1: /* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.105 2006/01/05 20:23:19 lievre
5: *** empty log message ***
6:
7: Revision 1.104 2005/09/30 16:11:43 lievre
8: (Module): sump fixed, loop imx fixed, and simplifications.
9: (Module): If the status is missing at the last wave but we know
10: that the person is alive, then we can code his/her status as -2
11: (instead of missing=-1 in earlier versions) and his/her
12: contributions to the likelihood is 1 - Prob of dying from last
13: health status (= 1-p13= p11+p12 in the easiest case of somebody in
14: the healthy state at last known wave). Version is 0.98
15:
16: Revision 1.103 2005/09/30 15:54:49 lievre
17: (Module): sump fixed, loop imx fixed, and simplifications.
18:
19: Revision 1.102 2004/09/15 17:31:30 brouard
20: Add the possibility to read data file including tab characters.
21:
22: Revision 1.101 2004/09/15 10:38:38 brouard
23: Fix on curr_time
24:
25: Revision 1.100 2004/07/12 18:29:06 brouard
26: Add version for Mac OS X. Just define UNIX in Makefile
27:
28: Revision 1.99 2004/06/05 08:57:40 brouard
29: *** empty log message ***
30:
31: Revision 1.98 2004/05/16 15:05:56 brouard
32: New version 0.97 . First attempt to estimate force of mortality
33: directly from the data i.e. without the need of knowing the health
34: state at each age, but using a Gompertz model: log u =a + b*age .
35: This is the basic analysis of mortality and should be done before any
36: other analysis, in order to test if the mortality estimated from the
37: cross-longitudinal survey is different from the mortality estimated
38: from other sources like vital statistic data.
39:
40: The same imach parameter file can be used but the option for mle should be -3.
41:
42: Agnès, who wrote this part of the code, tried to keep most of the
43: former routines in order to include the new code within the former code.
44:
45: The output is very simple: only an estimate of the intercept and of
46: the slope with 95% confident intervals.
47:
48: Current limitations:
49: A) Even if you enter covariates, i.e. with the
50: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
51: B) There is no computation of Life Expectancy nor Life Table.
52:
53: Revision 1.97 2004/02/20 13:25:42 lievre
54: Version 0.96d. Population forecasting command line is (temporarily)
55: suppressed.
56:
57: Revision 1.96 2003/07/15 15:38:55 brouard
58: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
59: rewritten within the same printf. Workaround: many printfs.
60:
61: Revision 1.95 2003/07/08 07:54:34 brouard
62: * imach.c (Repository):
63: (Repository): Using imachwizard code to output a more meaningful covariance
64: matrix (cov(a12,c31) instead of numbers.
65:
66: Revision 1.94 2003/06/27 13:00:02 brouard
67: Just cleaning
68:
69: Revision 1.93 2003/06/25 16:33:55 brouard
70: (Module): On windows (cygwin) function asctime_r doesn't
71: exist so I changed back to asctime which exists.
72: (Module): Version 0.96b
73:
74: Revision 1.92 2003/06/25 16:30:45 brouard
75: (Module): On windows (cygwin) function asctime_r doesn't
76: exist so I changed back to asctime which exists.
77:
78: Revision 1.91 2003/06/25 15:30:29 brouard
79: * imach.c (Repository): Duplicated warning errors corrected.
80: (Repository): Elapsed time after each iteration is now output. It
81: helps to forecast when convergence will be reached. Elapsed time
82: is stamped in powell. We created a new html file for the graphs
83: concerning matrix of covariance. It has extension -cov.htm.
84:
85: Revision 1.90 2003/06/24 12:34:15 brouard
86: (Module): Some bugs corrected for windows. Also, when
87: mle=-1 a template is output in file "or"mypar.txt with the design
88: of the covariance matrix to be input.
89:
90: Revision 1.89 2003/06/24 12:30:52 brouard
91: (Module): Some bugs corrected for windows. Also, when
92: mle=-1 a template is output in file "or"mypar.txt with the design
93: of the covariance matrix to be input.
94:
95: Revision 1.88 2003/06/23 17:54:56 brouard
96: * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
97:
98: Revision 1.87 2003/06/18 12:26:01 brouard
99: Version 0.96
100:
101: Revision 1.86 2003/06/17 20:04:08 brouard
102: (Module): Change position of html and gnuplot routines and added
103: routine fileappend.
104:
105: Revision 1.85 2003/06/17 13:12:43 brouard
106: * imach.c (Repository): Check when date of death was earlier that
107: current date of interview. It may happen when the death was just
108: prior to the death. In this case, dh was negative and likelihood
109: was wrong (infinity). We still send an "Error" but patch by
110: assuming that the date of death was just one stepm after the
111: interview.
112: (Repository): Because some people have very long ID (first column)
113: we changed int to long in num[] and we added a new lvector for
114: memory allocation. But we also truncated to 8 characters (left
115: truncation)
116: (Repository): No more line truncation errors.
117:
118: Revision 1.84 2003/06/13 21:44:43 brouard
119: * imach.c (Repository): Replace "freqsummary" at a correct
120: place. It differs from routine "prevalence" which may be called
121: many times. Probs is memory consuming and must be used with
122: parcimony.
123: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
124:
125: Revision 1.83 2003/06/10 13:39:11 lievre
126: *** empty log message ***
127:
128: Revision 1.82 2003/06/05 15:57:20 brouard
129: Add log in imach.c and fullversion number is now printed.
130:
131: */
132: /*
133: Interpolated Markov Chain
134:
135: Short summary of the programme:
136:
137: This program computes Healthy Life Expectancies from
138: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
139: first survey ("cross") where individuals from different ages are
140: interviewed on their health status or degree of disability (in the
141: case of a health survey which is our main interest) -2- at least a
142: second wave of interviews ("longitudinal") which measure each change
143: (if any) in individual health status. Health expectancies are
144: computed from the time spent in each health state according to a
145: model. More health states you consider, more time is necessary to reach the
146: Maximum Likelihood of the parameters involved in the model. The
147: simplest model is the multinomial logistic model where pij is the
148: probability to be observed in state j at the second wave
149: conditional to be observed in state i at the first wave. Therefore
150: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
151: 'age' is age and 'sex' is a covariate. If you want to have a more
152: complex model than "constant and age", you should modify the program
153: where the markup *Covariates have to be included here again* invites
154: you to do it. More covariates you add, slower the
155: convergence.
156:
157: The advantage of this computer programme, compared to a simple
158: multinomial logistic model, is clear when the delay between waves is not
159: identical for each individual. Also, if a individual missed an
160: intermediate interview, the information is lost, but taken into
161: account using an interpolation or extrapolation.
162:
163: hPijx is the probability to be observed in state i at age x+h
164: conditional to the observed state i at age x. The delay 'h' can be
165: split into an exact number (nh*stepm) of unobserved intermediate
166: states. This elementary transition (by month, quarter,
167: semester or year) is modelled as a multinomial logistic. The hPx
168: matrix is simply the matrix product of nh*stepm elementary matrices
169: and the contribution of each individual to the likelihood is simply
170: hPijx.
171:
172: Also this programme outputs the covariance matrix of the parameters but also
173: of the life expectancies. It also computes the stable prevalence.
174:
175: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
176: Institut national d'études démographiques, Paris.
177: This software have been partly granted by Euro-REVES, a concerted action
178: from the European Union.
179: It is copyrighted identically to a GNU software product, ie programme and
180: software can be distributed freely for non commercial use. Latest version
181: can be accessed at http://euroreves.ined.fr/imach .
182:
183: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
184: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
185:
186: **********************************************************************/
187: /*
188: main
189: read parameterfile
190: read datafile
191: concatwav
192: freqsummary
193: if (mle >= 1)
194: mlikeli
195: print results files
196: if mle==1
197: computes hessian
198: read end of parameter file: agemin, agemax, bage, fage, estepm
199: begin-prev-date,...
200: open gnuplot file
201: open html file
202: stable prevalence
203: for age prevalim()
204: h Pij x
205: variance of p varprob
206: forecasting if prevfcast==1 prevforecast call prevalence()
207: health expectancies
208: Variance-covariance of DFLE
209: prevalence()
210: movingaverage()
211: varevsij()
212: if popbased==1 varevsij(,popbased)
213: total life expectancies
214: Variance of stable prevalence
215: end
216: */
217:
218:
219:
220:
221: #include <math.h>
222: #include <stdio.h>
223: #include <stdlib.h>
224: #include <unistd.h>
225:
226: /* #include <sys/time.h> */
227: #include <time.h>
228: #include "timeval.h"
229:
230: /* #include <libintl.h> */
231: /* #define _(String) gettext (String) */
232:
233: #define MAXLINE 256
234: #define GNUPLOTPROGRAM "gnuplot"
235: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
236: #define FILENAMELENGTH 132
237: /*#define DEBUG*/
238: /*#define windows*/
239: #define GLOCK_ERROR_NOPATH -1 /* empty path */
240: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
241:
242: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
243: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
244:
245: #define NINTERVMAX 8
246: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
247: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
248: #define NCOVMAX 8 /* Maximum number of covariates */
249: #define MAXN 20000
250: #define YEARM 12. /* Number of months per year */
251: #define AGESUP 130
252: #define AGEBASE 40
253: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
254: #ifdef UNIX
255: #define DIRSEPARATOR '/'
256: #define ODIRSEPARATOR '\\'
257: #else
258: #define DIRSEPARATOR '\\'
259: #define ODIRSEPARATOR '/'
260: #endif
261:
262: /* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */
263: /* $State: Exp $ */
264:
265: char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
266: char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $";
267: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
268: int nvar;
269: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
270: int npar=NPARMAX;
271: int nlstate=2; /* Number of live states */
272: int ndeath=1; /* Number of dead states */
273: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
274: int popbased=0;
275:
276: int *wav; /* Number of waves for this individuual 0 is possible */
277: int maxwav; /* Maxim number of waves */
278: int jmin, jmax; /* min, max spacing between 2 waves */
279: int gipmx, gsw; /* Global variables on the number of contributions
280: to the likelihood and the sum of weights (done by funcone)*/
281: int mle, weightopt;
282: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
283: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
284: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
285: * wave mi and wave mi+1 is not an exact multiple of stepm. */
286: double jmean; /* Mean space between 2 waves */
287: double **oldm, **newm, **savm; /* Working pointers to matrices */
288: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
289: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
290: FILE *ficlog, *ficrespow;
291: int globpr; /* Global variable for printing or not */
292: double fretone; /* Only one call to likelihood */
293: long ipmx; /* Number of contributions */
294: double sw; /* Sum of weights */
295: char filerespow[FILENAMELENGTH];
296: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
297: FILE *ficresilk;
298: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
299: FILE *ficresprobmorprev;
300: FILE *fichtm, *fichtmcov; /* Html File */
301: FILE *ficreseij;
302: char filerese[FILENAMELENGTH];
303: FILE *ficresvij;
304: char fileresv[FILENAMELENGTH];
305: FILE *ficresvpl;
306: char fileresvpl[FILENAMELENGTH];
307: char title[MAXLINE];
308: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
309: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
310: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
311: char command[FILENAMELENGTH];
312: int outcmd=0;
313:
314: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
315:
316: char filelog[FILENAMELENGTH]; /* Log file */
317: char filerest[FILENAMELENGTH];
318: char fileregp[FILENAMELENGTH];
319: char popfile[FILENAMELENGTH];
320:
321: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
322:
323: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
324: struct timezone tzp;
325: extern int gettimeofday();
326: struct tm tmg, tm, tmf, *gmtime(), *localtime();
327: long time_value;
328: extern long time();
329: char strcurr[80], strfor[80];
330:
331: #define NR_END 1
332: #define FREE_ARG char*
333: #define FTOL 1.0e-10
334:
335: #define NRANSI
336: #define ITMAX 200
337:
338: #define TOL 2.0e-4
339:
340: #define CGOLD 0.3819660
341: #define ZEPS 1.0e-10
342: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
343:
344: #define GOLD 1.618034
345: #define GLIMIT 100.0
346: #define TINY 1.0e-20
347:
348: static double maxarg1,maxarg2;
349: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
350: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
351:
352: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
353: #define rint(a) floor(a+0.5)
354:
355: static double sqrarg;
356: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
357: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
358: int agegomp= AGEGOMP;
359:
360: int imx;
361: int stepm=1;
362: /* Stepm, step in month: minimum step interpolation*/
363:
364: int estepm;
365: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
366:
367: int m,nb;
368: long *num;
369: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
370: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
371: double **pmmij, ***probs;
372: double *ageexmed,*agecens;
373: double dateintmean=0;
374:
375: double *weight;
376: int **s; /* Status */
377: double *agedc, **covar, idx;
378: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
379: double *lsurv, *lpop, *tpop;
380:
381: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
382: double ftolhess; /* Tolerance for computing hessian */
383:
384: /**************** split *************************/
385: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
386: {
387: /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
388: the name of the file (name), its extension only (ext) and its first part of the name (finame)
389: */
390: char *ss; /* pointer */
391: int l1, l2; /* length counters */
392:
393: l1 = strlen(path ); /* length of path */
394: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
395: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
396: if ( ss == NULL ) { /* no directory, so use current */
397: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
398: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
399: /* get current working directory */
400: /* extern char* getcwd ( char *buf , int len);*/
401: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
402: return( GLOCK_ERROR_GETCWD );
403: }
404: strcpy( name, path ); /* we've got it */
405: } else { /* strip direcotry from path */
406: ss++; /* after this, the filename */
407: l2 = strlen( ss ); /* length of filename */
408: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
409: strcpy( name, ss ); /* save file name */
410: strncpy( dirc, path, l1 - l2 ); /* now the directory */
411: dirc[l1-l2] = 0; /* add zero */
412: }
413: l1 = strlen( dirc ); /* length of directory */
414: /*#ifdef windows
415: if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
416: #else
417: if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
418: #endif
419: */
420: ss = strrchr( name, '.' ); /* find last / */
421: if (ss >0){
422: ss++;
423: strcpy(ext,ss); /* save extension */
424: l1= strlen( name);
425: l2= strlen(ss)+1;
426: strncpy( finame, name, l1-l2);
427: finame[l1-l2]= 0;
428: }
429: return( 0 ); /* we're done */
430: }
431:
432:
433: /******************************************/
434:
435: void replace_back_to_slash(char *s, char*t)
436: {
437: int i;
438: int lg=0;
439: i=0;
440: lg=strlen(t);
441: for(i=0; i<= lg; i++) {
442: (s[i] = t[i]);
443: if (t[i]== '\\') s[i]='/';
444: }
445: }
446:
447: int nbocc(char *s, char occ)
448: {
449: int i,j=0;
450: int lg=20;
451: i=0;
452: lg=strlen(s);
453: for(i=0; i<= lg; i++) {
454: if (s[i] == occ ) j++;
455: }
456: return j;
457: }
458:
459: void cutv(char *u,char *v, char*t, char occ)
460: {
461: /* cuts string t into u and v where u ends before first occurence of char 'occ'
462: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
463: gives u="abcedf" and v="ghi2j" */
464: int i,lg,j,p=0;
465: i=0;
466: for(j=0; j<=strlen(t)-1; j++) {
467: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
468: }
469:
470: lg=strlen(t);
471: for(j=0; j<p; j++) {
472: (u[j] = t[j]);
473: }
474: u[p]='\0';
475:
476: for(j=0; j<= lg; j++) {
477: if (j>=(p+1))(v[j-p-1] = t[j]);
478: }
479: }
480:
481: /********************** nrerror ********************/
482:
483: void nrerror(char error_text[])
484: {
485: fprintf(stderr,"ERREUR ...\n");
486: fprintf(stderr,"%s\n",error_text);
487: exit(EXIT_FAILURE);
488: }
489: /*********************** vector *******************/
490: double *vector(int nl, int nh)
491: {
492: double *v;
493: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
494: if (!v) nrerror("allocation failure in vector");
495: return v-nl+NR_END;
496: }
497:
498: /************************ free vector ******************/
499: void free_vector(double*v, int nl, int nh)
500: {
501: free((FREE_ARG)(v+nl-NR_END));
502: }
503:
504: /************************ivector *******************************/
505: int *ivector(long nl,long nh)
506: {
507: int *v;
508: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
509: if (!v) nrerror("allocation failure in ivector");
510: return v-nl+NR_END;
511: }
512:
513: /******************free ivector **************************/
514: void free_ivector(int *v, long nl, long nh)
515: {
516: free((FREE_ARG)(v+nl-NR_END));
517: }
518:
519: /************************lvector *******************************/
520: long *lvector(long nl,long nh)
521: {
522: long *v;
523: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
524: if (!v) nrerror("allocation failure in ivector");
525: return v-nl+NR_END;
526: }
527:
528: /******************free lvector **************************/
529: void free_lvector(long *v, long nl, long nh)
530: {
531: free((FREE_ARG)(v+nl-NR_END));
532: }
533:
534: /******************* imatrix *******************************/
535: int **imatrix(long nrl, long nrh, long ncl, long nch)
536: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
537: {
538: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
539: int **m;
540:
541: /* allocate pointers to rows */
542: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
543: if (!m) nrerror("allocation failure 1 in matrix()");
544: m += NR_END;
545: m -= nrl;
546:
547:
548: /* allocate rows and set pointers to them */
549: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
550: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
551: m[nrl] += NR_END;
552: m[nrl] -= ncl;
553:
554: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
555:
556: /* return pointer to array of pointers to rows */
557: return m;
558: }
559:
560: /****************** free_imatrix *************************/
561: void free_imatrix(m,nrl,nrh,ncl,nch)
562: int **m;
563: long nch,ncl,nrh,nrl;
564: /* free an int matrix allocated by imatrix() */
565: {
566: free((FREE_ARG) (m[nrl]+ncl-NR_END));
567: free((FREE_ARG) (m+nrl-NR_END));
568: }
569:
570: /******************* matrix *******************************/
571: double **matrix(long nrl, long nrh, long ncl, long nch)
572: {
573: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
574: double **m;
575:
576: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
577: if (!m) nrerror("allocation failure 1 in matrix()");
578: m += NR_END;
579: m -= nrl;
580:
581: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
582: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
583: m[nrl] += NR_END;
584: m[nrl] -= ncl;
585:
586: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
587: return m;
588: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
589: */
590: }
591:
592: /*************************free matrix ************************/
593: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
594: {
595: free((FREE_ARG)(m[nrl]+ncl-NR_END));
596: free((FREE_ARG)(m+nrl-NR_END));
597: }
598:
599: /******************* ma3x *******************************/
600: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
601: {
602: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
603: double ***m;
604:
605: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
606: if (!m) nrerror("allocation failure 1 in matrix()");
607: m += NR_END;
