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Thu Mar 16 17:45:01 2006 UTC (18 years, 3 months ago) by
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* imach.c (Module): Comments concerning covariates added
* imach.c (Module): refinements in the computation of lli if
status=-2 in order to have more reliable computation if stepm is
not 1 month. Version 0.98f
1: /* $Id: imach.c,v 1.121 2006/03/16 17:45:01 lievre Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.121 2006/03/16 17:45:01 lievre
5: * imach.c (Module): Comments concerning covariates added
6:
7: * imach.c (Module): refinements in the computation of lli if
8: status=-2 in order to have more reliable computation if stepm is
9: not 1 month. Version 0.98f
10:
11: Revision 1.120 2006/03/16 15:10:38 lievre
12: (Module): refinements in the computation of lli if
13: status=-2 in order to have more reliable computation if stepm is
14: not 1 month. Version 0.98f
15:
16: Revision 1.119 2006/03/15 17:42:26 brouard
17: (Module): Bug if status = -2, the loglikelihood was
18: computed as likelihood omitting the logarithm. Version O.98e
19:
20: Revision 1.118 2006/03/14 18:20:07 brouard
21: (Module): varevsij Comments added explaining the second
22: table of variances if popbased=1 .
23: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
24: (Module): Function pstamp added
25: (Module): Version 0.98d
26:
27: Revision 1.117 2006/03/14 17:16:22 brouard
28: (Module): varevsij Comments added explaining the second
29: table of variances if popbased=1 .
30: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
31: (Module): Function pstamp added
32: (Module): Version 0.98d
33:
34: Revision 1.116 2006/03/06 10:29:27 brouard
35: (Module): Variance-covariance wrong links and
36: varian-covariance of ej. is needed (Saito).
37:
38: Revision 1.115 2006/02/27 12:17:45 brouard
39: (Module): One freematrix added in mlikeli! 0.98c
40:
41: Revision 1.114 2006/02/26 12:57:58 brouard
42: (Module): Some improvements in processing parameter
43: filename with strsep.
44:
45: Revision 1.113 2006/02/24 14:20:24 brouard
46: (Module): Memory leaks checks with valgrind and:
47: datafile was not closed, some imatrix were not freed and on matrix
48: allocation too.
49:
50: Revision 1.112 2006/01/30 09:55:26 brouard
51: (Module): Back to gnuplot.exe instead of wgnuplot.exe
52:
53: Revision 1.111 2006/01/25 20:38:18 brouard
54: (Module): Lots of cleaning and bugs added (Gompertz)
55: (Module): Comments can be added in data file. Missing date values
56: can be a simple dot '.'.
57:
58: Revision 1.110 2006/01/25 00:51:50 brouard
59: (Module): Lots of cleaning and bugs added (Gompertz)
60:
61: Revision 1.109 2006/01/24 19:37:15 brouard
62: (Module): Comments (lines starting with a #) are allowed in data.
63:
64: Revision 1.108 2006/01/19 18:05:42 lievre
65: Gnuplot problem appeared...
66: To be fixed
67:
68: Revision 1.107 2006/01/19 16:20:37 brouard
69: Test existence of gnuplot in imach path
70:
71: Revision 1.106 2006/01/19 13:24:36 brouard
72: Some cleaning and links added in html output
73:
74: Revision 1.105 2006/01/05 20:23:19 lievre
75: *** empty log message ***
76:
77: Revision 1.104 2005/09/30 16:11:43 lievre
78: (Module): sump fixed, loop imx fixed, and simplifications.
79: (Module): If the status is missing at the last wave but we know
80: that the person is alive, then we can code his/her status as -2
81: (instead of missing=-1 in earlier versions) and his/her
82: contributions to the likelihood is 1 - Prob of dying from last
83: health status (= 1-p13= p11+p12 in the easiest case of somebody in
84: the healthy state at last known wave). Version is 0.98
85:
86: Revision 1.103 2005/09/30 15:54:49 lievre
87: (Module): sump fixed, loop imx fixed, and simplifications.
88:
89: Revision 1.102 2004/09/15 17:31:30 brouard
90: Add the possibility to read data file including tab characters.
91:
92: Revision 1.101 2004/09/15 10:38:38 brouard
93: Fix on curr_time
94:
95: Revision 1.100 2004/07/12 18:29:06 brouard
96: Add version for Mac OS X. Just define UNIX in Makefile
97:
98: Revision 1.99 2004/06/05 08:57:40 brouard
99: *** empty log message ***
100:
101: Revision 1.98 2004/05/16 15:05:56 brouard
102: New version 0.97 . First attempt to estimate force of mortality
103: directly from the data i.e. without the need of knowing the health
104: state at each age, but using a Gompertz model: log u =a + b*age .
105: This is the basic analysis of mortality and should be done before any
106: other analysis, in order to test if the mortality estimated from the
107: cross-longitudinal survey is different from the mortality estimated
108: from other sources like vital statistic data.
109:
110: The same imach parameter file can be used but the option for mle should be -3.
111:
112: Agnès, who wrote this part of the code, tried to keep most of the
113: former routines in order to include the new code within the former code.
114:
115: The output is very simple: only an estimate of the intercept and of
116: the slope with 95% confident intervals.
117:
118: Current limitations:
119: A) Even if you enter covariates, i.e. with the
120: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
121: B) There is no computation of Life Expectancy nor Life Table.
122:
123: Revision 1.97 2004/02/20 13:25:42 lievre
124: Version 0.96d. Population forecasting command line is (temporarily)
125: suppressed.
126:
127: Revision 1.96 2003/07/15 15:38:55 brouard
128: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
129: rewritten within the same printf. Workaround: many printfs.
130:
131: Revision 1.95 2003/07/08 07:54:34 brouard
132: * imach.c (Repository):
133: (Repository): Using imachwizard code to output a more meaningful covariance
134: matrix (cov(a12,c31) instead of numbers.
135:
136: Revision 1.94 2003/06/27 13:00:02 brouard
137: Just cleaning
138:
139: Revision 1.93 2003/06/25 16:33:55 brouard
140: (Module): On windows (cygwin) function asctime_r doesn't
141: exist so I changed back to asctime which exists.
142: (Module): Version 0.96b
143:
144: Revision 1.92 2003/06/25 16:30:45 brouard
145: (Module): On windows (cygwin) function asctime_r doesn't
146: exist so I changed back to asctime which exists.
147:
148: Revision 1.91 2003/06/25 15:30:29 brouard
149: * imach.c (Repository): Duplicated warning errors corrected.
150: (Repository): Elapsed time after each iteration is now output. It
151: helps to forecast when convergence will be reached. Elapsed time
152: is stamped in powell. We created a new html file for the graphs
153: concerning matrix of covariance. It has extension -cov.htm.
154:
155: Revision 1.90 2003/06/24 12:34:15 brouard
156: (Module): Some bugs corrected for windows. Also, when
157: mle=-1 a template is output in file "or"mypar.txt with the design
158: of the covariance matrix to be input.
159:
160: Revision 1.89 2003/06/24 12:30:52 brouard
161: (Module): Some bugs corrected for windows. Also, when
162: mle=-1 a template is output in file "or"mypar.txt with the design
163: of the covariance matrix to be input.
164:
165: Revision 1.88 2003/06/23 17:54:56 brouard
166: * 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.
167:
168: Revision 1.87 2003/06/18 12:26:01 brouard
169: Version 0.96
170:
171: Revision 1.86 2003/06/17 20:04:08 brouard
172: (Module): Change position of html and gnuplot routines and added
173: routine fileappend.
174:
175: Revision 1.85 2003/06/17 13:12:43 brouard
176: * imach.c (Repository): Check when date of death was earlier that
177: current date of interview. It may happen when the death was just
178: prior to the death. In this case, dh was negative and likelihood
179: was wrong (infinity). We still send an "Error" but patch by
180: assuming that the date of death was just one stepm after the
181: interview.
182: (Repository): Because some people have very long ID (first column)
183: we changed int to long in num[] and we added a new lvector for
184: memory allocation. But we also truncated to 8 characters (left
185: truncation)
186: (Repository): No more line truncation errors.
187:
188: Revision 1.84 2003/06/13 21:44:43 brouard
189: * imach.c (Repository): Replace "freqsummary" at a correct
190: place. It differs from routine "prevalence" which may be called
191: many times. Probs is memory consuming and must be used with
192: parcimony.
193: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
194:
195: Revision 1.83 2003/06/10 13:39:11 lievre
196: *** empty log message ***
197:
198: Revision 1.82 2003/06/05 15:57:20 brouard
199: Add log in imach.c and fullversion number is now printed.
200:
201: */
202: /*
203: Interpolated Markov Chain
204:
205: Short summary of the programme:
206:
207: This program computes Healthy Life Expectancies from
208: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
209: first survey ("cross") where individuals from different ages are
210: interviewed on their health status or degree of disability (in the
211: case of a health survey which is our main interest) -2- at least a
212: second wave of interviews ("longitudinal") which measure each change
213: (if any) in individual health status. Health expectancies are
214: computed from the time spent in each health state according to a
215: model. More health states you consider, more time is necessary to reach the
216: Maximum Likelihood of the parameters involved in the model. The
217: simplest model is the multinomial logistic model where pij is the
218: probability to be observed in state j at the second wave
219: conditional to be observed in state i at the first wave. Therefore
220: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
221: 'age' is age and 'sex' is a covariate. If you want to have a more
222: complex model than "constant and age", you should modify the program
223: where the markup *Covariates have to be included here again* invites
224: you to do it. More covariates you add, slower the
225: convergence.
226:
227: The advantage of this computer programme, compared to a simple
228: multinomial logistic model, is clear when the delay between waves is not
229: identical for each individual. Also, if a individual missed an
230: intermediate interview, the information is lost, but taken into
231: account using an interpolation or extrapolation.
