1: /* $Id: imach.c,v 1.112 2006/01/30 09:55:26 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.112 2006/01/30 09:55:26 brouard
5: (Module): Back to gnuplot.exe instead of wgnuplot.exe
6:
7: Revision 1.111 2006/01/25 20:38:18 brouard
8: (Module): Lots of cleaning and bugs added (Gompertz)
9: (Module): Comments can be added in data file. Missing date values
10: can be a simple dot '.'.
11:
12: Revision 1.110 2006/01/25 00:51:50 brouard
13: (Module): Lots of cleaning and bugs added (Gompertz)
14:
15: Revision 1.109 2006/01/24 19:37:15 brouard
16: (Module): Comments (lines starting with a #) are allowed in data.
17:
18: Revision 1.108 2006/01/19 18:05:42 lievre
19: Gnuplot problem appeared...
20: To be fixed
21:
22: Revision 1.107 2006/01/19 16:20:37 brouard
23: Test existence of gnuplot in imach path
24:
25: Revision 1.106 2006/01/19 13:24:36 brouard
26: Some cleaning and links added in html output
27:
28: Revision 1.105 2006/01/05 20:23:19 lievre
29: *** empty log message ***
30:
31: Revision 1.104 2005/09/30 16:11:43 lievre
32: (Module): sump fixed, loop imx fixed, and simplifications.
33: (Module): If the status is missing at the last wave but we know
34: that the person is alive, then we can code his/her status as -2
35: (instead of missing=-1 in earlier versions) and his/her
36: contributions to the likelihood is 1 - Prob of dying from last
37: health status (= 1-p13= p11+p12 in the easiest case of somebody in
38: the healthy state at last known wave). Version is 0.98
39:
40: Revision 1.103 2005/09/30 15:54:49 lievre
41: (Module): sump fixed, loop imx fixed, and simplifications.
42:
43: Revision 1.102 2004/09/15 17:31:30 brouard
44: Add the possibility to read data file including tab characters.
45:
46: Revision 1.101 2004/09/15 10:38:38 brouard
47: Fix on curr_time
48:
49: Revision 1.100 2004/07/12 18:29:06 brouard
50: Add version for Mac OS X. Just define UNIX in Makefile
51:
52: Revision 1.99 2004/06/05 08:57:40 brouard
53: *** empty log message ***
54:
55: Revision 1.98 2004/05/16 15:05:56 brouard
56: New version 0.97 . First attempt to estimate force of mortality
57: directly from the data i.e. without the need of knowing the health
58: state at each age, but using a Gompertz model: log u =a + b*age .
59: This is the basic analysis of mortality and should be done before any
60: other analysis, in order to test if the mortality estimated from the
61: cross-longitudinal survey is different from the mortality estimated
62: from other sources like vital statistic data.
63:
64: The same imach parameter file can be used but the option for mle should be -3.
65:
66: Agnès, who wrote this part of the code, tried to keep most of the
67: former routines in order to include the new code within the former code.
68:
69: The output is very simple: only an estimate of the intercept and of
70: the slope with 95% confident intervals.
71:
72: Current limitations:
73: A) Even if you enter covariates, i.e. with the
74: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
75: B) There is no computation of Life Expectancy nor Life Table.
76:
77: Revision 1.97 2004/02/20 13:25:42 lievre
78: Version 0.96d. Population forecasting command line is (temporarily)
79: suppressed.
80:
81: Revision 1.96 2003/07/15 15:38:55 brouard
82: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
83: rewritten within the same printf. Workaround: many printfs.
84:
85: Revision 1.95 2003/07/08 07:54:34 brouard
86: * imach.c (Repository):
87: (Repository): Using imachwizard code to output a more meaningful covariance
88: matrix (cov(a12,c31) instead of numbers.
89:
90: Revision 1.94 2003/06/27 13:00:02 brouard
91: Just cleaning
92:
93: Revision 1.93 2003/06/25 16:33:55 brouard
94: (Module): On windows (cygwin) function asctime_r doesn't
95: exist so I changed back to asctime which exists.
96: (Module): Version 0.96b
97:
98: Revision 1.92 2003/06/25 16:30:45 brouard
99: (Module): On windows (cygwin) function asctime_r doesn't
100: exist so I changed back to asctime which exists.
101:
102: Revision 1.91 2003/06/25 15:30:29 brouard
103: * imach.c (Repository): Duplicated warning errors corrected.
104: (Repository): Elapsed time after each iteration is now output. It
105: helps to forecast when convergence will be reached. Elapsed time
106: is stamped in powell. We created a new html file for the graphs
107: concerning matrix of covariance. It has extension -cov.htm.
108:
109: Revision 1.90 2003/06/24 12:34:15 brouard
110: (Module): Some bugs corrected for windows. Also, when
111: mle=-1 a template is output in file "or"mypar.txt with the design
112: of the covariance matrix to be input.
113:
114: Revision 1.89 2003/06/24 12:30:52 brouard
115: (Module): Some bugs corrected for windows. Also, when
116: mle=-1 a template is output in file "or"mypar.txt with the design
117: of the covariance matrix to be input.
118:
119: Revision 1.88 2003/06/23 17:54:56 brouard
120: * 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.
121:
122: Revision 1.87 2003/06/18 12:26:01 brouard
123: Version 0.96
124:
125: Revision 1.86 2003/06/17 20:04:08 brouard
126: (Module): Change position of html and gnuplot routines and added
127: routine fileappend.
128:
129: Revision 1.85 2003/06/17 13:12:43 brouard
130: * imach.c (Repository): Check when date of death was earlier that
131: current date of interview. It may happen when the death was just
132: prior to the death. In this case, dh was negative and likelihood
133: was wrong (infinity). We still send an "Error" but patch by
134: assuming that the date of death was just one stepm after the
135: interview.
136: (Repository): Because some people have very long ID (first column)
137: we changed int to long in num[] and we added a new lvector for
138: memory allocation. But we also truncated to 8 characters (left
139: truncation)
140: (Repository): No more line truncation errors.
141:
142: Revision 1.84 2003/06/13 21:44:43 brouard
143: * imach.c (Repository): Replace "freqsummary" at a correct
144: place. It differs from routine "prevalence" which may be called
145: many times. Probs is memory consuming and must be used with
146: parcimony.
147: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
148:
149: Revision 1.83 2003/06/10 13:39:11 lievre
150: *** empty log message ***
151:
152: Revision 1.82 2003/06/05 15:57:20 brouard
153: Add log in imach.c and fullversion number is now printed.
154:
155: */
156: /*
157: Interpolated Markov Chain
158:
159: Short summary of the programme:
160:
161: This program computes Healthy Life Expectancies from
162: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
163: first survey ("cross") where individuals from different ages are
164: interviewed on their health status or degree of disability (in the
165: case of a health survey which is our main interest) -2- at least a
166: second wave of interviews ("longitudinal") which measure each change
167: (if any) in individual health status. Health expectancies are
168: computed from the time spent in each health state according to a
169: model. More health states you consider, more time is necessary to reach the
170: Maximum Likelihood of the parameters involved in the model. The
171: simplest model is the multinomial logistic model where pij is the
172: probability to be observed in state j at the second wave
173: conditional to be observed in state i at the first wave. Therefore
174: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
175: 'age' is age and 'sex' is a covariate. If you want to have a more
176: complex model than "constant and age", you should modify the program
177: where the markup *Covariates have to be included here again* invites
178: you to do it. More covariates you add, slower the
179: convergence.
180:
181: The advantage of this computer programme, compared to a simple
182: multinomial logistic model, is clear when the delay between waves is not
183: identical for each individual. Also, if a individual missed an
184: intermediate interview, the information is lost, but taken into
185: account using an interpolation or extrapolation.
186:
187: hPijx is the probability to be observed in state i at age x+h
188: conditional to the observed state i at age x. The delay 'h' can be
189: split into an exact number (nh*stepm) of unobserved intermediate
190: states. This elementary transition (by month, quarter,
191: semester or year) is modelled as a multinomial logistic. The hPx
192: matrix is simply the matrix product of nh*stepm elementary matrices
193: and the contribution of each individual to the likelihood is simply
194: hPijx.
195:
196: Also this programme outputs the covariance matrix of the parameters but also
197: of the life expectancies. It also computes the stable prevalence.
198:
199: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
200: Institut national d'études démographiques, Paris.
201: This software have been partly granted by Euro-REVES, a concerted action
202: from the European Union.
203: It is copyrighted identically to a GNU software product, ie programme and
204: software can be distributed freely for non commercial use. Latest version
205: can be accessed at http://euroreves.ined.fr/imach .
206:
207: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
208: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
209:
210: **********************************************************************/
211: /*
212: main
213: read parameterfile
214: read datafile
215: concatwav
216: freqsummary
217: if (mle >= 1)
218: mlikeli
219: print results files
220: if mle==1
221: computes hessian
222: read end of parameter file: agemin, agemax, bage, fage, estepm
223: begin-prev-date,...
224: open gnuplot file
225: open html file
226: stable prevalence
227: for age prevalim()
228: h Pij x
229: variance of p varprob
230: forecasting if prevfcast==1 prevforecast call prevalence()
231: health expectancies
232: Variance-covariance of DFLE
233: prevalence()
234: movingaverage()
235: varevsij()
236: if popbased==1 varevsij(,popbased)
237: total life expectancies
238: Variance of stable prevalence
239: end
240: */
241:
242:
243:
244:
245: #include <math.h>
246: #include <stdio.h>
247: #include <stdlib.h>
248: #include <string.h>
249: #include <unistd.h>
250:
251: #include <limits.h>
252: #include <sys/types.h>
253: #include <sys/stat.h>
254: #include <errno.h>
255: extern int errno;
256:
257: /* #include <sys/time.h> */
258: #include <time.h>
259: #include "timeval.h"
260:
261: /* #include <libintl.h> */
262: /* #define _(String) gettext (String) */
263:
264: #define MAXLINE 256
265:
266: #define GNUPLOTPROGRAM "gnuplot"
267: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
268: #define FILENAMELENGTH 132
269:
270: #define GLOCK_ERROR_NOPATH -1 /* empty path */
271: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
272:
273: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
274: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
275:
276: #define NINTERVMAX 8
277: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
278: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
279: #define NCOVMAX 8 /* Maximum number of covariates */
280: #define MAXN 20000
281: #define YEARM 12. /* Number of months per year */
282: #define AGESUP 130
283: #define AGEBASE 40
284: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
285: #ifdef UNIX
286: #define DIRSEPARATOR '/'
287: #define CHARSEPARATOR "/"
288: #define ODIRSEPARATOR '\\'
289: #else
290: #define DIRSEPARATOR '\\'
291: #define CHARSEPARATOR "\\"
292: #define ODIRSEPARATOR '/'
293: #endif
294:
295: /* $Id: imach.c,v 1.112 2006/01/30 09:55:26 brouard Exp $ */
296: /* $State: Exp $ */
297:
298: char version[]="Imach version 0.98b, January 2006, INED-EUROREVES ";
299: char fullversion[]="$Revision: 1.112 $ $Date: 2006/01/30 09:55:26 $";
300: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
301: int nvar;
302: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
303: int npar=NPARMAX;
304: int nlstate=2; /* Number of live states */
305: int ndeath=1; /* Number of dead states */
306: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
307: int popbased=0;
308:
309: int *wav; /* Number of waves for this individuual 0 is possible */
310: int maxwav; /* Maxim number of waves */
311: int jmin, jmax; /* min, max spacing between 2 waves */
312: int ijmin, ijmax; /* Individuals having jmin and jmax */
313: int gipmx, gsw; /* Global variables on the number of contributions
314: to the likelihood and the sum of weights (done by funcone)*/
315: int mle, weightopt;
316: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
317: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
318: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
319: * wave mi and wave mi+1 is not an exact multiple of stepm. */
320: double jmean; /* Mean space between 2 waves */
321: double **oldm, **newm, **savm; /* Working pointers to matrices */
322: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
323: FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
324: FILE *ficlog, *ficrespow;
325: int globpr; /* Global variable for printing or not */
326: double fretone; /* Only one call to likelihood */
327: long ipmx; /* Number of contributions */
328: double sw; /* Sum of weights */
329: char filerespow[FILENAMELENGTH];
330: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
331: FILE *ficresilk;
332: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
333: FILE *ficresprobmorprev;
334: FILE *fichtm, *fichtmcov; /* Html File */
335: FILE *ficreseij;
336: char filerese[FILENAMELENGTH];
337: FILE *ficresvij;
338: char fileresv[FILENAMELENGTH];
339: FILE *ficresvpl;
340: char fileresvpl[FILENAMELENGTH];
341: char title[MAXLINE];
342: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
343: char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
344: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
345: char command[FILENAMELENGTH];
346: int outcmd=0;
347:
348: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
349:
350: char filelog[FILENAMELENGTH]; /* Log file */
351: char filerest[FILENAMELENGTH];
352: char fileregp[FILENAMELENGTH];
353: char popfile[FILENAMELENGTH];
354:
355: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
356:
357: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
358: struct timezone tzp;
359: extern int gettimeofday();
360: struct tm tmg, tm, tmf, *gmtime(), *localtime();
361: long time_value;
362: extern long time();
363: char strcurr[80], strfor[80];
364:
365: char *endptr;
366: long lval;
367:
368: #define NR_END 1
369: #define FREE_ARG char*
370: #define FTOL 1.0e-10
371:
372: #define NRANSI
373: #define ITMAX 200
374:
375: #define TOL 2.0e-4
376:
377: #define CGOLD 0.3819660
378: #define ZEPS 1.0e-10
379: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
380:
381: #define GOLD 1.618034
382: #define GLIMIT 100.0
383: #define TINY 1.0e-20
384:
385: static double maxarg1,maxarg2;
386: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
387: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
388:
389: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
390: #define rint(a) floor(a+0.5)
391:
392: static double sqrarg;
393: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
394: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
395: int agegomp= AGEGOMP;
396:
397: int imx;
398: int stepm=1;
399: /* Stepm, step in month: minimum step interpolation*/
400:
401: int estepm;
402: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
403:
404: int m,nb;
405: long *num;
406: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
407: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
408: double **pmmij, ***probs;
409: double *ageexmed,*agecens;
410: double dateintmean=0;
411:
412: double *weight;
413: int **s; /* Status */
414: double *agedc, **covar, idx;
415: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
416: double *lsurv, *lpop, *tpop;
417:
418: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
419: double ftolhess; /* Tolerance for computing hessian */
420:
421: /**************** split *************************/
422: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
423: {
424: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
425: the name of the file (name), its extension only (ext) and its first part of the name (finame)
426: */
427: char *ss; /* pointer */
428: int l1, l2; /* length counters */
429:
430: l1 = strlen(path ); /* length of path */
431: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
432: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
433: if ( ss == NULL ) { /* no directory, so determine current directory */
434: strcpy( name, path ); /* we got the fullname name because no directory */
435: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
436: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
437: /* get current working directory */
438: /* extern char* getcwd ( char *buf , int len);*/
439: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
440: return( GLOCK_ERROR_GETCWD );
441: }
442: /* got dirc from getcwd*/
443: printf(" DIRC = %s \n",dirc);
444: } else { /* strip direcotry from path */
445: ss++; /* after this, the filename */
446: l2 = strlen( ss ); /* length of filename */
447: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
448: strcpy( name, ss ); /* save file name */
449: strncpy( dirc, path, l1 - l2 ); /* now the directory */
450: dirc[l1-l2] = 0; /* add zero */
451: printf(" DIRC2 = %s \n",dirc);
452: }
453: /* We add a separator at the end of dirc if not exists */
454: l1 = strlen( dirc ); /* length of directory */
455: if( dirc[l1-1] != DIRSEPARATOR ){
456: dirc[l1] = DIRSEPARATOR;
457: dirc[l1+1] = 0;
458: printf(" DIRC3 = %s \n",dirc);
459: }
460: ss = strrchr( name, '.' ); /* find last / */
461: if (ss >0){
462: ss++;
463: strcpy(ext,ss); /* save extension */
464: l1= strlen( name);
465: l2= strlen(ss)+1;
466: strncpy( finame, name, l1-l2);
467: finame[l1-l2]= 0;
468: }
469:
470: return( 0 ); /* we're done */
471: }
472:
473:
474: /******************************************/
475:
476: void replace_back_to_slash(char *s, char*t)
477: {
478: int i;
479: int lg=0;
480: i=0;
481: lg=strlen(t);
482: for(i=0; i<= lg; i++) {
483: (s[i] = t[i]);
484: if (t[i]== '\\') s[i]='/';
485: }
486: }
487:
488: int nbocc(char *s, char occ)
489: {
490: int i,j=0;
491: int lg=20;
492: i=0;
493: lg=strlen(s);
494: for(i=0; i<= lg; i++) {
495: if (s[i] == occ ) j++;
496: }
497: return j;
498: }
499:
500: void cutv(char *u,char *v, char*t, char occ)
501: {
502: /* cuts string t into u and v where u ends before first occurence of char 'occ'
503: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
504: gives u="abcedf" and v="ghi2j" */
505: int i,lg,j,p=0;
506: i=0;
507: for(j=0; j<=strlen(t)-1; j++) {
508: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
509: }
510:
511: lg=strlen(t);
512: for(j=0; j<p; j++) {
513: (u[j] = t[j]);
514: }
515: u[p]='\0';
516:
517: for(j=0; j<= lg; j++) {
518: if (j>=(p+1))(v[j-p-1] = t[j]);
519: }
520: }
521:
522: /********************** nrerror ********************/
523:
524: void nrerror(char error_text[])
525: {
526: fprintf(stderr,"ERREUR ...\n");
527: fprintf(stderr,"%s\n",error_text);
528: exit(EXIT_FAILURE);
529: }
530: /*********************** vector *******************/
531: double *vector(int nl, int nh)
532: {
533: double *v;
534: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
535: if (!v) nrerror("allocation failure in vector");
536: return v-nl+NR_END;
537: }
538:
539: /************************ free vector ******************/
540: void free_vector(double*v, int nl, int nh)
541: {
542: free((FREE_ARG)(v+nl-NR_END));
543: }
544:
545: /************************ivector *******************************/
546: int *ivector(long nl,long nh)
547: {
548: int *v;
549: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
550: if (!v) nrerror("allocation failure in ivector");
551: return v-nl+NR_END;
552: }
553:
554: /******************free ivector **************************/
555: void free_ivector(int *v, long nl, long nh)
556: {
557: free((FREE_ARG)(v+nl-NR_END));
558: }
559:
560: /************************lvector *******************************/
561: long *lvector(long nl,long nh)
562: {
563: long *v;
564: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
565: if (!v) nrerror("allocation failure in ivector");
566: return v-nl+NR_END;
567: }
568:
569: /******************free lvector **************************/
570: void free_lvector(long *v, long nl, long nh)
571: {
572: free((FREE_ARG)(v+nl-NR_END));
573: }
574:
575: /******************* imatrix *******************************/
576: int **imatrix(long nrl, long nrh, long ncl, long nch)
577: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
578: {
579: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
580: int **m;
581:
582: /* allocate pointers to rows */
583: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
584: if (!m) nrerror("allocation failure 1 in matrix()");
585: m += NR_END;
586: m -= nrl;
587:
588:
589: /* allocate rows and set pointers to them */
590: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
591: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
592: m[nrl] += NR_END;
593: m[nrl] -= ncl;
594:
595: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
596:
597: /* return pointer to array of pointers to rows */
598: return m;
599: }
600:
601: /****************** free_imatrix *************************/
602: void free_imatrix(m,nrl,nrh,ncl,nch)
603: int **m;
604: long nch,ncl,nrh,nrl;
605: /* free an int matrix allocated by imatrix() */
606: {
607: free((FREE_ARG) (m[nrl]+ncl-NR_END));
608: free((FREE_ARG) (m+nrl-NR_END));
609: }
610:
611: /******************* matrix *******************************/
612: double **matrix(long nrl, long nrh, long ncl, long nch)
613: {
614: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
615: double **m;
616:
617: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
618: if (!m) nrerror("allocation failure 1 in matrix()");
619: m += NR_END;
620: m -= nrl;
621:
622: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
623: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
624: m[nrl] += NR_END;
625: m[nrl] -= ncl;
626:
627: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