608: m -= nrl;
609:
610: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
611: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
612: m[nrl] += NR_END;
613: m[nrl] -= ncl;
614:
615: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
616:
617: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
618: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
619: m[nrl][ncl] += NR_END;
620: m[nrl][ncl] -= nll;
621: for (j=ncl+1; j<=nch; j++)
622: m[nrl][j]=m[nrl][j-1]+nlay;
623:
624: for (i=nrl+1; i<=nrh; i++) {
625: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
626: for (j=ncl+1; j<=nch; j++)
627: m[i][j]=m[i][j-1]+nlay;
628: }
629: return m;
630: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
631: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
632: */
633: }
634:
635: /*************************free ma3x ************************/
636: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
637: {
638: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
639: free((FREE_ARG)(m[nrl]+ncl-NR_END));
640: free((FREE_ARG)(m+nrl-NR_END));
641: }
642:
643: /*************** function subdirf ***********/
644: char *subdirf(char fileres[])
645: {
646: /* Caution optionfilefiname is hidden */
647: strcpy(tmpout,optionfilefiname);
648: strcat(tmpout,"/"); /* Add to the right */
649: strcat(tmpout,fileres);
650: return tmpout;
651: }
652:
653: /*************** function subdirf2 ***********/
654: char *subdirf2(char fileres[], char *preop)
655: {
656:
657: /* Caution optionfilefiname is hidden */
658: strcpy(tmpout,optionfilefiname);
659: strcat(tmpout,"/");
660: strcat(tmpout,preop);
661: strcat(tmpout,fileres);
662: return tmpout;
663: }
664:
665: /*************** function subdirf3 ***********/
666: char *subdirf3(char fileres[], char *preop, char *preop2)
667: {
668:
669: /* Caution optionfilefiname is hidden */
670: strcpy(tmpout,optionfilefiname);
671: strcat(tmpout,"/");
672: strcat(tmpout,preop);
673: strcat(tmpout,preop2);
674: strcat(tmpout,fileres);
675: return tmpout;
676: }
677:
678: /***************** f1dim *************************/
679: extern int ncom;
680: extern double *pcom,*xicom;
681: extern double (*nrfunc)(double []);
682:
683: double f1dim(double x)
684: {
685: int j;
686: double f;
687: double *xt;
688:
689: xt=vector(1,ncom);
690: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
691: f=(*nrfunc)(xt);
692: free_vector(xt,1,ncom);
693: return f;
694: }
695:
696: /*****************brent *************************/
697: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
698: {
699: int iter;
700: double a,b,d,etemp;
701: double fu,fv,fw,fx;
702: double ftemp;
703: double p,q,r,tol1,tol2,u,v,w,x,xm;
704: double e=0.0;
705:
706: a=(ax < cx ? ax : cx);
707: b=(ax > cx ? ax : cx);
708: x=w=v=bx;
709: fw=fv=fx=(*f)(x);
710: for (iter=1;iter<=ITMAX;iter++) {
711: xm=0.5*(a+b);
712: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
713: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
714: printf(".");fflush(stdout);
715: fprintf(ficlog,".");fflush(ficlog);
716: #ifdef DEBUG
717: 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);
718: 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);
719: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
720: #endif
721: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
722: *xmin=x;
723: return fx;
724: }
725: ftemp=fu;
726: if (fabs(e) > tol1) {
727: r=(x-w)*(fx-fv);
728: q=(x-v)*(fx-fw);
729: p=(x-v)*q-(x-w)*r;
730: q=2.0*(q-r);
731: if (q > 0.0) p = -p;
732: q=fabs(q);
733: etemp=e;
734: e=d;
735: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
736: d=CGOLD*(e=(x >= xm ? a-x : b-x));
737: else {
738: d=p/q;
739: u=x+d;
740: if (u-a < tol2 || b-u < tol2)
741: d=SIGN(tol1,xm-x);
742: }
743: } else {
744: d=CGOLD*(e=(x >= xm ? a-x : b-x));
745: }
746: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
747: fu=(*f)(u);
748: if (fu <= fx) {
749: if (u >= x) a=x; else b=x;
750: SHFT(v,w,x,u)
751: SHFT(fv,fw,fx,fu)
752: } else {
753: if (u < x) a=u; else b=u;
754: if (fu <= fw || w == x) {
755: v=w;
756: w=u;
757: fv=fw;
758: fw=fu;
759: } else if (fu <= fv || v == x || v == w) {
760: v=u;
761: fv=fu;
762: }
763: }
764: }
765: nrerror("Too many iterations in brent");
766: *xmin=x;
767: return fx;
768: }
769:
770: /****************** mnbrak ***********************/
771:
772: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
773: double (*func)(double))
774: {
775: double ulim,u,r,q, dum;
776: double fu;
777:
778: *fa=(*func)(*ax);
779: *fb=(*func)(*bx);
780: if (*fb > *fa) {
781: SHFT(dum,*ax,*bx,dum)
782: SHFT(dum,*fb,*fa,dum)
783: }
784: *cx=(*bx)+GOLD*(*bx-*ax);
785: *fc=(*func)(*cx);
786: while (*fb > *fc) {
787: r=(*bx-*ax)*(*fb-*fc);
788: q=(*bx-*cx)*(*fb-*fa);
789: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
790: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
791: ulim=(*bx)+GLIMIT*(*cx-*bx);
792: if ((*bx-u)*(u-*cx) > 0.0) {
793: fu=(*func)(u);
794: } else if ((*cx-u)*(u-ulim) > 0.0) {
795: fu=(*func)(u);
796: if (fu < *fc) {
797: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
798: SHFT(*fb,*fc,fu,(*func)(u))
799: }
800: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
801: u=ulim;
802: fu=(*func)(u);
803: } else {
804: u=(*cx)+GOLD*(*cx-*bx);
805: fu=(*func)(u);
806: }
807: SHFT(*ax,*bx,*cx,u)
808: SHFT(*fa,*fb,*fc,fu)
809: }
810: }
811:
812: /*************** linmin ************************/
813:
814: int ncom;
815: double *pcom,*xicom;
816: double (*nrfunc)(double []);
817:
818: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
819: {
820: double brent(double ax, double bx, double cx,
821: double (*f)(double), double tol, double *xmin);
822: double f1dim(double x);
823: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
824: double *fc, double (*func)(double));
825: int j;
826: double xx,xmin,bx,ax;
827: double fx,fb,fa;
828:
829: ncom=n;
830: pcom=vector(1,n);
831: xicom=vector(1,n);
832: nrfunc=func;
833: for (j=1;j<=n;j++) {
834: pcom[j]=p[j];
835: xicom[j]=xi[j];
836: }
837: ax=0.0;
838: xx=1.0;
839: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
840: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
841: #ifdef DEBUG
842: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
843: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
844: #endif
845: for (j=1;j<=n;j++) {
846: xi[j] *= xmin;
847: p[j] += xi[j];
848: }
849: free_vector(xicom,1,n);
850: free_vector(pcom,1,n);
851: }
852:
853: char *asc_diff_time(long time_sec, char ascdiff[])
854: {
855: long sec_left, days, hours, minutes;
856: days = (time_sec) / (60*60*24);
857: sec_left = (time_sec) % (60*60*24);
858: hours = (sec_left) / (60*60) ;
859: sec_left = (sec_left) %(60*60);
860: minutes = (sec_left) /60;
861: sec_left = (sec_left) % (60);
862: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
863: return ascdiff;
864: }
865:
866: /*************** powell ************************/
867: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
868: double (*func)(double []))
869: {
870: void linmin(double p[], double xi[], int n, double *fret,
871: double (*func)(double []));
872: int i,ibig,j;
873: double del,t,*pt,*ptt,*xit;
874: double fp,fptt;
875: double *xits;
876: int niterf, itmp;
877:
878: pt=vector(1,n);
879: ptt=vector(1,n);
880: xit=vector(1,n);
881: xits=vector(1,n);
882: *fret=(*func)(p);
883: for (j=1;j<=n;j++) pt[j]=p[j];
884: for (*iter=1;;++(*iter)) {
885: fp=(*fret);
886: ibig=0;
887: del=0.0;
888: last_time=curr_time;
889: (void) gettimeofday(&curr_time,&tzp);
890: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
891: /* fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
892: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
893: */
894: for (i=1;i<=n;i++) {
895: printf(" %d %.12f",i, p[i]);
896: fprintf(ficlog," %d %.12lf",i, p[i]);
897: fprintf(ficrespow," %.12lf", p[i]);
898: }
899: printf("\n");
900: fprintf(ficlog,"\n");
901: fprintf(ficrespow,"\n");fflush(ficrespow);
902: if(*iter <=3){
903: tm = *localtime(&curr_time.tv_sec);
904: strcpy(strcurr,asctime(&tm));
905: /* asctime_r(&tm,strcurr); */
906: forecast_time=curr_time;
907: itmp = strlen(strcurr);
908: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
909: strcurr[itmp-1]='\0';
910: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
911: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
912: for(niterf=10;niterf<=30;niterf+=10){
913: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
914: tmf = *localtime(&forecast_time.tv_sec);
915: /* asctime_r(&tmf,strfor); */
916: strcpy(strfor,asctime(&tmf));
917: itmp = strlen(strfor);
918: if(strfor[itmp-1]=='\n')
919: strfor[itmp-1]='\0';
920: printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
921: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
922: }
923: }
924: for (i=1;i<=n;i++) {
925: for (j=1;j<=n;j++) xit[j]=xi[j][i];
926: fptt=(*fret);
927: #ifdef DEBUG
928: printf("fret=%lf \n",*fret);
929: fprintf(ficlog,"fret=%lf \n",*fret);
930: #endif
931: printf("%d",i);fflush(stdout);
932: fprintf(ficlog,"%d",i);fflush(ficlog);
933: linmin(p,xit,n,fret,func);
934: if (fabs(fptt-(*fret)) > del) {
935: del=fabs(fptt-(*fret));
936: ibig=i;
937: }
938: #ifdef DEBUG
939: printf("%d %.12e",i,(*fret));
940: fprintf(ficlog,"%d %.12e",i,(*fret));
941: for (j=1;j<=n;j++) {
942: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
943: printf(" x(%d)=%.12e",j,xit[j]);
944: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
945: }
946: for(j=1;j<=n;j++) {
947: printf(" p=%.12e",p[j]);
948: fprintf(ficlog," p=%.12e",p[j]);
949: }
950: printf("\n");
951: fprintf(ficlog,"\n");
952: #endif
953: }
954: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
955: #ifdef DEBUG
956: int k[2],l;
957: k[0]=1;
958: k[1]=-1;
959: printf("Max: %.12e",(*func)(p));
960: fprintf(ficlog,"Max: %.12e",(*func)(p));
961: for (j=1;j<=n;j++) {
962: printf(" %.12e",p[j]);
963: fprintf(ficlog," %.12e",p[j]);
964: }
965: printf("\n");
966: fprintf(ficlog,"\n");
967: for(l=0;l<=1;l++) {
968: for (j=1;j<=n;j++) {
969: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
970: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
971: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
972: }
973: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
974: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
975: }
976: #endif
977:
978:
979: free_vector(xit,1,n);
980: free_vector(xits,1,n);
981: free_vector(ptt,1,n);
982: free_vector(pt,1,n);
983: return;
984: }
985: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
986: for (j=1;j<=n;j++) {
987: ptt[j]=2.0*p[j]-pt[j];
988: xit[j]=p[j]-pt[j];
989: pt[j]=p[j];
990: }
991: fptt=(*func)(ptt);
992: if (fptt < fp) {
993: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
994: if (t < 0.0) {
995: linmin(p,xit,n,fret,func);
996: for (j=1;j<=n;j++) {
997: xi[j][ibig]=xi[j][n];
998: xi[j][n]=xit[j];
999: }
1000: #ifdef DEBUG
1001: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1002: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1003: for(j=1;j<=n;j++){
1004: printf(" %.12e",xit[j]);
1005: fprintf(ficlog," %.12e",xit[j]);
1006: }
1007: printf("\n");
1008: fprintf(ficlog,"\n");
1009: #endif
1010: }
1011: }
1012: }
1013: }
1014:
1015: /**** Prevalence limit (stable prevalence) ****************/
1016:
1017: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1018: {
1019: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1020: matrix by transitions matrix until convergence is reached */
1021:
1022: int i, ii,j,k;
1023: double min, max, maxmin, maxmax,sumnew=0.;
1024: double **matprod2();
1025: double **out, cov[NCOVMAX], **pmij();
1026: double **newm;
1027: double agefin, delaymax=50 ; /* Max number of years to converge */
1028:
1029: for (ii=1;ii<=nlstate+ndeath;ii++)
1030: for (j=1;j<=nlstate+ndeath;j++){
1031: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1032: }
1033:
1034: cov[1]=1.;
1035:
1036: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1037: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1038: newm=savm;
1039: /* Covariates have to be included here again */
1040: cov[2]=agefin;
1041:
1042: for (k=1; k<=cptcovn;k++) {
1043: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1044: /* 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]]);*/
1045: }
1046: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1047: for (k=1; k<=cptcovprod;k++)
1048: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1049:
1050: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1051: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1052: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1053: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1054:
1055: savm=oldm;
1056: oldm=newm;
1057: maxmax=0.;
1058: for(j=1;j<=nlstate;j++){
1059: min=1.;
1060: max=0.;
1061: for(i=1; i<=nlstate; i++) {
1062: sumnew=0;
1063: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1064: prlim[i][j]= newm[i][j]/(1-sumnew);
1065: max=FMAX(max,prlim[i][j]);
1066: min=FMIN(min,prlim[i][j]);
1067: }
1068: maxmin=max-min;
1069: maxmax=FMAX(maxmax,maxmin);
1070: }
1071: if(maxmax < ftolpl){
1072: return prlim;
1073: }
1074: }
1075: }
1076:
1077: /*************** transition probabilities ***************/
1078:
1079: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1080: {
1081: double s1, s2;
1082: /*double t34;*/
1083: int i,j,j1, nc, ii, jj;
1084:
1085: for(i=1; i<= nlstate; i++){
1086: for(j=1; j<i;j++){
1087: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1088: /*s2 += param[i][j][nc]*cov[nc];*/
1089: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1090: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1091: }
1092: ps[i][j]=s2;
1093: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1094: }
1095: for(j=i+1; j<=nlstate+ndeath;j++){
1096: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1097: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1098: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1099: }
1100: ps[i][j]=s2;
1101: }
1102: }
1103: /*ps[3][2]=1;*/
1104:
1105: for(i=1; i<= nlstate; i++){
1106: s1=0;
1107: for(j=1; j<i; j++)
1108: s1+=exp(ps[i][j]);
1109: for(j=i+1; j<=nlstate+ndeath; j++)
1110: s1+=exp(ps[i][j]);
1111: ps[i][i]=1./(s1+1.);
1112: for(j=1; j<i; j++)
1113: ps[i][j]= exp(ps[i][j])*ps[i][i];
1114: for(j=i+1; j<=nlstate+ndeath; j++)
1115: ps[i][j]= exp(ps[i][j])*ps[i][i];
1116: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1117: } /* end i */
1118:
1119: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1120: for(jj=1; jj<= nlstate+ndeath; jj++){
1121: ps[ii][jj]=0;
1122: ps[ii][ii]=1;
1123: }
1124: }
1125:
1126:
1127: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1128: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1129: /* printf("ddd %lf ",ps[ii][jj]); */
1130: /* } */
1131: /* printf("\n "); */
1132: /* } */
1133: /* printf("\n ");printf("%lf ",cov[2]); */
1134: /*
1135: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1136: goto end;*/
1137: return ps;
1138: }
1139:
1140: /**************** Product of 2 matrices ******************/
1141:
1142: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1143: {
1144: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1145: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1146: /* in, b, out are matrice of pointers which should have been initialized
1147: before: only the contents of out is modified. The function returns
1148: a pointer to pointers identical to out */
1149: long i, j, k;
1150: for(i=nrl; i<= nrh; i++)
1151: for(k=ncolol; k<=ncoloh; k++)
1152: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1153: out[i][k] +=in[i][j]*b[j][k];
1154:
1155: return out;
1156: }
1157:
1158:
1159: /************* Higher Matrix Product ***************/
1160:
1161: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1162: {
1163: /* Computes the transition matrix starting at age 'age' over
1164: 'nhstepm*hstepm*stepm' months (i.e. until
1165: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1166: nhstepm*hstepm matrices.
1167: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1168: (typically every 2 years instead of every month which is too big
1169: for the memory).
1170: Model is determined by parameters x and covariates have to be
1171: included manually here.
1172:
1173: */
1174:
1175: int i, j, d, h, k;
1176: double **out, cov[NCOVMAX];
1177: double **newm;
1178:
1179: /* Hstepm could be zero and should return the unit matrix */
1180: for (i=1;i<=nlstate+ndeath;i++)
1181: for (j=1;j<=nlstate+ndeath;j++){
1182: oldm[i][j]=(i==j ? 1.0 : 0.0);
1183: po[i][j][0]=(i==j ? 1.0 : 0.0);
1184: }
1185: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1186: for(h=1; h <=nhstepm; h++){
1187: for(d=1; d <=hstepm; d++){
1188: newm=savm;
1189: /* Covariates have to be included here again */
1190: cov[1]=1.;
1191: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1192: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1193: for (k=1; k<=cptcovage;k++)
1194: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1195: for (k=1; k<=cptcovprod;k++)
1196: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1197:
1198:
1199: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1200: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1201: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1202: pmij(pmmij,cov,ncovmodel,x,nlstate));
1203: savm=oldm;
1204: oldm=newm;
1205: }
1206: for(i=1; i<=nlstate+ndeath; i++)
1207: for(j=1;j<=nlstate+ndeath;j++) {
1208: po[i][j][h]=newm[i][j];
1209: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1210: */
1211: }
1212: } /* end h */
1213: return po;
1214: }
1215:
1216:
1217: /*************** log-likelihood *************/
1218: double func( double *x)
1219: {
1220: int i, ii, j, k, mi, d, kk;
1221: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1222: double **out;
1223: double sw; /* Sum of weights */
1224: double lli; /* Individual log likelihood */
1225: int s1, s2;
1226: double bbh, survp;
1227: long ipmx;
1228: /*extern weight */
1229: /* We are differentiating ll according to initial status */
1230: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1231: /*for(i=1;i<imx;i++)
1232: printf(" %d\n",s[4][i]);
1233: */
1234: cov[1]=1.;
1235:
1236: for(k=1; k<=nlstate; k++) ll[k]=0.;
1237:
1238: if(mle==1){
1239: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1240: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1241: for(mi=1; mi<= wav[i]-1; mi++){
1242: for (ii=1;ii<=nlstate+ndeath;ii++)
1243: for (j=1;j<=nlstate+ndeath;j++){
1244: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1245: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1246: }
1247: for(d=0; d<dh[mi][i]; d++){
1248: newm=savm;
1249: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1250: for (kk=1; kk<=cptcovage;kk++) {
1251: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1252: }
1253: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1254: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1255: savm=oldm;
1256: oldm=newm;
1257: } /* end mult */
1258:
1259: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1260: /* But now since version 0.9 we anticipate for bias at large stepm.
1261: * If stepm is larger than one month (smallest stepm) and if the exact delay
1262: * (in months) between two waves is not a multiple of stepm, we rounded to
1263: * the nearest (and in case of equal distance, to the lowest) interval but now
1264: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1265: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1266: * probability in order to take into account the bias as a fraction of the way
1267: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1268: * -stepm/2 to stepm/2 .
1269: * For stepm=1 the results are the same as for previous versions of Imach.
1270: * For stepm > 1 the results are less biased than in previous versions.
1271: */
1272: s1=s[mw[mi][i]][i];
1273: s2=s[mw[mi+1][i]][i];
1274: bbh=(double)bh[mi][i]/(double)stepm;
1275: /* bias bh is positive if real duration
1276: * is higher than the multiple of stepm and negative otherwise.
1277: */
1278: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1279: if( s2 > nlstate){
1280: /* i.e. if s2 is a death state and if the date of death is known
1281: then the contribution to the likelihood is the probability to
1282: die between last step unit time and current step unit time,
1283: which is also equal to probability to die before dh
1284: minus probability to die before dh-stepm .
1285: In version up to 0.92 likelihood was computed
1286: as if date of death was unknown. Death was treated as any other
1287: health state: the date of the interview describes the actual state
1288: and not the date of a change in health state. The former idea was
1289: to consider that at each interview the state was recorded
1290: (healthy, disable or death) and IMaCh was corrected; but when we
1291: introduced the exact date of death then we should have modified
1292: the contribution of an exact death to the likelihood. This new
1293: contribution is smaller and very dependent of the step unit
1294: stepm. It is no more the probability to die between last interview
1295: and month of death but the probability to survive from last
1296: interview up to one month before death multiplied by the
1297: probability to die within a month. Thanks to Chris
1298: Jackson for correcting this bug. Former versions increased
1299: mortality artificially. The bad side is that we add another loop
1300: which slows down the processing. The difference can be up to 10%
1301: lower mortality.