232:
233: hPijx is the probability to be observed in state i at age x+h
234: conditional to the observed state i at age x. The delay 'h' can be
235: split into an exact number (nh*stepm) of unobserved intermediate
236: states. This elementary transition (by month, quarter,
237: semester or year) is modelled as a multinomial logistic. The hPx
238: matrix is simply the matrix product of nh*stepm elementary matrices
239: and the contribution of each individual to the likelihood is simply
240: hPijx.
241:
242: Also this programme outputs the covariance matrix of the parameters but also
243: of the life expectancies. It also computes the period (stable) prevalence.
244:
245: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
246: Institut national d'études démographiques, Paris.
247: This software have been partly granted by Euro-REVES, a concerted action
248: from the European Union.
249: It is copyrighted identically to a GNU software product, ie programme and
250: software can be distributed freely for non commercial use. Latest version
251: can be accessed at http://euroreves.ined.fr/imach .
252:
253: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
254: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
255:
256: **********************************************************************/
257: /*
258: main
259: read parameterfile
260: read datafile
261: concatwav
262: freqsummary
263: if (mle >= 1)
264: mlikeli
265: print results files
266: if mle==1
267: computes hessian
268: read end of parameter file: agemin, agemax, bage, fage, estepm
269: begin-prev-date,...
270: open gnuplot file
271: open html file
272: period (stable) prevalence
273: for age prevalim()
274: h Pij x
275: variance of p varprob
276: forecasting if prevfcast==1 prevforecast call prevalence()
277: health expectancies
278: Variance-covariance of DFLE
279: prevalence()
280: movingaverage()
281: varevsij()
282: if popbased==1 varevsij(,popbased)
283: total life expectancies
284: Variance of period (stable) prevalence
285: end
286: */
287:
288:
289:
290:
291: #include <math.h>
292: #include <stdio.h>
293: #include <stdlib.h>
294: #include <string.h>
295: #include <unistd.h>
296:
297: #include <limits.h>
298: #include <sys/types.h>
299: #include <sys/stat.h>
300: #include <errno.h>
301: extern int errno;
302:
303: /* #include <sys/time.h> */
304: #include <time.h>
305: #include "timeval.h"
306:
307: /* #include <libintl.h> */
308: /* #define _(String) gettext (String) */
309:
310: #define MAXLINE 256
311:
312: #define GNUPLOTPROGRAM "gnuplot"
313: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
314: #define FILENAMELENGTH 132
315:
316: #define GLOCK_ERROR_NOPATH -1 /* empty path */
317: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
318:
319: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
320: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
321:
322: #define NINTERVMAX 8
323: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
324: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
325: #define NCOVMAX 8 /* Maximum number of covariates */
326: #define MAXN 20000
327: #define YEARM 12. /* Number of months per year */
328: #define AGESUP 130
329: #define AGEBASE 40
330: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
331: #ifdef UNIX
332: #define DIRSEPARATOR '/'
333: #define CHARSEPARATOR "/"
334: #define ODIRSEPARATOR '\\'
335: #else
336: #define DIRSEPARATOR '\\'
337: #define CHARSEPARATOR "\\"
338: #define ODIRSEPARATOR '/'
339: #endif
340:
341: /* $Id: imach.c,v 1.121 2006/03/16 17:45:01 lievre Exp $ */
342: /* $State: Exp $ */
343:
344: char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";
345: char fullversion[]="$Revision: 1.121 $ $Date: 2006/03/16 17:45:01 $";
346: char strstart[80];
347: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
348: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
349: int nvar;
350: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
351: int npar=NPARMAX;
352: int nlstate=2; /* Number of live states */
353: int ndeath=1; /* Number of dead states */
354: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
355: int popbased=0;
356:
357: int *wav; /* Number of waves for this individuual 0 is possible */
358: int maxwav; /* Maxim number of waves */
359: int jmin, jmax; /* min, max spacing between 2 waves */
360: int ijmin, ijmax; /* Individuals having jmin and jmax */
361: int gipmx, gsw; /* Global variables on the number of contributions
362: to the likelihood and the sum of weights (done by funcone)*/
363: int mle, weightopt;
364: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
365: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
366: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
367: * wave mi and wave mi+1 is not an exact multiple of stepm. */
368: double jmean; /* Mean space between 2 waves */
369: double **oldm, **newm, **savm; /* Working pointers to matrices */
370: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
371: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
372: FILE *ficlog, *ficrespow;
373: int globpr; /* Global variable for printing or not */
374: double fretone; /* Only one call to likelihood */
375: long ipmx; /* Number of contributions */
376: double sw; /* Sum of weights */
377: char filerespow[FILENAMELENGTH];
378: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
379: FILE *ficresilk;
380: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
381: FILE *ficresprobmorprev;
382: FILE *fichtm, *fichtmcov; /* Html File */
383: FILE *ficreseij;
384: char filerese[FILENAMELENGTH];
385: FILE *ficresstdeij;
386: char fileresstde[FILENAMELENGTH];
387: FILE *ficrescveij;
388: char filerescve[FILENAMELENGTH];
389: FILE *ficresvij;
390: char fileresv[FILENAMELENGTH];
391: FILE *ficresvpl;
392: char fileresvpl[FILENAMELENGTH];
393: char title[MAXLINE];
394: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
395: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
396: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
397: char command[FILENAMELENGTH];
398: int outcmd=0;
399:
400: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
401:
402: char filelog[FILENAMELENGTH]; /* Log file */
403: char filerest[FILENAMELENGTH];
404: char fileregp[FILENAMELENGTH];
405: char popfile[FILENAMELENGTH];
406:
407: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
408:
409: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
410: struct timezone tzp;
411: extern int gettimeofday();
412: struct tm tmg, tm, tmf, *gmtime(), *localtime();
413: long time_value;
414: extern long time();
415: char strcurr[80], strfor[80];
416:
417: char *endptr;
418: long lval;
419:
420: #define NR_END 1
421: #define FREE_ARG char*
422: #define FTOL 1.0e-10
423:
424: #define NRANSI
425: #define ITMAX 200
426:
427: #define TOL 2.0e-4
428:
429: #define CGOLD 0.3819660
430: #define ZEPS 1.0e-10
431: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
432:
433: #define GOLD 1.618034
434: #define GLIMIT 100.0
435: #define TINY 1.0e-20
436:
437: static double maxarg1,maxarg2;
438: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
439: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
440:
441: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
442: #define rint(a) floor(a+0.5)
443:
444: static double sqrarg;
445: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
446: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
447: int agegomp= AGEGOMP;
448:
449: int imx;
450: int stepm=1;
451: /* Stepm, step in month: minimum step interpolation*/
452:
453: int estepm;
454: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
455:
456: int m,nb;
457: long *num;
458: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
459: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
460: double **pmmij, ***probs;
461: double *ageexmed,*agecens;
462: double dateintmean=0;
463:
464: double *weight;
465: int **s; /* Status */
466: double *agedc, **covar, idx;
467: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
468: double *lsurv, *lpop, *tpop;
469:
470: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
471: double ftolhess; /* Tolerance for computing hessian */
472:
473: /**************** split *************************/
474: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
475: {
476: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
477: the name of the file (name), its extension only (ext) and its first part of the name (finame)
478: */
479: char *ss; /* pointer */
480: int l1, l2; /* length counters */
481:
482: l1 = strlen(path ); /* length of path */
483: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
484: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
485: if ( ss == NULL ) { /* no directory, so determine current directory */
486: strcpy( name, path ); /* we got the fullname name because no directory */
487: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
488: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
489: /* get current working directory */
490: /* extern char* getcwd ( char *buf , int len);*/
491: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
492: return( GLOCK_ERROR_GETCWD );
493: }
494: /* got dirc from getcwd*/
495: printf(" DIRC = %s \n",dirc);
496: } else { /* strip direcotry from path */
497: ss++; /* after this, the filename */
498: l2 = strlen( ss ); /* length of filename */
499: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
500: strcpy( name, ss ); /* save file name */
501: strncpy( dirc, path, l1 - l2 ); /* now the directory */
502: dirc[l1-l2] = 0; /* add zero */
503: printf(" DIRC2 = %s \n",dirc);
504: }
505: /* We add a separator at the end of dirc if not exists */
506: l1 = strlen( dirc ); /* length of directory */
507: if( dirc[l1-1] != DIRSEPARATOR ){
508: dirc[l1] = DIRSEPARATOR;
509: dirc[l1+1] = 0;
510: printf(" DIRC3 = %s \n",dirc);
511: }
512: ss = strrchr( name, '.' ); /* find last / */
513: if (ss >0){
514: ss++;
515: strcpy(ext,ss); /* save extension */
516: l1= strlen( name);
517: l2= strlen(ss)+1;
518: strncpy( finame, name, l1-l2);
519: finame[l1-l2]= 0;
520: }
521:
522: return( 0 ); /* we're done */
523: }
524:
525:
526: /******************************************/
527:
528: void replace_back_to_slash(char *s, char*t)
529: {
530: int i;
531: int lg=0;
532: i=0;
533: lg=strlen(t);
534: for(i=0; i<= lg; i++) {
535: (s[i] = t[i]);
536: if (t[i]== '\\') s[i]='/';