628: return m;
629: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
630: */
631: }
632:
633: /*************************free matrix ************************/
634: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
635: {
636: free((FREE_ARG)(m[nrl]+ncl-NR_END));
637: free((FREE_ARG)(m+nrl-NR_END));
638: }
639:
640: /******************* ma3x *******************************/
641: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
642: {
643: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
644: double ***m;
645:
646: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
647: if (!m) nrerror("allocation failure 1 in matrix()");
648: m += NR_END;
649: m -= nrl;
650:
651: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
652: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
653: m[nrl] += NR_END;
654: m[nrl] -= ncl;
655:
656: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
657:
658: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
659: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
660: m[nrl][ncl] += NR_END;
661: m[nrl][ncl] -= nll;
662: for (j=ncl+1; j<=nch; j++)
663: m[nrl][j]=m[nrl][j-1]+nlay;
664:
665: for (i=nrl+1; i<=nrh; i++) {
666: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
667: for (j=ncl+1; j<=nch; j++)
668: m[i][j]=m[i][j-1]+nlay;
669: }
670: return m;
671: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
672: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
673: */
674: }
675:
676: /*************************free ma3x ************************/
677: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
678: {
679: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
680: free((FREE_ARG)(m[nrl]+ncl-NR_END));
681: free((FREE_ARG)(m+nrl-NR_END));
682: }
683:
684: /*************** function subdirf ***********/
685: char *subdirf(char fileres[])
686: {
687: /* Caution optionfilefiname is hidden */
688: strcpy(tmpout,optionfilefiname);
689: strcat(tmpout,"/"); /* Add to the right */
690: strcat(tmpout,fileres);
691: return tmpout;
692: }
693:
694: /*************** function subdirf2 ***********/
695: char *subdirf2(char fileres[], char *preop)
696: {
697:
698: /* Caution optionfilefiname is hidden */
699: strcpy(tmpout,optionfilefiname);
700: strcat(tmpout,"/");
701: strcat(tmpout,preop);
702: strcat(tmpout,fileres);
703: return tmpout;
704: }
705:
706: /*************** function subdirf3 ***********/
707: char *subdirf3(char fileres[], char *preop, char *preop2)
708: {
709:
710: /* Caution optionfilefiname is hidden */
711: strcpy(tmpout,optionfilefiname);
712: strcat(tmpout,"/");
713: strcat(tmpout,preop);
714: strcat(tmpout,preop2);
715: strcat(tmpout,fileres);
716: return tmpout;
717: }
718:
719: /***************** f1dim *************************/
720: extern int ncom;
721: extern double *pcom,*xicom;
722: extern double (*nrfunc)(double []);
723:
724: double f1dim(double x)
725: {
726: int j;
727: double f;
728: double *xt;
729:
730: xt=vector(1,ncom);
731: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
732: f=(*nrfunc)(xt);
733: free_vector(xt,1,ncom);
734: return f;
735: }
736:
737: /*****************brent *************************/
738: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
739: {
740: int iter;
741: double a,b,d,etemp;
742: double fu,fv,fw,fx;
743: double ftemp;
744: double p,q,r,tol1,tol2,u,v,w,x,xm;
745: double e=0.0;
746:
747: a=(ax < cx ? ax : cx);
748: b=(ax > cx ? ax : cx);
749: x=w=v=bx;
750: fw=fv=fx=(*f)(x);
751: for (iter=1;iter<=ITMAX;iter++) {
752: xm=0.5*(a+b);
753: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
754: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
755: printf(".");fflush(stdout);
756: fprintf(ficlog,".");fflush(ficlog);
757: #ifdef DEBUG
758: 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);
759: 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);
760: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
761: #endif
762: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
763: *xmin=x;
764: return fx;
765: }
766: ftemp=fu;
767: if (fabs(e) > tol1) {
768: r=(x-w)*(fx-fv);
769: q=(x-v)*(fx-fw);
770: p=(x-v)*q-(x-w)*r;
771: q=2.0*(q-r);
772: if (q > 0.0) p = -p;
773: q=fabs(q);
774: etemp=e;
775: e=d;
776: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
777: d=CGOLD*(e=(x >= xm ? a-x : b-x));
778: else {
779: d=p/q;
780: u=x+d;
781: if (u-a < tol2 || b-u < tol2)
782: d=SIGN(tol1,xm-x);
783: }
784: } else {
785: d=CGOLD*(e=(x >= xm ? a-x : b-x));
786: }
787: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
788: fu=(*f)(u);
789: if (fu <= fx) {
790: if (u >= x) a=x; else b=x;
791: SHFT(v,w,x,u)
792: SHFT(fv,fw,fx,fu)
793: } else {
794: if (u < x) a=u; else b=u;
795: if (fu <= fw || w == x) {
796: v=w;
797: w=u;
798: fv=fw;
799: fw=fu;
800: } else if (fu <= fv || v == x || v == w) {
801: v=u;
802: fv=fu;
803: }
804: }
805: }
806: nrerror("Too many iterations in brent");
807: *xmin=x;
808: return fx;
809: }
810:
811: /****************** mnbrak ***********************/
812:
813: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
814: double (*func)(double))
815: {
816: double ulim,u,r,q, dum;
817: double fu;
818:
819: *fa=(*func)(*ax);
820: *fb=(*func)(*bx);
821: if (*fb > *fa) {
822: SHFT(dum,*ax,*bx,dum)
823: SHFT(dum,*fb,*fa,dum)
824: }
825: *cx=(*bx)+GOLD*(*bx-*ax);
826: *fc=(*func)(*cx);
827: while (*fb > *fc) {
828: r=(*bx-*ax)*(*fb-*fc);
829: q=(*bx-*cx)*(*fb-*fa);
830: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
831: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
832: ulim=(*bx)+GLIMIT*(*cx-*bx);
833: if ((*bx-u)*(u-*cx) > 0.0) {
834: fu=(*func)(u);
835: } else if ((*cx-u)*(u-ulim) > 0.0) {
836: fu=(*func)(u);
837: if (fu < *fc) {
838: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
839: SHFT(*fb,*fc,fu,(*func)(u))
840: }
841: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
842: u=ulim;
843: fu=(*func)(u);
844: } else {
845: u=(*cx)+GOLD*(*cx-*bx);
846: fu=(*func)(u);
847: }
848: SHFT(*ax,*bx,*cx,u)
849: SHFT(*fa,*fb,*fc,fu)
850: }
851: }
852:
853: /*************** linmin ************************/
854:
855: int ncom;
856: double *pcom,*xicom;
857: double (*nrfunc)(double []);
858:
859: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
860: {
861: double brent(double ax, double bx, double cx,
862: double (*f)(double), double tol, double *xmin);
863: double f1dim(double x);
864: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
865: double *fc, double (*func)(double));
866: int j;
867: double xx,xmin,bx,ax;
868: double fx,fb,fa;
869:
870: ncom=n;
871: pcom=vector(1,n);
872: xicom=vector(1,n);
873: nrfunc=func;
874: for (j=1;j<=n;j++) {
875: pcom[j]=p[j];
876: xicom[j]=xi[j];
877: }
878: ax=0.0;
879: xx=1.0;
880: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
881: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
882: #ifdef DEBUG
883: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
884: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
885: #endif
886: for (j=1;j<=n;j++) {
887: xi[j] *= xmin;
888: p[j] += xi[j];
889: }
890: free_vector(xicom,1,n);
891: free_vector(pcom,1,n);
892: }
893:
894: char *asc_diff_time(long time_sec, char ascdiff[])
895: {
896: long sec_left, days, hours, minutes;
897: days = (time_sec) / (60*60*24);
898: sec_left = (time_sec) % (60*60*24);
899: hours = (sec_left) / (60*60) ;
900: sec_left = (sec_left) %(60*60);
901: minutes = (sec_left) /60;
902: sec_left = (sec_left) % (60);
903: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
904: return ascdiff;
905: }
906:
907: /*************** powell ************************/
908: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
909: double (*func)(double []))
910: {
911: void linmin(double p[], double xi[], int n, double *fret,
912: double (*func)(double []));
913: int i,ibig,j;
914: double del,t,*pt,*ptt,*xit;
915: double fp,fptt;
916: double *xits;
917: int niterf, itmp;
918:
919: pt=vector(1,n);
920: ptt=vector(1,n);
921: xit=vector(1,n);
922: xits=vector(1,n);
923: *fret=(*func)(p);
924: for (j=1;j<=n;j++) pt[j]=p[j];
925: for (*iter=1;;++(*iter)) {
926: fp=(*fret);
927: ibig=0;
928: del=0.0;
929: last_time=curr_time;
930: (void) gettimeofday(&curr_time,&tzp);
931: 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);
932: /* 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);
933: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
934: */
935: for (i=1;i<=n;i++) {
936: printf(" %d %.12f",i, p[i]);
937: fprintf(ficlog," %d %.12lf",i, p[i]);
938: fprintf(ficrespow," %.12lf", p[i]);
939: }
940: printf("\n");
941: fprintf(ficlog,"\n");
942: fprintf(ficrespow,"\n");fflush(ficrespow);
943: if(*iter <=3){
944: tm = *localtime(&curr_time.tv_sec);
945: strcpy(strcurr,asctime(&tm));
946: /* asctime_r(&tm,strcurr); */
947: forecast_time=curr_time;
948: itmp = strlen(strcurr);
949: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
950: strcurr[itmp-1]='\0';
951: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
952: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
953: for(niterf=10;niterf<=30;niterf+=10){
954: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
955: tmf = *localtime(&forecast_time.tv_sec);
956: /* asctime_r(&tmf,strfor); */
957: strcpy(strfor,asctime(&tmf));
958: itmp = strlen(strfor);
959: if(strfor[itmp-1]=='\n')
960: strfor[itmp-1]='\0';
961: 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);
962: 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);
963: }
964: }
965: for (i=1;i<=n;i++) {
966: for (j=1;j<=n;j++) xit[j]=xi[j][i];
967: fptt=(*fret);
968: #ifdef DEBUG
969: printf("fret=%lf \n",*fret);
970: fprintf(ficlog,"fret=%lf \n",*fret);
971: #endif
972: printf("%d",i);fflush(stdout);
973: fprintf(ficlog,"%d",i);fflush(ficlog);
974: linmin(p,xit,n,fret,func);
975: if (fabs(fptt-(*fret)) > del) {
976: del=fabs(fptt-(*fret));
977: ibig=i;
978: }
979: #ifdef DEBUG
980: printf("%d %.12e",i,(*fret));
981: fprintf(ficlog,"%d %.12e",i,(*fret));
982: for (j=1;j<=n;j++) {
983: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
984: printf(" x(%d)=%.12e",j,xit[j]);
985: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
986: }
987: for(j=1;j<=n;j++) {
988: printf(" p=%.12e",p[j]);
989: fprintf(ficlog," p=%.12e",p[j]);
990: }
991: printf("\n");
992: fprintf(ficlog,"\n");
993: #endif
994: }
995: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
996: #ifdef DEBUG
997: int k[2],l;
998: k[0]=1;
999: k[1]=-1;
1000: printf("Max: %.12e",(*func)(p));
1001: fprintf(ficlog,"Max: %.12e",(*func)(p));
1002: for (j=1;j<=n;j++) {
1003: printf(" %.12e",p[j]);
1004: fprintf(ficlog," %.12e",p[j]);
1005: }
1006: printf("\n");
1007: fprintf(ficlog,"\n");
1008: for(l=0;l<=1;l++) {
1009: for (j=1;j<=n;j++) {
1010: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1011: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1012: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1013: }
1014: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1015: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1016: }
1017: #endif
1018:
1019:
1020: free_vector(xit,1,n);
1021: free_vector(xits,1,n);
1022: free_vector(ptt,1,n);
1023: free_vector(pt,1,n);
1024: return;
1025: }
1026: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1027: for (j=1;j<=n;j++) {
1028: ptt[j]=2.0*p[j]-pt[j];
1029: xit[j]=p[j]-pt[j];
1030: pt[j]=p[j];
1031: }
1032: fptt=(*func)(ptt);
1033: if (fptt < fp) {
1034: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1035: if (t < 0.0) {
1036: linmin(p,xit,n,fret,func);
1037: for (j=1;j<=n;j++) {
1038: xi[j][ibig]=xi[j][n];
1039: xi[j][n]=xit[j];
1040: }
1041: #ifdef DEBUG
1042: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1043: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1044: for(j=1;j<=n;j++){
1045: printf(" %.12e",xit[j]);
1046: fprintf(ficlog," %.12e",xit[j]);
1047: }
1048: printf("\n");
1049: fprintf(ficlog,"\n");
1050: #endif
1051: }
1052: }
1053: }
1054: }
1055:
1056: /**** Prevalence limit (stable prevalence) ****************/
1057:
1058: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1059: {
1060: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1061: matrix by transitions matrix until convergence is reached */
1062:
1063: int i, ii,j,k;
1064: double min, max, maxmin, maxmax,sumnew=0.;
1065: double **matprod2();
1066: double **out, cov[NCOVMAX], **pmij();
1067: double **newm;
1068: double agefin, delaymax=50 ; /* Max number of years to converge */
1069:
1070: for (ii=1;ii<=nlstate+ndeath;ii++)
1071: for (j=1;j<=nlstate+ndeath;j++){
1072: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1073: }
1074:
1075: cov[1]=1.;
1076:
1077: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1078: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1079: newm=savm;
1080: /* Covariates have to be included here again */
1081: cov[2]=agefin;
1082:
1083: for (k=1; k<=cptcovn;k++) {
1084: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1085: /* 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]]);*/
1086: }
1087: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1088: for (k=1; k<=cptcovprod;k++)
1089: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1090:
1091: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1092: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1093: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1094: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1095:
1096: savm=oldm;
1097: oldm=newm;
1098: maxmax=0.;
1099: for(j=1;j<=nlstate;j++){
1100: min=1.;
1101: max=0.;
1102: for(i=1; i<=nlstate; i++) {
1103: sumnew=0;
1104: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1105: prlim[i][j]= newm[i][j]/(1-sumnew);
1106: max=FMAX(max,prlim[i][j]);
1107: min=FMIN(min,prlim[i][j]);
1108: }
1109: maxmin=max-min;
1110: maxmax=FMAX(maxmax,maxmin);
1111: }
1112: if(maxmax < ftolpl){
1113: return prlim;
1114: }
1115: }
1116: }
1117:
1118: /*************** transition probabilities ***************/
1119:
1120: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1121: {
1122: double s1, s2;
1123: /*double t34;*/
1124: int i,j,j1, nc, ii, jj;
1125:
1126: for(i=1; i<= nlstate; i++){
1127: for(j=1; j<i;j++){
1128: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1129: /*s2 += param[i][j][nc]*cov[nc];*/
1130: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1131: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1132: }
1133: ps[i][j]=s2;
1134: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1135: }
1136: for(j=i+1; j<=nlstate+ndeath;j++){
1137: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1138: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1139: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1140: }
1141: ps[i][j]=s2;
1142: }
1143: }
1144: /*ps[3][2]=1;*/
1145:
1146: for(i=1; i<= nlstate; i++){
1147: s1=0;
1148: for(j=1; j<i; j++)
1149: s1+=exp(ps[i][j]);
1150: for(j=i+1; j<=nlstate+ndeath; j++)
1151: s1+=exp(ps[i][j]);
1152: ps[i][i]=1./(s1+1.);
1153: for(j=1; j<i; j++)
1154: ps[i][j]= exp(ps[i][j])*ps[i][i];
1155: for(j=i+1; j<=nlstate+ndeath; j++)
1156: ps[i][j]= exp(ps[i][j])*ps[i][i];
1157: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1158: } /* end i */
1159:
1160: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1161: for(jj=1; jj<= nlstate+ndeath; jj++){
1162: ps[ii][jj]=0;
1163: ps[ii][ii]=1;
1164: }
1165: }
1166:
1167:
1168: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1169: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1170: /* printf("ddd %lf ",ps[ii][jj]); */
1171: /* } */
1172: /* printf("\n "); */
1173: /* } */
1174: /* printf("\n ");printf("%lf ",cov[2]); */
1175: /*
1176: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1177: goto end;*/
1178: return ps;
1179: }
1180:
1181: /**************** Product of 2 matrices ******************/
1182:
1183: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1184: {
1185: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1186: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1187: /* in, b, out are matrice of pointers which should have been initialized
1188: before: only the contents of out is modified. The function returns
1189: a pointer to pointers identical to out */
1190: long i, j, k;
1191: for(i=nrl; i<= nrh; i++)
1192: for(k=ncolol; k<=ncoloh; k++)
1193: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1194: out[i][k] +=in[i][j]*b[j][k];
1195:
1196: return out;
1197: }
1198:
1199:
1200: /************* Higher Matrix Product ***************/
1201:
1202: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1203: {
1204: /* Computes the transition matrix starting at age 'age' over
1205: 'nhstepm*hstepm*stepm' months (i.e. until
1206: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1207: nhstepm*hstepm matrices.
1208: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1209: (typically every 2 years instead of every month which is too big
1210: for the memory).
1211: Model is determined by parameters x and covariates have to be
1212: included manually here.
1213:
1214: */
1215:
1216: int i, j, d, h, k;
1217: double **out, cov[NCOVMAX];
1218: double **newm;
1219:
1220: /* Hstepm could be zero and should return the unit matrix */
1221: for (i=1;i<=nlstate+ndeath;i++)
1222: for (j=1;j<=nlstate+ndeath;j++){
1223: oldm[i][j]=(i==j ? 1.0 : 0.0);
1224: po[i][j][0]=(i==j ? 1.0 : 0.0);
1225: }
1226: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1227: for(h=1; h <=nhstepm; h++){
1228: for(d=1; d <=hstepm; d++){
1229: newm=savm;
1230: /* Covariates have to be included here again */
1231: cov[1]=1.;
1232: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1233: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1234: for (k=1; k<=cptcovage;k++)
1235: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1236: for (k=1; k<=cptcovprod;k++)
1237: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1238:
1239:
1240: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1241: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1242: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1243: pmij(pmmij,cov,ncovmodel,x,nlstate));
1244: savm=oldm;
1245: oldm=newm;
1246: }
1247: for(i=1; i<=nlstate+ndeath; i++)
1248: for(j=1;j<=nlstate+ndeath;j++) {
1249: po[i][j][h]=newm[i][j];
1250: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1251: */
1252: }
1253: } /* end h */
1254: return po;
1255: }
1256:
1257:
1258: /*************** log-likelihood *************/
1259: double func( double *x)
1260: {
1261: int i, ii, j, k, mi, d, kk;
1262: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1263: double **out;
1264: double sw; /* Sum of weights */
1265: double lli; /* Individual log likelihood */
1266: int s1, s2;
1267: double bbh, survp;
1268: long ipmx;
1269: /*extern weight */
1270: /* We are differentiating ll according to initial status */
1271: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1272: /*for(i=1;i<imx;i++)
1273: printf(" %d\n",s[4][i]);
1274: */
1275: cov[1]=1.;
1276:
1277: for(k=1; k<=nlstate; k++) ll[k]=0.;
1278:
1279: if(mle==1){
1280: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1281: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1282: for(mi=1; mi<= wav[i]-1; mi++){
1283: for (ii=1;ii<=nlstate+ndeath;ii++)
1284: for (j=1;j<=nlstate+ndeath;j++){
1285: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1286: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1287: }
1288: for(d=0; d<dh[mi][i]; d++){
1289: newm=savm;
1290: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1291: for (kk=1; kk<=cptcovage;kk++) {
1292: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1293: }
1294: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1295: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1296: savm=oldm;
1297: oldm=newm;
1298: } /* end mult */
1299:
1300: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1301: /* But now since version 0.9 we anticipate for bias at large stepm.
1302: * If stepm is larger than one month (smallest stepm) and if the exact delay
1303: * (in months) between two waves is not a multiple of stepm, we rounded to
1304: * the nearest (and in case of equal distance, to the lowest) interval but now
1305: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1306: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1307: * probability in order to take into account the bias as a fraction of the way
1308: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1309: * -stepm/2 to stepm/2 .
1310: * For stepm=1 the results are the same as for previous versions of Imach.
1311: * For stepm > 1 the results are less biased than in previous versions.
1312: */
1313: s1=s[mw[mi][i]][i];
1314: s2=s[mw[mi+1][i]][i];
1315: bbh=(double)bh[mi][i]/(double)stepm;
1316: /* bias bh is positive if real duration
1317: * is higher than the multiple of stepm and negative otherwise.
1318: */
1319: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1320: if( s2 > nlstate){
1321: /* i.e. if s2 is a death state and if the date of death is known
1322: then the contribution to the likelihood is the probability to
1323: die between last step unit time and current step unit time,
1324: which is also equal to probability to die before dh
1325: minus probability to die before dh-stepm .
1326: In version up to 0.92 likelihood was computed
1327: as if date of death was unknown. Death was treated as any other
1328: health state: the date of the interview describes the actual state
1329: and not the date of a change in health state. The former idea was
1330: to consider that at each interview the state was recorded
1331: (healthy, disable or death) and IMaCh was corrected; but when we
1332: introduced the exact date of death then we should have modified
1333: the contribution of an exact death to the likelihood. This new
1334: contribution is smaller and very dependent of the step unit
1335: stepm. It is no more the probability to die between last interview
1336: and month of death but the probability to survive from last
1337: interview up to one month before death multiplied by the
1338: probability to die within a month. Thanks to Chris
1339: Jackson for correcting this bug. Former versions increased
1340: mortality artificially. The bad side is that we add another loop
1341: which slows down the processing. The difference can be up to 10%
1342: lower mortality.