1302: */
1303: lli=log(out[s1][s2] - savm[s1][s2]);
1304:
1305:
1306: } else if (s2==-2) {
1307: for (j=1,survp=0. ; j<=nlstate; j++)
1308: survp += out[s1][j];
1309: lli= survp;
1310: }
1311:
1312: else if (s2==-4) {
1313: for (j=3,survp=0. ; j<=nlstate; j++)
1314: survp += out[s1][j];
1315: lli= survp;
1316: }
1317:
1318: else if (s2==-5) {
1319: for (j=1,survp=0. ; j<=2; j++)
1320: survp += out[s1][j];
1321: lli= survp;
1322: }
1323:
1324:
1325: else{
1326: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1327: /* 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 */
1328: }
1329: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1330: /*if(lli ==000.0)*/
1331: /*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); */
1332: ipmx +=1;
1333: sw += weight[i];
1334: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1335: } /* end of wave */
1336: } /* end of individual */
1337: } else if(mle==2){
1338: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1339: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1340: for(mi=1; mi<= wav[i]-1; mi++){
1341: for (ii=1;ii<=nlstate+ndeath;ii++)
1342: for (j=1;j<=nlstate+ndeath;j++){
1343: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1344: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1345: }
1346: for(d=0; d<=dh[mi][i]; d++){
1347: newm=savm;
1348: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1349: for (kk=1; kk<=cptcovage;kk++) {
1350: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1351: }
1352: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1353: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1354: savm=oldm;
1355: oldm=newm;
1356: } /* end mult */
1357:
1358: s1=s[mw[mi][i]][i];
1359: s2=s[mw[mi+1][i]][i];
1360: bbh=(double)bh[mi][i]/(double)stepm;
1361: 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 */
1362: ipmx +=1;
1363: sw += weight[i];
1364: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1365: } /* end of wave */
1366: } /* end of individual */
1367: } else if(mle==3){ /* exponential inter-extrapolation */
1368: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1369: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1370: for(mi=1; mi<= wav[i]-1; mi++){
1371: for (ii=1;ii<=nlstate+ndeath;ii++)
1372: for (j=1;j<=nlstate+ndeath;j++){
1373: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1374: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1375: }
1376: for(d=0; d<dh[mi][i]; d++){
1377: newm=savm;
1378: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1379: for (kk=1; kk<=cptcovage;kk++) {
1380: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1381: }
1382: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1383: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1384: savm=oldm;
1385: oldm=newm;
1386: } /* end mult */
1387:
1388: s1=s[mw[mi][i]][i];
1389: s2=s[mw[mi+1][i]][i];
1390: bbh=(double)bh[mi][i]/(double)stepm;
1391: 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 */
1392: ipmx +=1;
1393: sw += weight[i];
1394: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1395: } /* end of wave */
1396: } /* end of individual */
1397: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1398: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1399: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1400: for(mi=1; mi<= wav[i]-1; mi++){
1401: for (ii=1;ii<=nlstate+ndeath;ii++)
1402: for (j=1;j<=nlstate+ndeath;j++){
1403: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1404: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1405: }
1406: for(d=0; d<dh[mi][i]; d++){
1407: newm=savm;
1408: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1409: for (kk=1; kk<=cptcovage;kk++) {
1410: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1411: }
1412:
1413: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1414: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1415: savm=oldm;
1416: oldm=newm;
1417: } /* end mult */
1418:
1419: s1=s[mw[mi][i]][i];
1420: s2=s[mw[mi+1][i]][i];
1421: if( s2 > nlstate){
1422: lli=log(out[s1][s2] - savm[s1][s2]);
1423: }else{
1424: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1425: }
1426: ipmx +=1;
1427: sw += weight[i];
1428: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1429: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1430: } /* end of wave */
1431: } /* end of individual */
1432: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1433: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1434: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1435: for(mi=1; mi<= wav[i]-1; mi++){
1436: for (ii=1;ii<=nlstate+ndeath;ii++)
1437: for (j=1;j<=nlstate+ndeath;j++){
1438: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1439: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1440: }
1441: for(d=0; d<dh[mi][i]; d++){
1442: newm=savm;
1443: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1444: for (kk=1; kk<=cptcovage;kk++) {
1445: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1446: }
1447:
1448: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1449: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1450: savm=oldm;
1451: oldm=newm;
1452: } /* end mult */
1453:
1454: s1=s[mw[mi][i]][i];
1455: s2=s[mw[mi+1][i]][i];
1456: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1457: ipmx +=1;
1458: sw += weight[i];
1459: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1460: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
1461: } /* end of wave */
1462: } /* end of individual */
1463: } /* End of if */
1464: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1465: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1466: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1467: return -l;
1468: }
1469:
1470: /*************** log-likelihood *************/
1471: double funcone( double *x)
1472: {
1473: /* Same as likeli but slower because of a lot of printf and if */
1474: int i, ii, j, k, mi, d, kk;
1475: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1476: double **out;
1477: double lli; /* Individual log likelihood */
1478: double llt;
1479: int s1, s2;
1480: double bbh, survp;
1481: /*extern weight */
1482: /* We are differentiating ll according to initial status */
1483: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1484: /*for(i=1;i<imx;i++)
1485: printf(" %d\n",s[4][i]);
1486: */
1487: cov[1]=1.;
1488:
1489: for(k=1; k<=nlstate; k++) ll[k]=0.;
1490:
1491: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1492: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1493: for(mi=1; mi<= wav[i]-1; mi++){
1494: for (ii=1;ii<=nlstate+ndeath;ii++)
1495: for (j=1;j<=nlstate+ndeath;j++){
1496: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1497: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1498: }
1499: for(d=0; d<dh[mi][i]; d++){
1500: newm=savm;
1501: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1502: for (kk=1; kk<=cptcovage;kk++) {
1503: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1504: }
1505: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1506: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1507: savm=oldm;
1508: oldm=newm;
1509: } /* end mult */
1510:
1511: s1=s[mw[mi][i]][i];
1512: s2=s[mw[mi+1][i]][i];
1513: bbh=(double)bh[mi][i]/(double)stepm;
1514: /* bias is positive if real duration
1515: * is higher than the multiple of stepm and negative otherwise.
1516: */
1517: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1518: lli=log(out[s1][s2] - savm[s1][s2]);
1519: } else if (mle==1){
1520: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1521: } else if(mle==2){
1522: 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 */
1523: } else if(mle==3){ /* exponential inter-extrapolation */
1524: lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
1525: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1526: lli=log(out[s1][s2]); /* Original formula */
1527: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1528: lli=log(out[s1][s2]); /* Original formula */
1529: } /* End of if */
1530: ipmx +=1;
1531: sw += weight[i];
1532: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1533: /* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1534: if(globpr){
1535: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1536: %10.6f %10.6f %10.6f ", \
1537: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1538: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1539: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1540: llt +=ll[k]*gipmx/gsw;
1541: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1542: }
1543: fprintf(ficresilk," %10.6f\n", -llt);
1544: }
1545: } /* end of wave */
1546: } /* end of individual */
1547: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1548: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1549: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1550: if(globpr==0){ /* First time we count the contributions and weights */
1551: gipmx=ipmx;
1552: gsw=sw;
1553: }
1554: return -l;
1555: }
1556:
1557:
1558: /*************** function likelione ***********/
1559: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1560: {
1561: /* This routine should help understanding what is done with
1562: the selection of individuals/waves and
1563: to check the exact contribution to the likelihood.
1564: Plotting could be done.
1565: */
1566: int k;
1567:
1568: if(*globpri !=0){ /* Just counts and sums, no printings */
1569: strcpy(fileresilk,"ilk");
1570: strcat(fileresilk,fileres);
1571: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1572: printf("Problem with resultfile: %s\n", fileresilk);
1573: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1574: }
1575: fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
1576: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1577: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1578: for(k=1; k<=nlstate; k++)
1579: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1580: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1581: }
1582:
1583: *fretone=(*funcone)(p);
1584: if(*globpri !=0){
1585: fclose(ficresilk);
1586: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1587: fflush(fichtm);
1588: }
1589: return;
1590: }
1591:
1592:
1593: /*********** Maximum Likelihood Estimation ***************/
1594:
1595: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1596: {
1597: int i,j, iter;
1598: double **xi;
1599: double fret;
1600: double fretone; /* Only one call to likelihood */
1601: /* char filerespow[FILENAMELENGTH];*/
1602: xi=matrix(1,npar,1,npar);
1603: for (i=1;i<=npar;i++)
1604: for (j=1;j<=npar;j++)
1605: xi[i][j]=(i==j ? 1.0 : 0.0);
1606: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1607: strcpy(filerespow,"pow");
1608: strcat(filerespow,fileres);
1609: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1610: printf("Problem with resultfile: %s\n", filerespow);
1611: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1612: }
1613: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1614: for (i=1;i<=nlstate;i++)
1615: for(j=1;j<=nlstate+ndeath;j++)
1616: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1617: fprintf(ficrespow,"\n");
1618:
1619: powell(p,xi,npar,ftol,&iter,&fret,func);
1620:
1621: fclose(ficrespow);
1622: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1623: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1624: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1625:
1626: }
1627:
1628: /**** Computes Hessian and covariance matrix ***/
1629: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1630: {
1631: double **a,**y,*x,pd;
1632: double **hess;
1633: int i, j,jk;
1634: int *indx;
1635:
1636: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1637: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1638: void lubksb(double **a, int npar, int *indx, double b[]) ;
1639: void ludcmp(double **a, int npar, int *indx, double *d) ;
1640: double gompertz(double p[]);
1641: hess=matrix(1,npar,1,npar);
1642:
1643: printf("\nCalculation of the hessian matrix. Wait...\n");
1644: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1645: for (i=1;i<=npar;i++){
1646: printf("%d",i);fflush(stdout);
1647: fprintf(ficlog,"%d",i);fflush(ficlog);
1648:
1649: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1650:
1651: /* printf(" %f ",p[i]);
1652: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1653: }
1654:
1655: for (i=1;i<=npar;i++) {
1656: for (j=1;j<=npar;j++) {
1657: if (j>i) {
1658: printf(".%d%d",i,j);fflush(stdout);
1659: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1660: hess[i][j]=hessij(p,delti,i,j,func,npar);
1661:
1662: hess[j][i]=hess[i][j];
1663: /*printf(" %lf ",hess[i][j]);*/
1664: }
1665: }
1666: }
1667: printf("\n");
1668: fprintf(ficlog,"\n");
1669:
1670: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1671: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1672:
1673: a=matrix(1,npar,1,npar);
1674: y=matrix(1,npar,1,npar);
1675: x=vector(1,npar);
1676: indx=ivector(1,npar);
1677: for (i=1;i<=npar;i++)
1678: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1679: ludcmp(a,npar,indx,&pd);
1680:
1681: for (j=1;j<=npar;j++) {
1682: for (i=1;i<=npar;i++) x[i]=0;
1683: x[j]=1;
1684: lubksb(a,npar,indx,x);
1685: for (i=1;i<=npar;i++){
1686: matcov[i][j]=x[i];
1687: }
1688: }
1689:
1690: printf("\n#Hessian matrix#\n");
1691: fprintf(ficlog,"\n#Hessian matrix#\n");
1692: for (i=1;i<=npar;i++) {
1693: for (j=1;j<=npar;j++) {
1694: printf("%.3e ",hess[i][j]);
1695: fprintf(ficlog,"%.3e ",hess[i][j]);
1696: }
1697: printf("\n");
1698: fprintf(ficlog,"\n");
1699: }
1700:
1701: /* Recompute Inverse */
1702: for (i=1;i<=npar;i++)
1703: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1704: ludcmp(a,npar,indx,&pd);
1705:
1706: /* printf("\n#Hessian matrix recomputed#\n");
1707:
1708: for (j=1;j<=npar;j++) {
1709: for (i=1;i<=npar;i++) x[i]=0;
1710: x[j]=1;
1711: lubksb(a,npar,indx,x);
1712: for (i=1;i<=npar;i++){
1713: y[i][j]=x[i];
1714: printf("%.3e ",y[i][j]);
1715: fprintf(ficlog,"%.3e ",y[i][j]);
1716: }
1717: printf("\n");
1718: fprintf(ficlog,"\n");
1719: }
1720: */
1721:
1722: free_matrix(a,1,npar,1,npar);
1723: free_matrix(y,1,npar,1,npar);
1724: free_vector(x,1,npar);
1725: free_ivector(indx,1,npar);
1726: free_matrix(hess,1,npar,1,npar);
1727:
1728:
1729: }
1730:
1731: /*************** hessian matrix ****************/
1732: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1733: {
1734: int i;
1735: int l=1, lmax=20;
1736: double k1,k2;
1737: double p2[NPARMAX+1];
1738: double res;
1739: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1740: double fx;
1741: int k=0,kmax=10;
1742: double l1;
1743:
1744: fx=func(x);
1745: for (i=1;i<=npar;i++) p2[i]=x[i];
1746: for(l=0 ; l <=lmax; l++){
1747: l1=pow(10,l);
1748: delts=delt;
1749: for(k=1 ; k <kmax; k=k+1){
1750: delt = delta*(l1*k);
1751: p2[theta]=x[theta] +delt;
1752: k1=func(p2)-fx;
1753: p2[theta]=x[theta]-delt;
1754: k2=func(p2)-fx;
1755: /*res= (k1-2.0*fx+k2)/delt/delt; */
1756: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1757:
1758: #ifdef DEBUG
1759: 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);
1760: 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);
1761: #endif
1762: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1763: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1764: k=kmax;
1765: }
1766: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1767: k=kmax; l=lmax*10.;
1768: }
1769: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1770: delts=delt;
1771: }
1772: }
1773: }
1774: delti[theta]=delts;
1775: return res;
1776:
1777: }
1778:
1779: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1780: {
1781: int i;
1782: int l=1, l1, lmax=20;
1783: double k1,k2,k3,k4,res,fx;
1784: double p2[NPARMAX+1];
1785: int k;
1786:
1787: fx=func(x);
1788: for (k=1; k<=2; k++) {
1789: for (i=1;i<=npar;i++) p2[i]=x[i];
1790: p2[thetai]=x[thetai]+delti[thetai]/k;
1791: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1792: k1=func(p2)-fx;
1793:
1794: p2[thetai]=x[thetai]+delti[thetai]/k;
1795: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1796: k2=func(p2)-fx;
1797:
1798: p2[thetai]=x[thetai]-delti[thetai]/k;
1799: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1800: k3=func(p2)-fx;
1801:
1802: p2[thetai]=x[thetai]-delti[thetai]/k;
1803: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1804: k4=func(p2)-fx;
1805: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1806: #ifdef DEBUG
1807: 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);
1808: 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);
1809: #endif
1810: }
1811: return res;
1812: }
1813:
1814: /************** Inverse of matrix **************/
1815: void ludcmp(double **a, int n, int *indx, double *d)
1816: {
1817: int i,imax,j,k;
1818: double big,dum,sum,temp;
1819: double *vv;
1820:
1821: vv=vector(1,n);
1822: *d=1.0;
1823: for (i=1;i<=n;i++) {
1824: big=0.0;
1825: for (j=1;j<=n;j++)
1826: if ((temp=fabs(a[i][j])) > big) big=temp;
1827: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1828: vv[i]=1.0/big;
1829: }
1830: for (j=1;j<=n;j++) {
1831: for (i=1;i<j;i++) {
1832: sum=a[i][j];
1833: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1834: a[i][j]=sum;
1835: }
1836: big=0.0;
1837: for (i=j;i<=n;i++) {
1838: sum=a[i][j];
1839: for (k=1;k<j;k++)
1840: sum -= a[i][k]*a[k][j];
1841: a[i][j]=sum;
1842: if ( (dum=vv[i]*fabs(sum)) >= big) {
1843: big=dum;
1844: imax=i;
1845: }
1846: }
1847: if (j != imax) {
1848: for (k=1;k<=n;k++) {
1849: dum=a[imax][k];
1850: a[imax][k]=a[j][k];
1851: a[j][k]=dum;
1852: }
1853: *d = -(*d);
1854: vv[imax]=vv[j];
1855: }
1856: indx[j]=imax;
1857: if (a[j][j] == 0.0) a[j][j]=TINY;
1858: if (j != n) {
1859: dum=1.0/(a[j][j]);
1860: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1861: }
1862: }
1863: free_vector(vv,1,n); /* Doesn't work */
1864: ;
1865: }
1866:
1867: void lubksb(double **a, int n, int *indx, double b[])
1868: {
1869: int i,ii=0,ip,j;
1870: double sum;
1871:
1872: for (i=1;i<=n;i++) {
1873: ip=indx[i];
1874: sum=b[ip];
1875: b[ip]=b[i];
1876: if (ii)
1877: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1878: else if (sum) ii=i;
1879: b[i]=sum;
1880: }
1881: for (i=n;i>=1;i--) {
1882: sum=b[i];
1883: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1884: b[i]=sum/a[i][i];
1885: }
1886: }
1887:
1888: /************ Frequencies ********************/
1889: 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, char strstart[])
1890: { /* Some frequencies */
1891:
1892: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1893: int first;
1894: double ***freq; /* Frequencies */
1895: double *pp, **prop;
1896: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1897: FILE *ficresp;
1898: char fileresp[FILENAMELENGTH];
1899:
1900: pp=vector(1,nlstate);
1901: prop=matrix(1,nlstate,iagemin,iagemax+3);
1902: strcpy(fileresp,"p");
1903: strcat(fileresp,fileres);
1904: if((ficresp=fopen(fileresp,"w"))==NULL) {
1905: printf("Problem with prevalence resultfile: %s\n", fileresp);
1906: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1907: exit(0);
1908: }
1909: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1910: j1=0;
1911:
1912: j=cptcoveff;
1913: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1914:
1915: first=1;
1916:
1917: for(k1=1; k1<=j;k1++){
1918: for(i1=1; i1<=ncodemax[k1];i1++){
1919: j1++;
1920: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1921: scanf("%d", i);*/
1922: for (i=-5; i<=nlstate+ndeath; i++)
1923: for (jk=-5; jk<=nlstate+ndeath; jk++)
1924: for(m=iagemin; m <= iagemax+3; m++)
1925: freq[i][jk][m]=0;
1926:
1927: for (i=1; i<=nlstate; i++)
1928: for(m=iagemin; m <= iagemax+3; m++)
1929: prop[i][m]=0;
1930:
1931: dateintsum=0;
1932: k2cpt=0;
1933: for (i=1; i<=imx; i++) {
1934: bool=1;
1935: if (cptcovn>0) {
1936: for (z1=1; z1<=cptcoveff; z1++)
1937: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1938: bool=0;
1939: }
1940: if (bool==1){
1941: for(m=firstpass; m<=lastpass; m++){
1942: k2=anint[m][i]+(mint[m][i]/12.);
1943: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1944: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1945: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1946: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1947: if (m<lastpass) {
1948: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1949: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1950: }
1951:
1952: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1953: dateintsum=dateintsum+k2;
1954: k2cpt++;
1955: }
1956: /*}*/
1957: }
1958: }
1959: }
1960:
1961: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
1962: fprintf(ficresp, "#Local time at start: %s", strstart);
1963: if (cptcovn>0) {
1964: fprintf(ficresp, "\n#********** Variable ");
1965: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
1966: fprintf(ficresp, "**********\n#");
1967: }
1968: for(i=1; i<=nlstate;i++)
1969: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1970: fprintf(ficresp, "\n");
1971:
1972: for(i=iagemin; i <= iagemax+3; i++){
1973: if(i==iagemax+3){
1974: fprintf(ficlog,"Total");
1975: }else{
1976: if(first==1){
1977: first=0;
1978: printf("See log file for details...\n");
1979: }
1980: fprintf(ficlog,"Age %d", i);
1981: }
1982: for(jk=1; jk <=nlstate ; jk++){
1983: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
1984: pp[jk] += freq[jk][m][i];
1985: }
1986: for(jk=1; jk <=nlstate ; jk++){
1987: for(m=-1, pos=0; m <=0 ; m++)
1988: pos += freq[jk][m][i];
1989: if(pp[jk]>=1.e-10){
1990: if(first==1){
1991: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1992: }
1993: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1994: }else{
1995: if(first==1)
1996: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1997: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
1998: }
1999: }
2000:
2001: for(jk=1; jk <=nlstate ; jk++){
2002: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2003: pp[jk] += freq[jk][m][i];
2004: }
2005: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2006: pos += pp[jk];
2007: posprop += prop[jk][i];
2008: }
2009: for(jk=1; jk <=nlstate ; jk++){
2010: if(pos>=1.e-5){
2011: if(first==1)
2012: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2013: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2014: }else{
2015: if(first==1)
2016: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2017: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2018: }
2019: if( i <= iagemax){
2020: if(pos>=1.e-5){
2021: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2022: /*probs[i][jk][j1]= pp[jk]/pos;*/
2023: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2024: }
2025: else
2026: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2027: }
2028: }
2029:
2030: for(jk=-1; jk <=nlstate+ndeath; jk++)
2031: for(m=-1; m <=nlstate+ndeath; m++)
2032: if(freq[jk][m][i] !=0 ) {
2033: if(first==1)
2034: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2035: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2036: }
2037: if(i <= iagemax)
2038: fprintf(ficresp,"\n");
2039: if(first==1)
2040: printf("Others in log...\n");
2041: fprintf(ficlog,"\n");
2042: }
2043: }
2044: }
2045: dateintmean=dateintsum/k2cpt;
2046:
2047: fclose(ficresp);
2048: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2049: free_vector(pp,1,nlstate);
2050: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2051: /* End of Freq */
2052: }
2053:
2054: /************ Prevalence ********************/
2055: void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
2056: {
2057: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2058: in each health status at the date of interview (if between dateprev1 and dateprev2).