537: }
538: }
539:
540: int nbocc(char *s, char occ)
541: {
542: int i,j=0;
543: int lg=20;
544: i=0;
545: lg=strlen(s);
546: for(i=0; i<= lg; i++) {
547: if (s[i] == occ ) j++;
548: }
549: return j;
550: }
551:
552: void cutv(char *u,char *v, char*t, char occ)
553: {
554: /* cuts string t into u and v where u ends before first occurence of char 'occ'
555: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
556: gives u="abcedf" and v="ghi2j" */
557: int i,lg,j,p=0;
558: i=0;
559: for(j=0; j<=strlen(t)-1; j++) {
560: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
561: }
562:
563: lg=strlen(t);
564: for(j=0; j<p; j++) {
565: (u[j] = t[j]);
566: }
567: u[p]='\0';
568:
569: for(j=0; j<= lg; j++) {
570: if (j>=(p+1))(v[j-p-1] = t[j]);
571: }
572: }
573:
574: /********************** nrerror ********************/
575:
576: void nrerror(char error_text[])
577: {
578: fprintf(stderr,"ERREUR ...\n");
579: fprintf(stderr,"%s\n",error_text);
580: exit(EXIT_FAILURE);
581: }
582: /*********************** vector *******************/
583: double *vector(int nl, int nh)
584: {
585: double *v;
586: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
587: if (!v) nrerror("allocation failure in vector");
588: return v-nl+NR_END;
589: }
590:
591: /************************ free vector ******************/
592: void free_vector(double*v, int nl, int nh)
593: {
594: free((FREE_ARG)(v+nl-NR_END));
595: }
596:
597: /************************ivector *******************************/
598: int *ivector(long nl,long nh)
599: {
600: int *v;
601: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
602: if (!v) nrerror("allocation failure in ivector");
603: return v-nl+NR_END;
604: }
605:
606: /******************free ivector **************************/
607: void free_ivector(int *v, long nl, long nh)
608: {
609: free((FREE_ARG)(v+nl-NR_END));
610: }
611:
612: /************************lvector *******************************/
613: long *lvector(long nl,long nh)
614: {
615: long *v;
616: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
617: if (!v) nrerror("allocation failure in ivector");
618: return v-nl+NR_END;
619: }
620:
621: /******************free lvector **************************/
622: void free_lvector(long *v, long nl, long nh)
623: {
624: free((FREE_ARG)(v+nl-NR_END));
625: }
626:
627: /******************* imatrix *******************************/
628: int **imatrix(long nrl, long nrh, long ncl, long nch)
629: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
630: {
631: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
632: int **m;
633:
634: /* allocate pointers to rows */
635: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
636: if (!m) nrerror("allocation failure 1 in matrix()");
637: m += NR_END;
638: m -= nrl;
639:
640:
641: /* allocate rows and set pointers to them */
642: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
643: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
644: m[nrl] += NR_END;
645: m[nrl] -= ncl;
646:
647: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
648:
649: /* return pointer to array of pointers to rows */
650: return m;
651: }
652:
653: /****************** free_imatrix *************************/
654: void free_imatrix(m,nrl,nrh,ncl,nch)
655: int **m;
656: long nch,ncl,nrh,nrl;
657: /* free an int matrix allocated by imatrix() */
658: {
659: free((FREE_ARG) (m[nrl]+ncl-NR_END));
660: free((FREE_ARG) (m+nrl-NR_END));
661: }
662:
663: /******************* matrix *******************************/
664: double **matrix(long nrl, long nrh, long ncl, long nch)
665: {
666: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
667: double **m;
668:
669: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
670: if (!m) nrerror("allocation failure 1 in matrix()");
671: m += NR_END;
672: m -= nrl;
673:
674: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
675: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
676: m[nrl] += NR_END;
677: m[nrl] -= ncl;
678:
679: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
680: return m;
681: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
682: */
683: }
684:
685: /*************************free matrix ************************/
686: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
687: {
688: free((FREE_ARG)(m[nrl]+ncl-NR_END));
689: free((FREE_ARG)(m+nrl-NR_END));
690: }
691:
692: /******************* ma3x *******************************/
693: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
694: {
695: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
696: double ***m;
697:
698: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
699: if (!m) nrerror("allocation failure 1 in matrix()");
700: m += NR_END;
701: m -= nrl;
702:
703: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
704: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
705: m[nrl] += NR_END;
706: m[nrl] -= ncl;
707:
708: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
709:
710: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
711: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
712: m[nrl][ncl] += NR_END;
713: m[nrl][ncl] -= nll;
714: for (j=ncl+1; j<=nch; j++)
715: m[nrl][j]=m[nrl][j-1]+nlay;
716:
717: for (i=nrl+1; i<=nrh; i++) {
718: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
719: for (j=ncl+1; j<=nch; j++)
720: m[i][j]=m[i][j-1]+nlay;
721: }
722: return m;
723: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
724: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
725: */
726: }
727:
728: /*************************free ma3x ************************/
729: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
730: {
731: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
732: free((FREE_ARG)(m[nrl]+ncl-NR_END));
733: free((FREE_ARG)(m+nrl-NR_END));
734: }
735:
736: /*************** function subdirf ***********/
737: char *subdirf(char fileres[])
738: {
739: /* Caution optionfilefiname is hidden */
740: strcpy(tmpout,optionfilefiname);
741: strcat(tmpout,"/"); /* Add to the right */
742: strcat(tmpout,fileres);
743: return tmpout;
744: }
745:
746: /*************** function subdirf2 ***********/
747: char *subdirf2(char fileres[], char *preop)
748: {
749:
750: /* Caution optionfilefiname is hidden */
751: strcpy(tmpout,optionfilefiname);
752: strcat(tmpout,"/");
753: strcat(tmpout,preop);
754: strcat(tmpout,fileres);
755: return tmpout;
756: }
757:
758: /*************** function subdirf3 ***********/
759: char *subdirf3(char fileres[], char *preop, char *preop2)
760: {
761:
762: /* Caution optionfilefiname is hidden */
763: strcpy(tmpout,optionfilefiname);
764: strcat(tmpout,"/");
765: strcat(tmpout,preop);
766: strcat(tmpout,preop2);
767: strcat(tmpout,fileres);
768: return tmpout;
769: }
770:
771: /***************** f1dim *************************/
772: extern int ncom;
773: extern double *pcom,*xicom;
774: extern double (*nrfunc)(double []);
775:
776: double f1dim(double x)
777: {
778: int j;
779: double f;
780: double *xt;
781:
782: xt=vector(1,ncom);
783: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
784: f=(*nrfunc)(xt);
785: free_vector(xt,1,ncom);
786: return f;
787: }
788:
789: /*****************brent *************************/
790: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
791: {
792: int iter;
793: double a,b,d,etemp;
794: double fu,fv,fw,fx;
795: double ftemp;
796: double p,q,r,tol1,tol2,u,v,w,x,xm;
797: double e=0.0;
798:
799: a=(ax < cx ? ax : cx);
800: b=(ax > cx ? ax : cx);
801: x=w=v=bx;
802: fw=fv=fx=(*f)(x);
803: for (iter=1;iter<=ITMAX;iter++) {
804: xm=0.5*(a+b);
805: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
806: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
807: printf(".");fflush(stdout);
808: fprintf(ficlog,".");fflush(ficlog);
809: #ifdef DEBUG
810: 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);
811: 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);
812: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
813: #endif
814: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
815: *xmin=x;
816: return fx;
817: }
818: ftemp=fu;
819: if (fabs(e) > tol1) {
820: r=(x-w)*(fx-fv);
821: q=(x-v)*(fx-fw);
822: p=(x-v)*q-(x-w)*r;
823: q=2.0*(q-r);
824: if (q > 0.0) p = -p;
825: q=fabs(q);
826: etemp=e;
827: e=d;
828: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
829: d=CGOLD*(e=(x >= xm ? a-x : b-x));
830: else {
831: d=p/q;
832: u=x+d;
833: if (u-a < tol2 || b-u < tol2)
834: d=SIGN(tol1,xm-x);
835: }
836: } else {
837: d=CGOLD*(e=(x >= xm ? a-x : b-x));
838: }
839: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
840: fu=(*f)(u);
841: if (fu <= fx) {
842: if (u >= x) a=x; else b=x;
843: SHFT(v,w,x,u)
844: SHFT(fv,fw,fx,fu)
845: } else {
846: if (u < x) a=u; else b=u;
847: if (fu <= fw || w == x) {
848: v=w;
849: w=u;
850: fv=fw;
851: fw=fu;
852: } else if (fu <= fv || v == x || v == w) {
853: v=u;
854: fv=fu;
855: }
856: }
857: }
858: nrerror("Too many iterations in brent");
859: *xmin=x;
860: return fx;
861: }
862:
863: /****************** mnbrak ***********************/
864:
865: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
866: double (*func)(double))
867: {
868: double ulim,u,r,q, dum;
869: double fu;
870:
871: *fa=(*func)(*ax);
872: *fb=(*func)(*bx);
873: if (*fb > *fa) {
874: SHFT(dum,*ax,*bx,dum)
875: SHFT(dum,*fb,*fa,dum)
876: }
877: *cx=(*bx)+GOLD*(*bx-*ax);
878: *fc=(*func)(*cx);
879: while (*fb > *fc) {
880: r=(*bx-*ax)*(*fb-*fc);
881: q=(*bx-*cx)*(*fb-*fa);
882: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
883: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
884: ulim=(*bx)+GLIMIT*(*cx-*bx);
885: if ((*bx-u)*(u-*cx) > 0.0) {
886: fu=(*func)(u);
887: } else if ((*cx-u)*(u-ulim) > 0.0) {
888: fu=(*func)(u);
889: if (fu < *fc) {
890: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
891: SHFT(*fb,*fc,fu,(*func)(u))
892: }
893: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
894: u=ulim;
895: fu=(*func)(u);
896: } else {
897: u=(*cx)+GOLD*(*cx-*bx);
898: fu=(*func)(u);
899: }
900: SHFT(*ax,*bx,*cx,u)
901: SHFT(*fa,*fb,*fc,fu)
902: }
903: }
904:
905: /*************** linmin ************************/
906:
907: int ncom;
908: double *pcom,*xicom;
909: double (*nrfunc)(double []);
910:
911: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
912: {
913: double brent(double ax, double bx, double cx,
914: double (*f)(double), double tol, double *xmin);
915: double f1dim(double x);