1343: */
1344: lli=log(out[s1][s2] - savm[s1][s2]);
1345:
1346:
1347: } else if (s2==-2) {
1348: for (j=1,survp=0. ; j<=nlstate; j++)
1349: survp += out[s1][j];
1350: lli= survp;
1351: }
1352:
1353: else if (s2==-4) {
1354: for (j=3,survp=0. ; j<=nlstate; j++)
1355: survp += out[s1][j];
1356: lli= survp;
1357: }
1358:
1359: else if (s2==-5) {
1360: for (j=1,survp=0. ; j<=2; j++)
1361: survp += out[s1][j];
1362: lli= survp;
1363: }
1364:
1365:
1366: else{
1367: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1368: /* 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 */
1369: }
1370: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1371: /*if(lli ==000.0)*/
1372: /*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); */
1373: ipmx +=1;
1374: sw += weight[i];
1375: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1376: } /* end of wave */
1377: } /* end of individual */
1378: } else if(mle==2){
1379: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1380: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1381: for(mi=1; mi<= wav[i]-1; mi++){
1382: for (ii=1;ii<=nlstate+ndeath;ii++)
1383: for (j=1;j<=nlstate+ndeath;j++){
1384: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1385: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1386: }
1387: for(d=0; d<=dh[mi][i]; d++){
1388: newm=savm;
1389: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1390: for (kk=1; kk<=cptcovage;kk++) {
1391: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1392: }
1393: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1394: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1395: savm=oldm;
1396: oldm=newm;
1397: } /* end mult */
1398:
1399: s1=s[mw[mi][i]][i];
1400: s2=s[mw[mi+1][i]][i];
1401: bbh=(double)bh[mi][i]/(double)stepm;
1402: 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 */
1403: ipmx +=1;
1404: sw += weight[i];
1405: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1406: } /* end of wave */
1407: } /* end of individual */
1408: } else if(mle==3){ /* exponential inter-extrapolation */
1409: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1410: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1411: for(mi=1; mi<= wav[i]-1; mi++){
1412: for (ii=1;ii<=nlstate+ndeath;ii++)
1413: for (j=1;j<=nlstate+ndeath;j++){
1414: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1415: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1416: }
1417: for(d=0; d<dh[mi][i]; d++){
1418: newm=savm;
1419: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1420: for (kk=1; kk<=cptcovage;kk++) {
1421: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1422: }
1423: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1424: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1425: savm=oldm;
1426: oldm=newm;
1427: } /* end mult */
1428:
1429: s1=s[mw[mi][i]][i];
1430: s2=s[mw[mi+1][i]][i];
1431: bbh=(double)bh[mi][i]/(double)stepm;
1432: 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 */
1433: ipmx +=1;
1434: sw += weight[i];
1435: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1436: } /* end of wave */
1437: } /* end of individual */
1438: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1439: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1440: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1441: for(mi=1; mi<= wav[i]-1; mi++){
1442: for (ii=1;ii<=nlstate+ndeath;ii++)
1443: for (j=1;j<=nlstate+ndeath;j++){
1444: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1445: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1446: }
1447: for(d=0; d<dh[mi][i]; d++){
1448: newm=savm;
1449: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1450: for (kk=1; kk<=cptcovage;kk++) {
1451: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1452: }
1453:
1454: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1455: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1456: savm=oldm;
1457: oldm=newm;
1458: } /* end mult */
1459:
1460: s1=s[mw[mi][i]][i];
1461: s2=s[mw[mi+1][i]][i];
1462: if( s2 > nlstate){
1463: lli=log(out[s1][s2] - savm[s1][s2]);
1464: }else{
1465: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1466: }
1467: ipmx +=1;
1468: sw += weight[i];
1469: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1470: /* 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]); */
1471: } /* end of wave */
1472: } /* end of individual */
1473: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1474: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1475: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1476: for(mi=1; mi<= wav[i]-1; mi++){
1477: for (ii=1;ii<=nlstate+ndeath;ii++)
1478: for (j=1;j<=nlstate+ndeath;j++){
1479: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1480: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1481: }
1482: for(d=0; d<dh[mi][i]; d++){
1483: newm=savm;
1484: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1485: for (kk=1; kk<=cptcovage;kk++) {
1486: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1487: }
1488:
1489: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1490: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1491: savm=oldm;
1492: oldm=newm;
1493: } /* end mult */
1494:
1495: s1=s[mw[mi][i]][i];
1496: s2=s[mw[mi+1][i]][i];
1497: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1498: ipmx +=1;
1499: sw += weight[i];
1500: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1501: /*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]);*/
1502: } /* end of wave */
1503: } /* end of individual */
1504: } /* End of if */
1505: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1506: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1507: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1508: return -l;
1509: }
1510:
1511: /*************** log-likelihood *************/
1512: double funcone( double *x)
1513: {
1514: /* Same as likeli but slower because of a lot of printf and if */
1515: int i, ii, j, k, mi, d, kk;
1516: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1517: double **out;
1518: double lli; /* Individual log likelihood */
1519: double llt;
1520: int s1, s2;
1521: double bbh, survp;
1522: /*extern weight */
1523: /* We are differentiating ll according to initial status */
1524: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1525: /*for(i=1;i<imx;i++)
1526: printf(" %d\n",s[4][i]);
1527: */
1528: cov[1]=1.;
1529:
1530: for(k=1; k<=nlstate; k++) ll[k]=0.;
1531:
1532: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1533: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1534: for(mi=1; mi<= wav[i]-1; mi++){
1535: for (ii=1;ii<=nlstate+ndeath;ii++)
1536: for (j=1;j<=nlstate+ndeath;j++){
1537: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1538: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1539: }
1540: for(d=0; d<dh[mi][i]; d++){
1541: newm=savm;
1542: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1543: for (kk=1; kk<=cptcovage;kk++) {
1544: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1545: }
1546: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1547: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1548: savm=oldm;
1549: oldm=newm;
1550: } /* end mult */
1551:
1552: s1=s[mw[mi][i]][i];
1553: s2=s[mw[mi+1][i]][i];
1554: bbh=(double)bh[mi][i]/(double)stepm;
1555: /* bias is positive if real duration
1556: * is higher than the multiple of stepm and negative otherwise.
1557: */
1558: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1559: lli=log(out[s1][s2] - savm[s1][s2]);
1560: } else if (mle==1){
1561: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1562: } else if(mle==2){
1563: 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 */
1564: } else if(mle==3){ /* exponential inter-extrapolation */
1565: 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 */
1566: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1567: lli=log(out[s1][s2]); /* Original formula */
1568: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1569: lli=log(out[s1][s2]); /* Original formula */
1570: } /* End of if */
1571: ipmx +=1;
1572: sw += weight[i];
1573: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1574: /* 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]); */
1575: if(globpr){
1576: fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
1577: %10.6f %10.6f %10.6f ", \
1578: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1579: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1580: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1581: llt +=ll[k]*gipmx/gsw;
1582: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1583: }
1584: fprintf(ficresilk," %10.6f\n", -llt);
1585: }
1586: } /* end of wave */
1587: } /* end of individual */
1588: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1589: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1590: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1591: if(globpr==0){ /* First time we count the contributions and weights */
1592: gipmx=ipmx;
1593: gsw=sw;
1594: }
1595: return -l;
1596: }
1597:
1598:
1599: /*************** function likelione ***********/
1600: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1601: {
1602: /* This routine should help understanding what is done with
1603: the selection of individuals/waves and
1604: to check the exact contribution to the likelihood.
1605: Plotting could be done.
1606: */
1607: int k;
1608:
1609: if(*globpri !=0){ /* Just counts and sums, no printings */
1610: strcpy(fileresilk,"ilk");
1611: strcat(fileresilk,fileres);
1612: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1613: printf("Problem with resultfile: %s\n", fileresilk);
1614: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1615: }
1616: 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");
1617: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1618: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1619: for(k=1; k<=nlstate; k++)
1620: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1621: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1622: }
1623:
1624: *fretone=(*funcone)(p);
1625: if(*globpri !=0){
1626: fclose(ficresilk);
1627: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1628: fflush(fichtm);
1629: }
1630: return;
1631: }
1632:
1633:
1634: /*********** Maximum Likelihood Estimation ***************/
1635:
1636: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1637: {
1638: int i,j, iter;
1639: double **xi;
1640: double fret;
1641: double fretone; /* Only one call to likelihood */
1642: /* char filerespow[FILENAMELENGTH];*/
1643: xi=matrix(1,npar,1,npar);
1644: for (i=1;i<=npar;i++)
1645: for (j=1;j<=npar;j++)
1646: xi[i][j]=(i==j ? 1.0 : 0.0);
1647: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1648: strcpy(filerespow,"pow");
1649: strcat(filerespow,fileres);
1650: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1651: printf("Problem with resultfile: %s\n", filerespow);
1652: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1653: }
1654: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1655: for (i=1;i<=nlstate;i++)
1656: for(j=1;j<=nlstate+ndeath;j++)
1657: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1658: fprintf(ficrespow,"\n");
1659:
1660: powell(p,xi,npar,ftol,&iter,&fret,func);
1661:
1662: fclose(ficrespow);
1663: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1664: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1665: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1666:
1667: }
1668:
1669: /**** Computes Hessian and covariance matrix ***/
1670: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1671: {
1672: double **a,**y,*x,pd;
1673: double **hess;
1674: int i, j,jk;
1675: int *indx;
1676:
1677: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1678: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1679: void lubksb(double **a, int npar, int *indx, double b[]) ;
1680: void ludcmp(double **a, int npar, int *indx, double *d) ;
1681: double gompertz(double p[]);
1682: hess=matrix(1,npar,1,npar);
1683:
1684: printf("\nCalculation of the hessian matrix. Wait...\n");
1685: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1686: for (i=1;i<=npar;i++){
1687: printf("%d",i);fflush(stdout);
1688: fprintf(ficlog,"%d",i);fflush(ficlog);
1689:
1690: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1691:
1692: /* printf(" %f ",p[i]);
1693: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1694: }
1695:
1696: for (i=1;i<=npar;i++) {
1697: for (j=1;j<=npar;j++) {
1698: if (j>i) {
1699: printf(".%d%d",i,j);fflush(stdout);
1700: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1701: hess[i][j]=hessij(p,delti,i,j,func,npar);
1702:
1703: hess[j][i]=hess[i][j];
1704: /*printf(" %lf ",hess[i][j]);*/
1705: }
1706: }
1707: }
1708: printf("\n");
1709: fprintf(ficlog,"\n");
1710:
1711: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1712: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1713:
1714: a=matrix(1,npar,1,npar);
1715: y=matrix(1,npar,1,npar);
1716: x=vector(1,npar);
1717: indx=ivector(1,npar);
1718: for (i=1;i<=npar;i++)
1719: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1720: ludcmp(a,npar,indx,&pd);
1721:
1722: for (j=1;j<=npar;j++) {
1723: for (i=1;i<=npar;i++) x[i]=0;
1724: x[j]=1;
1725: lubksb(a,npar,indx,x);
1726: for (i=1;i<=npar;i++){
1727: matcov[i][j]=x[i];
1728: }
1729: }
1730:
1731: printf("\n#Hessian matrix#\n");
1732: fprintf(ficlog,"\n#Hessian matrix#\n");
1733: for (i=1;i<=npar;i++) {
1734: for (j=1;j<=npar;j++) {
1735: printf("%.3e ",hess[i][j]);
1736: fprintf(ficlog,"%.3e ",hess[i][j]);
1737: }
1738: printf("\n");
1739: fprintf(ficlog,"\n");
1740: }
1741:
1742: /* Recompute Inverse */
1743: for (i=1;i<=npar;i++)
1744: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1745: ludcmp(a,npar,indx,&pd);
1746:
1747: /* printf("\n#Hessian matrix recomputed#\n");
1748:
1749: for (j=1;j<=npar;j++) {
1750: for (i=1;i<=npar;i++) x[i]=0;
1751: x[j]=1;
1752: lubksb(a,npar,indx,x);
1753: for (i=1;i<=npar;i++){
1754: y[i][j]=x[i];
1755: printf("%.3e ",y[i][j]);
1756: fprintf(ficlog,"%.3e ",y[i][j]);
1757: }
1758: printf("\n");
1759: fprintf(ficlog,"\n");
1760: }
1761: */
1762:
1763: free_matrix(a,1,npar,1,npar);
1764: free_matrix(y,1,npar,1,npar);
1765: free_vector(x,1,npar);
1766: free_ivector(indx,1,npar);
1767: free_matrix(hess,1,npar,1,npar);
1768:
1769:
1770: }
1771:
1772: /*************** hessian matrix ****************/
1773: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1774: {
1775: int i;
1776: int l=1, lmax=20;
1777: double k1,k2;
1778: double p2[NPARMAX+1];
1779: double res;
1780: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1781: double fx;
1782: int k=0,kmax=10;
1783: double l1;
1784:
1785: fx=func(x);
1786: for (i=1;i<=npar;i++) p2[i]=x[i];
1787: for(l=0 ; l <=lmax; l++){
1788: l1=pow(10,l);
1789: delts=delt;
1790: for(k=1 ; k <kmax; k=k+1){
1791: delt = delta*(l1*k);
1792: p2[theta]=x[theta] +delt;
1793: k1=func(p2)-fx;
1794: p2[theta]=x[theta]-delt;
1795: k2=func(p2)-fx;
1796: /*res= (k1-2.0*fx+k2)/delt/delt; */
1797: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1798:
1799: #ifdef DEBUG
1800: 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);
1801: 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);
1802: #endif
1803: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1804: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1805: k=kmax;
1806: }
1807: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1808: k=kmax; l=lmax*10.;
1809: }
1810: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1811: delts=delt;
1812: }
1813: }
1814: }
1815: delti[theta]=delts;
1816: return res;
1817:
1818: }
1819:
1820: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1821: {
1822: int i;
1823: int l=1, l1, lmax=20;
1824: double k1,k2,k3,k4,res,fx;
1825: double p2[NPARMAX+1];
1826: int k;
1827:
1828: fx=func(x);
1829: for (k=1; k<=2; k++) {
1830: for (i=1;i<=npar;i++) p2[i]=x[i];
1831: p2[thetai]=x[thetai]+delti[thetai]/k;
1832: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1833: k1=func(p2)-fx;
1834:
1835: p2[thetai]=x[thetai]+delti[thetai]/k;
1836: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1837: k2=func(p2)-fx;
1838:
1839: p2[thetai]=x[thetai]-delti[thetai]/k;
1840: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1841: k3=func(p2)-fx;
1842:
1843: p2[thetai]=x[thetai]-delti[thetai]/k;
1844: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1845: k4=func(p2)-fx;
1846: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1847: #ifdef DEBUG
1848: 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);
1849: 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);
1850: #endif
1851: }
1852: return res;
1853: }
1854:
1855: /************** Inverse of matrix **************/
1856: void ludcmp(double **a, int n, int *indx, double *d)
1857: {
1858: int i,imax,j,k;
1859: double big,dum,sum,temp;
1860: double *vv;
1861:
1862: vv=vector(1,n);
1863: *d=1.0;
1864: for (i=1;i<=n;i++) {
1865: big=0.0;
1866: for (j=1;j<=n;j++)
1867: if ((temp=fabs(a[i][j])) > big) big=temp;
1868: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1869: vv[i]=1.0/big;
1870: }
1871: for (j=1;j<=n;j++) {
1872: for (i=1;i<j;i++) {
1873: sum=a[i][j];
1874: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1875: a[i][j]=sum;
1876: }
1877: big=0.0;
1878: for (i=j;i<=n;i++) {
1879: sum=a[i][j];
1880: for (k=1;k<j;k++)
1881: sum -= a[i][k]*a[k][j];
1882: a[i][j]=sum;
1883: if ( (dum=vv[i]*fabs(sum)) >= big) {
1884: big=dum;
1885: imax=i;
1886: }
1887: }
1888: if (j != imax) {
1889: for (k=1;k<=n;k++) {
1890: dum=a[imax][k];
1891: a[imax][k]=a[j][k];
1892: a[j][k]=dum;
1893: }
1894: *d = -(*d);
1895: vv[imax]=vv[j];
1896: }
1897: indx[j]=imax;
1898: if (a[j][j] == 0.0) a[j][j]=TINY;
1899: if (j != n) {
1900: dum=1.0/(a[j][j]);
1901: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1902: }
1903: }
1904: free_vector(vv,1,n); /* Doesn't work */
1905: ;
1906: }
1907:
1908: void lubksb(double **a, int n, int *indx, double b[])
1909: {
1910: int i,ii=0,ip,j;
1911: double sum;
1912:
1913: for (i=1;i<=n;i++) {
1914: ip=indx[i];
1915: sum=b[ip];
1916: b[ip]=b[i];
1917: if (ii)
1918: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1919: else if (sum) ii=i;
1920: b[i]=sum;
1921: }
1922: for (i=n;i>=1;i--) {
1923: sum=b[i];
1924: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1925: b[i]=sum/a[i][i];
1926: }
1927: }
1928:
1929: /************ Frequencies ********************/
1930: 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[])
1931: { /* Some frequencies */
1932:
1933: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1934: int first;
1935: double ***freq; /* Frequencies */
1936: double *pp, **prop;
1937: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1938: FILE *ficresp;
1939: char fileresp[FILENAMELENGTH];
1940:
1941: pp=vector(1,nlstate);
1942: prop=matrix(1,nlstate,iagemin,iagemax+3);
1943: strcpy(fileresp,"p");
1944: strcat(fileresp,fileres);
1945: if((ficresp=fopen(fileresp,"w"))==NULL) {
1946: printf("Problem with prevalence resultfile: %s\n", fileresp);
1947: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
1948: exit(0);
1949: }
1950: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
1951: j1=0;
1952:
1953: j=cptcoveff;
1954: if (cptcovn<1) {j=1;ncodemax[1]=1;}
1955:
1956: first=1;
1957:
1958: for(k1=1; k1<=j;k1++){
1959: for(i1=1; i1<=ncodemax[k1];i1++){
1960: j1++;
1961: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
1962: scanf("%d", i);*/
1963: for (i=-5; i<=nlstate+ndeath; i++)
1964: for (jk=-5; jk<=nlstate+ndeath; jk++)
1965: for(m=iagemin; m <= iagemax+3; m++)
1966: freq[i][jk][m]=0;
1967:
1968: for (i=1; i<=nlstate; i++)
1969: for(m=iagemin; m <= iagemax+3; m++)
1970: prop[i][m]=0;
1971:
1972: dateintsum=0;
1973: k2cpt=0;
1974: for (i=1; i<=imx; i++) {
1975: bool=1;
1976: if (cptcovn>0) {
1977: for (z1=1; z1<=cptcoveff; z1++)
1978: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
1979: bool=0;
1980: }
1981: if (bool==1){
1982: for(m=firstpass; m<=lastpass; m++){
1983: k2=anint[m][i]+(mint[m][i]/12.);
1984: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
1985: if(agev[m][i]==0) agev[m][i]=iagemax+1;
1986: if(agev[m][i]==1) agev[m][i]=iagemax+2;
1987: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
1988: if (m<lastpass) {
1989: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
1990: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
1991: }
1992:
1993: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
1994: dateintsum=dateintsum+k2;
1995: k2cpt++;
1996: }
1997: /*}*/
1998: }
1999: }
2000: }
2001:
2002: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2003: fprintf(ficresp, "#Local time at start: %s", strstart);
2004: if (cptcovn>0) {
2005: fprintf(ficresp, "\n#********** Variable ");
2006: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2007: fprintf(ficresp, "**********\n#");
2008: }
2009: for(i=1; i<=nlstate;i++)
2010: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2011: fprintf(ficresp, "\n");
2012:
2013: for(i=iagemin; i <= iagemax+3; i++){
2014: if(i==iagemax+3){
2015: fprintf(ficlog,"Total");
2016: }else{
2017: if(first==1){
2018: first=0;
2019: printf("See log file for details...\n");
2020: }
2021: fprintf(ficlog,"Age %d", i);
2022: }
2023: for(jk=1; jk <=nlstate ; jk++){
2024: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2025: pp[jk] += freq[jk][m][i];
2026: }
2027: for(jk=1; jk <=nlstate ; jk++){
2028: for(m=-1, pos=0; m <=0 ; m++)
2029: pos += freq[jk][m][i];
2030: if(pp[jk]>=1.e-10){
2031: if(first==1){
2032: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2033: }
2034: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2035: }else{
2036: if(first==1)
2037: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2038: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2039: }
2040: }
2041:
2042: for(jk=1; jk <=nlstate ; jk++){
2043: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2044: pp[jk] += freq[jk][m][i];
2045: }
2046: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2047: pos += pp[jk];
2048: posprop += prop[jk][i];
2049: }
2050: for(jk=1; jk <=nlstate ; jk++){
2051: if(pos>=1.e-5){
2052: if(first==1)
2053: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2054: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2055: }else{
2056: if(first==1)
2057: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2058: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2059: }
2060: if( i <= iagemax){
2061: if(pos>=1.e-5){
2062: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2063: /*probs[i][jk][j1]= pp[jk]/pos;*/
2064: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2065: }
2066: else
2067: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2068: }
2069: }
2070:
2071: for(jk=-1; jk <=nlstate+ndeath; jk++)
2072: for(m=-1; m <=nlstate+ndeath; m++)
2073: if(freq[jk][m][i] !=0 ) {
2074: if(first==1)
2075: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2076: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2077: }
2078: if(i <= iagemax)
2079: fprintf(ficresp,"\n");
2080: if(first==1)
2081: printf("Others in log...\n");
2082: fprintf(ficlog,"\n");
2083: }
2084: }
2085: }
2086: dateintmean=dateintsum/k2cpt;
2087:
2088: fclose(ficresp);
2089: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2090: free_vector(pp,1,nlstate);
2091: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2092: /* End of Freq */
2093: }
2094:
2095: /************ Prevalence ********************/
2096: 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)
2097: {
2098: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2099: in each health status at the date of interview (if between dateprev1 and dateprev2).