2059: We still use firstpass and lastpass as another selection.
2060: */
2061:
2062: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2063: double ***freq; /* Frequencies */
2064: double *pp, **prop;
2065: double pos,posprop;
2066: double y2; /* in fractional years */
2067: int iagemin, iagemax;
2068:
2069: iagemin= (int) agemin;
2070: iagemax= (int) agemax;
2071: /*pp=vector(1,nlstate);*/
2072: prop=matrix(1,nlstate,iagemin,iagemax+3);
2073: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2074: j1=0;
2075:
2076: j=cptcoveff;
2077: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2078:
2079: for(k1=1; k1<=j;k1++){
2080: for(i1=1; i1<=ncodemax[k1];i1++){
2081: j1++;
2082:
2083: for (i=1; i<=nlstate; i++)
2084: for(m=iagemin; m <= iagemax+3; m++)
2085: prop[i][m]=0.0;
2086:
2087: for (i=1; i<=imx; i++) { /* Each individual */
2088: bool=1;
2089: if (cptcovn>0) {
2090: for (z1=1; z1<=cptcoveff; z1++)
2091: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2092: bool=0;
2093: }
2094: if (bool==1) {
2095: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2096: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2097: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2098: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2099: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2100: 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);
2101: if (s[m][i]>0 && s[m][i]<=nlstate) {
2102: /*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]]);*/
2103: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2104: prop[s[m][i]][iagemax+3] += weight[i];
2105: }
2106: }
2107: } /* end selection of waves */
2108: }
2109: }
2110: for(i=iagemin; i <= iagemax+3; i++){
2111:
2112: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2113: posprop += prop[jk][i];
2114: }
2115:
2116: for(jk=1; jk <=nlstate ; jk++){
2117: if( i <= iagemax){
2118: if(posprop>=1.e-5){
2119: probs[i][jk][j1]= prop[jk][i]/posprop;
2120: }
2121: }
2122: }/* end jk */
2123: }/* end i */
2124: } /* end i1 */
2125: } /* end k1 */
2126:
2127: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2128: /*free_vector(pp,1,nlstate);*/
2129: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2130: } /* End of prevalence */
2131:
2132: /************* Waves Concatenation ***************/
2133:
2134: 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)
2135: {
2136: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2137: Death is a valid wave (if date is known).
2138: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2139: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2140: and mw[mi+1][i]. dh depends on stepm.
2141: */
2142:
2143: int i, mi, m;
2144: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2145: double sum=0., jmean=0.;*/
2146: int first;
2147: int j, k=0,jk, ju, jl;
2148: double sum=0.;
2149: first=0;
2150: jmin=1e+5;
2151: jmax=-1;
2152: jmean=0.;
2153: for(i=1; i<=imx; i++){
2154: mi=0;
2155: m=firstpass;
2156: while(s[m][i] <= nlstate){
2157: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2158: mw[++mi][i]=m;
2159: if(m >=lastpass)
2160: break;
2161: else
2162: m++;
2163: }/* end while */
2164: if (s[m][i] > nlstate){
2165: mi++; /* Death is another wave */
2166: /* if(mi==0) never been interviewed correctly before death */
2167: /* Only death is a correct wave */
2168: mw[mi][i]=m;
2169: }
2170:
2171: wav[i]=mi;
2172: if(mi==0){
2173: nbwarn++;
2174: if(first==0){
2175: printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2176: first=1;
2177: }
2178: if(first==1){
2179: fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
2180: }
2181: } /* end mi==0 */
2182: } /* End individuals */
2183:
2184: for(i=1; i<=imx; i++){
2185: for(mi=1; mi<wav[i];mi++){
2186: if (stepm <=0)
2187: dh[mi][i]=1;
2188: else{
2189: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2190: if (agedc[i] < 2*AGESUP) {
2191: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2192: if(j==0) j=1; /* Survives at least one month after exam */
2193: else if(j<0){
2194: nberr++;
2195: printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2196: j=1; /* Temporary Dangerous patch */
2197: printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
2198: fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2199: fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
2200: }
2201: k=k+1;
2202: if (j >= jmax) jmax=j;
2203: if (j <= jmin) jmin=j;
2204: sum=sum+j;
2205: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2206: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2207: }
2208: }
2209: else{
2210: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2211: /* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
2212:
2213: k=k+1;
2214: if (j >= jmax) jmax=j;
2215: else if (j <= jmin)jmin=j;
2216: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2217: /*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]);*/
2218: if(j<0){
2219: nberr++;
2220: printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2221: fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
2222: }
2223: sum=sum+j;
2224: }
2225: jk= j/stepm;
2226: jl= j -jk*stepm;
2227: ju= j -(jk+1)*stepm;
2228: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2229: if(jl==0){
2230: dh[mi][i]=jk;
2231: bh[mi][i]=0;
2232: }else{ /* We want a negative bias in order to only have interpolation ie
2233: * at the price of an extra matrix product in likelihood */
2234: dh[mi][i]=jk+1;
2235: bh[mi][i]=ju;
2236: }
2237: }else{
2238: if(jl <= -ju){
2239: dh[mi][i]=jk;
2240: bh[mi][i]=jl; /* bias is positive if real duration
2241: * is higher than the multiple of stepm and negative otherwise.
2242: */
2243: }
2244: else{
2245: dh[mi][i]=jk+1;
2246: bh[mi][i]=ju;
2247: }
2248: if(dh[mi][i]==0){
2249: dh[mi][i]=1; /* At least one step */
2250: bh[mi][i]=ju; /* At least one step */
2251: /* 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);*/
2252: }
2253: } /* end if mle */
2254: }
2255: } /* end wave */
2256: }
2257: jmean=sum/k;
2258: printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2259: fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
2260: }
2261:
2262: /*********** Tricode ****************************/
2263: void tricode(int *Tvar, int **nbcode, int imx)
2264: {
2265:
2266: int Ndum[20],ij=1, k, j, i, maxncov=19;
2267: int cptcode=0;
2268: cptcoveff=0;
2269:
2270: for (k=0; k<maxncov; k++) Ndum[k]=0;
2271: for (k=1; k<=7; k++) ncodemax[k]=0;
2272:
2273: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2274: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2275: modality*/
2276: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2277: Ndum[ij]++; /*store the modality */
2278: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2279: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2280: Tvar[j]. If V=sex and male is 0 and
2281: female is 1, then cptcode=1.*/
2282: }
2283:
2284: for (i=0; i<=cptcode; i++) {
2285: 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 */
2286: }
2287:
2288: ij=1;
2289: for (i=1; i<=ncodemax[j]; i++) {
2290: for (k=0; k<= maxncov; k++) {
2291: if (Ndum[k] != 0) {
2292: nbcode[Tvar[j]][ij]=k;
2293: /* 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; */
2294:
2295: ij++;
2296: }
2297: if (ij > ncodemax[j]) break;
2298: }
2299: }
2300: }
2301:
2302: for (k=0; k< maxncov; k++) Ndum[k]=0;
2303:
2304: for (i=1; i<=ncovmodel-2; i++) {
2305: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2306: ij=Tvar[i];
2307: Ndum[ij]++;
2308: }
2309:
2310: ij=1;
2311: for (i=1; i<= maxncov; i++) {
2312: if((Ndum[i]!=0) && (i<=ncovcol)){
2313: Tvaraff[ij]=i; /*For printing */
2314: ij++;
2315: }
2316: }
2317:
2318: cptcoveff=ij-1; /*Number of simple covariates*/
2319: }
2320:
2321: /*********** Health Expectancies ****************/
2322:
2323: 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,char strstart[] )
2324:
2325: {
2326: /* Health expectancies */
2327: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2328: double age, agelim, hf;
2329: double ***p3mat,***varhe;
2330: double **dnewm,**doldm;
2331: double *xp;
2332: double **gp, **gm;
2333: double ***gradg, ***trgradg;
2334: int theta;
2335:
2336: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2337: xp=vector(1,npar);
2338: dnewm=matrix(1,nlstate*nlstate,1,npar);
2339: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2340:
2341: fprintf(ficreseij,"# Local time at start: %s", strstart);
2342: fprintf(ficreseij,"# Health expectancies\n");
2343: fprintf(ficreseij,"# Age");
2344: for(i=1; i<=nlstate;i++)
2345: for(j=1; j<=nlstate;j++)
2346: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2347: fprintf(ficreseij,"\n");
2348:
2349: if(estepm < stepm){
2350: printf ("Problem %d lower than %d\n",estepm, stepm);
2351: }
2352: else hstepm=estepm;
2353: /* We compute the life expectancy from trapezoids spaced every estepm months
2354: * This is mainly to measure the difference between two models: for example
2355: * if stepm=24 months pijx are given only every 2 years and by summing them
2356: * we are calculating an estimate of the Life Expectancy assuming a linear
2357: * progression in between and thus overestimating or underestimating according
2358: * to the curvature of the survival function. If, for the same date, we
2359: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2360: * to compare the new estimate of Life expectancy with the same linear
2361: * hypothesis. A more precise result, taking into account a more precise
2362: * curvature will be obtained if estepm is as small as stepm. */
2363:
2364: /* For example we decided to compute the life expectancy with the smallest unit */
2365: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2366: nhstepm is the number of hstepm from age to agelim
2367: nstepm is the number of stepm from age to agelin.
2368: Look at hpijx to understand the reason of that which relies in memory size
2369: and note for a fixed period like estepm months */
2370: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2371: survival function given by stepm (the optimization length). Unfortunately it
2372: means that if the survival funtion is printed only each two years of age and if
2373: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2374: results. So we changed our mind and took the option of the best precision.
2375: */
2376: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2377:
2378: agelim=AGESUP;
2379: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2380: /* nhstepm age range expressed in number of stepm */
2381: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2382: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2383: /* if (stepm >= YEARM) hstepm=1;*/
2384: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2385: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2386: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2387: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2388: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2389:
2390: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2391: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2392: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2393:
2394:
2395: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2396:
2397: /* Computing Variances of health expectancies */
2398:
2399: for(theta=1; theta <=npar; theta++){
2400: for(i=1; i<=npar; i++){
2401: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2402: }
2403: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2404:
2405: cptj=0;
2406: for(j=1; j<= nlstate; j++){
2407: for(i=1; i<=nlstate; i++){
2408: cptj=cptj+1;
2409: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2410: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2411: }
2412: }
2413: }
2414:
2415:
2416: for(i=1; i<=npar; i++)
2417: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2418: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2419:
2420: cptj=0;
2421: for(j=1; j<= nlstate; j++){
2422: for(i=1;i<=nlstate;i++){
2423: cptj=cptj+1;
2424: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2425:
2426: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2427: }
2428: }
2429: }
2430: for(j=1; j<= nlstate*nlstate; j++)
2431: for(h=0; h<=nhstepm-1; h++){
2432: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2433: }
2434: }
2435:
2436: /* End theta */
2437:
2438: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2439:
2440: for(h=0; h<=nhstepm-1; h++)
2441: for(j=1; j<=nlstate*nlstate;j++)
2442: for(theta=1; theta <=npar; theta++)
2443: trgradg[h][j][theta]=gradg[h][theta][j];
2444:
2445:
2446: for(i=1;i<=nlstate*nlstate;i++)
2447: for(j=1;j<=nlstate*nlstate;j++)
2448: varhe[i][j][(int)age] =0.;
2449:
2450: printf("%d|",(int)age);fflush(stdout);
2451: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2452: for(h=0;h<=nhstepm-1;h++){
2453: for(k=0;k<=nhstepm-1;k++){
2454: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2455: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2456: for(i=1;i<=nlstate*nlstate;i++)
2457: for(j=1;j<=nlstate*nlstate;j++)
2458: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2459: }
2460: }
2461: /* Computing expectancies */
2462: for(i=1; i<=nlstate;i++)
2463: for(j=1; j<=nlstate;j++)
2464: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2465: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2466:
2467: /* 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]);*/
2468:
2469: }
2470:
2471: fprintf(ficreseij,"%3.0f",age );
2472: cptj=0;
2473: for(i=1; i<=nlstate;i++)
2474: for(j=1; j<=nlstate;j++){
2475: cptj++;
2476: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2477: }
2478: fprintf(ficreseij,"\n");
2479:
2480: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2481: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2482: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2483: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2484: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2485: }
2486: printf("\n");
2487: fprintf(ficlog,"\n");
2488:
2489: free_vector(xp,1,npar);
2490: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2491: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2492: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2493: }
2494:
2495: /************ Variance ******************/
2496: 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, char strstart[])
2497: {
2498: /* Variance of health expectancies */
2499: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2500: /* double **newm;*/
2501: double **dnewm,**doldm;
2502: double **dnewmp,**doldmp;
2503: int i, j, nhstepm, hstepm, h, nstepm ;
2504: int k, cptcode;
2505: double *xp;
2506: double **gp, **gm; /* for var eij */
2507: double ***gradg, ***trgradg; /*for var eij */
2508: double **gradgp, **trgradgp; /* for var p point j */
2509: double *gpp, *gmp; /* for var p point j */
2510: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2511: double ***p3mat;
2512: double age,agelim, hf;
2513: double ***mobaverage;
2514: int theta;
2515: char digit[4];
2516: char digitp[25];
2517:
2518: char fileresprobmorprev[FILENAMELENGTH];
2519:
2520: if(popbased==1){
2521: if(mobilav!=0)
2522: strcpy(digitp,"-populbased-mobilav-");
2523: else strcpy(digitp,"-populbased-nomobil-");
2524: }
2525: else
2526: strcpy(digitp,"-stablbased-");
2527:
2528: if (mobilav!=0) {
2529: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2530: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2531: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2532: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2533: }
2534: }
2535:
2536: strcpy(fileresprobmorprev,"prmorprev");
2537: sprintf(digit,"%-d",ij);
2538: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2539: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2540: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2541: strcat(fileresprobmorprev,fileres);
2542: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2543: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2544: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2545: }
2546: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2547:
2548: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2549: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
2550: 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);
2551: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2552: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2553: fprintf(ficresprobmorprev," p.%-d SE",j);
2554: for(i=1; i<=nlstate;i++)
2555: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2556: }
2557: fprintf(ficresprobmorprev,"\n");
2558: fprintf(ficgp,"\n# Routine varevsij");
2559: fprintf(fichtm, "#Local time at start: %s", strstart);
2560: 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");
2561: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2562: /* } */
2563: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2564: fprintf(ficresvij, "#Local time at start: %s", strstart);
2565: 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");
2566: fprintf(ficresvij,"# Age");
2567: for(i=1; i<=nlstate;i++)
2568: for(j=1; j<=nlstate;j++)
2569: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2570: fprintf(ficresvij,"\n");
2571:
2572: xp=vector(1,npar);
2573: dnewm=matrix(1,nlstate,1,npar);
2574: doldm=matrix(1,nlstate,1,nlstate);
2575: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2576: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2577:
2578: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2579: gpp=vector(nlstate+1,nlstate+ndeath);
2580: gmp=vector(nlstate+1,nlstate+ndeath);
2581: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2582:
2583: if(estepm < stepm){
2584: printf ("Problem %d lower than %d\n",estepm, stepm);
2585: }
2586: else hstepm=estepm;
2587: /* For example we decided to compute the life expectancy with the smallest unit */
2588: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2589: nhstepm is the number of hstepm from age to agelim
2590: nstepm is the number of stepm from age to agelin.
2591: Look at hpijx to understand the reason of that which relies in memory size
2592: and note for a fixed period like k years */
2593: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2594: survival function given by stepm (the optimization length). Unfortunately it
2595: means that if the survival funtion is printed every two years of age and if
2596: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2597: results. So we changed our mind and took the option of the best precision.
2598: */
2599: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2600: agelim = AGESUP;
2601: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2602: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2603: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2604: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2605: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2606: gp=matrix(0,nhstepm,1,nlstate);
2607: gm=matrix(0,nhstepm,1,nlstate);
2608:
2609:
2610: for(theta=1; theta <=npar; theta++){
2611: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2612: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2613: }
2614: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2615: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2616:
2617: if (popbased==1) {
2618: if(mobilav ==0){
2619: for(i=1; i<=nlstate;i++)
2620: prlim[i][i]=probs[(int)age][i][ij];
2621: }else{ /* mobilav */
2622: for(i=1; i<=nlstate;i++)
2623: prlim[i][i]=mobaverage[(int)age][i][ij];
2624: }
2625: }
2626:
2627: for(j=1; j<= nlstate; j++){
2628: for(h=0; h<=nhstepm; h++){
2629: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2630: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2631: }
2632: }
2633: /* This for computing probability of death (h=1 means
2634: computed over hstepm matrices product = hstepm*stepm months)
2635: as a weighted average of prlim.
2636: */
2637: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2638: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2639: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2640: }
2641: /* end probability of death */
2642:
2643: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2644: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2645: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2646: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2647:
2648: if (popbased==1) {
2649: if(mobilav ==0){
2650: for(i=1; i<=nlstate;i++)
2651: prlim[i][i]=probs[(int)age][i][ij];
2652: }else{ /* mobilav */
2653: for(i=1; i<=nlstate;i++)
2654: prlim[i][i]=mobaverage[(int)age][i][ij];
2655: }
2656: }
2657:
2658: for(j=1; j<= nlstate; j++){
2659: for(h=0; h<=nhstepm; h++){
2660: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2661: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2662: }
2663: }
2664: /* This for computing probability of death (h=1 means
2665: computed over hstepm matrices product = hstepm*stepm months)
2666: as a weighted average of prlim.
2667: */
2668: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2669: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2670: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2671: }
2672: /* end probability of death */
2673:
2674: for(j=1; j<= nlstate; j++) /* vareij */
2675: for(h=0; h<=nhstepm; h++){
2676: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2677: }
2678:
2679: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2680: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2681: }
2682:
2683: } /* End theta */
2684:
2685: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2686:
2687: for(h=0; h<=nhstepm; h++) /* veij */
2688: for(j=1; j<=nlstate;j++)
2689: for(theta=1; theta <=npar; theta++)
2690: trgradg[h][j][theta]=gradg[h][theta][j];
2691:
2692: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2693: for(theta=1; theta <=npar; theta++)
2694: trgradgp[j][theta]=gradgp[theta][j];
2695:
2696:
2697: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2698: for(i=1;i<=nlstate;i++)
2699: for(j=1;j<=nlstate;j++)
2700: vareij[i][j][(int)age] =0.;
2701:
2702: for(h=0;h<=nhstepm;h++){
2703: for(k=0;k<=nhstepm;k++){
2704: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2705: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2706: for(i=1;i<=nlstate;i++)
2707: for(j=1;j<=nlstate;j++)
2708: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2709: }
2710: }
2711:
2712: /* pptj */
2713: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2714: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2715: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2716: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2717: varppt[j][i]=doldmp[j][i];
2718: /* end ppptj */
2719: /* x centered again */
2720: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2721: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2722:
2723: if (popbased==1) {
2724: if(mobilav ==0){
2725: for(i=1; i<=nlstate;i++)
2726: prlim[i][i]=probs[(int)age][i][ij];
2727: }else{ /* mobilav */
2728: for(i=1; i<=nlstate;i++)
2729: prlim[i][i]=mobaverage[(int)age][i][ij];
2730: }
2731: }
2732:
2733: /* This for computing probability of death (h=1 means
2734: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2735: as a weighted average of prlim.