916: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
917: double *fc, double (*func)(double));
918: int j;
919: double xx,xmin,bx,ax;
920: double fx,fb,fa;
921:
922: ncom=n;
923: pcom=vector(1,n);
924: xicom=vector(1,n);
925: nrfunc=func;
926: for (j=1;j<=n;j++) {
927: pcom[j]=p[j];
928: xicom[j]=xi[j];
929: }
930: ax=0.0;
931: xx=1.0;
932: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
933: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
934: #ifdef DEBUG
935: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
936: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
937: #endif
938: for (j=1;j<=n;j++) {
939: xi[j] *= xmin;
940: p[j] += xi[j];
941: }
942: free_vector(xicom,1,n);
943: free_vector(pcom,1,n);
944: }
945:
946: char *asc_diff_time(long time_sec, char ascdiff[])
947: {
948: long sec_left, days, hours, minutes;
949: days = (time_sec) / (60*60*24);
950: sec_left = (time_sec) % (60*60*24);
951: hours = (sec_left) / (60*60) ;
952: sec_left = (sec_left) %(60*60);
953: minutes = (sec_left) /60;
954: sec_left = (sec_left) % (60);
955: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
956: return ascdiff;
957: }
958:
959: /*************** powell ************************/
960: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
961: double (*func)(double []))
962: {
963: void linmin(double p[], double xi[], int n, double *fret,
964: double (*func)(double []));
965: int i,ibig,j;
966: double del,t,*pt,*ptt,*xit;
967: double fp,fptt;
968: double *xits;
969: int niterf, itmp;
970:
971: pt=vector(1,n);
972: ptt=vector(1,n);
973: xit=vector(1,n);
974: xits=vector(1,n);
975: *fret=(*func)(p);
976: for (j=1;j<=n;j++) pt[j]=p[j];
977: for (*iter=1;;++(*iter)) {
978: fp=(*fret);
979: ibig=0;
980: del=0.0;
981: last_time=curr_time;
982: (void) gettimeofday(&curr_time,&tzp);
983: 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);
984: /* 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);
985: fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
986: */
987: for (i=1;i<=n;i++) {
988: printf(" %d %.12f",i, p[i]);
989: fprintf(ficlog," %d %.12lf",i, p[i]);
990: fprintf(ficrespow," %.12lf", p[i]);
991: }
992: printf("\n");
993: fprintf(ficlog,"\n");
994: fprintf(ficrespow,"\n");fflush(ficrespow);
995: if(*iter <=3){
996: tm = *localtime(&curr_time.tv_sec);
997: strcpy(strcurr,asctime(&tm));
998: /* asctime_r(&tm,strcurr); */
999: forecast_time=curr_time;
1000: itmp = strlen(strcurr);
1001: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1002: strcurr[itmp-1]='\0';
1003: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1004: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1005: for(niterf=10;niterf<=30;niterf+=10){
1006: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1007: tmf = *localtime(&forecast_time.tv_sec);
1008: /* asctime_r(&tmf,strfor); */
1009: strcpy(strfor,asctime(&tmf));
1010: itmp = strlen(strfor);
1011: if(strfor[itmp-1]=='\n')
1012: strfor[itmp-1]='\0';
1013: 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);
1014: 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);
1015: }
1016: }
1017: for (i=1;i<=n;i++) {
1018: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1019: fptt=(*fret);
1020: #ifdef DEBUG
1021: printf("fret=%lf \n",*fret);
1022: fprintf(ficlog,"fret=%lf \n",*fret);
1023: #endif
1024: printf("%d",i);fflush(stdout);
1025: fprintf(ficlog,"%d",i);fflush(ficlog);
1026: linmin(p,xit,n,fret,func);
1027: if (fabs(fptt-(*fret)) > del) {
1028: del=fabs(fptt-(*fret));
1029: ibig=i;
1030: }
1031: #ifdef DEBUG
1032: printf("%d %.12e",i,(*fret));
1033: fprintf(ficlog,"%d %.12e",i,(*fret));
1034: for (j=1;j<=n;j++) {
1035: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1036: printf(" x(%d)=%.12e",j,xit[j]);
1037: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1038: }
1039: for(j=1;j<=n;j++) {
1040: printf(" p=%.12e",p[j]);
1041: fprintf(ficlog," p=%.12e",p[j]);
1042: }
1043: printf("\n");
1044: fprintf(ficlog,"\n");
1045: #endif
1046: }
1047: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1048: #ifdef DEBUG
1049: int k[2],l;
1050: k[0]=1;
1051: k[1]=-1;
1052: printf("Max: %.12e",(*func)(p));
1053: fprintf(ficlog,"Max: %.12e",(*func)(p));
1054: for (j=1;j<=n;j++) {
1055: printf(" %.12e",p[j]);
1056: fprintf(ficlog," %.12e",p[j]);
1057: }
1058: printf("\n");
1059: fprintf(ficlog,"\n");
1060: for(l=0;l<=1;l++) {
1061: for (j=1;j<=n;j++) {
1062: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1063: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1064: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1065: }
1066: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1067: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1068: }
1069: #endif
1070:
1071:
1072: free_vector(xit,1,n);
1073: free_vector(xits,1,n);
1074: free_vector(ptt,1,n);
1075: free_vector(pt,1,n);
1076: return;
1077: }
1078: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1079: for (j=1;j<=n;j++) {
1080: ptt[j]=2.0*p[j]-pt[j];
1081: xit[j]=p[j]-pt[j];
1082: pt[j]=p[j];
1083: }
1084: fptt=(*func)(ptt);
1085: if (fptt < fp) {
1086: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1087: if (t < 0.0) {
1088: linmin(p,xit,n,fret,func);
1089: for (j=1;j<=n;j++) {
1090: xi[j][ibig]=xi[j][n];
1091: xi[j][n]=xit[j];
1092: }
1093: #ifdef DEBUG
1094: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1095: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1096: for(j=1;j<=n;j++){
1097: printf(" %.12e",xit[j]);
1098: fprintf(ficlog," %.12e",xit[j]);
1099: }
1100: printf("\n");
1101: fprintf(ficlog,"\n");
1102: #endif
1103: }
1104: }
1105: }
1106: }
1107:
1108: /**** Prevalence limit (stable or period prevalence) ****************/
1109:
1110: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1111: {
1112: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1113: matrix by transitions matrix until convergence is reached */
1114:
1115: int i, ii,j,k;
1116: double min, max, maxmin, maxmax,sumnew=0.;
1117: double **matprod2();
1118: double **out, cov[NCOVMAX], **pmij();
1119: double **newm;
1120: double agefin, delaymax=50 ; /* Max number of years to converge */
1121:
1122: for (ii=1;ii<=nlstate+ndeath;ii++)
1123: for (j=1;j<=nlstate+ndeath;j++){
1124: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1125: }
1126:
1127: cov[1]=1.;
1128:
1129: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1130: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1131: newm=savm;
1132: /* Covariates have to be included here again */
1133: cov[2]=agefin;
1134:
1135: for (k=1; k<=cptcovn;k++) {
1136: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1137: /* 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]]);*/
1138: }
1139: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1140: for (k=1; k<=cptcovprod;k++)
1141: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1142:
1143: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1144: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1145: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1146: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1147:
1148: savm=oldm;
1149: oldm=newm;
1150: maxmax=0.;
1151: for(j=1;j<=nlstate;j++){
1152: min=1.;
1153: max=0.;
1154: for(i=1; i<=nlstate; i++) {
1155: sumnew=0;
1156: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1157: prlim[i][j]= newm[i][j]/(1-sumnew);
1158: max=FMAX(max,prlim[i][j]);
1159: min=FMIN(min,prlim[i][j]);
1160: }
1161: maxmin=max-min;
1162: maxmax=FMAX(maxmax,maxmin);
1163: }
1164: if(maxmax < ftolpl){
1165: return prlim;
1166: }
1167: }
1168: }
1169:
1170: /*************** transition probabilities ***************/
1171:
1172: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1173: {
1174: double s1, s2;
1175: /*double t34;*/
1176: int i,j,j1, nc, ii, jj;
1177:
1178: for(i=1; i<= nlstate; i++){
1179: for(j=1; j<i;j++){
1180: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1181: /*s2 += param[i][j][nc]*cov[nc];*/
1182: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1183: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1184: }
1185: ps[i][j]=s2;
1186: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1187: }
1188: for(j=i+1; j<=nlstate+ndeath;j++){
1189: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1190: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1191: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1192: }
1193: ps[i][j]=s2;
1194: }
1195: }
1196: /*ps[3][2]=1;*/
1197:
1198: for(i=1; i<= nlstate; i++){
1199: s1=0;
1200: for(j=1; j<i; j++)
1201: s1+=exp(ps[i][j]);
1202: for(j=i+1; j<=nlstate+ndeath; j++)
1203: s1+=exp(ps[i][j]);
1204: ps[i][i]=1./(s1+1.);
1205: for(j=1; j<i; j++)
1206: ps[i][j]= exp(ps[i][j])*ps[i][i];
1207: for(j=i+1; j<=nlstate+ndeath; j++)
1208: ps[i][j]= exp(ps[i][j])*ps[i][i];
1209: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1210: } /* end i */
1211:
1212: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1213: for(jj=1; jj<= nlstate+ndeath; jj++){
1214: ps[ii][jj]=0;
1215: ps[ii][ii]=1;
1216: }
1217: }
1218:
1219:
1220: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1221: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1222: /* printf("ddd %lf ",ps[ii][jj]); */
1223: /* } */
1224: /* printf("\n "); */
1225: /* } */
1226: /* printf("\n ");printf("%lf ",cov[2]); */
1227: /*
1228: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1229: goto end;*/
1230: return ps;
1231: }
1232:
1233: /**************** Product of 2 matrices ******************/
1234:
1235: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1236: {
1237: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1238: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1239: /* in, b, out are matrice of pointers which should have been initialized
1240: before: only the contents of out is modified. The function returns
1241: a pointer to pointers identical to out */
1242: long i, j, k;
1243: for(i=nrl; i<= nrh; i++)
1244: for(k=ncolol; k<=ncoloh; k++)
1245: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1246: out[i][k] +=in[i][j]*b[j][k];
1247:
1248: return out;
1249: }
1250:
1251:
1252: /************* Higher Matrix Product ***************/
1253:
1254: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1255: {
1256: /* Computes the transition matrix starting at age 'age' over
1257: 'nhstepm*hstepm*stepm' months (i.e. until
1258: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1259: nhstepm*hstepm matrices.