2100: We still use firstpass and lastpass as another selection.
2101: */
2102:
2103: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2104: double ***freq; /* Frequencies */
2105: double *pp, **prop;
2106: double pos,posprop;
2107: double y2; /* in fractional years */
2108: int iagemin, iagemax;
2109:
2110: iagemin= (int) agemin;
2111: iagemax= (int) agemax;
2112: /*pp=vector(1,nlstate);*/
2113: prop=matrix(1,nlstate,iagemin,iagemax+3);
2114: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2115: j1=0;
2116:
2117: j=cptcoveff;
2118: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2119:
2120: for(k1=1; k1<=j;k1++){
2121: for(i1=1; i1<=ncodemax[k1];i1++){
2122: j1++;
2123:
2124: for (i=1; i<=nlstate; i++)
2125: for(m=iagemin; m <= iagemax+3; m++)
2126: prop[i][m]=0.0;
2127:
2128: for (i=1; i<=imx; i++) { /* Each individual */
2129: bool=1;
2130: if (cptcovn>0) {
2131: for (z1=1; z1<=cptcoveff; z1++)
2132: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2133: bool=0;
2134: }
2135: if (bool==1) {
2136: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2137: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2138: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2139: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2140: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2141: 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);
2142: if (s[m][i]>0 && s[m][i]<=nlstate) {
2143: /*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]]);*/
2144: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2145: prop[s[m][i]][iagemax+3] += weight[i];
2146: }
2147: }
2148: } /* end selection of waves */
2149: }
2150: }
2151: for(i=iagemin; i <= iagemax+3; i++){
2152:
2153: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2154: posprop += prop[jk][i];
2155: }
2156:
2157: for(jk=1; jk <=nlstate ; jk++){
2158: if( i <= iagemax){
2159: if(posprop>=1.e-5){
2160: probs[i][jk][j1]= prop[jk][i]/posprop;
2161: }
2162: }
2163: }/* end jk */
2164: }/* end i */
2165: } /* end i1 */
2166: } /* end k1 */
2167:
2168: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2169: /*free_vector(pp,1,nlstate);*/
2170: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2171: } /* End of prevalence */
2172:
2173: /************* Waves Concatenation ***************/
2174:
2175: 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)
2176: {
2177: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2178: Death is a valid wave (if date is known).
2179: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2180: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2181: and mw[mi+1][i]. dh depends on stepm.
2182: */
2183:
2184: int i, mi, m;
2185: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2186: double sum=0., jmean=0.;*/
2187: int first;
2188: int j, k=0,jk, ju, jl;
2189: double sum=0.;
2190: first=0;
2191: jmin=1e+5;
2192: jmax=-1;
2193: jmean=0.;
2194: for(i=1; i<=imx; i++){
2195: mi=0;
2196: m=firstpass;
2197: while(s[m][i] <= nlstate){
2198: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2199: mw[++mi][i]=m;
2200: if(m >=lastpass)
2201: break;
2202: else
2203: m++;
2204: }/* end while */
2205: if (s[m][i] > nlstate){
2206: mi++; /* Death is another wave */
2207: /* if(mi==0) never been interviewed correctly before death */
2208: /* Only death is a correct wave */
2209: mw[mi][i]=m;
2210: }
2211:
2212: wav[i]=mi;
2213: if(mi==0){
2214: nbwarn++;
2215: if(first==0){
2216: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2217: first=1;
2218: }
2219: if(first==1){
2220: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2221: }
2222: } /* end mi==0 */
2223: } /* End individuals */
2224:
2225: for(i=1; i<=imx; i++){
2226: for(mi=1; mi<wav[i];mi++){
2227: if (stepm <=0)
2228: dh[mi][i]=1;
2229: else{
2230: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2231: if (agedc[i] < 2*AGESUP) {
2232: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2233: if(j==0) j=1; /* Survives at least one month after exam */
2234: else if(j<0){
2235: nberr++;
2236: 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]);
2237: j=1; /* Temporary Dangerous patch */
2238: 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);
2239: 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]);
2240: 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);
2241: }
2242: k=k+1;
2243: if (j >= jmax){
2244: jmax=j;
2245: ijmax=i;
2246: }
2247: if (j <= jmin){
2248: jmin=j;
2249: ijmin=i;
2250: }
2251: sum=sum+j;
2252: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2253: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2254: }
2255: }
2256: else{
2257: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2258: /* 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]); */
2259:
2260: k=k+1;
2261: if (j >= jmax) {
2262: jmax=j;
2263: ijmax=i;
2264: }
2265: else if (j <= jmin){
2266: jmin=j;
2267: ijmin=i;
2268: }
2269: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2270: /*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]);*/
2271: if(j<0){
2272: nberr++;
2273: 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]);
2274: 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]);
2275: }
2276: sum=sum+j;
2277: }
2278: jk= j/stepm;
2279: jl= j -jk*stepm;
2280: ju= j -(jk+1)*stepm;
2281: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2282: if(jl==0){
2283: dh[mi][i]=jk;
2284: bh[mi][i]=0;
2285: }else{ /* We want a negative bias in order to only have interpolation ie
2286: * at the price of an extra matrix product in likelihood */
2287: dh[mi][i]=jk+1;
2288: bh[mi][i]=ju;
2289: }
2290: }else{
2291: if(jl <= -ju){
2292: dh[mi][i]=jk;
2293: bh[mi][i]=jl; /* bias is positive if real duration
2294: * is higher than the multiple of stepm and negative otherwise.
2295: */
2296: }
2297: else{
2298: dh[mi][i]=jk+1;
2299: bh[mi][i]=ju;
2300: }
2301: if(dh[mi][i]==0){
2302: dh[mi][i]=1; /* At least one step */
2303: bh[mi][i]=ju; /* At least one step */
2304: /* 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);*/
2305: }
2306: } /* end if mle */
2307: }
2308: } /* end wave */
2309: }
2310: jmean=sum/k;
2311: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
2312: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
2313: }
2314:
2315: /*********** Tricode ****************************/
2316: void tricode(int *Tvar, int **nbcode, int imx)
2317: {
2318:
2319: int Ndum[20],ij=1, k, j, i, maxncov=19;
2320: int cptcode=0;
2321: cptcoveff=0;
2322:
2323: for (k=0; k<maxncov; k++) Ndum[k]=0;
2324: for (k=1; k<=7; k++) ncodemax[k]=0;
2325:
2326: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2327: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2328: modality*/
2329: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2330: Ndum[ij]++; /*store the modality */
2331: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2332: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2333: Tvar[j]. If V=sex and male is 0 and
2334: female is 1, then cptcode=1.*/
2335: }
2336:
2337: for (i=0; i<=cptcode; i++) {
2338: 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 */
2339: }
2340:
2341: ij=1;
2342: for (i=1; i<=ncodemax[j]; i++) {
2343: for (k=0; k<= maxncov; k++) {
2344: if (Ndum[k] != 0) {
2345: nbcode[Tvar[j]][ij]=k;
2346: /* 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; */
2347:
2348: ij++;
2349: }
2350: if (ij > ncodemax[j]) break;
2351: }
2352: }
2353: }
2354:
2355: for (k=0; k< maxncov; k++) Ndum[k]=0;
2356:
2357: for (i=1; i<=ncovmodel-2; i++) {
2358: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2359: ij=Tvar[i];
2360: Ndum[ij]++;
2361: }
2362:
2363: ij=1;
2364: for (i=1; i<= maxncov; i++) {
2365: if((Ndum[i]!=0) && (i<=ncovcol)){
2366: Tvaraff[ij]=i; /*For printing */
2367: ij++;
2368: }
2369: }
2370:
2371: cptcoveff=ij-1; /*Number of simple covariates*/
2372: }
2373:
2374: /*********** Health Expectancies ****************/
2375:
2376: 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[] )
2377:
2378: {
2379: /* Health expectancies */
2380: int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
2381: double age, agelim, hf;
2382: double ***p3mat,***varhe;
2383: double **dnewm,**doldm;
2384: double *xp;
2385: double **gp, **gm;
2386: double ***gradg, ***trgradg;
2387: int theta;
2388:
2389: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2390: xp=vector(1,npar);
2391: dnewm=matrix(1,nlstate*nlstate,1,npar);
2392: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2393:
2394: fprintf(ficreseij,"# Local time at start: %s", strstart);
2395: fprintf(ficreseij,"# Health expectancies\n");
2396: fprintf(ficreseij,"# Age");
2397: for(i=1; i<=nlstate;i++)
2398: for(j=1; j<=nlstate;j++)
2399: fprintf(ficreseij," %1d-%1d (SE)",i,j);
2400: fprintf(ficreseij,"\n");
2401:
2402: if(estepm < stepm){
2403: printf ("Problem %d lower than %d\n",estepm, stepm);
2404: }
2405: else hstepm=estepm;
2406: /* We compute the life expectancy from trapezoids spaced every estepm months
2407: * This is mainly to measure the difference between two models: for example
2408: * if stepm=24 months pijx are given only every 2 years and by summing them
2409: * we are calculating an estimate of the Life Expectancy assuming a linear
2410: * progression in between and thus overestimating or underestimating according
2411: * to the curvature of the survival function. If, for the same date, we
2412: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2413: * to compare the new estimate of Life expectancy with the same linear
2414: * hypothesis. A more precise result, taking into account a more precise
2415: * curvature will be obtained if estepm is as small as stepm. */
2416:
2417: /* For example we decided to compute the life expectancy with the smallest unit */
2418: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2419: nhstepm is the number of hstepm from age to agelim
2420: nstepm is the number of stepm from age to agelin.
2421: Look at hpijx to understand the reason of that which relies in memory size
2422: and note for a fixed period like estepm months */
2423: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2424: survival function given by stepm (the optimization length). Unfortunately it
2425: means that if the survival funtion is printed only each two years of age and if
2426: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2427: results. So we changed our mind and took the option of the best precision.
2428: */
2429: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2430:
2431: agelim=AGESUP;
2432: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2433: /* nhstepm age range expressed in number of stepm */
2434: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2435: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2436: /* if (stepm >= YEARM) hstepm=1;*/
2437: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2438: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2439: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2440: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2441: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2442:
2443: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2444: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2445: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
2446:
2447:
2448: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2449:
2450: /* Computing Variances of health expectancies */
2451:
2452: for(theta=1; theta <=npar; theta++){
2453: for(i=1; i<=npar; i++){
2454: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2455: }
2456: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2457:
2458: cptj=0;
2459: for(j=1; j<= nlstate; j++){
2460: for(i=1; i<=nlstate; i++){
2461: cptj=cptj+1;
2462: for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
2463: gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2464: }
2465: }
2466: }
2467:
2468:
2469: for(i=1; i<=npar; i++)
2470: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2471: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2472:
2473: cptj=0;
2474: for(j=1; j<= nlstate; j++){
2475: for(i=1;i<=nlstate;i++){
2476: cptj=cptj+1;
2477: for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
2478:
2479: gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
2480: }
2481: }
2482: }
2483: for(j=1; j<= nlstate*nlstate; j++)
2484: for(h=0; h<=nhstepm-1; h++){
2485: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2486: }
2487: }
2488:
2489: /* End theta */
2490:
2491: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2492:
2493: for(h=0; h<=nhstepm-1; h++)
2494: for(j=1; j<=nlstate*nlstate;j++)
2495: for(theta=1; theta <=npar; theta++)
2496: trgradg[h][j][theta]=gradg[h][theta][j];
2497:
2498:
2499: for(i=1;i<=nlstate*nlstate;i++)
2500: for(j=1;j<=nlstate*nlstate;j++)
2501: varhe[i][j][(int)age] =0.;
2502:
2503: printf("%d|",(int)age);fflush(stdout);
2504: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2505: for(h=0;h<=nhstepm-1;h++){
2506: for(k=0;k<=nhstepm-1;k++){
2507: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2508: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2509: for(i=1;i<=nlstate*nlstate;i++)
2510: for(j=1;j<=nlstate*nlstate;j++)
2511: varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
2512: }
2513: }
2514: /* Computing expectancies */
2515: for(i=1; i<=nlstate;i++)
2516: for(j=1; j<=nlstate;j++)
2517: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2518: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2519:
2520: /* 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]);*/
2521:
2522: }
2523:
2524: fprintf(ficreseij,"%3.0f",age );
2525: cptj=0;
2526: for(i=1; i<=nlstate;i++)
2527: for(j=1; j<=nlstate;j++){
2528: cptj++;
2529: fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
2530: }
2531: fprintf(ficreseij,"\n");
2532:
2533: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2534: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2535: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2536: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2537: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2538: }
2539: printf("\n");
2540: fprintf(ficlog,"\n");
2541:
2542: free_vector(xp,1,npar);
2543: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2544: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2545: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2546: }
2547:
2548: /************ Variance ******************/
2549: 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[])
2550: {
2551: /* Variance of health expectancies */
2552: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2553: /* double **newm;*/
2554: double **dnewm,**doldm;
2555: double **dnewmp,**doldmp;
2556: int i, j, nhstepm, hstepm, h, nstepm ;
2557: int k, cptcode;
2558: double *xp;
2559: double **gp, **gm; /* for var eij */
2560: double ***gradg, ***trgradg; /*for var eij */
2561: double **gradgp, **trgradgp; /* for var p point j */
2562: double *gpp, *gmp; /* for var p point j */
2563: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2564: double ***p3mat;
2565: double age,agelim, hf;
2566: double ***mobaverage;
2567: int theta;
2568: char digit[4];
2569: char digitp[25];
2570:
2571: char fileresprobmorprev[FILENAMELENGTH];
2572:
2573: if(popbased==1){
2574: if(mobilav!=0)
2575: strcpy(digitp,"-populbased-mobilav-");
2576: else strcpy(digitp,"-populbased-nomobil-");
2577: }
2578: else
2579: strcpy(digitp,"-stablbased-");
2580:
2581: if (mobilav!=0) {
2582: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2583: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2584: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2585: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2586: }
2587: }
2588:
2589: strcpy(fileresprobmorprev,"prmorprev");
2590: sprintf(digit,"%-d",ij);
2591: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2592: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2593: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2594: strcat(fileresprobmorprev,fileres);
2595: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2596: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2597: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2598: }
2599: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2600:
2601: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2602: fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
2603: 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);
2604: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2605: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2606: fprintf(ficresprobmorprev," p.%-d SE",j);
2607: for(i=1; i<=nlstate;i++)
2608: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2609: }
2610: fprintf(ficresprobmorprev,"\n");
2611: fprintf(ficgp,"\n# Routine varevsij");
2612: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2613: 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");
2614: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2615: /* } */
2616: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2617: fprintf(ficresvij, "#Local time at start: %s", strstart);
2618: 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");
2619: fprintf(ficresvij,"# Age");
2620: for(i=1; i<=nlstate;i++)
2621: for(j=1; j<=nlstate;j++)
2622: fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
2623: fprintf(ficresvij,"\n");
2624:
2625: xp=vector(1,npar);
2626: dnewm=matrix(1,nlstate,1,npar);
2627: doldm=matrix(1,nlstate,1,nlstate);
2628: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2629: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2630:
2631: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2632: gpp=vector(nlstate+1,nlstate+ndeath);
2633: gmp=vector(nlstate+1,nlstate+ndeath);
2634: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2635:
2636: if(estepm < stepm){
2637: printf ("Problem %d lower than %d\n",estepm, stepm);
2638: }
2639: else hstepm=estepm;
2640: /* For example we decided to compute the life expectancy with the smallest unit */
2641: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2642: nhstepm is the number of hstepm from age to agelim
2643: nstepm is the number of stepm from age to agelin.
2644: Look at hpijx to understand the reason of that which relies in memory size
2645: and note for a fixed period like k years */
2646: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2647: survival function given by stepm (the optimization length). Unfortunately it
2648: means that if the survival funtion is printed every two years of age and if
2649: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2650: results. So we changed our mind and took the option of the best precision.
2651: */
2652: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2653: agelim = AGESUP;
2654: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2655: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2656: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2657: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2658: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2659: gp=matrix(0,nhstepm,1,nlstate);
2660: gm=matrix(0,nhstepm,1,nlstate);
2661:
2662:
2663: for(theta=1; theta <=npar; theta++){
2664: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2665: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2666: }
2667: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2668: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2669:
2670: if (popbased==1) {
2671: if(mobilav ==0){
2672: for(i=1; i<=nlstate;i++)
2673: prlim[i][i]=probs[(int)age][i][ij];
2674: }else{ /* mobilav */
2675: for(i=1; i<=nlstate;i++)
2676: prlim[i][i]=mobaverage[(int)age][i][ij];
2677: }
2678: }
2679:
2680: for(j=1; j<= nlstate; j++){
2681: for(h=0; h<=nhstepm; h++){
2682: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2683: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2684: }
2685: }
2686: /* This for computing probability of death (h=1 means
2687: computed over hstepm matrices product = hstepm*stepm months)
2688: as a weighted average of prlim.
2689: */
2690: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2691: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2692: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2693: }
2694: /* end probability of death */
2695:
2696: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2697: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2698: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2699: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2700:
2701: if (popbased==1) {
2702: if(mobilav ==0){
2703: for(i=1; i<=nlstate;i++)
2704: prlim[i][i]=probs[(int)age][i][ij];
2705: }else{ /* mobilav */
2706: for(i=1; i<=nlstate;i++)
2707: prlim[i][i]=mobaverage[(int)age][i][ij];
2708: }
2709: }
2710:
2711: for(j=1; j<= nlstate; j++){
2712: for(h=0; h<=nhstepm; h++){
2713: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2714: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2715: }
2716: }
2717: /* This for computing probability of death (h=1 means
2718: computed over hstepm matrices product = hstepm*stepm months)
2719: as a weighted average of prlim.
2720: */
2721: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2722: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2723: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2724: }
2725: /* end probability of death */
2726:
2727: for(j=1; j<= nlstate; j++) /* vareij */
2728: for(h=0; h<=nhstepm; h++){
2729: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2730: }
2731:
2732: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2733: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2734: }
2735:
2736: } /* End theta */
2737:
2738: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2739:
2740: for(h=0; h<=nhstepm; h++) /* veij */
2741: for(j=1; j<=nlstate;j++)
2742: for(theta=1; theta <=npar; theta++)
2743: trgradg[h][j][theta]=gradg[h][theta][j];
2744:
2745: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2746: for(theta=1; theta <=npar; theta++)
2747: trgradgp[j][theta]=gradgp[theta][j];
2748:
2749:
2750: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2751: for(i=1;i<=nlstate;i++)
2752: for(j=1;j<=nlstate;j++)
2753: vareij[i][j][(int)age] =0.;
2754:
2755: for(h=0;h<=nhstepm;h++){
2756: for(k=0;k<=nhstepm;k++){
2757: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2758: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2759: for(i=1;i<=nlstate;i++)
2760: for(j=1;j<=nlstate;j++)
2761: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2762: }
2763: }
2764:
2765: /* pptj */
2766: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2767: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2768: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2769: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2770: varppt[j][i]=doldmp[j][i];
2771: /* end ppptj */
2772: /* x centered again */
2773: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2774: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2775:
2776: if (popbased==1) {
2777: if(mobilav ==0){
2778: for(i=1; i<=nlstate;i++)
2779: prlim[i][i]=probs[(int)age][i][ij];
2780: }else{ /* mobilav */
2781: for(i=1; i<=nlstate;i++)
2782: prlim[i][i]=mobaverage[(int)age][i][ij];
2783: }
2784: }
2785:
2786: /* This for computing probability of death (h=1 means
2787: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2788: as a weighted average of prlim.