2736: */
2737: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2738: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2739: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2740: }
2741: /* end probability of death */
2742:
2743: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2744: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2745: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2746: for(i=1; i<=nlstate;i++){
2747: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2748: }
2749: }
2750: fprintf(ficresprobmorprev,"\n");
2751:
2752: fprintf(ficresvij,"%.0f ",age );
2753: for(i=1; i<=nlstate;i++)
2754: for(j=1; j<=nlstate;j++){
2755: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2756: }
2757: fprintf(ficresvij,"\n");
2758: free_matrix(gp,0,nhstepm,1,nlstate);
2759: free_matrix(gm,0,nhstepm,1,nlstate);
2760: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2761: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2762: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2763: } /* End age */
2764: free_vector(gpp,nlstate+1,nlstate+ndeath);
2765: free_vector(gmp,nlstate+1,nlstate+ndeath);
2766: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2767: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2768: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2769: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2770: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2771: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2772: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2773: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2774: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2775: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2776: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2777: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2778: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2779: /* 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);
2780: */
2781: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2782: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2783:
2784: free_vector(xp,1,npar);
2785: free_matrix(doldm,1,nlstate,1,nlstate);
2786: free_matrix(dnewm,1,nlstate,1,npar);
2787: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2788: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2789: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2790: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2791: fclose(ficresprobmorprev);
2792: fflush(ficgp);
2793: fflush(fichtm);
2794: } /* end varevsij */
2795:
2796: /************ Variance of prevlim ******************/
2797: 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, char strstart[])
2798: {
2799: /* Variance of prevalence limit */
2800: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2801: double **newm;
2802: double **dnewm,**doldm;
2803: int i, j, nhstepm, hstepm;
2804: int k, cptcode;
2805: double *xp;
2806: double *gp, *gm;
2807: double **gradg, **trgradg;
2808: double age,agelim;
2809: int theta;
2810: fprintf(ficresvpl, "#Local time at start: %s", strstart);
2811: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2812: fprintf(ficresvpl,"# Age");
2813: for(i=1; i<=nlstate;i++)
2814: fprintf(ficresvpl," %1d-%1d",i,i);
2815: fprintf(ficresvpl,"\n");
2816:
2817: xp=vector(1,npar);
2818: dnewm=matrix(1,nlstate,1,npar);
2819: doldm=matrix(1,nlstate,1,nlstate);
2820:
2821: hstepm=1*YEARM; /* Every year of age */
2822: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2823: agelim = AGESUP;
2824: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2825: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2826: if (stepm >= YEARM) hstepm=1;
2827: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2828: gradg=matrix(1,npar,1,nlstate);
2829: gp=vector(1,nlstate);
2830: gm=vector(1,nlstate);
2831:
2832: for(theta=1; theta <=npar; theta++){
2833: for(i=1; i<=npar; i++){ /* Computes gradient */
2834: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2835: }
2836: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2837: for(i=1;i<=nlstate;i++)
2838: gp[i] = prlim[i][i];
2839:
2840: for(i=1; i<=npar; i++) /* Computes gradient */
2841: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2842: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2843: for(i=1;i<=nlstate;i++)
2844: gm[i] = prlim[i][i];
2845:
2846: for(i=1;i<=nlstate;i++)
2847: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2848: } /* End theta */
2849:
2850: trgradg =matrix(1,nlstate,1,npar);
2851:
2852: for(j=1; j<=nlstate;j++)
2853: for(theta=1; theta <=npar; theta++)
2854: trgradg[j][theta]=gradg[theta][j];
2855:
2856: for(i=1;i<=nlstate;i++)
2857: varpl[i][(int)age] =0.;
2858: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2859: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2860: for(i=1;i<=nlstate;i++)
2861: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2862:
2863: fprintf(ficresvpl,"%.0f ",age );
2864: for(i=1; i<=nlstate;i++)
2865: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2866: fprintf(ficresvpl,"\n");
2867: free_vector(gp,1,nlstate);
2868: free_vector(gm,1,nlstate);
2869: free_matrix(gradg,1,npar,1,nlstate);
2870: free_matrix(trgradg,1,nlstate,1,npar);
2871: } /* End age */
2872:
2873: free_vector(xp,1,npar);
2874: free_matrix(doldm,1,nlstate,1,npar);
2875: free_matrix(dnewm,1,nlstate,1,nlstate);
2876:
2877: }
2878:
2879: /************ Variance of one-step probabilities ******************/
2880: void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
2881: {
2882: int i, j=0, i1, k1, l1, t, tj;
2883: int k2, l2, j1, z1;
2884: int k=0,l, cptcode;
2885: int first=1, first1;
2886: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2887: double **dnewm,**doldm;
2888: double *xp;
2889: double *gp, *gm;
2890: double **gradg, **trgradg;
2891: double **mu;
2892: double age,agelim, cov[NCOVMAX];
2893: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2894: int theta;
2895: char fileresprob[FILENAMELENGTH];
2896: char fileresprobcov[FILENAMELENGTH];
2897: char fileresprobcor[FILENAMELENGTH];
2898:
2899: double ***varpij;
2900:
2901: strcpy(fileresprob,"prob");
2902: strcat(fileresprob,fileres);
2903: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2904: printf("Problem with resultfile: %s\n", fileresprob);
2905: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2906: }
2907: strcpy(fileresprobcov,"probcov");
2908: strcat(fileresprobcov,fileres);
2909: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2910: printf("Problem with resultfile: %s\n", fileresprobcov);
2911: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2912: }
2913: strcpy(fileresprobcor,"probcor");
2914: strcat(fileresprobcor,fileres);
2915: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2916: printf("Problem with resultfile: %s\n", fileresprobcor);
2917: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2918: }
2919: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2920: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2921: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2922: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2923: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2924: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2925: fprintf(ficresprob, "#Local time at start: %s", strstart);
2926: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2927: fprintf(ficresprob,"# Age");
2928: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
2929: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2930: fprintf(ficresprobcov,"# Age");
2931: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
2932: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2933: fprintf(ficresprobcov,"# Age");
2934:
2935:
2936: for(i=1; i<=nlstate;i++)
2937: for(j=1; j<=(nlstate+ndeath);j++){
2938: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2939: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2940: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2941: }
2942: /* fprintf(ficresprob,"\n");
2943: fprintf(ficresprobcov,"\n");
2944: fprintf(ficresprobcor,"\n");
2945: */
2946: xp=vector(1,npar);
2947: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
2948: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
2949: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
2950: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
2951: first=1;
2952: fprintf(ficgp,"\n# Routine varprob");
2953: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
2954: fprintf(fichtm,"\n");
2955:
2956: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
2957: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
2958: file %s<br>\n",optionfilehtmcov);
2959: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
2960: and drawn. It helps understanding how is the covariance between two incidences.\
2961: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
2962: fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
2963: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
2964: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
2965: standard deviations wide on each axis. <br>\
2966: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
2967: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
2968: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
2969:
2970: cov[1]=1;
2971: tj=cptcoveff;
2972: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
2973: j1=0;
2974: for(t=1; t<=tj;t++){
2975: for(i1=1; i1<=ncodemax[t];i1++){
2976: j1++;
2977: if (cptcovn>0) {
2978: fprintf(ficresprob, "\n#********** Variable ");
2979: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2980: fprintf(ficresprob, "**********\n#\n");
2981: fprintf(ficresprobcov, "\n#********** Variable ");
2982: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2983: fprintf(ficresprobcov, "**********\n#\n");
2984:
2985: fprintf(ficgp, "\n#********** Variable ");
2986: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2987: fprintf(ficgp, "**********\n#\n");
2988:
2989:
2990: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
2991: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2992: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
2993:
2994: fprintf(ficresprobcor, "\n#********** Variable ");
2995: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2996: fprintf(ficresprobcor, "**********\n#");
2997: }
2998:
2999: for (age=bage; age<=fage; age ++){
3000: cov[2]=age;
3001: for (k=1; k<=cptcovn;k++) {
3002: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3003: }
3004: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3005: for (k=1; k<=cptcovprod;k++)
3006: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3007:
3008: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3009: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3010: gp=vector(1,(nlstate)*(nlstate+ndeath));
3011: gm=vector(1,(nlstate)*(nlstate+ndeath));
3012:
3013: for(theta=1; theta <=npar; theta++){
3014: for(i=1; i<=npar; i++)
3015: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3016:
3017: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3018:
3019: k=0;
3020: for(i=1; i<= (nlstate); i++){
3021: for(j=1; j<=(nlstate+ndeath);j++){
3022: k=k+1;
3023: gp[k]=pmmij[i][j];
3024: }
3025: }
3026:
3027: for(i=1; i<=npar; i++)
3028: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3029:
3030: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3031: k=0;
3032: for(i=1; i<=(nlstate); i++){
3033: for(j=1; j<=(nlstate+ndeath);j++){
3034: k=k+1;
3035: gm[k]=pmmij[i][j];
3036: }
3037: }
3038:
3039: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3040: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3041: }
3042:
3043: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3044: for(theta=1; theta <=npar; theta++)
3045: trgradg[j][theta]=gradg[theta][j];
3046:
3047: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3048: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3049: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3050: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3051: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3052: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3053:
3054: pmij(pmmij,cov,ncovmodel,x,nlstate);
3055:
3056: k=0;
3057: for(i=1; i<=(nlstate); i++){
3058: for(j=1; j<=(nlstate+ndeath);j++){
3059: k=k+1;
3060: mu[k][(int) age]=pmmij[i][j];
3061: }
3062: }
3063: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3064: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3065: varpij[i][j][(int)age] = doldm[i][j];
3066:
3067: /*printf("\n%d ",(int)age);
3068: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3069: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3070: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3071: }*/
3072:
3073: fprintf(ficresprob,"\n%d ",(int)age);
3074: fprintf(ficresprobcov,"\n%d ",(int)age);
3075: fprintf(ficresprobcor,"\n%d ",(int)age);
3076:
3077: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3078: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3079: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3080: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3081: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3082: }
3083: i=0;
3084: for (k=1; k<=(nlstate);k++){
3085: for (l=1; l<=(nlstate+ndeath);l++){
3086: i=i++;
3087: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3088: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3089: for (j=1; j<=i;j++){
3090: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3091: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3092: }
3093: }
3094: }/* end of loop for state */
3095: } /* end of loop for age */
3096:
3097: /* Confidence intervalle of pij */
3098: /*
3099: fprintf(ficgp,"\nset noparametric;unset label");
3100: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3101: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3102: 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);
3103: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3104: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3105: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3106: */
3107:
3108: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3109: first1=1;
3110: for (k2=1; k2<=(nlstate);k2++){
3111: for (l2=1; l2<=(nlstate+ndeath);l2++){
3112: if(l2==k2) continue;
3113: j=(k2-1)*(nlstate+ndeath)+l2;
3114: for (k1=1; k1<=(nlstate);k1++){
3115: for (l1=1; l1<=(nlstate+ndeath);l1++){
3116: if(l1==k1) continue;
3117: i=(k1-1)*(nlstate+ndeath)+l1;
3118: if(i<=j) continue;
3119: for (age=bage; age<=fage; age ++){
3120: if ((int)age %5==0){
3121: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3122: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3123: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3124: mu1=mu[i][(int) age]/stepm*YEARM ;
3125: mu2=mu[j][(int) age]/stepm*YEARM;
3126: c12=cv12/sqrt(v1*v2);
3127: /* Computing eigen value of matrix of covariance */
3128: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3129: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3130: /* Eigen vectors */
3131: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3132: /*v21=sqrt(1.-v11*v11); *//* error */
3133: v21=(lc1-v1)/cv12*v11;
3134: v12=-v21;
3135: v22=v11;
3136: tnalp=v21/v11;
3137: if(first1==1){
3138: first1=0;
3139: 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);
3140: }
3141: 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);
3142: /*printf(fignu*/
3143: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3144: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3145: if(first==1){
3146: first=0;
3147: fprintf(ficgp,"\nset parametric;unset label");
3148: 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);
3149: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3150: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3151: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3152: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3153: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3154: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3155: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3156: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3157: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3158: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3159: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3160: 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",\
3161: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3162: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3163: }else{
3164: first=0;
3165: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3166: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3167: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3168: 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",\
3169: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3170: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3171: }/* if first */
3172: } /* age mod 5 */
3173: } /* end loop age */
3174: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3175: first=1;
3176: } /*l12 */
3177: } /* k12 */
3178: } /*l1 */
3179: }/* k1 */
3180: } /* loop covariates */
3181: }
3182: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3183: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3184: free_vector(xp,1,npar);
3185: fclose(ficresprob);
3186: fclose(ficresprobcov);
3187: fclose(ficresprobcor);
3188: fflush(ficgp);
3189: fflush(fichtmcov);
3190: }
3191:
3192:
3193: /******************* Printing html file ***********/
3194: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3195: int lastpass, int stepm, int weightopt, char model[],\
3196: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3197: int popforecast, int estepm ,\
3198: double jprev1, double mprev1,double anprev1, \
3199: double jprev2, double mprev2,double anprev2){
3200: int jj1, k1, i1, cpt;
3201:
3202: fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
3203: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3204: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3205: fprintf(fichtm,"\
3206: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3207: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3208: fprintf(fichtm,"\
3209: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3210: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3211: fprintf(fichtm,"\
3212: - Life expectancies by age and initial health status (estepm=%2d months): \
3213: <a href=\"%s\">%s</a> <br>\n</li>",
3214: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3215:
3216: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3217:
3218: m=cptcoveff;
3219: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3220:
3221: jj1=0;
3222: for(k1=1; k1<=m;k1++){
3223: for(i1=1; i1<=ncodemax[k1];i1++){
3224: jj1++;
3225: if (cptcovn > 0) {
3226: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3227: for (cpt=1; cpt<=cptcoveff;cpt++)
3228: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3229: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3230: }
3231: /* Pij */
3232: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
3233: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3234: /* Quasi-incidences */
3235: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3236: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3237: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3238: /* Stable prevalence in each health state */
3239: for(cpt=1; cpt<nlstate;cpt++){
3240: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3241: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3242: }
3243: for(cpt=1; cpt<=nlstate;cpt++) {
3244: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3245: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3246: }
3247: } /* end i1 */
3248: }/* End k1 */
3249: fprintf(fichtm,"</ul>");
3250:
3251:
3252: fprintf(fichtm,"\
3253: \n<br><li><h4> Result files (second order: variances)</h4>\n\
3254: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3255:
3256: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3257: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3258: fprintf(fichtm,"\
3259: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3260: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3261:
3262: fprintf(fichtm,"\
3263: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3264: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3265: fprintf(fichtm,"\
3266: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3267: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3268: fprintf(fichtm,"\
3269: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3270: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3271: fprintf(fichtm,"\
3272: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3273: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3274:
3275: /* if(popforecast==1) fprintf(fichtm,"\n */
3276: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3277: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3278: /* <br>",fileres,fileres,fileres,fileres); */
3279: /* else */
3280: /* 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); */
3281: fflush(fichtm);
3282: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3283:
3284: m=cptcoveff;
3285: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3286:
3287: jj1=0;
3288: for(k1=1; k1<=m;k1++){
3289: for(i1=1; i1<=ncodemax[k1];i1++){
3290: jj1++;
3291: if (cptcovn > 0) {
3292: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3293: for (cpt=1; cpt<=cptcoveff;cpt++)
3294: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3295: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3296: }
3297: for(cpt=1; cpt<=nlstate;cpt++) {
3298: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3299: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3300: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3301: }
3302: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3303: health expectancies in states (1) and (2): %s%d.png<br>\
3304: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3305: } /* end i1 */
3306: }/* End k1 */
3307: fprintf(fichtm,"</ul>");
3308: fflush(fichtm);
3309: }
3310:
3311: /******************* Gnuplot file **************/
3312: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3313:
3314: char dirfileres[132],optfileres[132];
3315: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3316: int ng;
3317: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3318: /* printf("Problem with file %s",optionfilegnuplot); */
3319: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3320: /* } */
3321:
3322: /*#ifdef windows */
3323: fprintf(ficgp,"cd \"%s\" \n",pathc);
3324: /*#endif */
3325: m=pow(2,cptcoveff);
3326:
3327: strcpy(dirfileres,optionfilefiname);
3328: strcpy(optfileres,"vpl");
3329: /* 1eme*/
3330: for (cpt=1; cpt<= nlstate ; cpt ++) {
3331: for (k1=1; k1<= m ; k1 ++) {
3332: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3333: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3334: fprintf(ficgp,"set xlabel \"Age\" \n\
3335: set ylabel \"Probability\" \n\
3336: set ter png small\n\
3337: set size 0.65,0.65\n\
3338: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3339:
3340: for (i=1; i<= nlstate ; i ++) {
3341: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3342: else fprintf(ficgp," \%%*lf (\%%*lf)");
3343: }
3344: fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3345: for (i=1; i<= nlstate ; i ++) {
3346: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3347: else fprintf(ficgp," \%%*lf (\%%*lf)");
3348: }
3349: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3350: for (i=1; i<= nlstate ; i ++) {
3351: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3352: else fprintf(ficgp," \%%*lf (\%%*lf)");
3353: }
3354: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3355: }
3356: }
3357: /*2 eme*/
3358:
3359: for (k1=1; k1<= m ; k1 ++) {
3360: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3361: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3362:
3363: for (i=1; i<= nlstate+1 ; i ++) {
3364: k=2*i;
3365: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3366: for (j=1; j<= nlstate+1 ; j ++) {
3367: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3368: else fprintf(ficgp," \%%*lf (\%%*lf)");
3369: }
3370: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3371: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3372: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3373: for (j=1; j<= nlstate+1 ; j ++) {
3374: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3375: else fprintf(ficgp," \%%*lf (\%%*lf)");
3376: }
3377: fprintf(ficgp,"\" t\"\" w l 0,");
3378: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3379: for (j=1; j<= nlstate+1 ; j ++) {
3380: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3381: else fprintf(ficgp," \%%*lf (\%%*lf)");
3382: }
3383: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3384: else fprintf(ficgp,"\" t\"\" w l 0,");
3385: }
3386: }
3387:
3388: /*3eme*/
3389:
3390: for (k1=1; k1<= m ; k1 ++) {
3391: for (cpt=1; cpt<= nlstate ; cpt ++) {
3392: k=2+nlstate*(2*cpt-2);
3393: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3394: fprintf(ficgp,"set ter png small\n\
3395: set size 0.65,0.65\n\
3396: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3397: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3398: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3399: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3400: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3401: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3402: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3403:
3404: */
3405: for (i=1; i< nlstate ; i ++) {
3406: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
3407:
3408: }
3409: }
3410: }
3411:
3412: /* CV preval stable (period) */
3413: for (k1=1; k1<= m ; k1 ++) {
3414: for (cpt=1; cpt<=nlstate ; cpt ++) {
3415: k=3;
3416: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3417: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3418: set ter png small\nset size 0.65,0.65\n\
3419: unset log y\n\
3420: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3421:
3422: for (i=1; i< nlstate ; i ++)
3423: fprintf(ficgp,"+$%d",k+i+1);
3424: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3425:
3426: l=3+(nlstate+ndeath)*cpt;
3427: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3428: for (i=1; i< nlstate ; i ++) {
3429: l=3+(nlstate+ndeath)*cpt;
3430: fprintf(ficgp,"+$%d",l+i+1);
3431: }
3432: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3433: }
3434: }
3435:
3436: /* proba elementaires */
3437: for(i=1,jk=1; i <=nlstate; i++){
3438: for(k=1; k <=(nlstate+ndeath); k++){
3439: if (k != i) {
3440: for(j=1; j <=ncovmodel; j++){
3441: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3442: jk++;
3443: fprintf(ficgp,"\n");
3444: }
3445: }
3446: }
3447: }
3448:
3449: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3450: for(jk=1; jk <=m; jk++) {
3451: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3452: if (ng==2)
3453: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3454: else
3455: fprintf(ficgp,"\nset title \"Probability\"\n");
3456: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3457: i=1;
3458: for(k2=1; k2<=nlstate; k2++) {
3459: k3=i;
3460: for(k=1; k<=(nlstate+ndeath); k++) {
3461: if (k != k2){
3462: if(ng==2)
3463: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3464: else
3465: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3466: ij=1;
3467: for(j=3; j <=ncovmodel; j++) {
3468: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3469: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3470: ij++;
3471: }
3472: else
3473: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3474: }
3475: fprintf(ficgp,")/(1");
3476:
3477: for(k1=1; k1 <=nlstate; k1++){
3478: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3479: ij=1;
3480: for(j=3; j <=ncovmodel; j++){
3481: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3482: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3483: ij++;
3484: }
3485: else
3486: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3487: }
3488: fprintf(ficgp,")");
3489: }
3490: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3491: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3492: i=i+ncovmodel;
3493: }
3494: } /* end k */
3495: } /* end k2 */
3496: } /* end jk */
3497: } /* end ng */
3498: fflush(ficgp);
3499: } /* end gnuplot */
3500:
3501:
3502: /*************** Moving average **************/
3503: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3504:
3505: int i, cpt, cptcod;
3506: int modcovmax =1;
3507: int mobilavrange, mob;
3508: double age;
3509:
3510: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3511: a covariate has 2 modalities */
3512: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3513:
3514: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3515: if(mobilav==1) mobilavrange=5; /* default */
3516: else mobilavrange=mobilav;
3517: for (age=bage; age<=fage; age++)
3518: for (i=1; i<=nlstate;i++)
3519: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3520: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3521: /* We keep the original values on the extreme ages bage, fage and for
3522: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3523: we use a 5 terms etc. until the borders are no more concerned.