1260: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1261: (typically every 2 years instead of every month which is too big
1262: for the memory).
1263: Model is determined by parameters x and covariates have to be
1264: included manually here.
1265:
1266: */
1267:
1268: int i, j, d, h, k;
1269: double **out, cov[NCOVMAX];
1270: double **newm;
1271:
1272: /* Hstepm could be zero and should return the unit matrix */
1273: for (i=1;i<=nlstate+ndeath;i++)
1274: for (j=1;j<=nlstate+ndeath;j++){
1275: oldm[i][j]=(i==j ? 1.0 : 0.0);
1276: po[i][j][0]=(i==j ? 1.0 : 0.0);
1277: }
1278: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1279: for(h=1; h <=nhstepm; h++){
1280: for(d=1; d <=hstepm; d++){
1281: newm=savm;
1282: /* Covariates have to be included here again */
1283: cov[1]=1.;
1284: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1285: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1286: for (k=1; k<=cptcovage;k++)
1287: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1288: for (k=1; k<=cptcovprod;k++)
1289: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1290:
1291:
1292: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1293: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1294: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1295: pmij(pmmij,cov,ncovmodel,x,nlstate));
1296: savm=oldm;
1297: oldm=newm;
1298: }
1299: for(i=1; i<=nlstate+ndeath; i++)
1300: for(j=1;j<=nlstate+ndeath;j++) {
1301: po[i][j][h]=newm[i][j];
1302: /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
1303: */
1304: }
1305: } /* end h */
1306: return po;
1307: }
1308:
1309:
1310: /*************** log-likelihood *************/
1311: double func( double *x)
1312: {
1313: int i, ii, j, k, mi, d, kk;
1314: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1315: double **out;
1316: double sw; /* Sum of weights */
1317: double lli; /* Individual log likelihood */
1318: int s1, s2;
1319: double bbh, survp;
1320: long ipmx;
1321: /*extern weight */
1322: /* We are differentiating ll according to initial status */
1323: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1324: /*for(i=1;i<imx;i++)
1325: printf(" %d\n",s[4][i]);
1326: */
1327: cov[1]=1.;
1328:
1329: for(k=1; k<=nlstate; k++) ll[k]=0.;
1330:
1331: if(mle==1){
1332: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1333: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1334: for(mi=1; mi<= wav[i]-1; mi++){
1335: for (ii=1;ii<=nlstate+ndeath;ii++)
1336: for (j=1;j<=nlstate+ndeath;j++){
1337: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1338: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1339: }
1340: for(d=0; d<dh[mi][i]; d++){
1341: newm=savm;
1342: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1343: for (kk=1; kk<=cptcovage;kk++) {
1344: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1345: }
1346: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1347: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1348: savm=oldm;
1349: oldm=newm;
1350: } /* end mult */
1351:
1352: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1353: /* But now since version 0.9 we anticipate for bias at large stepm.
1354: * If stepm is larger than one month (smallest stepm) and if the exact delay
1355: * (in months) between two waves is not a multiple of stepm, we rounded to
1356: * the nearest (and in case of equal distance, to the lowest) interval but now
1357: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1358: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1359: * probability in order to take into account the bias as a fraction of the way
1360: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1361: * -stepm/2 to stepm/2 .
1362: * For stepm=1 the results are the same as for previous versions of Imach.
1363: * For stepm > 1 the results are less biased than in previous versions.
1364: */
1365: s1=s[mw[mi][i]][i];
1366: s2=s[mw[mi+1][i]][i];
1367: bbh=(double)bh[mi][i]/(double)stepm;
1368: /* bias bh is positive if real duration
1369: * is higher than the multiple of stepm and negative otherwise.
1370: */
1371: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1372: if( s2 > nlstate){
1373: /* i.e. if s2 is a death state and if the date of death is known
1374: then the contribution to the likelihood is the probability to
1375: die between last step unit time and current step unit time,
1376: which is also equal to probability to die before dh
1377: minus probability to die before dh-stepm .
1378: In version up to 0.92 likelihood was computed
1379: as if date of death was unknown. Death was treated as any other
1380: health state: the date of the interview describes the actual state
1381: and not the date of a change in health state. The former idea was
1382: to consider that at each interview the state was recorded
1383: (healthy, disable or death) and IMaCh was corrected; but when we
1384: introduced the exact date of death then we should have modified
1385: the contribution of an exact death to the likelihood. This new
1386: contribution is smaller and very dependent of the step unit
1387: stepm. It is no more the probability to die between last interview
1388: and month of death but the probability to survive from last
1389: interview up to one month before death multiplied by the
1390: probability to die within a month. Thanks to Chris
1391: Jackson for correcting this bug. Former versions increased
1392: mortality artificially. The bad side is that we add another loop
1393: which slows down the processing. The difference can be up to 10%
1394: lower mortality.
1395: */
1396: lli=log(out[s1][s2] - savm[s1][s2]);
1397:
1398:
1399: } else if (s2==-2) {
1400: for (j=1,survp=0. ; j<=nlstate; j++)
1401: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1402: /*survp += out[s1][j]; */
1403: lli= log(survp);
1404: }
1405:
1406: else if (s2==-4) {
1407: for (j=3,survp=0. ; j<=nlstate; j++)
1408: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1409: lli= log(survp);
1410: }
1411:
1412: else if (s2==-5) {
1413: for (j=1,survp=0. ; j<=2; j++)
1414: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1415: lli= log(survp);
1416: }
1417:
1418: else{
1419: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1420: /* 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 */
1421: }
1422: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1423: /*if(lli ==000.0)*/
1424: /*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); */
1425: ipmx +=1;
1426: sw += weight[i];
1427: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1428: } /* end of wave */
1429: } /* end of individual */
1430: } else if(mle==2){
1431: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1432: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1433: for(mi=1; mi<= wav[i]-1; mi++){
1434: for (ii=1;ii<=nlstate+ndeath;ii++)
1435: for (j=1;j<=nlstate+ndeath;j++){
1436: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1437: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1438: }
1439: for(d=0; d<=dh[mi][i]; d++){
1440: newm=savm;
1441: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1442: for (kk=1; kk<=cptcovage;kk++) {
1443: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1444: }
1445: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1446: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1447: savm=oldm;
1448: oldm=newm;
1449: } /* end mult */
1450:
1451: s1=s[mw[mi][i]][i];
1452: s2=s[mw[mi+1][i]][i];
1453: bbh=(double)bh[mi][i]/(double)stepm;
1454: 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 */
1455: ipmx +=1;
1456: sw += weight[i];
1457: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1458: } /* end of wave */
1459: } /* end of individual */
1460: } else if(mle==3){ /* exponential inter-extrapolation */
1461: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1462: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1463: for(mi=1; mi<= wav[i]-1; mi++){
1464: for (ii=1;ii<=nlstate+ndeath;ii++)
1465: for (j=1;j<=nlstate+ndeath;j++){
1466: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1467: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1468: }
1469: for(d=0; d<dh[mi][i]; d++){
1470: newm=savm;
1471: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1472: for (kk=1; kk<=cptcovage;kk++) {
1473: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1474: }
1475: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1476: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1477: savm=oldm;
1478: oldm=newm;
1479: } /* end mult */
1480:
1481: s1=s[mw[mi][i]][i];
1482: s2=s[mw[mi+1][i]][i];
1483: bbh=(double)bh[mi][i]/(double)stepm;
1484: 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 */
1485: ipmx +=1;
1486: sw += weight[i];
1487: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1488: } /* end of wave */
1489: } /* end of individual */
1490: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1491: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1492: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1493: for(mi=1; mi<= wav[i]-1; mi++){
1494: for (ii=1;ii<=nlstate+ndeath;ii++)
1495: for (j=1;j<=nlstate+ndeath;j++){
1496: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1497: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1498: }
1499: for(d=0; d<dh[mi][i]; d++){
1500: newm=savm;
1501: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1502: for (kk=1; kk<=cptcovage;kk++) {
1503: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1504: }
1505:
1506: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1507: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1508: savm=oldm;
1509: oldm=newm;
1510: } /* end mult */
1511:
1512: s1=s[mw[mi][i]][i];
1513: s2=s[mw[mi+1][i]][i];
1514: if( s2 > nlstate){
1515: lli=log(out[s1][s2] - savm[s1][s2]);
1516: }else{
1517: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1518: }
1519: ipmx +=1;
1520: sw += weight[i];
1521: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1522: /* 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]); */
1523: } /* end of wave */
1524: } /* end of individual */
1525: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1526: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1527: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1528: for(mi=1; mi<= wav[i]-1; mi++){
1529: for (ii=1;ii<=nlstate+ndeath;ii++)
1530: for (j=1;j<=nlstate+ndeath;j++){
1531: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1532: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1533: }
1534: for(d=0; d<dh[mi][i]; d++){
1535: newm=savm;
1536: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1537: for (kk=1; kk<=cptcovage;kk++) {
1538: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1539: }
1540:
1541: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1542: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1543: savm=oldm;
1544: oldm=newm;
1545: } /* end mult */
1546:
1547: s1=s[mw[mi][i]][i];
1548: s2=s[mw[mi+1][i]][i];
1549: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1550: ipmx +=1;
1551: sw += weight[i];
1552: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1553: /*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]);*/
1554: } /* end of wave */
1555: } /* end of individual */
1556: } /* End of if */
1557: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1558: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1559: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1560: return -l;
1561: }
1562:
1563: /*************** log-likelihood *************/
1564: double funcone( double *x)
1565: {
1566: /* Same as likeli but slower because of a lot of printf and if */
1567: int i, ii, j, k, mi, d, kk;
1568: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1569: double **out;
1570: double lli; /* Individual log likelihood */
1571: double llt;
1572: int s1, s2;
1573: double bbh, survp;
1574: /*extern weight */
1575: /* We are differentiating ll according to initial status */
1576: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1577: /*for(i=1;i<imx;i++)
1578: printf(" %d\n",s[4][i]);
1579: */
1580: cov[1]=1.;
1581:
1582: for(k=1; k<=nlstate; k++) ll[k]=0.;
1583:
1584: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1585: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1586: for(mi=1; mi<= wav[i]-1; mi++){
1587: for (ii=1;ii<=nlstate+ndeath;ii++)
1588: for (j=1;j<=nlstate+ndeath;j++){
1589: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1590: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1591: }
1592: for(d=0; d<dh[mi][i]; d++){
1593: newm=savm;
1594: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1595: for (kk=1; kk<=cptcovage;kk++) {
1596: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1597: }
1598: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1599: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1600: savm=oldm;
1601: oldm=newm;
1602: } /* end mult */
1603:
1604: s1=s[mw[mi][i]][i];
1605: s2=s[mw[mi+1][i]][i];
1606: bbh=(double)bh[mi][i]/(double)stepm;
1607: /* bias is positive if real duration
1608: * is higher than the multiple of stepm and negative otherwise.