2789: */
2790: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2791: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2792: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2793: }
2794: /* end probability of death */
2795:
2796: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2797: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2798: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2799: for(i=1; i<=nlstate;i++){
2800: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2801: }
2802: }
2803: fprintf(ficresprobmorprev,"\n");
2804:
2805: fprintf(ficresvij,"%.0f ",age );
2806: for(i=1; i<=nlstate;i++)
2807: for(j=1; j<=nlstate;j++){
2808: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
2809: }
2810: fprintf(ficresvij,"\n");
2811: free_matrix(gp,0,nhstepm,1,nlstate);
2812: free_matrix(gm,0,nhstepm,1,nlstate);
2813: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
2814: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
2815: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2816: } /* End age */
2817: free_vector(gpp,nlstate+1,nlstate+ndeath);
2818: free_vector(gmp,nlstate+1,nlstate+ndeath);
2819: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
2820: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2821: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
2822: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
2823: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
2824: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
2825: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
2826: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
2827: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
2828: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
2829: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
2830: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
2831: 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);
2832: /* 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);
2833: */
2834: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
2835: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
2836:
2837: free_vector(xp,1,npar);
2838: free_matrix(doldm,1,nlstate,1,nlstate);
2839: free_matrix(dnewm,1,nlstate,1,npar);
2840: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2841: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
2842: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2843: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2844: fclose(ficresprobmorprev);
2845: fflush(ficgp);
2846: fflush(fichtm);
2847: } /* end varevsij */
2848:
2849: /************ Variance of prevlim ******************/
2850: 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[])
2851: {
2852: /* Variance of prevalence limit */
2853: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
2854: double **newm;
2855: double **dnewm,**doldm;
2856: int i, j, nhstepm, hstepm;
2857: int k, cptcode;
2858: double *xp;
2859: double *gp, *gm;
2860: double **gradg, **trgradg;
2861: double age,agelim;
2862: int theta;
2863: fprintf(ficresvpl, "#Local time at start: %s", strstart);
2864: fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
2865: fprintf(ficresvpl,"# Age");
2866: for(i=1; i<=nlstate;i++)
2867: fprintf(ficresvpl," %1d-%1d",i,i);
2868: fprintf(ficresvpl,"\n");
2869:
2870: xp=vector(1,npar);
2871: dnewm=matrix(1,nlstate,1,npar);
2872: doldm=matrix(1,nlstate,1,nlstate);
2873:
2874: hstepm=1*YEARM; /* Every year of age */
2875: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
2876: agelim = AGESUP;
2877: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2878: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2879: if (stepm >= YEARM) hstepm=1;
2880: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
2881: gradg=matrix(1,npar,1,nlstate);
2882: gp=vector(1,nlstate);
2883: gm=vector(1,nlstate);
2884:
2885: for(theta=1; theta <=npar; theta++){
2886: for(i=1; i<=npar; i++){ /* Computes gradient */
2887: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2888: }
2889: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2890: for(i=1;i<=nlstate;i++)
2891: gp[i] = prlim[i][i];
2892:
2893: for(i=1; i<=npar; i++) /* Computes gradient */
2894: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2895: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2896: for(i=1;i<=nlstate;i++)
2897: gm[i] = prlim[i][i];
2898:
2899: for(i=1;i<=nlstate;i++)
2900: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
2901: } /* End theta */
2902:
2903: trgradg =matrix(1,nlstate,1,npar);
2904:
2905: for(j=1; j<=nlstate;j++)
2906: for(theta=1; theta <=npar; theta++)
2907: trgradg[j][theta]=gradg[theta][j];
2908:
2909: for(i=1;i<=nlstate;i++)
2910: varpl[i][(int)age] =0.;
2911: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
2912: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
2913: for(i=1;i<=nlstate;i++)
2914: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
2915:
2916: fprintf(ficresvpl,"%.0f ",age );
2917: for(i=1; i<=nlstate;i++)
2918: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
2919: fprintf(ficresvpl,"\n");
2920: free_vector(gp,1,nlstate);
2921: free_vector(gm,1,nlstate);
2922: free_matrix(gradg,1,npar,1,nlstate);
2923: free_matrix(trgradg,1,nlstate,1,npar);
2924: } /* End age */
2925:
2926: free_vector(xp,1,npar);
2927: free_matrix(doldm,1,nlstate,1,npar);
2928: free_matrix(dnewm,1,nlstate,1,nlstate);
2929:
2930: }
2931:
2932: /************ Variance of one-step probabilities ******************/
2933: 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[])
2934: {
2935: int i, j=0, i1, k1, l1, t, tj;
2936: int k2, l2, j1, z1;
2937: int k=0,l, cptcode;
2938: int first=1, first1;
2939: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
2940: double **dnewm,**doldm;
2941: double *xp;
2942: double *gp, *gm;
2943: double **gradg, **trgradg;
2944: double **mu;
2945: double age,agelim, cov[NCOVMAX];
2946: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
2947: int theta;
2948: char fileresprob[FILENAMELENGTH];
2949: char fileresprobcov[FILENAMELENGTH];
2950: char fileresprobcor[FILENAMELENGTH];
2951:
2952: double ***varpij;
2953:
2954: strcpy(fileresprob,"prob");
2955: strcat(fileresprob,fileres);
2956: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
2957: printf("Problem with resultfile: %s\n", fileresprob);
2958: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
2959: }
2960: strcpy(fileresprobcov,"probcov");
2961: strcat(fileresprobcov,fileres);
2962: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
2963: printf("Problem with resultfile: %s\n", fileresprobcov);
2964: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
2965: }
2966: strcpy(fileresprobcor,"probcor");
2967: strcat(fileresprobcor,fileres);
2968: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
2969: printf("Problem with resultfile: %s\n", fileresprobcor);
2970: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
2971: }
2972: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2973: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
2974: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2975: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
2976: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2977: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
2978: fprintf(ficresprob, "#Local time at start: %s", strstart);
2979: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
2980: fprintf(ficresprob,"# Age");
2981: fprintf(ficresprobcov, "#Local time at start: %s", strstart);
2982: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
2983: fprintf(ficresprobcov,"# Age");
2984: fprintf(ficresprobcor, "#Local time at start: %s", strstart);
2985: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
2986: fprintf(ficresprobcov,"# Age");
2987:
2988:
2989: for(i=1; i<=nlstate;i++)
2990: for(j=1; j<=(nlstate+ndeath);j++){
2991: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
2992: fprintf(ficresprobcov," p%1d-%1d ",i,j);
2993: fprintf(ficresprobcor," p%1d-%1d ",i,j);
2994: }
2995: /* fprintf(ficresprob,"\n");
2996: fprintf(ficresprobcov,"\n");
2997: fprintf(ficresprobcor,"\n");
2998: */
2999: xp=vector(1,npar);
3000: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3001: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3002: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3003: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3004: first=1;
3005: fprintf(ficgp,"\n# Routine varprob");
3006: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3007: fprintf(fichtm,"\n");
3008:
3009: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3010: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3011: file %s<br>\n",optionfilehtmcov);
3012: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3013: and drawn. It helps understanding how is the covariance between two incidences.\
3014: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3015: 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. \
3016: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3017: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3018: standard deviations wide on each axis. <br>\
3019: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3020: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3021: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3022:
3023: cov[1]=1;
3024: tj=cptcoveff;
3025: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3026: j1=0;
3027: for(t=1; t<=tj;t++){
3028: for(i1=1; i1<=ncodemax[t];i1++){
3029: j1++;
3030: if (cptcovn>0) {
3031: fprintf(ficresprob, "\n#********** Variable ");
3032: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3033: fprintf(ficresprob, "**********\n#\n");
3034: fprintf(ficresprobcov, "\n#********** Variable ");
3035: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3036: fprintf(ficresprobcov, "**********\n#\n");
3037:
3038: fprintf(ficgp, "\n#********** Variable ");
3039: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3040: fprintf(ficgp, "**********\n#\n");
3041:
3042:
3043: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3044: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3045: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3046:
3047: fprintf(ficresprobcor, "\n#********** Variable ");
3048: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3049: fprintf(ficresprobcor, "**********\n#");
3050: }
3051:
3052: for (age=bage; age<=fage; age ++){
3053: cov[2]=age;
3054: for (k=1; k<=cptcovn;k++) {
3055: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3056: }
3057: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3058: for (k=1; k<=cptcovprod;k++)
3059: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3060:
3061: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3062: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3063: gp=vector(1,(nlstate)*(nlstate+ndeath));
3064: gm=vector(1,(nlstate)*(nlstate+ndeath));
3065:
3066: for(theta=1; theta <=npar; theta++){
3067: for(i=1; i<=npar; i++)
3068: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3069:
3070: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3071:
3072: k=0;
3073: for(i=1; i<= (nlstate); i++){
3074: for(j=1; j<=(nlstate+ndeath);j++){
3075: k=k+1;
3076: gp[k]=pmmij[i][j];
3077: }
3078: }
3079:
3080: for(i=1; i<=npar; i++)
3081: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3082:
3083: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3084: k=0;
3085: for(i=1; i<=(nlstate); i++){
3086: for(j=1; j<=(nlstate+ndeath);j++){
3087: k=k+1;
3088: gm[k]=pmmij[i][j];
3089: }
3090: }
3091:
3092: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3093: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3094: }
3095:
3096: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3097: for(theta=1; theta <=npar; theta++)
3098: trgradg[j][theta]=gradg[theta][j];
3099:
3100: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3101: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3102: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3103: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3104: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3105: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3106:
3107: pmij(pmmij,cov,ncovmodel,x,nlstate);
3108:
3109: k=0;
3110: for(i=1; i<=(nlstate); i++){
3111: for(j=1; j<=(nlstate+ndeath);j++){
3112: k=k+1;
3113: mu[k][(int) age]=pmmij[i][j];
3114: }
3115: }
3116: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3117: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3118: varpij[i][j][(int)age] = doldm[i][j];
3119:
3120: /*printf("\n%d ",(int)age);
3121: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3122: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3123: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3124: }*/
3125:
3126: fprintf(ficresprob,"\n%d ",(int)age);
3127: fprintf(ficresprobcov,"\n%d ",(int)age);
3128: fprintf(ficresprobcor,"\n%d ",(int)age);
3129:
3130: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3131: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3132: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3133: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3134: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3135: }
3136: i=0;
3137: for (k=1; k<=(nlstate);k++){
3138: for (l=1; l<=(nlstate+ndeath);l++){
3139: i=i++;
3140: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3141: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3142: for (j=1; j<=i;j++){
3143: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3144: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3145: }
3146: }
3147: }/* end of loop for state */
3148: } /* end of loop for age */
3149:
3150: /* Confidence intervalle of pij */
3151: /*
3152: fprintf(ficgp,"\nset noparametric;unset label");
3153: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3154: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3155: 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);
3156: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3157: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3158: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3159: */
3160:
3161: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3162: first1=1;
3163: for (k2=1; k2<=(nlstate);k2++){
3164: for (l2=1; l2<=(nlstate+ndeath);l2++){
3165: if(l2==k2) continue;
3166: j=(k2-1)*(nlstate+ndeath)+l2;
3167: for (k1=1; k1<=(nlstate);k1++){
3168: for (l1=1; l1<=(nlstate+ndeath);l1++){
3169: if(l1==k1) continue;
3170: i=(k1-1)*(nlstate+ndeath)+l1;
3171: if(i<=j) continue;
3172: for (age=bage; age<=fage; age ++){
3173: if ((int)age %5==0){
3174: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3175: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3176: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3177: mu1=mu[i][(int) age]/stepm*YEARM ;
3178: mu2=mu[j][(int) age]/stepm*YEARM;
3179: c12=cv12/sqrt(v1*v2);
3180: /* Computing eigen value of matrix of covariance */
3181: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3182: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3183: /* Eigen vectors */
3184: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3185: /*v21=sqrt(1.-v11*v11); *//* error */
3186: v21=(lc1-v1)/cv12*v11;
3187: v12=-v21;
3188: v22=v11;
3189: tnalp=v21/v11;
3190: if(first1==1){
3191: first1=0;
3192: 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);
3193: }
3194: 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);
3195: /*printf(fignu*/
3196: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3197: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3198: if(first==1){
3199: first=0;
3200: fprintf(ficgp,"\nset parametric;unset label");
3201: 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);
3202: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3203: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3204: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3205: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3206: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3207: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3208: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3209: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3210: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3211: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3212: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3213: 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",\
3214: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3215: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3216: }else{
3217: first=0;
3218: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3219: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3220: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3221: 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",\
3222: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3223: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3224: }/* if first */
3225: } /* age mod 5 */
3226: } /* end loop age */
3227: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3228: first=1;
3229: } /*l12 */
3230: } /* k12 */
3231: } /*l1 */
3232: }/* k1 */
3233: } /* loop covariates */
3234: }
3235: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3236: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3237: free_vector(xp,1,npar);
3238: fclose(ficresprob);
3239: fclose(ficresprobcov);
3240: fclose(ficresprobcor);
3241: fflush(ficgp);
3242: fflush(fichtmcov);
3243: }
3244:
3245:
3246: /******************* Printing html file ***********/
3247: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3248: int lastpass, int stepm, int weightopt, char model[],\
3249: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3250: int popforecast, int estepm ,\
3251: double jprev1, double mprev1,double anprev1, \
3252: double jprev2, double mprev2,double anprev2){
3253: int jj1, k1, i1, cpt;
3254:
3255: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3256: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3257: </ul>");
3258: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3259: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3260: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3261: fprintf(fichtm,"\
3262: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3263: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3264: fprintf(fichtm,"\
3265: - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3266: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3267: fprintf(fichtm,"\
3268: - Life expectancies by age and initial health status (estepm=%2d months): \
3269: <a href=\"%s\">%s</a> <br>\n</li>",
3270: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3271:
3272: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3273:
3274: m=cptcoveff;
3275: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3276:
3277: jj1=0;
3278: for(k1=1; k1<=m;k1++){
3279: for(i1=1; i1<=ncodemax[k1];i1++){
3280: jj1++;
3281: if (cptcovn > 0) {
3282: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3283: for (cpt=1; cpt<=cptcoveff;cpt++)
3284: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3285: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3286: }
3287: /* Pij */
3288: 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> \
3289: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3290: /* Quasi-incidences */
3291: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3292: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
3293: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3294: /* Stable prevalence in each health state */
3295: for(cpt=1; cpt<nlstate;cpt++){
3296: fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
3297: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3298: }
3299: for(cpt=1; cpt<=nlstate;cpt++) {
3300: fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
3301: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3302: }
3303: } /* end i1 */
3304: }/* End k1 */
3305: fprintf(fichtm,"</ul>");
3306:
3307:
3308: fprintf(fichtm,"\
3309: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3310: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3311:
3312: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3313: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3314: fprintf(fichtm,"\
3315: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3316: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3317:
3318: fprintf(fichtm,"\
3319: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3320: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3321: fprintf(fichtm,"\
3322: - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3323: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3324: fprintf(fichtm,"\
3325: - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
3326: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3327: fprintf(fichtm,"\
3328: - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
3329: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3330:
3331: /* if(popforecast==1) fprintf(fichtm,"\n */
3332: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3333: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3334: /* <br>",fileres,fileres,fileres,fileres); */
3335: /* else */
3336: /* 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); */
3337: fflush(fichtm);
3338: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3339:
3340: m=cptcoveff;
3341: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3342:
3343: jj1=0;
3344: for(k1=1; k1<=m;k1++){
3345: for(i1=1; i1<=ncodemax[k1];i1++){
3346: jj1++;
3347: if (cptcovn > 0) {
3348: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3349: for (cpt=1; cpt<=cptcoveff;cpt++)
3350: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3351: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3352: }
3353: for(cpt=1; cpt<=nlstate;cpt++) {
3354: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3355: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3356: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3357: }
3358: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3359: health expectancies in states (1) and (2): %s%d.png<br>\
3360: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3361: } /* end i1 */
3362: }/* End k1 */
3363: fprintf(fichtm,"</ul>");
3364: fflush(fichtm);
3365: }
3366:
3367: /******************* Gnuplot file **************/
3368: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3369:
3370: char dirfileres[132],optfileres[132];
3371: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3372: int ng;
3373: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3374: /* printf("Problem with file %s",optionfilegnuplot); */
3375: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3376: /* } */
3377:
3378: /*#ifdef windows */
3379: fprintf(ficgp,"cd \"%s\" \n",pathc);
3380: /*#endif */
3381: m=pow(2,cptcoveff);
3382:
3383: strcpy(dirfileres,optionfilefiname);
3384: strcpy(optfileres,"vpl");
3385: /* 1eme*/
3386: for (cpt=1; cpt<= nlstate ; cpt ++) {
3387: for (k1=1; k1<= m ; k1 ++) {
3388: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3389: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3390: fprintf(ficgp,"set xlabel \"Age\" \n\
3391: set ylabel \"Probability\" \n\
3392: set ter png small\n\
3393: set size 0.65,0.65\n\
3394: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3395:
3396: for (i=1; i<= nlstate ; i ++) {
3397: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3398: else fprintf(ficgp," \%%*lf (\%%*lf)");
3399: }
3400: 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);
3401: for (i=1; i<= nlstate ; i ++) {
3402: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3403: else fprintf(ficgp," \%%*lf (\%%*lf)");
3404: }
3405: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3406: for (i=1; i<= nlstate ; i ++) {
3407: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3408: else fprintf(ficgp," \%%*lf (\%%*lf)");
3409: }
3410: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3411: }
3412: }
3413: /*2 eme*/
3414:
3415: for (k1=1; k1<= m ; k1 ++) {
3416: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3417: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3418:
3419: for (i=1; i<= nlstate+1 ; i ++) {
3420: k=2*i;
3421: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3422: for (j=1; j<= nlstate+1 ; j ++) {
3423: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3424: else fprintf(ficgp," \%%*lf (\%%*lf)");
3425: }
3426: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3427: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3428: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3429: for (j=1; j<= nlstate+1 ; j ++) {
3430: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3431: else fprintf(ficgp," \%%*lf (\%%*lf)");
3432: }
3433: fprintf(ficgp,"\" t\"\" w l 0,");
3434: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3435: for (j=1; j<= nlstate+1 ; j ++) {
3436: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3437: else fprintf(ficgp," \%%*lf (\%%*lf)");
3438: }
3439: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3440: else fprintf(ficgp,"\" t\"\" w l 0,");
3441: }
3442: }
3443:
3444: /*3eme*/
3445:
3446: for (k1=1; k1<= m ; k1 ++) {
3447: for (cpt=1; cpt<= nlstate ; cpt ++) {
3448: k=2+nlstate*(2*cpt-2);
3449: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3450: fprintf(ficgp,"set ter png small\n\
3451: set size 0.65,0.65\n\
3452: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3453: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3454: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3455: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3456: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3457: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3458: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3459:
3460: */
3461: for (i=1; i< nlstate ; i ++) {
3462: 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);
3463:
3464: }
3465: }
3466: }
3467:
3468: /* CV preval stable (period) */
3469: for (k1=1; k1<= m ; k1 ++) {
3470: for (cpt=1; cpt<=nlstate ; cpt ++) {
3471: k=3;
3472: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3473: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3474: set ter png small\nset size 0.65,0.65\n\
3475: unset log y\n\
3476: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3477:
3478: for (i=1; i< nlstate ; i ++)
3479: fprintf(ficgp,"+$%d",k+i+1);
3480: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3481:
3482: l=3+(nlstate+ndeath)*cpt;
3483: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3484: for (i=1; i< nlstate ; i ++) {
3485: l=3+(nlstate+ndeath)*cpt;
3486: fprintf(ficgp,"+$%d",l+i+1);
3487: }
3488: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3489: }
3490: }
3491:
3492: /* proba elementaires */
3493: for(i=1,jk=1; i <=nlstate; i++){
3494: for(k=1; k <=(nlstate+ndeath); k++){
3495: if (k != i) {
3496: for(j=1; j <=ncovmodel; j++){
3497: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3498: jk++;
3499: fprintf(ficgp,"\n");
3500: }
3501: }
3502: }
3503: }
3504:
3505: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3506: for(jk=1; jk <=m; jk++) {
3507: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3508: if (ng==2)
3509: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3510: else
3511: fprintf(ficgp,"\nset title \"Probability\"\n");
3512: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3513: i=1;
3514: for(k2=1; k2<=nlstate; k2++) {
3515: k3=i;
3516: for(k=1; k<=(nlstate+ndeath); k++) {
3517: if (k != k2){
3518: if(ng==2)
3519: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3520: else
3521: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3522: ij=1;
3523: for(j=3; j <=ncovmodel; j++) {
3524: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3525: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3526: ij++;
3527: }
3528: else
3529: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3530: }
3531: fprintf(ficgp,")/(1");
3532:
3533: for(k1=1; k1 <=nlstate; k1++){
3534: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3535: ij=1;
3536: for(j=3; j <=ncovmodel; j++){
3537: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3538: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3539: ij++;
3540: }
3541: else
3542: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3543: }
3544: fprintf(ficgp,")");
3545: }
3546: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3547: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3548: i=i+ncovmodel;
3549: }
3550: } /* end k */
3551: } /* end k2 */
3552: } /* end jk */
3553: } /* end ng */
3554: fflush(ficgp);
3555: } /* end gnuplot */
3556:
3557:
3558: /*************** Moving average **************/
3559: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3560:
3561: int i, cpt, cptcod;
3562: int modcovmax =1;
3563: int mobilavrange, mob;
3564: double age;
3565:
3566: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3567: a covariate has 2 modalities */
3568: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3569:
3570: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3571: if(mobilav==1) mobilavrange=5; /* default */
3572: else mobilavrange=mobilav;
3573: for (age=bage; age<=fage; age++)
3574: for (i=1; i<=nlstate;i++)
3575: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3576: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3577: /* We keep the original values on the extreme ages bage, fage and for
3578: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3579: we use a 5 terms etc. until the borders are no more concerned.