3524: */
3525: for (mob=3;mob <=mobilavrange;mob=mob+2){
3526: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3527: for (i=1; i<=nlstate;i++){
3528: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3529: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3530: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3531: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3532: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3533: }
3534: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3535: }
3536: }
3537: }/* end age */
3538: }/* end mob */
3539: }else return -1;
3540: return 0;
3541: }/* End movingaverage */
3542:
3543:
3544: /************** Forecasting ******************/
3545: 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){
3546: /* proj1, year, month, day of starting projection
3547: agemin, agemax range of age
3548: dateprev1 dateprev2 range of dates during which prevalence is computed
3549: anproj2 year of en of projection (same day and month as proj1).
3550: */
3551: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3552: int *popage;
3553: double agec; /* generic age */
3554: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3555: double *popeffectif,*popcount;
3556: double ***p3mat;
3557: double ***mobaverage;
3558: char fileresf[FILENAMELENGTH];
3559:
3560: agelim=AGESUP;
3561: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3562:
3563: strcpy(fileresf,"f");
3564: strcat(fileresf,fileres);
3565: if((ficresf=fopen(fileresf,"w"))==NULL) {
3566: printf("Problem with forecast resultfile: %s\n", fileresf);
3567: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3568: }
3569: printf("Computing forecasting: result on file '%s' \n", fileresf);
3570: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3571:
3572: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3573:
3574: if (mobilav!=0) {
3575: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3576: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3577: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3578: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3579: }
3580: }
3581:
3582: stepsize=(int) (stepm+YEARM-1)/YEARM;
3583: if (stepm<=12) stepsize=1;
3584: if(estepm < stepm){
3585: printf ("Problem %d lower than %d\n",estepm, stepm);
3586: }
3587: else hstepm=estepm;
3588:
3589: hstepm=hstepm/stepm;
3590: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3591: fractional in yp1 */
3592: anprojmean=yp;
3593: yp2=modf((yp1*12),&yp);
3594: mprojmean=yp;
3595: yp1=modf((yp2*30.5),&yp);
3596: jprojmean=yp;
3597: if(jprojmean==0) jprojmean=1;
3598: if(mprojmean==0) jprojmean=1;
3599:
3600: i1=cptcoveff;
3601: if (cptcovn < 1){i1=1;}
3602:
3603: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3604:
3605: fprintf(ficresf,"#****** Routine prevforecast **\n");
3606:
3607: /* if (h==(int)(YEARM*yearp)){ */
3608: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3609: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3610: k=k+1;
3611: fprintf(ficresf,"\n#******");
3612: for(j=1;j<=cptcoveff;j++) {
3613: 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]]);
3614: }
3615: fprintf(ficresf,"******\n");
3616: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3617: for(j=1; j<=nlstate+ndeath;j++){
3618: for(i=1; i<=nlstate;i++)
3619: fprintf(ficresf," p%d%d",i,j);
3620: fprintf(ficresf," p.%d",j);
3621: }
3622: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3623: fprintf(ficresf,"\n");
3624: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3625:
3626: for (agec=fage; agec>=(ageminpar-1); agec--){
3627: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3628: nhstepm = nhstepm/hstepm;
3629: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3630: oldm=oldms;savm=savms;
3631: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3632:
3633: for (h=0; h<=nhstepm; h++){
3634: if (h*hstepm/YEARM*stepm ==yearp) {
3635: fprintf(ficresf,"\n");
3636: for(j=1;j<=cptcoveff;j++)
3637: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3638: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3639: }
3640: for(j=1; j<=nlstate+ndeath;j++) {
3641: ppij=0.;
3642: for(i=1; i<=nlstate;i++) {
3643: if (mobilav==1)
3644: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3645: else {
3646: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3647: }
3648: if (h*hstepm/YEARM*stepm== yearp) {
3649: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3650: }
3651: } /* end i */
3652: if (h*hstepm/YEARM*stepm==yearp) {
3653: fprintf(ficresf," %.3f", ppij);
3654: }
3655: }/* end j */
3656: } /* end h */
3657: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3658: } /* end agec */
3659: } /* end yearp */
3660: } /* end cptcod */
3661: } /* end cptcov */
3662:
3663: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3664:
3665: fclose(ficresf);
3666: }
3667:
3668: /************** Forecasting *****not tested NB*************/
3669: 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){
3670:
3671: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3672: int *popage;
3673: double calagedatem, agelim, kk1, kk2;
3674: double *popeffectif,*popcount;
3675: double ***p3mat,***tabpop,***tabpopprev;
3676: double ***mobaverage;
3677: char filerespop[FILENAMELENGTH];
3678:
3679: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3680: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3681: agelim=AGESUP;
3682: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3683:
3684: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3685:
3686:
3687: strcpy(filerespop,"pop");
3688: strcat(filerespop,fileres);
3689: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3690: printf("Problem with forecast resultfile: %s\n", filerespop);
3691: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3692: }
3693: printf("Computing forecasting: result on file '%s' \n", filerespop);
3694: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3695:
3696: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3697:
3698: if (mobilav!=0) {
3699: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3700: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3701: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3702: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3703: }
3704: }
3705:
3706: stepsize=(int) (stepm+YEARM-1)/YEARM;
3707: if (stepm<=12) stepsize=1;
3708:
3709: agelim=AGESUP;
3710:
3711: hstepm=1;
3712: hstepm=hstepm/stepm;
3713:
3714: if (popforecast==1) {
3715: if((ficpop=fopen(popfile,"r"))==NULL) {
3716: printf("Problem with population file : %s\n",popfile);exit(0);
3717: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3718: }
3719: popage=ivector(0,AGESUP);
3720: popeffectif=vector(0,AGESUP);
3721: popcount=vector(0,AGESUP);
3722:
3723: i=1;
3724: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3725:
3726: imx=i;
3727: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3728: }
3729:
3730: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3731: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3732: k=k+1;
3733: fprintf(ficrespop,"\n#******");
3734: for(j=1;j<=cptcoveff;j++) {
3735: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3736: }
3737: fprintf(ficrespop,"******\n");
3738: fprintf(ficrespop,"# Age");
3739: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3740: if (popforecast==1) fprintf(ficrespop," [Population]");
3741:
3742: for (cpt=0; cpt<=0;cpt++) {
3743: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3744:
3745: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3746: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3747: nhstepm = nhstepm/hstepm;
3748:
3749: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3750: oldm=oldms;savm=savms;
3751: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3752:
3753: for (h=0; h<=nhstepm; h++){
3754: if (h==(int) (calagedatem+YEARM*cpt)) {
3755: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3756: }
3757: for(j=1; j<=nlstate+ndeath;j++) {
3758: kk1=0.;kk2=0;
3759: for(i=1; i<=nlstate;i++) {
3760: if (mobilav==1)
3761: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3762: else {
3763: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3764: }
3765: }
3766: if (h==(int)(calagedatem+12*cpt)){
3767: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3768: /*fprintf(ficrespop," %.3f", kk1);
3769: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3770: }
3771: }
3772: for(i=1; i<=nlstate;i++){
3773: kk1=0.;
3774: for(j=1; j<=nlstate;j++){
3775: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3776: }
3777: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3778: }
3779:
3780: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3781: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3782: }
3783: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3784: }
3785: }
3786:
3787: /******/
3788:
3789: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3790: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3791: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3792: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3793: nhstepm = nhstepm/hstepm;
3794:
3795: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3796: oldm=oldms;savm=savms;
3797: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3798: for (h=0; h<=nhstepm; h++){
3799: if (h==(int) (calagedatem+YEARM*cpt)) {
3800: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3801: }
3802: for(j=1; j<=nlstate+ndeath;j++) {
3803: kk1=0.;kk2=0;
3804: for(i=1; i<=nlstate;i++) {
3805: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3806: }
3807: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3808: }
3809: }
3810: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3811: }
3812: }
3813: }
3814: }
3815:
3816: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3817:
3818: if (popforecast==1) {
3819: free_ivector(popage,0,AGESUP);
3820: free_vector(popeffectif,0,AGESUP);
3821: free_vector(popcount,0,AGESUP);
3822: }
3823: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3824: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3825: fclose(ficrespop);
3826: } /* End of popforecast */
3827:
3828: int fileappend(FILE *fichier, char *optionfich)
3829: {
3830: if((fichier=fopen(optionfich,"a"))==NULL) {
3831: printf("Problem with file: %s\n", optionfich);
3832: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3833: return (0);
3834: }
3835: fflush(fichier);
3836: return (1);
3837: }
3838:
3839:
3840: /**************** function prwizard **********************/
3841: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3842: {
3843:
3844: /* Wizard to print covariance matrix template */
3845:
3846: char ca[32], cb[32], cc[32];
3847: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3848: int numlinepar;
3849:
3850: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3851: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3852: for(i=1; i <=nlstate; i++){
3853: jj=0;
3854: for(j=1; j <=nlstate+ndeath; j++){
3855: if(j==i) continue;
3856: jj++;
3857: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3858: printf("%1d%1d",i,j);
3859: fprintf(ficparo,"%1d%1d",i,j);
3860: for(k=1; k<=ncovmodel;k++){
3861: /* printf(" %lf",param[i][j][k]); */
3862: /* fprintf(ficparo," %lf",param[i][j][k]); */
3863: printf(" 0.");
3864: fprintf(ficparo," 0.");
3865: }
3866: printf("\n");
3867: fprintf(ficparo,"\n");
3868: }
3869: }
3870: printf("# Scales (for hessian or gradient estimation)\n");
3871: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3872: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3873: for(i=1; i <=nlstate; i++){
3874: jj=0;
3875: for(j=1; j <=nlstate+ndeath; j++){
3876: if(j==i) continue;
3877: jj++;
3878: fprintf(ficparo,"%1d%1d",i,j);
3879: printf("%1d%1d",i,j);
3880: fflush(stdout);
3881: for(k=1; k<=ncovmodel;k++){
3882: /* printf(" %le",delti3[i][j][k]); */
3883: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3884: printf(" 0.");
3885: fprintf(ficparo," 0.");
3886: }
3887: numlinepar++;
3888: printf("\n");
3889: fprintf(ficparo,"\n");
3890: }
3891: }
3892: printf("# Covariance matrix\n");
3893: /* # 121 Var(a12)\n\ */
3894: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3895: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3896: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3897: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3898: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3899: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3900: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3901: fflush(stdout);
3902: fprintf(ficparo,"# Covariance matrix\n");
3903: /* # 121 Var(a12)\n\ */
3904: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3905: /* # ...\n\ */
3906: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3907:
3908: for(itimes=1;itimes<=2;itimes++){
3909: jj=0;
3910: for(i=1; i <=nlstate; i++){
3911: for(j=1; j <=nlstate+ndeath; j++){
3912: if(j==i) continue;
3913: for(k=1; k<=ncovmodel;k++){
3914: jj++;
3915: ca[0]= k+'a'-1;ca[1]='\0';
3916: if(itimes==1){
3917: printf("#%1d%1d%d",i,j,k);
3918: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3919: }else{
3920: printf("%1d%1d%d",i,j,k);
3921: fprintf(ficparo,"%1d%1d%d",i,j,k);
3922: /* printf(" %.5le",matcov[i][j]); */
3923: }
3924: ll=0;
3925: for(li=1;li <=nlstate; li++){
3926: for(lj=1;lj <=nlstate+ndeath; lj++){
3927: if(lj==li) continue;
3928: for(lk=1;lk<=ncovmodel;lk++){
3929: ll++;
3930: if(ll<=jj){
3931: cb[0]= lk +'a'-1;cb[1]='\0';
3932: if(ll<jj){
3933: if(itimes==1){
3934: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3935: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3936: }else{
3937: printf(" 0.");
3938: fprintf(ficparo," 0.");
3939: }
3940: }else{
3941: if(itimes==1){
3942: printf(" Var(%s%1d%1d)",ca,i,j);
3943: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
3944: }else{
3945: printf(" 0.");
3946: fprintf(ficparo," 0.");
3947: }
3948: }
3949: }
3950: } /* end lk */
3951: } /* end lj */
3952: } /* end li */
3953: printf("\n");
3954: fprintf(ficparo,"\n");
3955: numlinepar++;
3956: } /* end k*/
3957: } /*end j */
3958: } /* end i */
3959: } /* end itimes */
3960:
3961: } /* end of prwizard */
3962: /******************* Gompertz Likelihood ******************************/
3963: double gompertz(double x[])
3964: {
3965: double A,B,L=0.0,sump=0.,num=0.;
3966: int i,n=0; /* n is the size of the sample */
3967: for (i=0;i<=imx-1 ; i++) {
3968: sump=sump+weight[i];
3969: /* sump=sump+1;*/
3970: num=num+1;
3971: }
3972:
3973:
3974: /* for (i=0; i<=imx; i++)
3975: if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
3976:
3977: for (i=1;i<=imx ; i++)
3978: {
3979: if (cens[i]==1 & wav[i]>1)
3980: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
3981:
3982: if (cens[i]==0 & wav[i]>1)
3983: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
3984: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
3985:
3986: if (wav[i]>1 & agecens[i]>15) {
3987: L=L+A*weight[i];
3988: /* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
3989: }
3990: }
3991:
3992: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
3993:
3994: return -2*L*num/sump;
3995: }
3996:
3997: /******************* Printing html file ***********/
3998: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
3999: int lastpass, int stepm, int weightopt, char model[],\
4000: int imx, double p[],double **matcov,double agemortsup){
4001: int i,k;
4002:
4003: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4004: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4005: for (i=1;i<=2;i++)
4006: fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4007: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4008: fprintf(fichtm,"</ul>");
4009:
4010: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4011:
4012: fprintf(fichtm,"\nAge lx qx dx Lx Tx e(x)<br>");
4013:
4014: for (k=agegomp;k<(agemortsup-2);k++)
4015: fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4016:
4017:
4018: fflush(fichtm);
4019: }
4020:
4021: /******************* Gnuplot file **************/
4022: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4023:
4024: char dirfileres[132],optfileres[132];
4025: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4026: int ng;
4027:
4028:
4029: /*#ifdef windows */
4030: fprintf(ficgp,"cd \"%s\" \n",pathc);
4031: /*#endif */
4032:
4033:
4034: strcpy(dirfileres,optionfilefiname);
4035: strcpy(optfileres,"vpl");
4036: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4037: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4038: fprintf(ficgp, "set ter png small\n set log y\n");
4039: fprintf(ficgp, "set size 0.65,0.65\n");
4040: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4041:
4042: }
4043:
4044:
4045:
4046:
4047: /***********************************************/
4048: /**************** Main Program *****************/
4049: /***********************************************/
4050:
4051: int main(int argc, char *argv[])
4052: {
4053: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4054: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4055: int jj, ll, li, lj, lk, imk;
4056: int numlinepar=0; /* Current linenumber of parameter file */
4057: int itimes;
4058: int NDIM=2;
4059:
4060: char ca[32], cb[32], cc[32];
4061: /* FILE *fichtm; *//* Html File */
4062: /* FILE *ficgp;*/ /*Gnuplot File */
4063: double agedeb, agefin,hf;
4064: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4065:
4066: double fret;
4067: double **xi,tmp,delta;
4068:
4069: double dum; /* Dummy variable */
4070: double ***p3mat;
4071: double ***mobaverage;
4072: int *indx;
4073: char line[MAXLINE], linepar[MAXLINE];
4074: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4075: char pathr[MAXLINE], pathimach[MAXLINE];
4076: int firstobs=1, lastobs=10;
4077: int sdeb, sfin; /* Status at beginning and end */
4078: int c, h , cpt,l;
4079: int ju,jl, mi;
4080: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4081: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4082: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4083: int mobilav=0,popforecast=0;
4084: int hstepm, nhstepm;
4085: int agemortsup;
4086: float sumlpop=0.;
4087: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4088: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4089:
4090: double bage, fage, age, agelim, agebase;
4091: double ftolpl=FTOL;
4092: double **prlim;
4093: double *severity;
4094: double ***param; /* Matrix of parameters */
4095: double *p;
4096: double **matcov; /* Matrix of covariance */
4097: double ***delti3; /* Scale */
4098: double *delti; /* Scale */
4099: double ***eij, ***vareij;
4100: double **varpl; /* Variances of prevalence limits by age */
4101: double *epj, vepp;
4102: double kk1, kk2;
4103: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4104: double **ximort;
4105: char *alph[]={"a","a","b","c","d","e"}, str[4];
4106: int *dcwave;
4107:
4108: char z[1]="c", occ;
4109:
4110: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4111: char strstart[80], *strt, strtend[80];
4112: char *stratrunc;
4113: int lstra;
4114:
4115: long total_usecs;
4116:
4117: /* setlocale (LC_ALL, ""); */
4118: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4119: /* textdomain (PACKAGE); */
4120: /* setlocale (LC_CTYPE, ""); */
4121: /* setlocale (LC_MESSAGES, ""); */
4122:
4123: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4124: (void) gettimeofday(&start_time,&tzp);
4125: curr_time=start_time;
4126: tm = *localtime(&start_time.tv_sec);
4127: tmg = *gmtime(&start_time.tv_sec);
4128: strcpy(strstart,asctime(&tm));
4129:
4130: /* printf("Localtime (at start)=%s",strstart); */
4131: /* tp.tv_sec = tp.tv_sec +86400; */
4132: /* tm = *localtime(&start_time.tv_sec); */
4133: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4134: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4135: /* tmg.tm_hour=tmg.tm_hour + 1; */
4136: /* tp.tv_sec = mktime(&tmg); */
4137: /* strt=asctime(&tmg); */
4138: /* printf("Time(after) =%s",strstart); */
4139: /* (void) time (&time_value);
4140: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4141: * tm = *localtime(&time_value);
4142: * strstart=asctime(&tm);
4143: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4144: */
4145:
4146: nberr=0; /* Number of errors and warnings */
4147: nbwarn=0;
4148: getcwd(pathcd, size);
4149:
4150: printf("\n%s\n%s",version,fullversion);
4151: if(argc <=1){
4152: printf("\nEnter the parameter file name: ");
4153: scanf("%s",pathtot);
4154: }
4155: else{
4156: strcpy(pathtot,argv[1]);
4157: }
4158: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4159: /*cygwin_split_path(pathtot,path,optionfile);
4160: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4161: /* cutv(path,optionfile,pathtot,'\\');*/
4162:
4163: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4164: /* strcpy(pathimach,argv[0]); */
4165: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4166: printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4167: chdir(path);
4168: strcpy(command,"mkdir ");
4169: strcat(command,optionfilefiname);
4170: if((outcmd=system(command)) != 0){
4171: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4172: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4173: /* fclose(ficlog); */
4174: /* exit(1); */
4175: }
4176: /* if((imk=mkdir(optionfilefiname))<0){ */
4177: /* perror("mkdir"); */
4178: /* } */
4179:
4180: /*-------- arguments in the command line --------*/
4181:
4182: /* Log file */
4183: strcat(filelog, optionfilefiname);
4184: strcat(filelog,".log"); /* */
4185: if((ficlog=fopen(filelog,"w"))==NULL) {
4186: printf("Problem with logfile %s\n",filelog);
4187: goto end;
4188: }
4189: fprintf(ficlog,"Log filename:%s\n",filelog);
4190: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4191: fprintf(ficlog,"\nEnter the parameter file name: \n");
4192: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4193: path=%s \n\
4194: optionfile=%s\n\
4195: optionfilext=%s\n\
4196: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4197:
4198: printf("Local time (at start):%s",strstart);
4199: fprintf(ficlog,"Local time (at start): %s",strstart);
4200: fflush(ficlog);
