
4072: /* day and month of proj2 are not used but only year anproj2.*/
4073:
4074: while((c=getc(ficpar))=='#' && c!= EOF){
4075: ungetc(c,ficpar);
4076: fgets(line, MAXLINE, ficpar);
4077: puts(line);
4078: fputs(line,ficparo);
4079: }
4080: ungetc(c,ficpar);
4081:
4082: fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
4083: fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4084: fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
4085:
4086: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4087: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
4088:
4089: /*------------ gnuplot -------------*/
4090: strcpy(optionfilegnuplot,optionfilefiname);
4091: strcat(optionfilegnuplot,".gp");
4092: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4093: printf("Problem with file %s",optionfilegnuplot);
4094: }
4095: else{
4096: fprintf(ficgp,"\n# %s\n", version);
4097: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4098: fprintf(ficgp,"set missing 'NaNq'\n");
4099: }
4100: fclose(ficgp);
4101: printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
4102: /*--------- index.htm --------*/
4103:
4104: strcpy(optionfilehtm,optionfile);
4105: strcat(optionfilehtm,".htm");
4106: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4107: printf("Problem with %s \n",optionfilehtm), exit(0);
4108: }
4109:
4110: fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
4111: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
4112: \n
4113: Total number of observations=%d <br>\n
4114: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
4115: <hr size=\"2\" color=\"#EC5E5E\">
4116: <ul><li><h4>Parameter files</h4>\n
4117: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
4118: - Log file of the run: <a href=\"%s\">%s</a><br>\n
4119: - 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);
4120: fclose(fichtm);
4121:
4122: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
4123:
4124: /*------------ free_vector -------------*/
4125: chdir(path);
4126:
4127: free_ivector(wav,1,imx);
4128: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
4129: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
4130: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
4131: free_ivector(num,1,n);
4132: free_vector(agedc,1,n);
4133: /*free_matrix(covar,0,NCOVMAX,1,n);*/
4134: /*free_matrix(covar,1,NCOVMAX,1,n);*/
4135: fclose(ficparo);
4136: fclose(ficres);
4137:
4138:
4139: /*--------------- Prevalence limit (stable prevalence) --------------*/
4140:
4141: strcpy(filerespl,"pl");
4142: strcat(filerespl,fileres);
4143: if((ficrespl=fopen(filerespl,"w"))==NULL) {
4144: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4145: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
4146: }
4147: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
4148: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
4149: fprintf(ficrespl,"#Stable prevalence \n");
4150: fprintf(ficrespl,"#Age ");
4151: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
4152: fprintf(ficrespl,"\n");
4153:
4154: prlim=matrix(1,nlstate,1,nlstate);
4155:
4156: agebase=ageminpar;
4157: agelim=agemaxpar;
4158: ftolpl=1.e-10;
4159: i1=cptcoveff;
4160: if (cptcovn < 1){i1=1;}
4161:
4162: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4163: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4164: k=k+1;
4165: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
4166: fprintf(ficrespl,"\n#******");
4167: printf("\n#******");
4168: fprintf(ficlog,"\n#******");
4169: for(j=1;j<=cptcoveff;j++) {
4170: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4171: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4172: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4173: }
4174: fprintf(ficrespl,"******\n");
4175: printf("******\n");
4176: fprintf(ficlog,"******\n");
4177:
4178: for (age=agebase; age<=agelim; age++){
4179: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4180: fprintf(ficrespl,"%.0f ",age );
4181: for(j=1;j<=cptcoveff;j++)
4182: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4183: for(i=1; i<=nlstate;i++)
4184: fprintf(ficrespl," %.5f", prlim[i][i]);
4185: fprintf(ficrespl,"\n");
4186: }
4187: }
4188: }
4189: fclose(ficrespl);
4190:
4191: /*------------- h Pij x at various ages ------------*/
4192:
4193: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
4194: if((ficrespij=fopen(filerespij,"w"))==NULL) {
4195: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
4196: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
4197: }
4198: printf("Computing pij: result on file '%s' \n", filerespij);
4199: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
4200:
4201: stepsize=(int) (stepm+YEARM-1)/YEARM;
4202: /*if (stepm<=24) stepsize=2;*/
4203:
4204: agelim=AGESUP;
4205: hstepm=stepsize*YEARM; /* Every year of age */
4206: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