3580: */
3581: for (mob=3;mob <=mobilavrange;mob=mob+2){
3582: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3583: for (i=1; i<=nlstate;i++){
3584: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3585: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3586: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3587: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3588: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3589: }
3590: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3591: }
3592: }
3593: }/* end age */
3594: }/* end mob */
3595: }else return -1;
3596: return 0;
3597: }/* End movingaverage */
3598:
3599:
3600: /************** Forecasting ******************/
3601: 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){
3602: /* proj1, year, month, day of starting projection
3603: agemin, agemax range of age
3604: dateprev1 dateprev2 range of dates during which prevalence is computed
3605: anproj2 year of en of projection (same day and month as proj1).
3606: */
3607: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3608: int *popage;
3609: double agec; /* generic age */
3610: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3611: double *popeffectif,*popcount;
3612: double ***p3mat;
3613: double ***mobaverage;
3614: char fileresf[FILENAMELENGTH];
3615:
3616: agelim=AGESUP;
3617: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3618:
3619: strcpy(fileresf,"f");
3620: strcat(fileresf,fileres);
3621: if((ficresf=fopen(fileresf,"w"))==NULL) {
3622: printf("Problem with forecast resultfile: %s\n", fileresf);
3623: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3624: }
3625: printf("Computing forecasting: result on file '%s' \n", fileresf);
3626: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3627:
3628: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3629:
3630: if (mobilav!=0) {
3631: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3632: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3633: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3634: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3635: }
3636: }
3637:
3638: stepsize=(int) (stepm+YEARM-1)/YEARM;
3639: if (stepm<=12) stepsize=1;
3640: if(estepm < stepm){
3641: printf ("Problem %d lower than %d\n",estepm, stepm);
3642: }
3643: else hstepm=estepm;
3644:
3645: hstepm=hstepm/stepm;
3646: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3647: fractional in yp1 */
3648: anprojmean=yp;
3649: yp2=modf((yp1*12),&yp);
3650: mprojmean=yp;
3651: yp1=modf((yp2*30.5),&yp);
3652: jprojmean=yp;
3653: if(jprojmean==0) jprojmean=1;
3654: if(mprojmean==0) jprojmean=1;
3655:
3656: i1=cptcoveff;
3657: if (cptcovn < 1){i1=1;}
3658:
3659: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3660:
3661: fprintf(ficresf,"#****** Routine prevforecast **\n");
3662:
3663: /* if (h==(int)(YEARM*yearp)){ */
3664: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3665: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3666: k=k+1;
3667: fprintf(ficresf,"\n#******");
3668: for(j=1;j<=cptcoveff;j++) {
3669: 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]]);
3670: }
3671: fprintf(ficresf,"******\n");
3672: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3673: for(j=1; j<=nlstate+ndeath;j++){
3674: for(i=1; i<=nlstate;i++)
3675: fprintf(ficresf," p%d%d",i,j);
3676: fprintf(ficresf," p.%d",j);
3677: }
3678: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3679: fprintf(ficresf,"\n");
3680: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3681:
3682: for (agec=fage; agec>=(ageminpar-1); agec--){
3683: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3684: nhstepm = nhstepm/hstepm;
3685: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3686: oldm=oldms;savm=savms;
3687: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3688:
3689: for (h=0; h<=nhstepm; h++){
3690: if (h*hstepm/YEARM*stepm ==yearp) {
3691: fprintf(ficresf,"\n");
3692: for(j=1;j<=cptcoveff;j++)
3693: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3694: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3695: }
3696: for(j=1; j<=nlstate+ndeath;j++) {
3697: ppij=0.;
3698: for(i=1; i<=nlstate;i++) {
3699: if (mobilav==1)
3700: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3701: else {
3702: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3703: }
3704: if (h*hstepm/YEARM*stepm== yearp) {
3705: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3706: }
3707: } /* end i */
3708: if (h*hstepm/YEARM*stepm==yearp) {
3709: fprintf(ficresf," %.3f", ppij);
3710: }
3711: }/* end j */
3712: } /* end h */
3713: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3714: } /* end agec */
3715: } /* end yearp */
3716: } /* end cptcod */
3717: } /* end cptcov */
3718:
3719: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3720:
3721: fclose(ficresf);
3722: }
3723:
3724: /************** Forecasting *****not tested NB*************/
3725: 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){
3726:
3727: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3728: int *popage;
3729: double calagedatem, agelim, kk1, kk2;
3730: double *popeffectif,*popcount;
3731: double ***p3mat,***tabpop,***tabpopprev;
3732: double ***mobaverage;
3733: char filerespop[FILENAMELENGTH];
3734:
3735: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3736: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3737: agelim=AGESUP;
3738: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3739:
3740: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3741:
3742:
3743: strcpy(filerespop,"pop");
3744: strcat(filerespop,fileres);
3745: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3746: printf("Problem with forecast resultfile: %s\n", filerespop);
3747: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3748: }
3749: printf("Computing forecasting: result on file '%s' \n", filerespop);
3750: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3751:
3752: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3753:
3754: if (mobilav!=0) {
3755: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3756: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3757: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3758: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3759: }
3760: }
3761:
3762: stepsize=(int) (stepm+YEARM-1)/YEARM;
3763: if (stepm<=12) stepsize=1;
3764:
3765: agelim=AGESUP;
3766:
3767: hstepm=1;
3768: hstepm=hstepm/stepm;
3769:
3770: if (popforecast==1) {
3771: if((ficpop=fopen(popfile,"r"))==NULL) {
3772: printf("Problem with population file : %s\n",popfile);exit(0);
3773: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3774: }
3775: popage=ivector(0,AGESUP);
3776: popeffectif=vector(0,AGESUP);
3777: popcount=vector(0,AGESUP);
3778:
3779: i=1;
3780: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3781:
3782: imx=i;
3783: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3784: }
3785:
3786: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3787: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3788: k=k+1;
3789: fprintf(ficrespop,"\n#******");
3790: for(j=1;j<=cptcoveff;j++) {
3791: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3792: }
3793: fprintf(ficrespop,"******\n");
3794: fprintf(ficrespop,"# Age");
3795: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
3796: if (popforecast==1) fprintf(ficrespop," [Population]");
3797:
3798: for (cpt=0; cpt<=0;cpt++) {
3799: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3800:
3801: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3802: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3803: nhstepm = nhstepm/hstepm;
3804:
3805: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3806: oldm=oldms;savm=savms;
3807: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3808:
3809: for (h=0; h<=nhstepm; h++){
3810: if (h==(int) (calagedatem+YEARM*cpt)) {
3811: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3812: }
3813: for(j=1; j<=nlstate+ndeath;j++) {
3814: kk1=0.;kk2=0;
3815: for(i=1; i<=nlstate;i++) {
3816: if (mobilav==1)
3817: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
3818: else {
3819: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
3820: }
3821: }
3822: if (h==(int)(calagedatem+12*cpt)){
3823: tabpop[(int)(agedeb)][j][cptcod]=kk1;
3824: /*fprintf(ficrespop," %.3f", kk1);
3825: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
3826: }
3827: }
3828: for(i=1; i<=nlstate;i++){
3829: kk1=0.;
3830: for(j=1; j<=nlstate;j++){
3831: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
3832: }
3833: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
3834: }
3835:
3836: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
3837: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
3838: }
3839: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3840: }
3841: }
3842:
3843: /******/
3844:
3845: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
3846: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
3847: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
3848: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
3849: nhstepm = nhstepm/hstepm;
3850:
3851: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3852: oldm=oldms;savm=savms;
3853: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
3854: for (h=0; h<=nhstepm; h++){
3855: if (h==(int) (calagedatem+YEARM*cpt)) {
3856: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
3857: }
3858: for(j=1; j<=nlstate+ndeath;j++) {
3859: kk1=0.;kk2=0;
3860: for(i=1; i<=nlstate;i++) {
3861: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
3862: }
3863: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
3864: }
3865: }
3866: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3867: }
3868: }
3869: }
3870: }
3871:
3872: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3873:
3874: if (popforecast==1) {
3875: free_ivector(popage,0,AGESUP);
3876: free_vector(popeffectif,0,AGESUP);
3877: free_vector(popcount,0,AGESUP);
3878: }
3879: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3880: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3881: fclose(ficrespop);
3882: } /* End of popforecast */
3883:
3884: int fileappend(FILE *fichier, char *optionfich)
3885: {
3886: if((fichier=fopen(optionfich,"a"))==NULL) {
3887: printf("Problem with file: %s\n", optionfich);
3888: fprintf(ficlog,"Problem with file: %s\n", optionfich);
3889: return (0);
3890: }
3891: fflush(fichier);
3892: return (1);
3893: }
3894:
3895:
3896: /**************** function prwizard **********************/
3897: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
3898: {
3899:
3900: /* Wizard to print covariance matrix template */
3901:
3902: char ca[32], cb[32], cc[32];
3903: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
3904: int numlinepar;
3905:
3906: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3907: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
3908: for(i=1; i <=nlstate; i++){
3909: jj=0;
3910: for(j=1; j <=nlstate+ndeath; j++){
3911: if(j==i) continue;
3912: jj++;
3913: /*ca[0]= k+'a'-1;ca[1]='\0';*/
3914: printf("%1d%1d",i,j);
3915: fprintf(ficparo,"%1d%1d",i,j);
3916: for(k=1; k<=ncovmodel;k++){
3917: /* printf(" %lf",param[i][j][k]); */
3918: /* fprintf(ficparo," %lf",param[i][j][k]); */
3919: printf(" 0.");
3920: fprintf(ficparo," 0.");
3921: }
3922: printf("\n");
3923: fprintf(ficparo,"\n");
3924: }
3925: }
3926: printf("# Scales (for hessian or gradient estimation)\n");
3927: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
3928: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
3929: for(i=1; i <=nlstate; i++){
3930: jj=0;
3931: for(j=1; j <=nlstate+ndeath; j++){
3932: if(j==i) continue;
3933: jj++;
3934: fprintf(ficparo,"%1d%1d",i,j);
3935: printf("%1d%1d",i,j);
3936: fflush(stdout);
3937: for(k=1; k<=ncovmodel;k++){
3938: /* printf(" %le",delti3[i][j][k]); */
3939: /* fprintf(ficparo," %le",delti3[i][j][k]); */
3940: printf(" 0.");
3941: fprintf(ficparo," 0.");
3942: }
3943: numlinepar++;
3944: printf("\n");
3945: fprintf(ficparo,"\n");
3946: }
3947: }
3948: printf("# Covariance matrix\n");
3949: /* # 121 Var(a12)\n\ */
3950: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3951: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
3952: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
3953: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
3954: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
3955: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
3956: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3957: fflush(stdout);
3958: fprintf(ficparo,"# Covariance matrix\n");
3959: /* # 121 Var(a12)\n\ */
3960: /* # 122 Cov(b12,a12) Var(b12)\n\ */
3961: /* # ...\n\ */
3962: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
3963:
3964: for(itimes=1;itimes<=2;itimes++){
3965: jj=0;
3966: for(i=1; i <=nlstate; i++){
3967: for(j=1; j <=nlstate+ndeath; j++){
3968: if(j==i) continue;
3969: for(k=1; k<=ncovmodel;k++){
3970: jj++;
3971: ca[0]= k+'a'-1;ca[1]='\0';
3972: if(itimes==1){
3973: printf("#%1d%1d%d",i,j,k);
3974: fprintf(ficparo,"#%1d%1d%d",i,j,k);
3975: }else{
3976: printf("%1d%1d%d",i,j,k);
3977: fprintf(ficparo,"%1d%1d%d",i,j,k);
3978: /* printf(" %.5le",matcov[i][j]); */
3979: }
3980: ll=0;
3981: for(li=1;li <=nlstate; li++){
3982: for(lj=1;lj <=nlstate+ndeath; lj++){
3983: if(lj==li) continue;
3984: for(lk=1;lk<=ncovmodel;lk++){
3985: ll++;
3986: if(ll<=jj){
3987: cb[0]= lk +'a'-1;cb[1]='\0';
3988: if(ll<jj){
3989: if(itimes==1){
3990: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3991: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
3992: }else{
3993: printf(" 0.");
3994: fprintf(ficparo," 0.");
3995: }
3996: }else{
3997: if(itimes==1){
3998: printf(" Var(%s%1d%1d)",ca,i,j);
3999: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4000: }else{
4001: printf(" 0.");
4002: fprintf(ficparo," 0.");
4003: }
4004: }
4005: }
4006: } /* end lk */
4007: } /* end lj */
4008: } /* end li */
4009: printf("\n");
4010: fprintf(ficparo,"\n");
4011: numlinepar++;
4012: } /* end k*/
4013: } /*end j */
4014: } /* end i */
4015: } /* end itimes */
4016:
4017: } /* end of prwizard */
4018: /******************* Gompertz Likelihood ******************************/
4019: double gompertz(double x[])
4020: {
4021: double A,B,L=0.0,sump=0.,num=0.;
4022: int i,n=0; /* n is the size of the sample */
4023:
4024: for (i=0;i<=imx-1 ; i++) {
4025: sump=sump+weight[i];
4026: /* sump=sump+1;*/
4027: num=num+1;
4028: }
4029:
4030:
4031: /* for (i=0; i<=imx; i++)
4032: 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]);*/
4033:
4034: for (i=1;i<=imx ; i++)
4035: {
4036: if (cens[i] == 1 && wav[i]>1)
4037: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4038:
4039: if (cens[i] == 0 && wav[i]>1)
4040: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4041: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4042:
4043: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4044: if (wav[i] > 1 ) { /* ??? */
4045: L=L+A*weight[i];
4046: /* 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]);*/
4047: }
4048: }
4049:
4050: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4051:
4052: return -2*L*num/sump;
4053: }
4054:
4055: /******************* Printing html file ***********/
4056: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4057: int lastpass, int stepm, int weightopt, char model[],\
4058: int imx, double p[],double **matcov,double agemortsup){
4059: int i,k;
4060:
4061: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4062: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4063: for (i=1;i<=2;i++)
4064: 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]));
4065: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4066: fprintf(fichtm,"</ul>");
4067:
4068: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4069:
4070: fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
4071:
4072: for (k=agegomp;k<(agemortsup-2);k++)
4073: 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]);
4074:
4075:
4076: fflush(fichtm);
4077: }
4078:
4079: /******************* Gnuplot file **************/
4080: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4081:
4082: char dirfileres[132],optfileres[132];
4083: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4084: int ng;
4085:
4086:
4087: /*#ifdef windows */
4088: fprintf(ficgp,"cd \"%s\" \n",pathc);
4089: /*#endif */
4090:
4091:
4092: strcpy(dirfileres,optionfilefiname);
4093: strcpy(optfileres,"vpl");
4094: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4095: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4096: fprintf(ficgp, "set ter png small\n set log y\n");
4097: fprintf(ficgp, "set size 0.65,0.65\n");
4098: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4099:
4100: }
4101:
4102:
4103:
4104:
4105: /***********************************************/
4106: /**************** Main Program *****************/
4107: /***********************************************/
4108:
4109: int main(int argc, char *argv[])
4110: {
4111: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4112: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4113: int linei, month, year,iout;
4114: int jj, ll, li, lj, lk, imk;
4115: int numlinepar=0; /* Current linenumber of parameter file */
4116: int itimes;
4117: int NDIM=2;
4118:
4119: char ca[32], cb[32], cc[32];
4120: char dummy[]=" ";
4121: /* FILE *fichtm; *//* Html File */
4122: /* FILE *ficgp;*/ /*Gnuplot File */
4123: struct stat info;
4124: double agedeb, agefin,hf;
4125: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4126:
4127: double fret;
4128: double **xi,tmp,delta;
4129:
4130: double dum; /* Dummy variable */
4131: double ***p3mat;
4132: double ***mobaverage;
4133: int *indx;
4134: char line[MAXLINE], linepar[MAXLINE];
4135: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4136: char pathr[MAXLINE], pathimach[MAXLINE];
4137: int firstobs=1, lastobs=10;
4138: int sdeb, sfin; /* Status at beginning and end */
4139: int c, h , cpt,l;
4140: int ju,jl, mi;
4141: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4142: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4143: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4144: int mobilav=0,popforecast=0;
4145: int hstepm, nhstepm;
4146: int agemortsup;
4147: float sumlpop=0.;
4148: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4149: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4150:
4151: double bage, fage, age, agelim, agebase;
4152: double ftolpl=FTOL;
4153: double **prlim;
4154: double *severity;
4155: double ***param; /* Matrix of parameters */
4156: double *p;
4157: double **matcov; /* Matrix of covariance */
4158: double ***delti3; /* Scale */
4159: double *delti; /* Scale */
4160: double ***eij, ***vareij;
4161: double **varpl; /* Variances of prevalence limits by age */
4162: double *epj, vepp;
4163: double kk1, kk2;
4164: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4165: double **ximort;
4166: char *alph[]={"a","a","b","c","d","e"}, str[4];
4167: int *dcwave;
4168:
4169: char z[1]="c", occ;
4170:
4171: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4172: char strstart[80], *strt, strtend[80];
4173: char *stratrunc;
4174: int lstra;
4175:
4176: long total_usecs;
4177:
4178: /* setlocale (LC_ALL, ""); */
4179: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4180: /* textdomain (PACKAGE); */
4181: /* setlocale (LC_CTYPE, ""); */
4182: /* setlocale (LC_MESSAGES, ""); */
4183:
4184: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4185: (void) gettimeofday(&start_time,&tzp);
4186: curr_time=start_time;
4187: tm = *localtime(&start_time.tv_sec);
4188: tmg = *gmtime(&start_time.tv_sec);
4189: strcpy(strstart,asctime(&tm));
4190:
4191: /* printf("Localtime (at start)=%s",strstart); */
4192: /* tp.tv_sec = tp.tv_sec +86400; */
4193: /* tm = *localtime(&start_time.tv_sec); */
4194: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4195: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4196: /* tmg.tm_hour=tmg.tm_hour + 1; */
4197: /* tp.tv_sec = mktime(&tmg); */
4198: /* strt=asctime(&tmg); */
4199: /* printf("Time(after) =%s",strstart); */
4200: /* (void) time (&time_value);
4201: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4202: * tm = *localtime(&time_value);
4203: * strstart=asctime(&tm);
4204: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4205: */
4206:
4207: nberr=0; /* Number of errors and warnings */
4208: nbwarn=0;
4209: getcwd(pathcd, size);
4210:
4211: printf("\n%s\n%s",version,fullversion);
4212: if(argc <=1){
4213: printf("\nEnter the parameter file name: ");
4214: scanf("%s",pathtot);
4215: }
4216: else{
4217: strcpy(pathtot,argv[1]);
4218: }
4219: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4220: /*cygwin_split_path(pathtot,path,optionfile);
4221: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4222: /* cutv(path,optionfile,pathtot,'\\');*/
4223:
4224: /* Split argv[0], imach program to get pathimach */
4225: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4226: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4227: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4228: /* strcpy(pathimach,argv[0]); */
4229: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4230: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4231: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4232: chdir(path);
4233: strcpy(command,"mkdir ");
4234: strcat(command,optionfilefiname);
4235: if((outcmd=system(command)) != 0){
4236: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4237: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4238: /* fclose(ficlog); */
4239: /* exit(1); */
4240: }
4241: /* if((imk=mkdir(optionfilefiname))<0){ */
4242: /* perror("mkdir"); */
4243: /* } */
4244:
4245: /*-------- arguments in the command line --------*/
4246:
4247: /* Log file */
4248: strcat(filelog, optionfilefiname);
4249: strcat(filelog,".log"); /* */
4250: if((ficlog=fopen(filelog,"w"))==NULL) {
4251: printf("Problem with logfile %s\n",filelog);
4252: goto end;
4253: }
4254: fprintf(ficlog,"Log filename:%s\n",filelog);
4255: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4256: fprintf(ficlog,"\nEnter the parameter file name: \n");
4257: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4258: path=%s \n\
4259: optionfile=%s\n\
4260: optionfilext=%s\n\
4261: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4262:
4263: printf("Local time (at start):%s",strstart);
4264: fprintf(ficlog,"Local time (at start): %s",strstart);
4265: fflush(ficlog);
4266: /* (void) gettimeofday(&curr_time,&tzp); */
4267: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4268:
4269: /* */
4270: strcpy(fileres,"r");
4271: strcat(fileres, optionfilefiname);
4272: strcat(fileres,".txt"); /* Other files have txt extension */
4273:
4274: /*---------arguments file --------*/
4275:
4276: if((ficpar=fopen(optionfile,"r"))==NULL) {
4277: printf("Problem with optionfile %s\n",optionfile);
4278: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4279: fflush(ficlog);
4280: goto end;
4281: }
4282:
4283:
4284:
4285: strcpy(filereso,"o");