1609: */
1610: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1611: lli=log(out[s1][s2] - savm[s1][s2]);
1612: } else if (s2==-2) {
1613: for (j=1,survp=0. ; j<=nlstate; j++)
1614: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1615: lli= log(survp);
1616: }else if (mle==1){
1617: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1618: } else if(mle==2){
1619: 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 */
1620: } else if(mle==3){ /* exponential inter-extrapolation */
1621: 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 */
1622: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1623: lli=log(out[s1][s2]); /* Original formula */
1624: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1625: lli=log(out[s1][s2]); /* Original formula */
1626: } /* End of if */
1627: ipmx +=1;
1628: sw += weight[i];
1629: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1630: /* 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]); */
1631: if(globpr){
1632: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1633: %11.6f %11.6f %11.6f ", \
1634: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1635: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1636: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1637: llt +=ll[k]*gipmx/gsw;
1638: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1639: }
1640: fprintf(ficresilk," %10.6f\n", -llt);
1641: }
1642: } /* end of wave */
1643: } /* end of individual */
1644: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1645: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1646: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1647: if(globpr==0){ /* First time we count the contributions and weights */
1648: gipmx=ipmx;
1649: gsw=sw;
1650: }
1651: return -l;
1652: }
1653:
1654:
1655: /*************** function likelione ***********/
1656: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1657: {
1658: /* This routine should help understanding what is done with
1659: the selection of individuals/waves and
1660: to check the exact contribution to the likelihood.
1661: Plotting could be done.
1662: */
1663: int k;
1664:
1665: if(*globpri !=0){ /* Just counts and sums, no printings */
1666: strcpy(fileresilk,"ilk");
1667: strcat(fileresilk,fileres);
1668: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1669: printf("Problem with resultfile: %s\n", fileresilk);
1670: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1671: }
1672: 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");
1673: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1674: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1675: for(k=1; k<=nlstate; k++)
1676: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1677: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1678: }
1679:
1680: *fretone=(*funcone)(p);
1681: if(*globpri !=0){
1682: fclose(ficresilk);
1683: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1684: fflush(fichtm);
1685: }
1686: return;
1687: }
1688:
1689:
1690: /*********** Maximum Likelihood Estimation ***************/
1691:
1692: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1693: {
1694: int i,j, iter;
1695: double **xi;
1696: double fret;
1697: double fretone; /* Only one call to likelihood */
1698: /* char filerespow[FILENAMELENGTH];*/
1699: xi=matrix(1,npar,1,npar);
1700: for (i=1;i<=npar;i++)
1701: for (j=1;j<=npar;j++)
1702: xi[i][j]=(i==j ? 1.0 : 0.0);
1703: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1704: strcpy(filerespow,"pow");
1705: strcat(filerespow,fileres);
1706: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1707: printf("Problem with resultfile: %s\n", filerespow);
1708: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1709: }
1710: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1711: for (i=1;i<=nlstate;i++)
1712: for(j=1;j<=nlstate+ndeath;j++)
1713: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1714: fprintf(ficrespow,"\n");
1715:
1716: powell(p,xi,npar,ftol,&iter,&fret,func);
1717:
1718: free_matrix(xi,1,npar,1,npar);
1719: fclose(ficrespow);
1720: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1721: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1722: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1723:
1724: }
1725:
1726: /**** Computes Hessian and covariance matrix ***/
1727: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1728: {
1729: double **a,**y,*x,pd;
1730: double **hess;
1731: int i, j,jk;
1732: int *indx;
1733:
1734: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1735: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1736: void lubksb(double **a, int npar, int *indx, double b[]) ;
1737: void ludcmp(double **a, int npar, int *indx, double *d) ;
1738: double gompertz(double p[]);
1739: hess=matrix(1,npar,1,npar);
1740:
1741: printf("\nCalculation of the hessian matrix. Wait...\n");
1742: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1743: for (i=1;i<=npar;i++){
1744: printf("%d",i);fflush(stdout);
1745: fprintf(ficlog,"%d",i);fflush(ficlog);
1746:
1747: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1748:
1749: /* printf(" %f ",p[i]);
1750: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1751: }
1752:
1753: for (i=1;i<=npar;i++) {
1754: for (j=1;j<=npar;j++) {
1755: if (j>i) {
1756: printf(".%d%d",i,j);fflush(stdout);
1757: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1758: hess[i][j]=hessij(p,delti,i,j,func,npar);
1759:
1760: hess[j][i]=hess[i][j];
1761: /*printf(" %lf ",hess[i][j]);*/
1762: }
1763: }
1764: }
1765: printf("\n");
1766: fprintf(ficlog,"\n");
1767:
1768: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1769: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1770:
1771: a=matrix(1,npar,1,npar);
1772: y=matrix(1,npar,1,npar);
1773: x=vector(1,npar);
1774: indx=ivector(1,npar);
1775: for (i=1;i<=npar;i++)
1776: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1777: ludcmp(a,npar,indx,&pd);
1778:
1779: for (j=1;j<=npar;j++) {
1780: for (i=1;i<=npar;i++) x[i]=0;
1781: x[j]=1;
1782: lubksb(a,npar,indx,x);
1783: for (i=1;i<=npar;i++){
1784: matcov[i][j]=x[i];
1785: }
1786: }
1787:
1788: printf("\n#Hessian matrix#\n");
1789: fprintf(ficlog,"\n#Hessian matrix#\n");
1790: for (i=1;i<=npar;i++) {
1791: for (j=1;j<=npar;j++) {
1792: printf("%.3e ",hess[i][j]);
1793: fprintf(ficlog,"%.3e ",hess[i][j]);
1794: }
1795: printf("\n");
1796: fprintf(ficlog,"\n");
1797: }
1798:
1799: /* Recompute Inverse */
1800: for (i=1;i<=npar;i++)
1801: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1802: ludcmp(a,npar,indx,&pd);
1803:
1804: /* printf("\n#Hessian matrix recomputed#\n");
1805:
1806: for (j=1;j<=npar;j++) {
1807: for (i=1;i<=npar;i++) x[i]=0;
1808: x[j]=1;
1809: lubksb(a,npar,indx,x);
1810: for (i=1;i<=npar;i++){
1811: y[i][j]=x[i];
1812: printf("%.3e ",y[i][j]);
1813: fprintf(ficlog,"%.3e ",y[i][j]);
1814: }
1815: printf("\n");
1816: fprintf(ficlog,"\n");
1817: }
1818: */
1819:
1820: free_matrix(a,1,npar,1,npar);
1821: free_matrix(y,1,npar,1,npar);
1822: free_vector(x,1,npar);
1823: free_ivector(indx,1,npar);
1824: free_matrix(hess,1,npar,1,npar);
1825:
1826:
1827: }
1828:
1829: /*************** hessian matrix ****************/
1830: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1831: {
1832: int i;
1833: int l=1, lmax=20;
1834: double k1,k2;
1835: double p2[NPARMAX+1];
1836: double res;
1837: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1838: double fx;
1839: int k=0,kmax=10;
1840: double l1;
1841:
1842: fx=func(x);
1843: for (i=1;i<=npar;i++) p2[i]=x[i];
1844: for(l=0 ; l <=lmax; l++){
1845: l1=pow(10,l);
1846: delts=delt;
1847: for(k=1 ; k <kmax; k=k+1){
1848: delt = delta*(l1*k);
1849: p2[theta]=x[theta] +delt;
1850: k1=func(p2)-fx;
1851: p2[theta]=x[theta]-delt;
1852: k2=func(p2)-fx;
1853: /*res= (k1-2.0*fx+k2)/delt/delt; */
1854: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1855:
1856: #ifdef DEBUG
1857: 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);
1858: 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);
1859: #endif
1860: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1861: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1862: k=kmax;
1863: }
1864: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1865: k=kmax; l=lmax*10.;
1866: }
1867: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1868: delts=delt;
1869: }
1870: }
1871: }
1872: delti[theta]=delts;
1873: return res;
1874:
1875: }
1876:
1877: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1878: {
1879: int i;
1880: int l=1, l1, lmax=20;
1881: double k1,k2,k3,k4,res,fx;
1882: double p2[NPARMAX+1];
1883: int k;
1884:
1885: fx=func(x);
1886: for (k=1; k<=2; k++) {
1887: for (i=1;i<=npar;i++) p2[i]=x[i];
1888: p2[thetai]=x[thetai]+delti[thetai]/k;
1889: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1890: k1=func(p2)-fx;
1891:
1892: p2[thetai]=x[thetai]+delti[thetai]/k;
1893: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1894: k2=func(p2)-fx;
1895:
1896: p2[thetai]=x[thetai]-delti[thetai]/k;
1897: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1898: k3=func(p2)-fx;
1899:
1900: p2[thetai]=x[thetai]-delti[thetai]/k;
1901: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1902: k4=func(p2)-fx;
1903: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1904: #ifdef DEBUG
1905: 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);
1906: 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);
1907: #endif
1908: }
1909: return res;
1910: }
1911:
1912: /************** Inverse of matrix **************/