4207:
4208: /* hstepm=1; aff par mois*/
4209:
4210: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
4211: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4212: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4213: k=k+1;
4214: fprintf(ficrespij,"\n#****** ");
4215: for(j=1;j<=cptcoveff;j++)
4216: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4217: fprintf(ficrespij,"******\n");
4218:
4219: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
4220: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4221: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4222:
4223: /* nhstepm=nhstepm*YEARM; aff par mois*/
4224:
4225: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4226: oldm=oldms;savm=savms;
4227: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4228: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
4229: for(i=1; i<=nlstate;i++)
4230: for(j=1; j<=nlstate+ndeath;j++)
4231: fprintf(ficrespij," %1d-%1d",i,j);
4232: fprintf(ficrespij,"\n");
4233: for (h=0; h<=nhstepm; h++){
4234: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
4235: for(i=1; i<=nlstate;i++)
4236: for(j=1; j<=nlstate+ndeath;j++)
4237: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
4238: fprintf(ficrespij,"\n");
4239: }
4240: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4241: fprintf(ficrespij,"\n");
4242: }
4243: }
4244: }
4245:
4246: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
4247:
4248: fclose(ficrespij);
4249:
4250:
4251: /*---------- Forecasting ------------------*/
4252: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
4253: if(prevfcast==1){
4254: /* if(stepm ==1){*/
4255: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
4256: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
4257: /* } */
4258: /* else{ */
4259: /* erreur=108; */
4260: /* 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); */
4261: /* 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); */
4262: /* } */
4263: }
4264:
4265:
4266: /*---------- Health expectancies and variances ------------*/
4267:
4268: strcpy(filerest,"t");
4269: strcat(filerest,fileres);
4270: if((ficrest=fopen(filerest,"w"))==NULL) {
4271: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
4272: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
4273: }
4274: printf("Computing Total LEs with variances: file '%s' \n", filerest);
4275: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
4276:
4277:
4278: strcpy(filerese,"e");
4279: strcat(filerese,fileres);
4280: if((ficreseij=fopen(filerese,"w"))==NULL) {
4281: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4282: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
4283: }
4284: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
4285: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
4286:
4287: strcpy(fileresv,"v");
4288: strcat(fileresv,fileres);
4289: if((ficresvij=fopen(fileresv,"w"))==NULL) {
4290: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
4291: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
4292: }
4293: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4294: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
4295:
4296: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
4297: prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4298: /* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
4299: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
4300: */
4301:
4302: if (mobilav!=0) {
4303: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4304: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4305: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4306: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4307: }
4308: }
4309:
4310: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4311: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4312: k=k+1;
4313: fprintf(ficrest,"\n#****** ");
4314: for(j=1;j<=cptcoveff;j++)
4315: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4316: fprintf(ficrest,"******\n");
4317:
4318: fprintf(ficreseij,"\n#****** ");
4319: for(j=1;j<=cptcoveff;j++)
4320: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4321: fprintf(ficreseij,"******\n");
4322:
4323: fprintf(ficresvij,"\n#****** ");
4324: for(j=1;j<=cptcoveff;j++)
4325: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4326: fprintf(ficresvij,"******\n");
4327:
4328: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4329: oldm=oldms;savm=savms;
4330: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);
4331:
4332: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
4333: oldm=oldms;savm=savms;
4334: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
4335: if(popbased==1){
4336: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
4337: }
4338:
4339:
4340: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
4341: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