4286: strcat(filereso,fileres);
4287: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4288: printf("Problem with Output resultfile: %s\n", filereso);
4289: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4290: fflush(ficlog);
4291: goto end;
4292: }
4293:
4294: /* Reads comments: lines beginning with '#' */
4295: numlinepar=0;
4296: while((c=getc(ficpar))=='#' && c!= EOF){
4297: ungetc(c,ficpar);
4298: fgets(line, MAXLINE, ficpar);
4299: numlinepar++;
4300: puts(line);
4301: fputs(line,ficparo);
4302: fputs(line,ficlog);
4303: }
4304: ungetc(c,ficpar);
4305:
4306: 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);
4307: numlinepar++;
4308: 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);
4309: 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);
4310: 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);
4311: fflush(ficlog);
4312: while((c=getc(ficpar))=='#' && c!= EOF){
4313: ungetc(c,ficpar);
4314: fgets(line, MAXLINE, ficpar);
4315: numlinepar++;
4316: puts(line);
4317: fputs(line,ficparo);
4318: fputs(line,ficlog);
4319: }
4320: ungetc(c,ficpar);
4321:
4322:
4323: covar=matrix(0,NCOVMAX,1,n);
4324: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4325: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4326:
4327: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4328: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4329: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4330:
4331: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4332: delti=delti3[1][1];
4333: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4334: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4335: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4336: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4337: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4338: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4339: fclose (ficparo);
4340: fclose (ficlog);
4341: exit(0);
4342: }
4343: else if(mle==-3) {
4344: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4345: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4346: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4347: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4348: matcov=matrix(1,npar,1,npar);
4349: }
4350: else{
4351: /* Read guess parameters */
4352: /* Reads comments: lines beginning with '#' */
4353: while((c=getc(ficpar))=='#' && c!= EOF){
4354: ungetc(c,ficpar);
4355: fgets(line, MAXLINE, ficpar);
4356: numlinepar++;
4357: puts(line);
4358: fputs(line,ficparo);
4359: fputs(line,ficlog);
4360: }
4361: ungetc(c,ficpar);
4362:
4363: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4364: for(i=1; i <=nlstate; i++){
4365: j=0;
4366: for(jj=1; jj <=nlstate+ndeath; jj++){
4367: if(jj==i) continue;
4368: j++;
4369: fscanf(ficpar,"%1d%1d",&i1,&j1);
4370: if ((i1 != i) && (j1 != j)){
4371: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4372: exit(1);
4373: }
4374: fprintf(ficparo,"%1d%1d",i1,j1);
4375: if(mle==1)
4376: printf("%1d%1d",i,j);
4377: fprintf(ficlog,"%1d%1d",i,j);
4378: for(k=1; k<=ncovmodel;k++){
4379: fscanf(ficpar," %lf",¶m[i][j][k]);
4380: if(mle==1){
4381: printf(" %lf",param[i][j][k]);
4382: fprintf(ficlog," %lf",param[i][j][k]);
4383: }
4384: else
4385: fprintf(ficlog," %lf",param[i][j][k]);
4386: fprintf(ficparo," %lf",param[i][j][k]);
4387: }
4388: fscanf(ficpar,"\n");
4389: numlinepar++;
4390: if(mle==1)
4391: printf("\n");
4392: fprintf(ficlog,"\n");
4393: fprintf(ficparo,"\n");
4394: }
4395: }
4396: fflush(ficlog);
4397:
4398: p=param[1][1];
4399:
4400: /* Reads comments: lines beginning with '#' */
4401: while((c=getc(ficpar))=='#' && c!= EOF){
4402: ungetc(c,ficpar);
4403: fgets(line, MAXLINE, ficpar);
4404: numlinepar++;
4405: puts(line);
4406: fputs(line,ficparo);
4407: fputs(line,ficlog);
4408: }
4409: ungetc(c,ficpar);
4410:
4411: for(i=1; i <=nlstate; i++){
4412: for(j=1; j <=nlstate+ndeath-1; j++){
4413: fscanf(ficpar,"%1d%1d",&i1,&j1);
4414: if ((i1-i)*(j1-j)!=0){
4415: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4416: exit(1);
4417: }
4418: printf("%1d%1d",i,j);
4419: fprintf(ficparo,"%1d%1d",i1,j1);
4420: fprintf(ficlog,"%1d%1d",i1,j1);
4421: for(k=1; k<=ncovmodel;k++){
4422: fscanf(ficpar,"%le",&delti3[i][j][k]);
4423: printf(" %le",delti3[i][j][k]);
4424: fprintf(ficparo," %le",delti3[i][j][k]);
4425: fprintf(ficlog," %le",delti3[i][j][k]);
4426: }
4427: fscanf(ficpar,"\n");
4428: numlinepar++;
4429: printf("\n");
4430: fprintf(ficparo,"\n");
4431: fprintf(ficlog,"\n");
4432: }
4433: }
4434: fflush(ficlog);
4435:
4436: delti=delti3[1][1];
4437:
4438:
4439: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4440:
4441: /* Reads comments: lines beginning with '#' */
4442: while((c=getc(ficpar))=='#' && c!= EOF){
4443: ungetc(c,ficpar);
4444: fgets(line, MAXLINE, ficpar);
4445: numlinepar++;
4446: puts(line);
4447: fputs(line,ficparo);
4448: fputs(line,ficlog);
4449: }
4450: ungetc(c,ficpar);
4451:
4452: matcov=matrix(1,npar,1,npar);
4453: for(i=1; i <=npar; i++){
4454: fscanf(ficpar,"%s",&str);
4455: if(mle==1)
4456: printf("%s",str);
4457: fprintf(ficlog,"%s",str);
4458: fprintf(ficparo,"%s",str);
4459: for(j=1; j <=i; j++){
4460: fscanf(ficpar," %le",&matcov[i][j]);
4461: if(mle==1){
4462: printf(" %.5le",matcov[i][j]);
4463: }
4464: fprintf(ficlog," %.5le",matcov[i][j]);
4465: fprintf(ficparo," %.5le",matcov[i][j]);
4466: }
4467: fscanf(ficpar,"\n");
4468: numlinepar++;
4469: if(mle==1)
4470: printf("\n");
4471: fprintf(ficlog,"\n");
4472: fprintf(ficparo,"\n");
4473: }
4474: for(i=1; i <=npar; i++)
4475: for(j=i+1;j<=npar;j++)
4476: matcov[i][j]=matcov[j][i];
4477:
4478: if(mle==1)
4479: printf("\n");
4480: fprintf(ficlog,"\n");
4481:
4482: fflush(ficlog);
4483:
4484: /*-------- Rewriting parameter file ----------*/
4485: strcpy(rfileres,"r"); /* "Rparameterfile */
4486: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4487: strcat(rfileres,"."); /* */
4488: strcat(rfileres,optionfilext); /* Other files have txt extension */
4489: if((ficres =fopen(rfileres,"w"))==NULL) {
4490: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4491: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4492: }
4493: fprintf(ficres,"#%s\n",version);
4494: } /* End of mle != -3 */
4495:
4496: /*-------- data file ----------*/
4497: if((fic=fopen(datafile,"r"))==NULL) {
4498: printf("Problem with datafile: %s\n", datafile);goto end;
4499: fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
4500: }
4501:
4502: n= lastobs;
4503: severity = vector(1,maxwav);
4504: outcome=imatrix(1,maxwav+1,1,n);
4505: num=lvector(1,n);
4506: moisnais=vector(1,n);
4507: annais=vector(1,n);
4508: moisdc=vector(1,n);
4509: andc=vector(1,n);
4510: agedc=vector(1,n);
4511: cod=ivector(1,n);
4512: weight=vector(1,n);
4513: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4514: mint=matrix(1,maxwav,1,n);
4515: anint=matrix(1,maxwav,1,n);
4516: s=imatrix(1,maxwav+1,1,n);
4517: tab=ivector(1,NCOVMAX);
4518: ncodemax=ivector(1,8);
4519:
4520: i=1;
4521: linei=0;
4522: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4523: linei=linei+1;
4524: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4525: if(line[j] == '\t')
4526: line[j] = ' ';
4527: }
4528: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4529: ;
4530: };
4531: line[j+1]=0; /* Trims blanks at end of line */
4532: if(line[0]=='#'){
4533: fprintf(ficlog,"Comment line\n%s\n",line);
4534: printf("Comment line\n%s\n",line);
4535: continue;
4536: }
4537:
4538: for (j=maxwav;j>=1;j--){
4539: cutv(stra, strb,line,' ');
4540: errno=0;
4541: lval=strtol(strb,&endptr,10);
4542: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4543: if( strb[0]=='\0' || (*endptr != '\0')){
4544: printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
4545: exit(1);
4546: }
4547: s[j][i]=lval;
4548:
4549: strcpy(line,stra);
4550: cutv(stra, strb,line,' ');
4551: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4552: }
4553: else if(iout=sscanf(strb,"%s.") != 0){
4554: month=99;
4555: year=9999;
4556: }else{
4557: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4558: exit(1);
4559: }
4560: anint[j][i]= (double) year;
4561: mint[j][i]= (double)month;
4562: strcpy(line,stra);
4563: } /* ENd Waves */
4564:
4565: cutv(stra, strb,line,' ');
4566: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4567: }
4568: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4569: month=99;
4570: year=9999;
4571: }else{
4572: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4573: exit(1);
4574: }
4575: andc[i]=(double) year;
4576: moisdc[i]=(double) month;
4577: strcpy(line,stra);
4578:
4579: cutv(stra, strb,line,' ');
4580: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4581: }
4582: else if(iout=sscanf(strb,"%s.") != 0){
4583: month=99;
4584: year=9999;
4585: }else{
4586: printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
4587: exit(1);
4588: }
4589: annais[i]=(double)(year);
4590: moisnais[i]=(double)(month);
4591: strcpy(line,stra);
4592:
4593: cutv(stra, strb,line,' ');
4594: errno=0;
4595: lval=strtol(strb,&endptr,10);
4596: if( strb[0]=='\0' || (*endptr != '\0')){
4597: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4598: exit(1);
4599: }
4600: weight[i]=(double)(lval);
4601: strcpy(line,stra);
4602:
4603: for (j=ncovcol;j>=1;j--){
4604: cutv(stra, strb,line,' ');
4605: errno=0;
4606: lval=strtol(strb,&endptr,10);
4607: if( strb[0]=='\0' || (*endptr != '\0')){
4608: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
4609: exit(1);
4610: }
4611: if(lval <-1 || lval >1){
4612: printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);
4613: exit(1);
4614: }
4615: covar[j][i]=(double)(lval);
4616: strcpy(line,stra);
4617: }
4618: lstra=strlen(stra);
4619:
4620: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4621: stratrunc = &(stra[lstra-9]);
4622: num[i]=atol(stratrunc);
4623: }
4624: else
4625: num[i]=atol(stra);
4626: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4627: 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;}*/
4628:
4629: i=i+1;
4630: } /* End loop reading data */
4631: /* printf("ii=%d", ij);
4632: scanf("%d",i);*/
4633: imx=i-1; /* Number of individuals */
4634:
4635: /* for (i=1; i<=imx; i++){
4636: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4637: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4638: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4639: }*/
4640: /* for (i=1; i<=imx; i++){
4641: if (s[4][i]==9) s[4][i]=-1;
4642: 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]));}*/
4643:
4644: /* for (i=1; i<=imx; i++) */
4645:
4646: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4647: else weight[i]=1;*/
4648:
4649: /* Calculation of the number of parameters from char model */
4650: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4651: Tprod=ivector(1,15);
4652: Tvaraff=ivector(1,15);
4653: Tvard=imatrix(1,15,1,2);
4654: Tage=ivector(1,15);
4655:
4656: if (strlen(model) >1){ /* If there is at least 1 covariate */
4657: j=0, j1=0, k1=1, k2=1;
4658: j=nbocc(model,'+'); /* j=Number of '+' */
4659: j1=nbocc(model,'*'); /* j1=Number of '*' */
4660: cptcovn=j+1;
4661: cptcovprod=j1; /*Number of products */
4662:
4663: strcpy(modelsav,model);
4664: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4665: printf("Error. Non available option model=%s ",model);
4666: fprintf(ficlog,"Error. Non available option model=%s ",model);
4667: goto end;
4668: }
4669:
4670: /* This loop fills the array Tvar from the string 'model'.*/
4671:
4672: for(i=(j+1); i>=1;i--){
4673: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4674: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4675: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4676: /*scanf("%d",i);*/
4677: if (strchr(strb,'*')) { /* Model includes a product */
4678: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4679: if (strcmp(strc,"age")==0) { /* Vn*age */
4680: cptcovprod--;
4681: cutv(strb,stre,strd,'V');
4682: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4683: cptcovage++;
4684: Tage[cptcovage]=i;
4685: /*printf("stre=%s ", stre);*/
4686: }
4687: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4688: cptcovprod--;
4689: cutv(strb,stre,strc,'V');
4690: Tvar[i]=atoi(stre);
4691: cptcovage++;
4692: Tage[cptcovage]=i;
4693: }
4694: else { /* Age is not in the model */
4695: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4696: Tvar[i]=ncovcol+k1;
4697: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4698: Tprod[k1]=i;
4699: Tvard[k1][1]=atoi(strc); /* m*/
4700: Tvard[k1][2]=atoi(stre); /* n */
4701: Tvar[cptcovn+k2]=Tvard[k1][1];
4702: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4703: for (k=1; k<=lastobs;k++)
4704: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4705: k1++;
4706: k2=k2+2;
4707: }
4708: }
4709: else { /* no more sum */
4710: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4711: /* scanf("%d",i);*/
4712: cutv(strd,strc,strb,'V');
4713: Tvar[i]=atoi(strc);
4714: }
4715: strcpy(modelsav,stra);
4716: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4717: scanf("%d",i);*/
4718: } /* end of loop + */
4719: } /* end model */
4720:
4721: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4722: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4723:
4724: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4725: printf("cptcovprod=%d ", cptcovprod);
4726: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4727:
4728: scanf("%d ",i);
4729: fclose(fic);*/
4730:
4731: /* if(mle==1){*/
4732: if (weightopt != 1) { /* Maximisation without weights*/
4733: for(i=1;i<=n;i++) weight[i]=1.0;
4734: }
4735: /*-calculation of age at interview from date of interview and age at death -*/
4736: agev=matrix(1,maxwav,1,imx);
4737:
4738: for (i=1; i<=imx; i++) {
4739: for(m=2; (m<= maxwav); m++) {
4740: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4741: anint[m][i]=9999;
4742: s[m][i]=-1;
4743: }
4744: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4745: nberr++;
4746: 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);
4747: 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);
4748: s[m][i]=-1;
4749: }
4750: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4751: nberr++;
4752: 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]);
4753: 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]);
4754: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4755: }
4756: }
4757: }
4758:
4759: for (i=1; i<=imx; i++) {
4760: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4761: for(m=firstpass; (m<= lastpass); m++){
4762: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4763: if (s[m][i] >= nlstate+1) {
4764: if(agedc[i]>0)
4765: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4766: agev[m][i]=agedc[i];
4767: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4768: else {
4769: if ((int)andc[i]!=9999){
4770: nbwarn++;
4771: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4772: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4773: agev[m][i]=-1;
4774: }
4775: }
4776: }
4777: else if(s[m][i] !=9){ /* Standard case, age in fractional
4778: years but with the precision of a month */
4779: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
4780: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
4781: agev[m][i]=1;
4782: else if(agev[m][i] <agemin){
4783: agemin=agev[m][i];
4784: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
4785: }
4786: else if(agev[m][i] >agemax){
4787: agemax=agev[m][i];
4788: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
4789: }
4790: /*agev[m][i]=anint[m][i]-annais[i];*/
4791: /* agev[m][i] = age[i]+2*m;*/
4792: }
4793: else { /* =9 */
4794: agev[m][i]=1;
4795: s[m][i]=-1;
4796: }
4797: }
4798: else /*= 0 Unknown */
4799: agev[m][i]=1;
4800: }
4801:
4802: }
4803: for (i=1; i<=imx; i++) {
4804: for(m=firstpass; (m<=lastpass); m++){
4805: if (s[m][i] > (nlstate+ndeath)) {
4806: nberr++;
4807: 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);
4808: 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);
4809: goto end;
4810: }
4811: }
4812: }
4813:
4814: /*for (i=1; i<=imx; i++){
4815: for (m=firstpass; (m<lastpass); m++){
4816: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
4817: }
4818:
4819: }*/
4820:
4821:
4822: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4823: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
4824:
4825: agegomp=(int)agemin;
4826: free_vector(severity,1,maxwav);
4827: free_imatrix(outcome,1,maxwav+1,1,n);
4828: free_vector(moisnais,1,n);
4829: free_vector(annais,1,n);
4830: /* free_matrix(mint,1,maxwav,1,n);
4831: free_matrix(anint,1,maxwav,1,n);*/
4832: free_vector(moisdc,1,n);
4833: free_vector(andc,1,n);
4834:
4835:
4836: wav=ivector(1,imx);
4837: dh=imatrix(1,lastpass-firstpass+1,1,imx);
4838: bh=imatrix(1,lastpass-firstpass+1,1,imx);
4839: mw=imatrix(1,lastpass-firstpass+1,1,imx);
4840:
4841: /* Concatenates waves */
4842: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
4843:
4844: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
4845:
4846: Tcode=ivector(1,100);
4847: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
4848: ncodemax[1]=1;
4849: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
4850:
4851: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
4852: the estimations*/
4853: h=0;
4854: m=pow(2,cptcoveff);
4855:
4856: for(k=1;k<=cptcoveff; k++){
4857: for(i=1; i <=(m/pow(2,k));i++){
4858: for(j=1; j <= ncodemax[k]; j++){
4859: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
4860: h++;
4861: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
4862: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
4863: }
4864: }
4865: }
4866: }
4867: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
4868: codtab[1][2]=1;codtab[2][2]=2; */
4869: /* for(i=1; i <=m ;i++){
4870: for(k=1; k <=cptcovn; k++){
4871: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
4872: }
4873: printf("\n");
4874: }
4875: scanf("%d",i);*/
4876:
4877: /*------------ gnuplot -------------*/
4878: strcpy(optionfilegnuplot,optionfilefiname);
4879: if(mle==-3)
4880: strcat(optionfilegnuplot,"-mort");
4881: strcat(optionfilegnuplot,".gp");
4882:
4883: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
4884: printf("Problem with file %s",optionfilegnuplot);
4885: }
4886: else{
4887: fprintf(ficgp,"\n# %s\n", version);
4888: fprintf(ficgp,"# %s\n", optionfilegnuplot);
4889: fprintf(ficgp,"set missing 'NaNq'\n");
4890: }
4891: /* fclose(ficgp);*/
4892: /*--------- index.htm --------*/
4893:
4894: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
4895: if(mle==-3)
4896: strcat(optionfilehtm,"-mort");
4897: strcat(optionfilehtm,".htm");
4898: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
4899: printf("Problem with %s \n",optionfilehtm), exit(0);
4900: }
4901:
4902: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
4903: strcat(optionfilehtmcov,"-cov.htm");
4904: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
4905: printf("Problem with %s \n",optionfilehtmcov), exit(0);
4906: }
4907: else{
4908: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
4909: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4910: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
4911: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
4912: }
4913:
4914: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
4915: <hr size=\"2\" color=\"#EC5E5E\"> \n\
4916: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
4917: \n\
4918: <hr size=\"2\" color=\"#EC5E5E\">\
4919: <ul><li><h4>Parameter files</h4>\n\
4920: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
4921: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
4922: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
4923: - Date and time at start: %s</ul>\n",\
4924: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
4925: fileres,fileres,\
4926: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
4927: fflush(fichtm);
4928:
4929: strcpy(pathr,path);
4930: strcat(pathr,optionfilefiname);
4931: chdir(optionfilefiname); /* Move to directory named optionfile */
4932:
4933: /* Calculates basic frequencies. Computes observed prevalence at single age
4934: and prints on file fileres'p'. */
4935: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
4936:
4937: fprintf(fichtm,"\n");
4938: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
4939: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
4940: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
4941: imx,agemin,agemax,jmin,jmax,jmean);
4942: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4943: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4944: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4945: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
4946: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
4947:
4948:
4949: /* For Powell, parameters are in a vector p[] starting at p[1]
4950: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
4951: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
4952:
4953: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
4954:
4955: if (mle==-3){
4956: ximort=matrix(1,NDIM,1,NDIM);
4957: cens=ivector(1,n);
4958: ageexmed=vector(1,n);
4959: agecens=vector(1,n);
4960: dcwave=ivector(1,n);
4961:
4962: for (i=1; i<=imx; i++){
4963: dcwave[i]=-1;
4964: for (m=firstpass; m<=lastpass; m++)
4965: if (s[m][i]>nlstate) {
4966: dcwave[i]=m;
4967: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
4968: break;
4969: }
4970: }
4971:
4972: for (i=1; i<=imx; i++) {
4973: if (wav[i]>0){
4974: ageexmed[i]=agev[mw[1][i]][i];
4975: j=wav[i];
4976: agecens[i]=1.;
4977:
4978: if (ageexmed[i]> 1 && wav[i] > 0){
4979: agecens[i]=agev[mw[j][i]][i];
4980: cens[i]= 1;
4981: }else if (ageexmed[i]< 1)
4982: cens[i]= -1;
4983: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
4984: cens[i]=0 ;
4985: }
4986: else cens[i]=-1;
4987: }
4988:
4989: for (i=1;i<=NDIM;i++) {
4990: for (j=1;j<=NDIM;j++)
4991: ximort[i][j]=(i == j ? 1.0 : 0.0);
4992: }
4993:
4994: p[1]=0.0268; p[NDIM]=0.083;
4995: /*printf("%lf %lf", p[1], p[2]);*/
4996:
4997:
4998: printf("Powell\n"); fprintf(ficlog,"Powell\n");
4999: strcpy(filerespow,"pow-mort");
5000: strcat(filerespow,fileres);
5001: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5002: printf("Problem with resultfile: %s\n", filerespow);
5003: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5004: }
5005: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5006: /* for (i=1;i<=nlstate;i++)
5007: for(j=1;j<=nlstate+ndeath;j++)
5008: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5009: */
5010: fprintf(ficrespow,"\n");
5011:
5012: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5013: fclose(ficrespow);
5014:
5015: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5016:
5017: for(i=1; i <=NDIM; i++)
5018: for(j=i+1;j<=NDIM;j++)
5019: matcov[i][j]=matcov[j][i];
5020:
5021: printf("\nCovariance matrix\n ");
5022: for(i=1; i <=NDIM; i++) {
5023: for(j=1;j<=NDIM;j++){
5024: printf("%f ",matcov[i][j]);
5025: }
5026: printf("\n ");
5027: }
5028:
5029: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5030: for (i=1;i<=NDIM;i++)
5031: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5032:
5033: lsurv=vector(1,AGESUP);
5034: lpop=vector(1,AGESUP);
5035: tpop=vector(1,AGESUP);
5036: lsurv[agegomp]=100000;
5037:
5038: for (k=agegomp;k<=AGESUP;k++) {
5039: agemortsup=k;
5040: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5041: }
5042:
5043: for (k=agegomp;k<agemortsup;k++)
5044: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5045:
5046: for (k=agegomp;k<agemortsup;k++){
5047: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5048: sumlpop=sumlpop+lpop[k];
5049: }
5050:
5051: tpop[agegomp]=sumlpop;
5052: for (k=agegomp;k<(agemortsup-3);k++){
5053: /* tpop[k+1]=2;*/
5054: tpop[k+1]=tpop[k]-lpop[k];
5055: }
5056:
5057:
5058: printf("\nAge lx qx dx Lx Tx e(x)\n");
5059: for (k=agegomp;k<(agemortsup-2);k++)
5060: 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]);
5061:
5062:
5063: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5064: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5065:
5066: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5067: stepm, weightopt,\
5068: model,imx,p,matcov,agemortsup);
5069:
5070: free_vector(lsurv,1,AGESUP);
5071: free_vector(lpop,1,AGESUP);
5072: free_vector(tpop,1,AGESUP);
5073: } /* Endof if mle==-3 */
5074:
5075: else{ /* For mle >=1 */
5076:
5077: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5078: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5079: for (k=1; k<=npar;k++)
5080: printf(" %d %8.5f",k,p[k]);
5081: printf("\n");
5082: globpr=1; /* to print the contributions */
5083: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5084: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5085: for (k=1; k<=npar;k++)
5086: printf(" %d %8.5f",k,p[k]);
5087: printf("\n");
5088: if(mle>=1){ /* Could be 1 or 2 */
5089: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5090: }
5091:
5092: /*--------- results files --------------*/
5093: 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);
5094:
5095:
5096: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5097: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5098: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5099: for(i=1,jk=1; i <=nlstate; i++){
5100: for(k=1; k <=(nlstate+ndeath); k++){
5101: if (k != i) {
5102: printf("%d%d ",i,k);
5103: fprintf(ficlog,"%d%d ",i,k);
5104: fprintf(ficres,"%1d%1d ",i,k);
5105: for(j=1; j <=ncovmodel; j++){
5106: printf("%f ",p[jk]);
5107: fprintf(ficlog,"%f ",p[jk]);
5108: fprintf(ficres,"%f ",p[jk]);
5109: jk++;
5110: }
5111: printf("\n");
5112: fprintf(ficlog,"\n");
5113: fprintf(ficres,"\n");
5114: }
5115: }
5116: }
5117: if(mle!=0){
5118: /* Computing hessian and covariance matrix */
5119: ftolhess=ftol; /* Usually correct */
5120: hesscov(matcov, p, npar, delti, ftolhess, func);
5121: }
5122: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5123: printf("# Scales (for hessian or gradient estimation)\n");
5124: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5125: for(i=1,jk=1; i <=nlstate; i++){
5126: for(j=1; j <=nlstate+ndeath; j++){
5127: if (j!=i) {
5128: fprintf(ficres,"%1d%1d",i,j);
5129: printf("%1d%1d",i,j);
5130: fprintf(ficlog,"%1d%1d",i,j);
5131: for(k=1; k<=ncovmodel;k++){
5132: printf(" %.5e",delti[jk]);
5133: fprintf(ficlog," %.5e",delti[jk]);
5134: fprintf(ficres," %.5e",delti[jk]);
5135: jk++;
5136: }
5137: printf("\n");
5138: fprintf(ficlog,"\n");
5139: fprintf(ficres,"\n");
5140: }
5141: }
5142: }
5143:
5144: 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");
5145: if(mle>=1)
5146: 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");
5147: 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");
5148: /* # 121 Var(a12)\n\ */
5149: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5150: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5151: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5152: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5153: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5154: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5155: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5156:
5157:
5158: /* Just to have a covariance matrix which will be more understandable
5159: even is we still don't want to manage dictionary of variables
5160: */
5161: for(itimes=1;itimes<=2;itimes++){
5162: jj=0;
5163: for(i=1; i <=nlstate; i++){
5164: for(j=1; j <=nlstate+ndeath; j++){
5165: if(j==i) continue;
5166: for(k=1; k<=ncovmodel;k++){
5167: jj++;
5168: ca[0]= k+'a'-1;ca[1]='\0';
5169: if(itimes==1){
5170: if(mle>=1)
5171: printf("#%1d%1d%d",i,j,k);
5172: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5173: fprintf(ficres,"#%1d%1d%d",i,j,k);
5174: }else{
5175: if(mle>=1)
5176: printf("%1d%1d%d",i,j,k);
5177: fprintf(ficlog,"%1d%1d%d",i,j,k);
5178: fprintf(ficres,"%1d%1d%d",i,j,k);
5179: }
5180: ll=0;
5181: for(li=1;li <=nlstate; li++){
5182: for(lj=1;lj <=nlstate+ndeath; lj++){
5183: if(lj==li) continue;
5184: for(lk=1;lk<=ncovmodel;lk++){
5185: ll++;
5186: if(ll<=jj){
5187: cb[0]= lk +'a'-1;cb[1]='\0';
5188: if(ll<jj){
5189: if(itimes==1){
5190: if(mle>=1)
5191: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5192: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5193: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5194: }else{
5195: if(mle>=1)
5196: printf(" %.5e",matcov[jj][ll]);
5197: fprintf(ficlog," %.5e",matcov[jj][ll]);
5198: fprintf(ficres," %.5e",matcov[jj][ll]);
5199: }
5200: }else{
5201: if(itimes==1){
5202: if(mle>=1)
5203: printf(" Var(%s%1d%1d)",ca,i,j);
5204: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5205: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5206: }else{
5207: if(mle>=1)
5208: printf(" %.5e",matcov[jj][ll]);
5209: fprintf(ficlog," %.5e",matcov[jj][ll]);
5210: fprintf(ficres," %.5e",matcov[jj][ll]);
5211: }
5212: }
5213: }
5214: } /* end lk */
5215: } /* end lj */
5216: } /* end li */
5217: if(mle>=1)
5218: printf("\n");
5219: fprintf(ficlog,"\n");
5220: fprintf(ficres,"\n");
5221: numlinepar++;
5222: } /* end k*/
5223: } /*end j */
5224: } /* end i */
5225: } /* end itimes */
5226:
5227: fflush(ficlog);
5228: fflush(ficres);
5229:
5230: while((c=getc(ficpar))=='#' && c!= EOF){
5231: ungetc(c,ficpar);
5232: fgets(line, MAXLINE, ficpar);
5233: puts(line);
5234: fputs(line,ficparo);
5235: }
5236: ungetc(c,ficpar);
5237:
5238: estepm=0;
5239: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5240: if (estepm==0 || estepm < stepm) estepm=stepm;
5241: if (fage <= 2) {
5242: bage = ageminpar;
5243: fage = agemaxpar;
5244: }
5245:
5246: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5247: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5248: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5249:
5250: while((c=getc(ficpar))=='#' && c!= EOF){
5251: ungetc(c,ficpar);
5252: fgets(line, MAXLINE, ficpar);
5253: puts(line);
5254: fputs(line,ficparo);
5255: }
5256: ungetc(c,ficpar);
5257:
5258: 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);
5259: 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);
5260: 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);
5261: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5262: 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);
5263:
5264: while((c=getc(ficpar))=='#' && c!= EOF){
5265: ungetc(c,ficpar);
5266: fgets(line, MAXLINE, ficpar);
5267: puts(line);
5268: fputs(line,ficparo);
5269: }
5270: ungetc(c,ficpar);
5271:
5272:
5273: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5274: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5275:
5276: fscanf(ficpar,"pop_based=%d\n",&popbased);
5277: fprintf(ficparo,"pop_based=%d\n",popbased);
5278: fprintf(ficres,"pop_based=%d\n",popbased);
5279:
5280: while((c=getc(ficpar))=='#' && c!= EOF){
5281: ungetc(c,ficpar);
5282: fgets(line, MAXLINE, ficpar);
5283: puts(line);
5284: fputs(line,ficparo);
5285: }
5286: ungetc(c,ficpar);
5287:
5288: 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);
5289: 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);
5290: 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);
5291: 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);
5292: 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);
5293: /* day and month of proj2 are not used but only year anproj2.*/
5294:
5295:
5296:
5297: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5298: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5299:
5300: replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
5301: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5302:
5303: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5304: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5305: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5306:
5307: /*------------ free_vector -------------*/
5308: /* chdir(path); */
5309:
5310: free_ivector(wav,1,imx);
5311: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5312: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5313: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5314: free_lvector(num,1,n);
5315: free_vector(agedc,1,n);
5316: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5317: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5318: fclose(ficparo);
5319: fclose(ficres);
5320:
5321:
5322: /*--------------- Prevalence limit (stable prevalence) --------------*/
5323:
5324: strcpy(filerespl,"pl");
5325: strcat(filerespl,fileres);
5326: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5327: printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5328: fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
5329: }
5330: printf("Computing stable prevalence: result on file '%s' \n", filerespl);
5331: fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
5332: fprintf(ficrespl, "#Local time at start: %s", strstart);
5333: fprintf(ficrespl,"#Stable prevalence \n");
5334: fprintf(ficrespl,"#Age ");
5335: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5336: fprintf(ficrespl,"\n");
5337:
5338: prlim=matrix(1,nlstate,1,nlstate);
5339:
5340: agebase=ageminpar;
5341: agelim=agemaxpar;
5342: ftolpl=1.e-10;
5343: i1=cptcoveff;
5344: if (cptcovn < 1){i1=1;}
5345:
5346: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5347: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5348: k=k+1;
5349: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5350: fprintf(ficrespl,"\n#******");
5351: printf("\n#******");
5352: fprintf(ficlog,"\n#******");
5353: for(j=1;j<=cptcoveff;j++) {
5354: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5355: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5356: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5357: }
5358: fprintf(ficrespl,"******\n");
5359: printf("******\n");
5360: fprintf(ficlog,"******\n");
5361:
5362: for (age=agebase; age<=agelim; age++){
5363: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5364: fprintf(ficrespl,"%.0f ",age );
5365: for(j=1;j<=cptcoveff;j++)
5366: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5367: for(i=1; i<=nlstate;i++)
5368: fprintf(ficrespl," %.5f", prlim[i][i]);
5369: fprintf(ficrespl,"\n");
5370: }
5371: }
5372: }
5373: fclose(ficrespl);
5374:
5375: /*------------- h Pij x at various ages ------------*/
5376:
5377: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5378: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5379: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5380: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5381: }
5382: printf("Computing pij: result on file '%s' \n", filerespij);
5383: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5384:
5385: stepsize=(int) (stepm+YEARM-1)/YEARM;
5386: /*if (stepm<=24) stepsize=2;*/
5387:
5388: agelim=AGESUP;
5389: hstepm=stepsize*YEARM; /* Every year of age */
5390: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5391:
5392: /* hstepm=1; aff par mois*/
5393: fprintf(ficrespij, "#Local time at start: %s", strstart);
5394: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5395: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5396: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5397: k=k+1;
5398: fprintf(ficrespij,"\n#****** ");
5399: for(j=1;j<=cptcoveff;j++)
5400: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5401: fprintf(ficrespij,"******\n");
5402:
5403: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5404: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5405: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5406:
5407: /* nhstepm=nhstepm*YEARM; aff par mois*/
5408:
5409: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5410: oldm=oldms;savm=savms;
5411: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5412: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5413: for(i=1; i<=nlstate;i++)
5414: for(j=1; j<=nlstate+ndeath;j++)
5415: fprintf(ficrespij," %1d-%1d",i,j);
5416: fprintf(ficrespij,"\n");
5417: for (h=0; h<=nhstepm; h++){
5418: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5419: for(i=1; i<=nlstate;i++)
5420: for(j=1; j<=nlstate+ndeath;j++)
5421: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5422: fprintf(ficrespij,"\n");
5423: }
5424: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5425: fprintf(ficrespij,"\n");
5426: }
5427: }
5428: }
5429:
5430: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5431:
5432: fclose(ficrespij);
5433:
5434: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5435: for(i=1;i<=AGESUP;i++)
5436: for(j=1;j<=NCOVMAX;j++)
5437: for(k=1;k<=NCOVMAX;k++)
5438: probs[i][j][k]=0.;
5439:
5440: /*---------- Forecasting ------------------*/
5441: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5442: if(prevfcast==1){
5443: /* if(stepm ==1){*/
5444: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5445: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5446: /* } */
5447: /* else{ */
5448: /* erreur=108; */
5449: /* 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); */
5450: /* 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); */
5451: /* } */
5452: }
5453:
5454:
5455: /*---------- Health expectancies and variances ------------*/
5456:
5457: strcpy(filerest,"t");
5458: strcat(filerest,fileres);
5459: if((ficrest=fopen(filerest,"w"))==NULL) {
5460: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5461: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5462: }
5463: printf("Computing Total LEs with variances: file '%s' \n", filerest);
5464: fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
5465:
5466:
5467: strcpy(filerese,"e");
5468: strcat(filerese,fileres);
5469: if((ficreseij=fopen(filerese,"w"))==NULL) {
5470: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5471: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5472: }
5473: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5474: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5475:
5476: strcpy(fileresv,"v");
5477: strcat(fileresv,fileres);
5478: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5479: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5480: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5481: }
5482: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5483: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5484:
5485: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5486: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5487: /* 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",\
5488: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5489: */
5490:
5491: if (mobilav!=0) {
5492: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5493: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5494: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5495: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5496: }
5497: }
5498:
5499: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5500: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5501: k=k+1;
5502: fprintf(ficrest,"\n#****** ");
5503: for(j=1;j<=cptcoveff;j++)
5504: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5505: fprintf(ficrest,"******\n");
5506:
5507: fprintf(ficreseij,"\n#****** ");
5508: for(j=1;j<=cptcoveff;j++)
5509: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5510: fprintf(ficreseij,"******\n");
5511:
5512: fprintf(ficresvij,"\n#****** ");
5513: for(j=1;j<=cptcoveff;j++)
5514: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5515: fprintf(ficresvij,"******\n");
5516:
5517: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5518: oldm=oldms;savm=savms;
5519: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5520:
5521: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5522: oldm=oldms;savm=savms;
5523: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5524: if(popbased==1){
5525: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5526: }
5527:
5528: fprintf(ficrest, "#Local time at start: %s", strstart);
5529: fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
5530: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5531: fprintf(ficrest,"\n");
5532:
5533: epj=vector(1,nlstate+1);
5534: for(age=bage; age <=fage ;age++){
5535: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5536: if (popbased==1) {
5537: if(mobilav ==0){
5538: for(i=1; i<=nlstate;i++)
5539: prlim[i][i]=probs[(int)age][i][k];
5540: }else{ /* mobilav */
5541: for(i=1; i<=nlstate;i++)
5542: prlim[i][i]=mobaverage[(int)age][i][k];
5543: }
5544: }
5545:
5546: fprintf(ficrest," %4.0f",age);
5547: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5548: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5549: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5550: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5551: }
5552: epj[nlstate+1] +=epj[j];
5553: }
5554:
5555: for(i=1, vepp=0.;i <=nlstate;i++)
5556: for(j=1;j <=nlstate;j++)
5557: vepp += vareij[i][j][(int)age];
5558: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5559: for(j=1;j <=nlstate;j++){
5560: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5561: }
5562: fprintf(ficrest,"\n");
5563: }
5564: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5565: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5566: free_vector(epj,1,nlstate+1);
5567: }
5568: }
5569: free_vector(weight,1,n);
5570: free_imatrix(Tvard,1,15,1,2);
5571: free_imatrix(s,1,maxwav+1,1,n);
5572: free_matrix(anint,1,maxwav,1,n);
5573: free_matrix(mint,1,maxwav,1,n);
5574: free_ivector(cod,1,n);
5575: free_ivector(tab,1,NCOVMAX);
5576: fclose(ficreseij);
5577: fclose(ficresvij);
5578: fclose(ficrest);
5579: fclose(ficpar);
5580:
5581: /*------- Variance of stable prevalence------*/
5582:
5583: strcpy(fileresvpl,"vpl");
5584: strcat(fileresvpl,fileres);
5585: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5586: printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
5587: exit(0);
5588: }
5589: printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
5590:
5591: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5592: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5593: k=k+1;
5594: fprintf(ficresvpl,"\n#****** ");
5595: for(j=1;j<=cptcoveff;j++)
5596: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5597: fprintf(ficresvpl,"******\n");
5598:
5599: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5600: oldm=oldms;savm=savms;
5601: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5602: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5603: }
5604: }
5605:
5606: fclose(ficresvpl);
5607:
5608: /*---------- End : free ----------------*/
5609: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5610: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5611:
5612: } /* mle==-3 arrives here for freeing */
5613: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5614: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5615: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5616: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5617:
5618: free_matrix(covar,0,NCOVMAX,1,n);
5619: free_matrix(matcov,1,npar,1,npar);
5620: /*free_vector(delti,1,npar);*/
5621: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5622: free_matrix(agev,1,maxwav,1,imx);
5623: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5624:
5625: free_ivector(ncodemax,1,8);
5626: free_ivector(Tvar,1,15);
5627: free_ivector(Tprod,1,15);
5628: free_ivector(Tvaraff,1,15);
5629: free_ivector(Tage,1,15);
5630: free_ivector(Tcode,1,100);
5631:
5632:
5633: fflush(fichtm);
5634: fflush(ficgp);
5635:
5636:
5637: if((nberr >0) || (nbwarn>0)){
5638: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5639: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5640: }else{
5641: printf("End of Imach\n");
5642: fprintf(ficlog,"End of Imach\n");
5643: }
5644: printf("See log file on %s\n",filelog);
5645: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5646: (void) gettimeofday(&end_time,&tzp);
5647: tm = *localtime(&end_time.tv_sec);
5648: tmg = *gmtime(&end_time.tv_sec);
5649: strcpy(strtend,asctime(&tm));
5650: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5651: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5652: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5653:
5654: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5655: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5656: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5657: /* printf("Total time was %d uSec.\n", total_usecs);*/
5658: /* if(fileappend(fichtm,optionfilehtm)){ */
5659: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5660: fclose(fichtm);
5661: fclose(fichtmcov);
5662: fclose(ficgp);
5663: fclose(ficlog);
5664: /*------ End -----------*/
5665:
5666: chdir(path);
5667: /*strcat(plotcmd,CHARSEPARATOR);*/
5668: sprintf(plotcmd,"gnuplot");
5669: #ifndef UNIX
5670: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5671: #endif
5672: if(!stat(plotcmd,&info)){
5673: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5674: if(!stat(getenv("GNUPLOTBIN"),&info)){
5675: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5676: }else
5677: strcpy(pplotcmd,plotcmd);
5678: #ifdef UNIX
5679: strcpy(plotcmd,GNUPLOTPROGRAM);
5680: if(!stat(plotcmd,&info)){
5681: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5682: }else
5683: strcpy(pplotcmd,plotcmd);
5684: #endif
5685: }else
5686: strcpy(pplotcmd,plotcmd);
5687:
5688: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5689: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5690:
5691: if((outcmd=system(plotcmd)) != 0){
5692: printf("\n Problem with gnuplot\n");
5693: }
5694: printf(" Wait...");
5695: while (z[0] != 'q') {
5696: /* chdir(path); */
5697: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5698: scanf("%s",z);
5699: /* if (z[0] == 'c') system("./imach"); */
5700: if (z[0] == 'e') {
5701: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5702: system(optionfilehtm);
5703: }
5704: else if (z[0] == 'g') system(plotcmd);
5705: else if (z[0] == 'q') exit(0);
5706: }
5707: end:
5708: while (z[0] != 'q') {
5709: printf("\nType q for exiting: ");
5710: scanf("%s",z);
5711: }
5712: }
5713:
5714:
5715:
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