1913: void ludcmp(double **a, int n, int *indx, double *d)
1914: {
1915: int i,imax,j,k;
1916: double big,dum,sum,temp;
1917: double *vv;
1918:
1919: vv=vector(1,n);
1920: *d=1.0;
1921: for (i=1;i<=n;i++) {
1922: big=0.0;
1923: for (j=1;j<=n;j++)
1924: if ((temp=fabs(a[i][j])) > big) big=temp;
1925: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1926: vv[i]=1.0/big;
1927: }
1928: for (j=1;j<=n;j++) {
1929: for (i=1;i<j;i++) {
1930: sum=a[i][j];
1931: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1932: a[i][j]=sum;
1933: }
1934: big=0.0;
1935: for (i=j;i<=n;i++) {
1936: sum=a[i][j];
1937: for (k=1;k<j;k++)
1938: sum -= a[i][k]*a[k][j];
1939: a[i][j]=sum;
1940: if ( (dum=vv[i]*fabs(sum)) >= big) {
1941: big=dum;
1942: imax=i;
1943: }
1944: }
1945: if (j != imax) {
1946: for (k=1;k<=n;k++) {
1947: dum=a[imax][k];
1948: a[imax][k]=a[j][k];
1949: a[j][k]=dum;
1950: }
1951: *d = -(*d);
1952: vv[imax]=vv[j];
1953: }
1954: indx[j]=imax;
1955: if (a[j][j] == 0.0) a[j][j]=TINY;
1956: if (j != n) {
1957: dum=1.0/(a[j][j]);
1958: for (i=j+1;i<=n;i++) a[i][j] *= dum;
1959: }
1960: }
1961: free_vector(vv,1,n); /* Doesn't work */
1962: ;
1963: }
1964:
1965: void lubksb(double **a, int n, int *indx, double b[])
1966: {
1967: int i,ii=0,ip,j;
1968: double sum;
1969:
1970: for (i=1;i<=n;i++) {
1971: ip=indx[i];
1972: sum=b[ip];
1973: b[ip]=b[i];
1974: if (ii)
1975: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
1976: else if (sum) ii=i;
1977: b[i]=sum;
1978: }
1979: for (i=n;i>=1;i--) {
1980: sum=b[i];
1981: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
1982: b[i]=sum/a[i][i];
1983: }
1984: }
1985:
1986: void pstamp(FILE *fichier)
1987: {
1988: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
1989: }
1990:
1991: /************ Frequencies ********************/
1992: 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[])
1993: { /* Some frequencies */
1994:
1995: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
1996: int first;
1997: double ***freq; /* Frequencies */
1998: double *pp, **prop;
1999: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2000: char fileresp[FILENAMELENGTH];
2001:
2002: pp=vector(1,nlstate);
2003: prop=matrix(1,nlstate,iagemin,iagemax+3);
2004: strcpy(fileresp,"p");
2005: strcat(fileresp,fileres);
2006: if((ficresp=fopen(fileresp,"w"))==NULL) {
2007: printf("Problem with prevalence resultfile: %s\n", fileresp);
2008: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2009: exit(0);
2010: }
2011: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2012: j1=0;
2013:
2014: j=cptcoveff;
2015: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2016:
2017: first=1;
2018:
2019: for(k1=1; k1<=j;k1++){
2020: for(i1=1; i1<=ncodemax[k1];i1++){
2021: j1++;
2022: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2023: scanf("%d", i);*/
2024: for (i=-5; i<=nlstate+ndeath; i++)
2025: for (jk=-5; jk<=nlstate+ndeath; jk++)
2026: for(m=iagemin; m <= iagemax+3; m++)
2027: freq[i][jk][m]=0;
2028:
2029: for (i=1; i<=nlstate; i++)
2030: for(m=iagemin; m <= iagemax+3; m++)
2031: prop[i][m]=0;
2032:
2033: dateintsum=0;
2034: k2cpt=0;
2035: for (i=1; i<=imx; i++) {
2036: bool=1;
2037: if (cptcovn>0) {
2038: for (z1=1; z1<=cptcoveff; z1++)
2039: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2040: bool=0;
2041: }
2042: if (bool==1){
2043: for(m=firstpass; m<=lastpass; m++){
2044: k2=anint[m][i]+(mint[m][i]/12.);
2045: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2046: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2047: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2048: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2049: if (m<lastpass) {
2050: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2051: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2052: }
2053:
2054: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2055: dateintsum=dateintsum+k2;
2056: k2cpt++;
2057: }
2058: /*}*/
2059: }
2060: }
2061: }
2062:
2063: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2064: pstamp(ficresp);
2065: if (cptcovn>0) {
2066: fprintf(ficresp, "\n#********** Variable ");
2067: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2068: fprintf(ficresp, "**********\n#");
2069: }
2070: for(i=1; i<=nlstate;i++)
2071: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2072: fprintf(ficresp, "\n");
2073:
2074: for(i=iagemin; i <= iagemax+3; i++){
2075: if(i==iagemax+3){
2076: fprintf(ficlog,"Total");
2077: }else{
2078: if(first==1){
2079: first=0;
2080: printf("See log file for details...\n");
2081: }
2082: fprintf(ficlog,"Age %d", i);
2083: }
2084: for(jk=1; jk <=nlstate ; jk++){
2085: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2086: pp[jk] += freq[jk][m][i];
2087: }
2088: for(jk=1; jk <=nlstate ; jk++){
2089: for(m=-1, pos=0; m <=0 ; m++)
2090: pos += freq[jk][m][i];
2091: if(pp[jk]>=1.e-10){
2092: if(first==1){
2093: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2094: }
2095: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2096: }else{
2097: if(first==1)
2098: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2099: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2100: }
2101: }
2102:
2103: for(jk=1; jk <=nlstate ; jk++){
2104: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2105: pp[jk] += freq[jk][m][i];
2106: }
2107: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2108: pos += pp[jk];
2109: posprop += prop[jk][i];
2110: }
2111: for(jk=1; jk <=nlstate ; jk++){
2112: if(pos>=1.e-5){
2113: if(first==1)
2114: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2115: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2116: }else{
2117: if(first==1)
2118: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2119: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2120: }
2121: if( i <= iagemax){
2122: if(pos>=1.e-5){
2123: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2124: /*probs[i][jk][j1]= pp[jk]/pos;*/
2125: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2126: }
2127: else
2128: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2129: }
2130: }
2131:
2132: for(jk=-1; jk <=nlstate+ndeath; jk++)
2133: for(m=-1; m <=nlstate+ndeath; m++)
2134: if(freq[jk][m][i] !=0 ) {
2135: if(first==1)
2136: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2137: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2138: }
2139: if(i <= iagemax)
2140: fprintf(ficresp,"\n");
2141: if(first==1)
2142: printf("Others in log...\n");
2143: fprintf(ficlog,"\n");
2144: }
2145: }
2146: }
2147: dateintmean=dateintsum/k2cpt;
2148:
2149: fclose(ficresp);
2150: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2151: free_vector(pp,1,nlstate);
2152: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2153: /* End of Freq */
2154: }
2155:
2156: /************ Prevalence ********************/
2157: 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)
2158: {
2159: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2160: in each health status at the date of interview (if between dateprev1 and dateprev2).
2161: We still use firstpass and lastpass as another selection.
2162: */
2163:
2164: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2165: double ***freq; /* Frequencies */
2166: double *pp, **prop;
2167: double pos,posprop;
2168: double y2; /* in fractional years */
2169: int iagemin, iagemax;
2170:
2171: iagemin= (int) agemin;
2172: iagemax= (int) agemax;
2173: /*pp=vector(1,nlstate);*/
2174: prop=matrix(1,nlstate,iagemin,iagemax+3);
2175: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2176: j1=0;
2177:
2178: j=cptcoveff;
2179: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2180:
2181: for(k1=1; k1<=j;k1++){
2182: for(i1=1; i1<=ncodemax[k1];i1++){
2183: j1++;
2184:
2185: for (i=1; i<=nlstate; i++)
2186: for(m=iagemin; m <= iagemax+3; m++)
2187: prop[i][m]=0.0;
2188:
2189: for (i=1; i<=imx; i++) { /* Each individual */
2190: bool=1;
2191: if (cptcovn>0) {
2192: for (z1=1; z1<=cptcoveff; z1++)
2193: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2194: bool=0;
2195: }
2196: if (bool==1) {
2197: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2198: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2199: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2200: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2201: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2202: 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);
2203: if (s[m][i]>0 && s[m][i]<=nlstate) {
2204: /*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]]);*/
2205: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2206: prop[s[m][i]][iagemax+3] += weight[i];
2207: }
2208: }
2209: } /* end selection of waves */
2210: }
2211: }
2212: for(i=iagemin; i <= iagemax+3; i++){
2213:
2214: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2215: posprop += prop[jk][i];
2216: }
2217:
2218: for(jk=1; jk <=nlstate ; jk++){
2219: if( i <= iagemax){
2220: if(posprop>=1.e-5){
2221: probs[i][jk][j1]= prop[jk][i]/posprop;
2222: }
2223: }
2224: }/* end jk */
2225: }/* end i */
2226: } /* end i1 */
2227: } /* end k1 */
2228:
2229: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2230: /*free_vector(pp,1,nlstate);*/
2231: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2232: } /* End of prevalence */
2233:
2234: /************* Waves Concatenation ***************/
2235:
2236: 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)
2237: {
2238: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2239: Death is a valid wave (if date is known).