4201: /* (void) gettimeofday(&curr_time,&tzp); */
4202: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4203:
4204: /* */
4205: strcpy(fileres,"r");
4206: strcat(fileres, optionfilefiname);
4207: strcat(fileres,".txt"); /* Other files have txt extension */
4208:
4209: /*---------arguments file --------*/
4210:
4211: if((ficpar=fopen(optionfile,"r"))==NULL) {
4212: printf("Problem with optionfile %s\n",optionfile);
4213: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4214: fflush(ficlog);
4215: goto end;
4216: }
4217:
4218:
4219:
4220: strcpy(filereso,"o");
4221: strcat(filereso,fileres);
4222: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4223: printf("Problem with Output resultfile: %s\n", filereso);
4224: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4225: fflush(ficlog);
4226: goto end;
4227: }
4228:
4229: /* Reads comments: lines beginning with '#' */
4230: numlinepar=0;
4231: while((c=getc(ficpar))=='#' && c!= EOF){
4232: ungetc(c,ficpar);
4233: fgets(line, MAXLINE, ficpar);
4234: numlinepar++;
4235: puts(line);
4236: fputs(line,ficparo);
4237: fputs(line,ficlog);
4238: }
4239: ungetc(c,ficpar);
4240:
4241: 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);
4242: numlinepar++;
4243: 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);
4244: 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);
4245: fprintf(ficlog,"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);
4246: fflush(ficlog);
4247: while((c=getc(ficpar))=='#' && c!= EOF){
4248: ungetc(c,ficpar);
4249: fgets(line, MAXLINE, ficpar);
4250: numlinepar++;
4251: puts(line);
4252: fputs(line,ficparo);
4253: fputs(line,ficlog);
4254: }
4255: ungetc(c,ficpar);
4256:
4257:
4258: covar=matrix(0,NCOVMAX,1,n);
4259: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4260: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4261:
4262: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4263: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4264: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4265:
4266: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4267: delti=delti3[1][1];
4268: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4269: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4270: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4271: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4272: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4273: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4274: fclose (ficparo);
4275: fclose (ficlog);
4276: exit(0);
4277: }
4278: else if(mle==-3) {
4279: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4280: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4281: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4282: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4283: matcov=matrix(1,npar,1,npar);
4284: }
4285: else{
4286: /* Read guess parameters */
4287: /* Reads comments: lines beginning with '#' */
4288: while((c=getc(ficpar))=='#' && c!= EOF){
4289: ungetc(c,ficpar);
4290: fgets(line, MAXLINE, ficpar);
4291: numlinepar++;
4292: puts(line);
4293: fputs(line,ficparo);
4294: fputs(line,ficlog);
4295: }
4296: ungetc(c,ficpar);
4297:
4298: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4299: for(i=1; i <=nlstate; i++){
4300: j=0;
4301: for(jj=1; jj <=nlstate+ndeath; jj++){
4302: if(jj==i) continue;
4303: j++;
4304: fscanf(ficpar,"%1d%1d",&i1,&j1);
4305: if ((i1 != i) && (j1 != j)){
4306: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4307: exit(1);
4308: }
4309: fprintf(ficparo,"%1d%1d",i1,j1);
4310: if(mle==1)
4311: printf("%1d%1d",i,j);
4312: fprintf(ficlog,"%1d%1d",i,j);
4313: for(k=1; k<=ncovmodel;k++){
4314: fscanf(ficpar," %lf",¶m[i][j][k]);
4315: if(mle==1){
4316: printf(" %lf",param[i][j][k]);
4317: fprintf(ficlog," %lf",param[i][j][k]);
4318: }
4319: else
4320: fprintf(ficlog," %lf",param[i][j][k]);
4321: fprintf(ficparo," %lf",param[i][j][k]);
4322: }
4323: fscanf(ficpar,"\n");
4324: numlinepar++;
4325: if(mle==1)
4326: printf("\n");
4327: fprintf(ficlog,"\n");
4328: fprintf(ficparo,"\n");
4329: }
4330: }
4331: fflush(ficlog);
4332:
4333:
4334: p=param[1][1];
4335:
4336: /* Reads comments: lines beginning with '#' */
4337: while((c=getc(ficpar))=='#' && c!= EOF){
4338: ungetc(c,ficpar);
4339: fgets(line, MAXLINE, ficpar);
4340: numlinepar++;
4341: puts(line);
4342: fputs(line,ficparo);
4343: fputs(line,ficlog);
4344: }
4345: ungetc(c,ficpar);
4346:
4347: for(i=1; i <=nlstate; i++){
4348: for(j=1; j <=nlstate+ndeath-1; j++){
4349: fscanf(ficpar,"%1d%1d",&i1,&j1);
4350: if ((i1-i)*(j1-j)!=0){
4351: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4352: exit(1);
4353: }
4354: printf("%1d%1d",i,j);
4355: fprintf(ficparo,"%1d%1d",i1,j1);
4356: fprintf(ficlog,"%1d%1d",i1,j1);
4357: for(k=1; k<=ncovmodel;k++){
4358: fscanf(ficpar,"%le",&delti3[i][j][k]);
4359: printf(" %le",delti3[i][j][k]);
4360: fprintf(ficparo," %le",delti3[i][j][k]);
4361: fprintf(ficlog," %le",delti3[i][j][k]);
4362: }
4363: fscanf(ficpar,"\n");
4364: numlinepar++;
4365: printf("\n");
4366: fprintf(ficparo,"\n");
4367: fprintf(ficlog,"\n");
4368: }
4369: }
4370: fflush(ficlog);
4371:
4372: delti=delti3[1][1];
4373:
4374:
4375: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4376:
4377: /* Reads comments: lines beginning with '#' */
4378: while((c=getc(ficpar))=='#' && c!= EOF){
4379: ungetc(c,ficpar);
4380: fgets(line, MAXLINE, ficpar);
4381: numlinepar++;
4382: puts(line);
4383: fputs(line,ficparo);
4384: fputs(line,ficlog);
4385: }
4386: ungetc(c,ficpar);
4387:
4388: matcov=matrix(1,npar,1,npar);
4389: for(i=1; i <=npar; i++){
4390: fscanf(ficpar,"%s",&str);
4391: if(mle==1)
4392: printf("%s",str);
4393: fprintf(ficlog,"%s",str);
4394: fprintf(ficparo,"%s",str);
4395: for(j=1; j <=i; j++){
4396: fscanf(ficpar," %le",&matcov[i][j]);
4397: if(mle==1){
4398: printf(" %.5le",matcov[i][j]);
4399: }
4400: fprintf(ficlog," %.5le",matcov[i][j]);
4401: fprintf(ficparo," %.5le",matcov[i][j]);
4402: }
4403: fscanf(ficpar,"\n");
4404: numlinepar++;
4405: if(mle==1)
4406: printf("\n");
4407: fprintf(ficlog,"\n");
4408: fprintf(ficparo,"\n");
4409: }
4410: for(i=1; i <=npar; i++)
4411: for(j=i+1;j<=npar;j++)
4412: matcov[i][j]=matcov[j][i];
4413:
4414: if(mle==1)
4415: printf("\n");
4416: fprintf(ficlog,"\n");
4417:
4418: fflush(ficlog);
4419:
4420: /*-------- Rewriting parameter file ----------*/
4421: strcpy(rfileres,"r"); /* "Rparameterfile */
4422: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4423: strcat(rfileres,"."); /* */
4424: strcat(rfileres,optionfilext); /* Other files have txt extension */
4425: if((ficres =fopen(rfileres,"w"))==NULL) {
4426: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4427: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4428: }
4429: fprintf(ficres,"#%s\n",version);
4430: } /* End of mle != -3 */
4431:
4432: /*-------- data file ----------*/
4433: if((fic=fopen(datafile,"r"))==NULL) {
4434: printf("Problem with datafile: %s\n", datafile);goto end;
4435: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4436: }
4437:
4438: n= lastobs;
4439: severity = vector(1,maxwav);
4440: outcome=imatrix(1,maxwav+1,1,n);
4441: num=lvector(1,n);
4442: moisnais=vector(1,n);
4443: annais=vector(1,n);
4444: moisdc=vector(1,n);
4445: andc=vector(1,n);
4446: agedc=vector(1,n);
4447: cod=ivector(1,n);
4448: weight=vector(1,n);
4449: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4450: mint=matrix(1,maxwav,1,n);
4451: anint=matrix(1,maxwav,1,n);
4452: s=imatrix(1,maxwav+1,1,n);
4453: tab=ivector(1,NCOVMAX);
4454: ncodemax=ivector(1,8);
4455:
4456: i=1;
4457: while (fgets(line, MAXLINE, fic) != NULL) {
4458: if ((i >= firstobs) && (i <=lastobs)) {
4459: for(j=0; line[j] != '\n';j++){ /* Untabifies line */
4460: if(line[j] == '\t')
4461: line[j] = ' ';
4462: }
4463: for (j=maxwav;j>=1;j--){
4464: cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
4465: strcpy(line,stra);
4466: cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4467: cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4468: }
4469:
4470: cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
4471: cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
4472:
4473: cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
4474: cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
4475:
4476: cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
4477: for (j=ncovcol;j>=1;j--){
4478: cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
4479: }
4480: lstra=strlen(stra);
4481: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4482: stratrunc = &(stra[lstra-9]);
4483: num[i]=atol(stratrunc);
4484: }
4485: else
4486: num[i]=atol(stra);
4487:
4488: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4489: printf("%ld %.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;}*/
4490:
4491: i=i+1;
4492: }
4493: }
4494: /* printf("ii=%d", ij);
4495: scanf("%d",i);*/
4496: imx=i-1; /* Number of individuals */
4497:
4498: /* for (i=1; i<=imx; i++){
4499: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4500: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4501: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4502: }*/
4503: /* for (i=1; i<=imx; i++){
4504: if (s[4][i]==9) s[4][i]=-1;
4505: printf("%ld %.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]));}*/
4506:
4507: for (i=1; i<=imx; i++)
4508:
4509: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4510: else weight[i]=1;*/
4511:
4512: /* Calculation of the number of parameter from char model*/
4513: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4514: Tprod=ivector(1,15);
4515: Tvaraff=ivector(1,15);
4516: Tvard=imatrix(1,15,1,2);
4517: Tage=ivector(1,15);
4518:
4519: if (strlen(model) >1){ /* If there is at least 1 covariate */
4520: j=0, j1=0, k1=1, k2=1;
4521: j=nbocc(model,'+'); /* j=Number of '+' */
4522: j1=nbocc(model,'*'); /* j1=Number of '*' */
4523: cptcovn=j+1;
4524: cptcovprod=j1; /*Number of products */
4525:
4526: strcpy(modelsav,model);
4527: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4528: printf("Error. Non available option model=%s ",model);
4529: fprintf(ficlog,"Error. Non available option model=%s ",model);
4530: goto end;
4531: }
4532:
4533: /* This loop fills the array Tvar from the string 'model'.*/
4534:
4535: for(i=(j+1); i>=1;i--){
4536: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4537: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4538: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4539: /*scanf("%d",i);*/
4540: if (strchr(strb,'*')) { /* Model includes a product */
4541: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4542: if (strcmp(strc,"age")==0) { /* Vn*age */
4543: cptcovprod--;
4544: cutv(strb,stre,strd,'V');
4545: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4546: cptcovage++;
4547: Tage[cptcovage]=i;
4548: /*printf("stre=%s ", stre);*/
4549: }
4550: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4551: cptcovprod--;
4552: cutv(strb,stre,strc,'V');
4553: Tvar[i]=atoi(stre);
4554: cptcovage++;
4555: Tage[cptcovage]=i;
4556: }
4557: else { /* Age is not in the model */
4558: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4559: Tvar[i]=ncovcol+k1;
4560: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4561: Tprod[k1]=i;
4562: Tvard[k1][1]=atoi(strc); /* m*/
4563: Tvard[k1][2]=atoi(stre); /* n */
4564: Tvar[cptcovn+k2]=Tvard[k1][1];
4565: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4566: for (k=1; k<=lastobs;k++)
4567: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4568: k1++;
4569: k2=k2+2;
4570: }
4571: }
4572: else { /* no more sum */
4573: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4574: /* scanf("%d",i);*/
4575: cutv(strd,strc,strb,'V');
4576: Tvar[i]=atoi(strc);
4577: }
4578: strcpy(modelsav,stra);
4579: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4580: scanf("%d",i);*/
4581: } /* end of loop + */
4582: } /* end model */
4583:
4584: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4585: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4586:
4587: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4588: printf("cptcovprod=%d ", cptcovprod);
4589: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4590:
4591: scanf("%d ",i);
4592: fclose(fic);*/
4593:
4594: /* if(mle==1){*/
4595: if (weightopt != 1) { /* Maximisation without weights*/
4596: for(i=1;i<=n;i++) weight[i]=1.0;
4597: }
4598: /*-calculation of age at interview from date of interview and age at death -*/
4599: agev=matrix(1,maxwav,1,imx);
4600:
4601: for (i=1; i<=imx; i++) {
4602: for(m=2; (m<= maxwav); m++) {
4603: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4604: anint[m][i]=9999;
4605: s[m][i]=-1;
4606: }
4607: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4608: nberr++;
4609: printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
4610: fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
4611: s[m][i]=-1;
4612: }
4613: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4614: nberr++;
4615: printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
4616: fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
4617: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4618: }
4619: }
4620: }
4621:
4622: for (i=1; i<=imx; i++) {
4623: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4624: for(m=firstpass; (m<= lastpass); m++){
4625: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4626: if (s[m][i] >= nlstate+1) {
4627: if(agedc[i]>0)
4628: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4629: agev[m][i]=agedc[i];
4630: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4631: else {
4632: if ((int)andc[i]!=9999){
4633: nbwarn++;
4634: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4635: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4636: agev[m][i]=-1;
4637: }
4638: }
4639: }
4640: else if(s[m][i] !=9){ /* Standard case, age in fractional
4641: years but with the precision of a
4642: month */
4643: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4644: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4645: agev[m][i]=1;
4646: else if(agev[m][i] <agemin){
4647: agemin=agev[m][i];
4648: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4649: }
4650: else if(agev[m][i] >agemax){
4651: agemax=agev[m][i];
4652: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4653: }
4654: /*agev[m][i]=anint[m][i]-annais[i];*/
4655: /* agev[m][i] = age[i]+2*m;*/
4656: }
4657: else { /* =9 */
4658: agev[m][i]=1;
4659: s[m][i]=-1;
4660: }
4661: }
4662: else /*= 0 Unknown */
4663: agev[m][i]=1;
4664: }
4665:
4666: }
4667: for (i=1; i<=imx; i++) {
4668: for(m=firstpass; (m<=lastpass); m++){
4669: if (s[m][i] > (nlstate+ndeath)) {
4670: nberr++;
4671: 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);
4672: 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);
4673: goto end;
4674: }
4675: }
4676: }
4677:
4678: /*for (i=1; i<=imx; i++){
4679: for (m=firstpass; (m<lastpass); m++){
4680: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4681: }
4682:
4683: }*/
4684:
4685:
4686: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4687: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4688:
4689: agegomp=(int)agemin;
4690: free_vector(severity,1,maxwav);
4691: free_imatrix(outcome,1,maxwav+1,1,n);
4692: free_vector(moisnais,1,n);
4693: free_vector(annais,1,n);
4694: /* free_matrix(mint,1,maxwav,1,n);
4695: free_matrix(anint,1,maxwav,1,n);*/
4696: free_vector(moisdc,1,n);
4697: free_vector(andc,1,n);
4698:
4699:
4700: wav=ivector(1,imx);
4701: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4702: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4703: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4704:
4705: /* Concatenates waves */
4706: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4707:
4708: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4709:
4710: Tcode=ivector(1,100);
4711: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4712: ncodemax[1]=1;
4713: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4714:
4715: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4716: the estimations*/
4717: h=0;
4718: m=pow(2,cptcoveff);
4719:
4720: for(k=1;k<=cptcoveff; k++){
4721: for(i=1; i <=(m/pow(2,k));i++){
4722: for(j=1; j <= ncodemax[k]; j++){
4723: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4724: h++;
4725: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4726: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4727: }
4728: }
4729: }
4730: }
4731: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4732: codtab[1][2]=1;codtab[2][2]=2; */
4733: /* for(i=1; i <=m ;i++){
4734: for(k=1; k <=cptcovn; k++){
4735: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4736: }
4737: printf("\n");
4738: }
4739: scanf("%d",i);*/
4740:
4741: /*------------ gnuplot -------------*/
4742: strcpy(optionfilegnuplot,optionfilefiname);
4743: if(mle==-3)
4744: strcat(optionfilegnuplot,"-mort");
4745: strcat(optionfilegnuplot,".gp");
4746:
4747: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4748: printf("Problem with file %s",optionfilegnuplot);
4749: }
4750: else{
4751: fprintf(ficgp,"\n# %s\n", version);
4752: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4753: fprintf(ficgp,"set missing 'NaNq'\n");
4754: }
4755: /* fclose(ficgp);*/
4756: /*--------- index.htm --------*/
4757:
4758: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4759: if(mle==-3)
4760: strcat(optionfilehtm,"-mort");
4761: strcat(optionfilehtm,".htm");
4762: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4763: printf("Problem with %s \n",optionfilehtm), exit(0);
4764: }
4765:
4766: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4767: strcat(optionfilehtmcov,"-cov.htm");
4768: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4769: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4770: }
4771: else{
4772: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4773: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4774: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4775: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4776: }
4777:
4778: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4779: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4780: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4781: \n\
4782: <hr size=\"2\" color=\"#EC5E5E\">\
4783: <ul><li><h4>Parameter files</h4>\n\
4784: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4785: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4786: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4787: - Date and time at start: %s</ul>\n",\
4788: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4789: fileres,fileres,\
4790: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4791: fflush(fichtm);
4792:
4793: strcpy(pathr,path);
4794: strcat(pathr,optionfilefiname);
4795: chdir(optionfilefiname); /* Move to directory named optionfile */
4796:
4797: /* Calculates basic frequencies. Computes observed prevalence at single age
4798: and prints on file fileres'p'. */
4799: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
4800:
4801: fprintf(fichtm,"\n");
4802: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4803: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4804: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4805: imx,agemin,agemax,jmin,jmax,jmean);
4806: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4807: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4808: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4809: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4810: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4811:
4812:
4813: /* For Powell, parameters are in a vector p[] starting at p[1]
4814: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4815: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4816:
4817: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4818: if (mle==-3){
4819: ximort=matrix(1,NDIM,1,NDIM);
4820: cens=ivector(1,n);
4821: ageexmed=vector(1,n);
4822: agecens=vector(1,n);
4823: dcwave=ivector(1,n);
4824:
4825: for (i=1; i<=imx; i++){
4826: dcwave[i]=-1;
4827: for (j=1; j<=lastpass; j++)
4828: if (s[j][i]>nlstate) {
4829: dcwave[i]=j;
4830: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4831: break;
4832: }
4833: }
4834:
4835: for (i=1; i<=imx; i++) {
4836: if (wav[i]>0){
4837: ageexmed[i]=agev[mw[1][i]][i];
4838: j=wav[i];agecens[i]=1.;
4839: if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
4840: cens[i]=1;
4841:
4842: if (ageexmed[i]<1) cens[i]=-1;
4843: if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
4844: }
4845: else cens[i]=-1;
4846: }
4847:
4848: for (i=1;i<=NDIM;i++) {
4849: for (j=1;j<=NDIM;j++)
4850: ximort[i][j]=(i == j ? 1.0 : 0.0);
4851: }
4852:
4853: p[1]=0.1; p[2]=0.1;
4854: /*printf("%lf %lf", p[1], p[2]);*/
4855:
4856:
4857: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4858: strcpy(filerespow,"pow-mort");
4859: strcat(filerespow,fileres);
4860: if((ficrespow=fopen(filerespow,"w"))==NULL) {
4861: printf("Problem with resultfile: %s\n", filerespow);
4862: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
4863: }
4864: fprintf(ficrespow,"# Powell\n# iter -2*LL");
4865: /* for (i=1;i<=nlstate;i++)
4866: for(j=1;j<=nlstate+ndeath;j++)
4867: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
4868: */
4869: fprintf(ficrespow,"\n");
4870:
4871: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
4872: fclose(ficrespow);
4873:
4874: hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
4875:
4876: for(i=1; i <=NDIM; i++)
4877: for(j=i+1;j<=NDIM;j++)
4878: matcov[i][j]=matcov[j][i];
4879:
4880: printf("\nCovariance matrix\n ");
4881: for(i=1; i <=NDIM; i++) {
4882: for(j=1;j<=NDIM;j++){
4883: printf("%f ",matcov[i][j]);
4884: }
4885: printf("\n ");
4886: }
4887:
4888: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
4889: for (i=1;i<=NDIM;i++)
4890: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
4891:
4892: lsurv=vector(1,AGESUP);
4893: lpop=vector(1,AGESUP);
4894: tpop=vector(1,AGESUP);
4895: lsurv[agegomp]=100000;
4896:
4897: for (k=agegomp;k<=AGESUP;k++) {
4898: agemortsup=k;
4899: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