4342: fprintf(ficrest,"\n");
4343:
4344: epj=vector(1,nlstate+1);
4345: for(age=bage; age <=fage ;age++){
4346: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
4347: if (popbased==1) {
4348: if(mobilav ==0){
4349: for(i=1; i<=nlstate;i++)
4350: prlim[i][i]=probs[(int)age][i][k];
4351: }else{ /* mobilav */
4352: for(i=1; i<=nlstate;i++)
4353: prlim[i][i]=mobaverage[(int)age][i][k];
4354: }
4355: }
4356:
4357: fprintf(ficrest," %4.0f",age);
4358: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
4359: for(i=1, epj[j]=0.;i <=nlstate;i++) {
4360: epj[j] += prlim[i][i]*eij[i][j][(int)age];
4361: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
4362: }
4363: epj[nlstate+1] +=epj[j];
4364: }
4365:
4366: for(i=1, vepp=0.;i <=nlstate;i++)
4367: for(j=1;j <=nlstate;j++)
4368: vepp += vareij[i][j][(int)age];
4369: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
4370: for(j=1;j <=nlstate;j++){
4371: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
4372: }
4373: fprintf(ficrest,"\n");
4374: }
4375: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4376: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
4377: free_vector(epj,1,nlstate+1);
4378: }
4379: }
4380: free_vector(weight,1,n);
4381: free_imatrix(Tvard,1,15,1,2);
4382: free_imatrix(s,1,maxwav+1,1,n);
4383: free_matrix(anint,1,maxwav,1,n);
4384: free_matrix(mint,1,maxwav,1,n);
4385: free_ivector(cod,1,n);
4386: free_ivector(tab,1,NCOVMAX);
4387: fclose(ficreseij);
4388: fclose(ficresvij);
4389: fclose(ficrest);
4390: fclose(ficpar);
4391:
4392: /*------- Variance of stable prevalence------*/
4393:
4394: strcpy(fileresvpl,"vpl");
4395: strcat(fileresvpl,fileres);
4396: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
4397: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
4398: exit(0);
4399: }
4400: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
4401:
4402: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
4403: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
4404: k=k+1;
4405: fprintf(ficresvpl,"\n#****** ");
4406: for(j=1;j<=cptcoveff;j++)
4407: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4408: fprintf(ficresvpl,"******\n");
4409:
4410: varpl=matrix(1,nlstate,(int) bage, (int) fage);
4411: oldm=oldms;savm=savms;
4412: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
4413: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
4414: }
4415: }
4416:
4417: fclose(ficresvpl);
4418:
4419: /*---------- End : free ----------------*/
4420: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
4421: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
4422: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
4423: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
4424:
4425: free_matrix(covar,0,NCOVMAX,1,n);
4426: free_matrix(matcov,1,npar,1,npar);
4427: /*free_vector(delti,1,npar);*/
4428: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4429: free_matrix(agev,1,maxwav,1,imx);
4430: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4431: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4432: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
4433:
4434: free_ivector(ncodemax,1,8);
4435: free_ivector(Tvar,1,15);
4436: free_ivector(Tprod,1,15);
4437: free_ivector(Tvaraff,1,15);
4438: free_ivector(Tage,1,15);
4439: free_ivector(Tcode,1,100);
4440:
4441: /* fclose(fichtm);*/
4442: /* fclose(ficgp);*/ /* ALready done */
4443:
4444:
4445: if(erreur >0){
4446: printf("End of Imach with error or warning %d\n",erreur);
4447: fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
4448: }else{
4449: printf("End of Imach\n");
4450: fprintf(ficlog,"End of Imach\n");
4451: }
4452: printf("See log file on %s\n",filelog);
4453: fclose(ficlog);
4454: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
4455:
4456: /* 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);*/
4457: /*printf("Total time was %d uSec.\n", total_usecs);*/
4458: /*------ End -----------*/
4459:
4460: end:
4461: #ifdef windows
4462: /* chdir(pathcd);*/
4463: #endif
4464: /*system("wgnuplot graph.plt");*/
4465: /*system("../gp37mgw/wgnuplot graph.plt");*/
4466: /*system("cd ../gp37mgw");*/
4467: /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
4468: strcpy(plotcmd,GNUPLOTPROGRAM);
4469: strcat(plotcmd," ");
4470: strcat(plotcmd,optionfilegnuplot);
4471: printf("Starting: %s\n",plotcmd);fflush(stdout);
4472: system(plotcmd);
4473:
4474: /*#ifdef windows*/
4475: while (z[0] != 'q') {
4476: /* chdir(path); */
4477: printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
4478: scanf("%s",z);
4479: if (z[0] == 'c') system("./imach");
4480: else if (z[0] == 'e') system(optionfilehtm);
4481: else if (z[0] == 'g') system(plotcmd);
4482: else if (z[0] == 'q') exit(0);
4483: }
4484: /*#endif */
4485: }
4486:
4487:
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