4900: }
4901:
4902: for (k=agegomp;k<agemortsup;k++)
4903: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
4904:
4905: for (k=agegomp;k<agemortsup;k++){
4906: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
4907: sumlpop=sumlpop+lpop[k];
4908: }
4909:
4910: tpop[agegomp]=sumlpop;
4911: for (k=agegomp;k<(agemortsup-3);k++){
4912: /* tpop[k+1]=2;*/
4913: tpop[k+1]=tpop[k]-lpop[k];
4914: }
4915:
4916:
4917: printf("\nAge lx qx dx Lx Tx e(x)\n");
4918: for (k=agegomp;k<(agemortsup-2);k++)
4919: printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
4920:
4921:
4922: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
4923: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
4924:
4925: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
4926: stepm, weightopt,\
4927: model,imx,p,matcov,agemortsup);
4928:
4929: free_vector(lsurv,1,AGESUP);
4930: free_vector(lpop,1,AGESUP);
4931: free_vector(tpop,1,AGESUP);
4932: } /* Endof if mle==-3 */
4933:
4934: else{ /* For mle >=1 */
4935:
4936: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4937: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4938: for (k=1; k<=npar;k++)
4939: printf(" %d %8.5f",k,p[k]);
4940: printf("\n");
4941: globpr=1; /* to print the contributions */
4942: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
4943: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
4944: for (k=1; k<=npar;k++)
4945: printf(" %d %8.5f",k,p[k]);
4946: printf("\n");
4947: if(mle>=1){ /* Could be 1 or 2 */
4948: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
4949: }
4950:
4951: /*--------- results files --------------*/
4952: 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);
4953:
4954:
4955: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4956: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4957: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4958: for(i=1,jk=1; i <=nlstate; i++){
4959: for(k=1; k <=(nlstate+ndeath); k++){
4960: if (k != i) {
4961: printf("%d%d ",i,k);
4962: fprintf(ficlog,"%d%d ",i,k);
4963: fprintf(ficres,"%1d%1d ",i,k);
4964: for(j=1; j <=ncovmodel; j++){
4965: printf("%f ",p[jk]);
4966: fprintf(ficlog,"%f ",p[jk]);
4967: fprintf(ficres,"%f ",p[jk]);
4968: jk++;
4969: }
4970: printf("\n");
4971: fprintf(ficlog,"\n");
4972: fprintf(ficres,"\n");
4973: }
4974: }
4975: }
4976: if(mle!=0){
4977: /* Computing hessian and covariance matrix */
4978: ftolhess=ftol; /* Usually correct */
4979: hesscov(matcov, p, npar, delti, ftolhess, func);
4980: }
4981: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
4982: printf("# Scales (for hessian or gradient estimation)\n");
4983: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
4984: for(i=1,jk=1; i <=nlstate; i++){
4985: for(j=1; j <=nlstate+ndeath; j++){
4986: if (j!=i) {
4987: fprintf(ficres,"%1d%1d",i,j);
4988: printf("%1d%1d",i,j);
4989: fprintf(ficlog,"%1d%1d",i,j);
4990: for(k=1; k<=ncovmodel;k++){
4991: printf(" %.5e",delti[jk]);
4992: fprintf(ficlog," %.5e",delti[jk]);
4993: fprintf(ficres," %.5e",delti[jk]);
4994: jk++;
4995: }
4996: printf("\n");
4997: fprintf(ficlog,"\n");
4998: fprintf(ficres,"\n");
4999: }
5000: }
5001: }
5002:
5003: 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");
5004: if(mle>=1)
5005: 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");
5006: 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");
5007: /* # 121 Var(a12)\n\ */
5008: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5009: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5010: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5011: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5012: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5013: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5014: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5015:
5016:
5017: /* Just to have a covariance matrix which will be more understandable
5018: even is we still don't want to manage dictionary of variables
5019: */
5020: for(itimes=1;itimes<=2;itimes++){
5021: jj=0;
5022: for(i=1; i <=nlstate; i++){
5023: for(j=1; j <=nlstate+ndeath; j++){
5024: if(j==i) continue;
5025: for(k=1; k<=ncovmodel;k++){
5026: jj++;
5027: ca[0]= k+'a'-1;ca[1]='\0';
5028: if(itimes==1){
5029: if(mle>=1)
5030: printf("#%1d%1d%d",i,j,k);
5031: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5032: fprintf(ficres,"#%1d%1d%d",i,j,k);
5033: }else{
5034: if(mle>=1)
5035: printf("%1d%1d%d",i,j,k);
5036: fprintf(ficlog,"%1d%1d%d",i,j,k);
5037: fprintf(ficres,"%1d%1d%d",i,j,k);
5038: }
5039: ll=0;
5040: for(li=1;li <=nlstate; li++){
5041: for(lj=1;lj <=nlstate+ndeath; lj++){
5042: if(lj==li) continue;
5043: for(lk=1;lk<=ncovmodel;lk++){
5044: ll++;
5045: if(ll<=jj){
5046: cb[0]= lk +'a'-1;cb[1]='\0';
5047: if(ll<jj){
5048: if(itimes==1){
5049: if(mle>=1)
5050: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5051: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5052: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5053: }else{
5054: if(mle>=1)
5055: printf(" %.5e",matcov[jj][ll]);
5056: fprintf(ficlog," %.5e",matcov[jj][ll]);
5057: fprintf(ficres," %.5e",matcov[jj][ll]);
5058: }
5059: }else{
5060: if(itimes==1){
5061: if(mle>=1)
5062: printf(" Var(%s%1d%1d)",ca,i,j);
5063: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5064: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5065: }else{
5066: if(mle>=1)
5067: printf(" %.5e",matcov[jj][ll]);
5068: fprintf(ficlog," %.5e",matcov[jj][ll]);
5069: fprintf(ficres," %.5e",matcov[jj][ll]);
5070: }
5071: }
5072: }
5073: } /* end lk */
5074: } /* end lj */
5075: } /* end li */
5076: if(mle>=1)
5077: printf("\n");
5078: fprintf(ficlog,"\n");
5079: fprintf(ficres,"\n");
5080: numlinepar++;
5081: } /* end k*/
5082: } /*end j */
5083: } /* end i */
5084: } /* end itimes */
5085:
5086: fflush(ficlog);
5087: fflush(ficres);
5088:
5089: while((c=getc(ficpar))=='#' && c!= EOF){
5090: ungetc(c,ficpar);
5091: fgets(line, MAXLINE, ficpar);
5092: puts(line);
5093: fputs(line,ficparo);
5094: }
5095: ungetc(c,ficpar);
5096:
5097: estepm=0;
5098: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5099: if (estepm==0 || estepm < stepm) estepm=stepm;
5100: if (fage <= 2) {
5101: bage = ageminpar;
5102: fage = agemaxpar;
5103: }
5104:
5105: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5106: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5107: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5108:
5109: while((c=getc(ficpar))=='#' && c!= EOF){
5110: ungetc(c,ficpar);
5111: fgets(line, MAXLINE, ficpar);
5112: puts(line);
5113: fputs(line,ficparo);
5114: }
5115: ungetc(c,ficpar);
5116:
5117: 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);
5118: 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);
5119: 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);
5120: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5121: 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);
5122:
5123: while((c=getc(ficpar))=='#' && c!= EOF){
5124: ungetc(c,ficpar);
5125: fgets(line, MAXLINE, ficpar);
5126: puts(line);
5127: fputs(line,ficparo);
5128: }
5129: ungetc(c,ficpar);
5130:
5131:
5132: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5133: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5134:
5135: fscanf(ficpar,"pop_based=%d\n",&popbased);
5136: fprintf(ficparo,"pop_based=%d\n",popbased);
5137: fprintf(ficres,"pop_based=%d\n",popbased);
5138:
5139: while((c=getc(ficpar))=='#' && c!= EOF){
5140: ungetc(c,ficpar);
5141: fgets(line, MAXLINE, ficpar);
5142: puts(line);
5143: fputs(line,ficparo);
5144: }
5145: ungetc(c,ficpar);
5146:
5147: 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);
5148: 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);
5149: 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);
5150: 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);
5151: 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);
5152: /* day and month of proj2 are not used but only year anproj2.*/
5153:
5154:
5155:
5156: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5157: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5158:
5159: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5160: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5161:
5162: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5163: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5164: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5165:
5166: /*------------ free_vector -------------*/
5167: /* chdir(path); */
5168:
5169: free_ivector(wav,1,imx);
5170: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5171: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5172: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5173: free_lvector(num,1,n);
5174: free_vector(agedc,1,n);
5175: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5176: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5177: fclose(ficparo);
5178: fclose(ficres);
5179:
5180:
5181: /*--------------- Prevalence limit (stable prevalence) --------------*/
5182:
5183: strcpy(filerespl,"pl");
5184: strcat(filerespl,fileres);
5185: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5186: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5187: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5188: }
5189: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5190: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5191: fprintf(ficrespl, "#Local time at start: %s", strstart);
5192: fprintf(ficrespl,"#Stable prevalence \n");
5193: fprintf(ficrespl,"#Age ");
5194: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5195: fprintf(ficrespl,"\n");
5196:
5197: prlim=matrix(1,nlstate,1,nlstate);
5198:
5199: agebase=ageminpar;
5200: agelim=agemaxpar;
5201: ftolpl=1.e-10;
5202: i1=cptcoveff;
5203: if (cptcovn < 1){i1=1;}
5204:
5205: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5206: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5207: k=k+1;
5208: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5209: fprintf(ficrespl,"\n#******");
5210: printf("\n#******");
5211: fprintf(ficlog,"\n#******");
5212: for(j=1;j<=cptcoveff;j++) {
5213: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5214: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5215: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5216: }
5217: fprintf(ficrespl,"******\n");
5218: printf("******\n");
5219: fprintf(ficlog,"******\n");
5220:
5221: for (age=agebase; age<=agelim; age++){
5222: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5223: fprintf(ficrespl,"%.0f ",age );
5224: for(j=1;j<=cptcoveff;j++)
5225: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5226: for(i=1; i<=nlstate;i++)
5227: fprintf(ficrespl," %.5f", prlim[i][i]);
5228: fprintf(ficrespl,"\n");
5229: }
5230: }
5231: }
5232: fclose(ficrespl);
5233:
5234: /*------------- h Pij x at various ages ------------*/
5235:
5236: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5237: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5238: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5239: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5240: }
5241: printf("Computing pij: result on file '%s' \n", filerespij);
5242: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5243:
5244: stepsize=(int) (stepm+YEARM-1)/YEARM;
5245: /*if (stepm<=24) stepsize=2;*/
5246:
5247: agelim=AGESUP;
5248: hstepm=stepsize*YEARM; /* Every year of age */
5249: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5250:
5251: /* hstepm=1; aff par mois*/
5252: fprintf(ficrespij, "#Local time at start: %s", strstart);
5253: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5254: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5255: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5256: k=k+1;
5257: fprintf(ficrespij,"\n#****** ");
5258: for(j=1;j<=cptcoveff;j++)
5259: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5260: fprintf(ficrespij,"******\n");
5261:
5262: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5263: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5264: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5265:
5266: /* nhstepm=nhstepm*YEARM; aff par mois*/
5267:
5268: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5269: oldm=oldms;savm=savms;
5270: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5271: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5272: for(i=1; i<=nlstate;i++)
5273: for(j=1; j<=nlstate+ndeath;j++)
5274: fprintf(ficrespij," %1d-%1d",i,j);
5275: fprintf(ficrespij,"\n");
5276: for (h=0; h<=nhstepm; h++){
5277: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5278: for(i=1; i<=nlstate;i++)
5279: for(j=1; j<=nlstate+ndeath;j++)
5280: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5281: fprintf(ficrespij,"\n");
5282: }
5283: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5284: fprintf(ficrespij,"\n");
5285: }
5286: }
5287: }
5288:
5289: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5290:
5291: fclose(ficrespij);
5292:
5293: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5294: for(i=1;i<=AGESUP;i++)
5295: for(j=1;j<=NCOVMAX;j++)
5296: for(k=1;k<=NCOVMAX;k++)
5297: probs[i][j][k]=0.;
5298:
5299: /*---------- Forecasting ------------------*/
5300: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5301: if(prevfcast==1){
5302: /* if(stepm ==1){*/
5303: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5304: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5305: /* } */
5306: /* else{ */
5307: /* erreur=108; */
5308: /* 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); */
5309: /* 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); */
5310: /* } */
5311: }
5312:
5313:
5314: /*---------- Health expectancies and variances ------------*/
5315:
5316: strcpy(filerest,"t");
5317: strcat(filerest,fileres);
5318: if((ficrest=fopen(filerest,"w"))==NULL) {
5319: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5320: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5321: }
5322: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5323: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5324:
5325:
5326: strcpy(filerese,"e");
5327: strcat(filerese,fileres);
5328: if((ficreseij=fopen(filerese,"w"))==NULL) {
5329: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5330: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5331: }
5332: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5333: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5334:
5335: strcpy(fileresv,"v");
5336: strcat(fileresv,fileres);
5337: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5338: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5339: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5340: }
5341: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5342: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5343:
5344: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5345: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5346: /* 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",\
5347: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5348: */
5349:
5350: if (mobilav!=0) {
5351: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5352: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5353: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5354: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5355: }
5356: }
5357:
5358: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5359: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5360: k=k+1;
5361: fprintf(ficrest,"\n#****** ");
5362: for(j=1;j<=cptcoveff;j++)
5363: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5364: fprintf(ficrest,"******\n");
5365:
5366: fprintf(ficreseij,"\n#****** ");
5367: for(j=1;j<=cptcoveff;j++)
5368: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5369: fprintf(ficreseij,"******\n");
5370:
5371: fprintf(ficresvij,"\n#****** ");
5372: for(j=1;j<=cptcoveff;j++)
5373: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5374: fprintf(ficresvij,"******\n");
5375:
5376: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5377: oldm=oldms;savm=savms;
5378: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5379:
5380: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5381: oldm=oldms;savm=savms;
5382: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5383: if(popbased==1){
5384: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5385: }
5386:
5387: fprintf(ficrest, "#Local time at start: %s", strstart);
5388: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5389: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5390: fprintf(ficrest,"\n");
5391:
5392: epj=vector(1,nlstate+1);
5393: for(age=bage; age <=fage ;age++){
5394: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5395: if (popbased==1) {
5396: if(mobilav ==0){
5397: for(i=1; i<=nlstate;i++)
5398: prlim[i][i]=probs[(int)age][i][k];
5399: }else{ /* mobilav */
5400: for(i=1; i<=nlstate;i++)
5401: prlim[i][i]=mobaverage[(int)age][i][k];
5402: }
5403: }
5404:
5405: fprintf(ficrest," %4.0f",age);
5406: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5407: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5408: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5409: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5410: }
5411: epj[nlstate+1] +=epj[j];
5412: }
5413:
5414: for(i=1, vepp=0.;i <=nlstate;i++)
5415: for(j=1;j <=nlstate;j++)
5416: vepp += vareij[i][j][(int)age];
5417: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5418: for(j=1;j <=nlstate;j++){
5419: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5420: }
5421: fprintf(ficrest,"\n");
5422: }
5423: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5424: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5425: free_vector(epj,1,nlstate+1);
5426: }
5427: }
5428: free_vector(weight,1,n);
5429: free_imatrix(Tvard,1,15,1,2);
5430: free_imatrix(s,1,maxwav+1,1,n);
5431: free_matrix(anint,1,maxwav,1,n);
5432: free_matrix(mint,1,maxwav,1,n);
5433: free_ivector(cod,1,n);
5434: free_ivector(tab,1,NCOVMAX);
5435: fclose(ficreseij);
5436: fclose(ficresvij);
5437: fclose(ficrest);
5438: fclose(ficpar);
5439:
5440: /*------- Variance of stable prevalence------*/
5441:
5442: strcpy(fileresvpl,"vpl");
5443: strcat(fileresvpl,fileres);
5444: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5445: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5446: exit(0);
5447: }
5448: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5449:
5450: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5451: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5452: k=k+1;
5453: fprintf(ficresvpl,"\n#****** ");
5454: for(j=1;j<=cptcoveff;j++)
5455: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5456: fprintf(ficresvpl,"******\n");
5457:
5458: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5459: oldm=oldms;savm=savms;
5460: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5461: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5462: }
5463: }
5464:
5465: fclose(ficresvpl);
5466:
5467: /*---------- End : free ----------------*/
5468: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5469: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5470:
5471: } /* mle==-3 arrives here for freeing */
5472: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5473: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5474: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5475: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5476:
5477: free_matrix(covar,0,NCOVMAX,1,n);
5478: free_matrix(matcov,1,npar,1,npar);
5479: /*free_vector(delti,1,npar);*/
5480: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5481: free_matrix(agev,1,maxwav,1,imx);
5482: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5483:
5484: free_ivector(ncodemax,1,8);
5485: free_ivector(Tvar,1,15);
5486: free_ivector(Tprod,1,15);
5487: free_ivector(Tvaraff,1,15);
5488: free_ivector(Tage,1,15);
5489: free_ivector(Tcode,1,100);
5490:
5491:
5492: fflush(fichtm);
5493: fflush(ficgp);
5494:
5495:
5496: if((nberr >0) || (nbwarn>0)){
5497: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5498: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5499: }else{
5500: printf("End of Imach\n");
5501: fprintf(ficlog,"End of Imach\n");
5502: }
5503: printf("See log file on %s\n",filelog);
5504: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5505: (void) gettimeofday(&end_time,&tzp);
5506: tm = *localtime(&end_time.tv_sec);
5507: tmg = *gmtime(&end_time.tv_sec);
5508: strcpy(strtend,asctime(&tm));
5509: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5510: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5511: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5512:
5513: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5514: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5515: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5516: /* printf("Total time was %d uSec.\n", total_usecs);*/
5517: /* if(fileappend(fichtm,optionfilehtm)){ */
5518: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5519: fclose(fichtm);
5520: fclose(fichtmcov);
5521: fclose(ficgp);
5522: fclose(ficlog);
5523: /*------ End -----------*/
5524:
5525: chdir(path);
5526: strcpy(plotcmd,"\"");
5527: strcat(plotcmd,pathimach);
5528: strcat(plotcmd,GNUPLOTPROGRAM);
5529: strcat(plotcmd,"\"");
5530: strcat(plotcmd," ");
5531: strcat(plotcmd,optionfilegnuplot);
5532: printf("Starting graphs with: %s",plotcmd);fflush(stdout);
5533: if((outcmd=system(plotcmd)) != 0){
5534: printf(" Problem with gnuplot\n");
5535: }
5536: printf(" Wait...");
5537: while (z[0] != 'q') {
5538: /* chdir(path); */
5539: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5540: scanf("%s",z);
5541: /* if (z[0] == 'c') system("./imach"); */
5542: if (z[0] == 'e') {
5543: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5544: system(optionfilehtm);
5545: }
5546: else if (z[0] == 'g') system(plotcmd);
5547: else if (z[0] == 'q') exit(0);
5548: }
5549: end:
5550: while (z[0] != 'q') {
5551: printf("\nType q for exiting: ");
5552: scanf("%s",z);
5553: }
5554: }
5555:
5556:
5557:
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