2240: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2241: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2242: and mw[mi+1][i]. dh depends on stepm.
2243: */
2244:
2245: int i, mi, m;
2246: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2247: double sum=0., jmean=0.;*/
2248: int first;
2249: int j, k=0,jk, ju, jl;
2250: double sum=0.;
2251: first=0;
2252: jmin=1e+5;
2253: jmax=-1;
2254: jmean=0.;
2255: for(i=1; i<=imx; i++){
2256: mi=0;
2257: m=firstpass;
2258: while(s[m][i] <= nlstate){
2259: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2260: mw[++mi][i]=m;
2261: if(m >=lastpass)
2262: break;
2263: else
2264: m++;
2265: }/* end while */
2266: if (s[m][i] > nlstate){
2267: mi++; /* Death is another wave */
2268: /* if(mi==0) never been interviewed correctly before death */
2269: /* Only death is a correct wave */
2270: mw[mi][i]=m;
2271: }
2272:
2273: wav[i]=mi;
2274: if(mi==0){
2275: nbwarn++;
2276: if(first==0){
2277: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2278: first=1;
2279: }
2280: if(first==1){
2281: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2282: }
2283: } /* end mi==0 */
2284: } /* End individuals */
2285:
2286: for(i=1; i<=imx; i++){
2287: for(mi=1; mi<wav[i];mi++){
2288: if (stepm <=0)
2289: dh[mi][i]=1;
2290: else{
2291: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2292: if (agedc[i] < 2*AGESUP) {
2293: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2294: if(j==0) j=1; /* Survives at least one month after exam */
2295: else if(j<0){
2296: nberr++;
2297: 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]);
2298: j=1; /* Temporary Dangerous patch */
2299: 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);
2300: 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]);
2301: 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);
2302: }
2303: k=k+1;
2304: if (j >= jmax){
2305: jmax=j;
2306: ijmax=i;
2307: }
2308: if (j <= jmin){
2309: jmin=j;
2310: ijmin=i;
2311: }
2312: sum=sum+j;
2313: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2314: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2315: }
2316: }
2317: else{
2318: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2319: /* 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]); */
2320:
2321: k=k+1;
2322: if (j >= jmax) {
2323: jmax=j;
2324: ijmax=i;
2325: }
2326: else if (j <= jmin){
2327: jmin=j;
2328: ijmin=i;
2329: }
2330: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2331: /*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]);*/
2332: if(j<0){
2333: nberr++;
2334: 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]);
2335: 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]);
2336: }
2337: sum=sum+j;
2338: }
2339: jk= j/stepm;
2340: jl= j -jk*stepm;
2341: ju= j -(jk+1)*stepm;
2342: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2343: if(jl==0){
2344: dh[mi][i]=jk;
2345: bh[mi][i]=0;
2346: }else{ /* We want a negative bias in order to only have interpolation ie
2347: * at the price of an extra matrix product in likelihood */
2348: dh[mi][i]=jk+1;
2349: bh[mi][i]=ju;
2350: }
2351: }else{
2352: if(jl <= -ju){
2353: dh[mi][i]=jk;
2354: bh[mi][i]=jl; /* bias is positive if real duration
2355: * is higher than the multiple of stepm and negative otherwise.
2356: */
2357: }
2358: else{
2359: dh[mi][i]=jk+1;
2360: bh[mi][i]=ju;
2361: }
2362: if(dh[mi][i]==0){
2363: dh[mi][i]=1; /* At least one step */
2364: bh[mi][i]=ju; /* At least one step */
2365: /* 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);*/
2366: }
2367: } /* end if mle */
2368: }
2369: } /* end wave */
2370: }
2371: jmean=sum/k;
2372: 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);
2373: 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);
2374: }
2375:
2376: /*********** Tricode ****************************/
2377: void tricode(int *Tvar, int **nbcode, int imx)
2378: {
2379:
2380: int Ndum[20],ij=1, k, j, i, maxncov=19;
2381: int cptcode=0;
2382: cptcoveff=0;
2383:
2384: for (k=0; k<maxncov; k++) Ndum[k]=0;
2385: for (k=1; k<=7; k++) ncodemax[k]=0;
2386:
2387: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2388: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2389: modality*/
2390: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2391: Ndum[ij]++; /*store the modality */
2392: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2393: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2394: Tvar[j]. If V=sex and male is 0 and
2395: female is 1, then cptcode=1.*/
2396: }
2397:
2398: for (i=0; i<=cptcode; i++) {
2399: 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 */
2400: }
2401:
2402: ij=1;
2403: for (i=1; i<=ncodemax[j]; i++) {
2404: for (k=0; k<= maxncov; k++) {
2405: if (Ndum[k] != 0) {
2406: nbcode[Tvar[j]][ij]=k;
2407: /* 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; */
2408:
2409: ij++;
2410: }
2411: if (ij > ncodemax[j]) break;
2412: }
2413: }
2414: }
2415:
2416: for (k=0; k< maxncov; k++) Ndum[k]=0;
2417:
2418: for (i=1; i<=ncovmodel-2; i++) {
2419: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2420: ij=Tvar[i];
2421: Ndum[ij]++;
2422: }
2423:
2424: ij=1;
2425: for (i=1; i<= maxncov; i++) {
2426: if((Ndum[i]!=0) && (i<=ncovcol)){
2427: Tvaraff[ij]=i; /*For printing */
2428: ij++;
2429: }
2430: }
2431:
2432: cptcoveff=ij-1; /*Number of simple covariates*/
2433: }
2434:
2435: /*********** Health Expectancies ****************/
2436:
2437: void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2438:
2439: {
2440: /* Health expectancies, no variances */
2441: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2442: double age, agelim, hf;
2443: double ***p3mat;
2444: double eip;
2445:
2446: pstamp(ficreseij);
2447: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2448: fprintf(ficreseij,"# Age");
2449: for(i=1; i<=nlstate;i++){
2450: for(j=1; j<=nlstate;j++){
2451: fprintf(ficreseij," e%1d%1d ",i,j);
2452: }
2453: fprintf(ficreseij," e%1d. ",i);
2454: }
2455: fprintf(ficreseij,"\n");
2456:
2457:
2458: if(estepm < stepm){
2459: printf ("Problem %d lower than %d\n",estepm, stepm);
2460: }
2461: else hstepm=estepm;
2462: /* We compute the life expectancy from trapezoids spaced every estepm months
2463: * This is mainly to measure the difference between two models: for example
2464: * if stepm=24 months pijx are given only every 2 years and by summing them
2465: * we are calculating an estimate of the Life Expectancy assuming a linear
2466: * progression in between and thus overestimating or underestimating according
2467: * to the curvature of the survival function. If, for the same date, we
2468: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2469: * to compare the new estimate of Life expectancy with the same linear
2470: * hypothesis. A more precise result, taking into account a more precise
2471: * curvature will be obtained if estepm is as small as stepm. */
2472:
2473: /* For example we decided to compute the life expectancy with the smallest unit */
2474: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2475: nhstepm is the number of hstepm from age to agelim
2476: nstepm is the number of stepm from age to agelin.
2477: Look at hpijx to understand the reason of that which relies in memory size
2478: and note for a fixed period like estepm months */
2479: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2480: survival function given by stepm (the optimization length). Unfortunately it
2481: means that if the survival funtion is printed only each two years of age and if
2482: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2483: results. So we changed our mind and took the option of the best precision.
2484: */
2485: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2486:
2487: agelim=AGESUP;
2488: /* nhstepm age range expressed in number of stepm */
2489: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2490: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2491: /* if (stepm >= YEARM) hstepm=1;*/
2492: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2493: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2494:
2495: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2496: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2497: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2498:
2499: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2500:
2501: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2502:
2503: printf("%d|",(int)age);fflush(stdout);
2504: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2505:
2506: /* Computing expectancies */
2507: for(i=1; i<=nlstate;i++)
2508: for(j=1; j<=nlstate;j++)
2509: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2510: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2511:
2512: /* 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]);*/
2513:
2514: }
2515:
2516: fprintf(ficreseij,"%3.0f",age );
2517: for(i=1; i<=nlstate;i++){
2518: eip=0;
2519: for(j=1; j<=nlstate;j++){
2520: eip +=eij[i][j][(int)age];
2521: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2522: }
2523: fprintf(ficreseij,"%9.4f", eip );
2524: }
2525: fprintf(ficreseij,"\n");
2526:
2527: }
2528: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2529: printf("\n");
2530: fprintf(ficlog,"\n");
2531:
2532: }
2533:
2534: void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
2535:
2536: {
2537: /* Covariances of health expectancies eij and of total life expectancies according
2538: to initial status i, ei. .
2539: */
2540: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2541: double age, agelim, hf;
2542: double ***p3matp, ***p3matm, ***varhe;
2543: double **dnewm,**doldm;
2544: double *xp, *xm;
2545: double **gp, **gm;
2546: double ***gradg, ***trgradg;
2547: int theta;
2548:
2549: double eip, vip;
2550:
2551: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2552: xp=vector(1,npar);
2553: xm=vector(1,npar);
2554: dnewm=matrix(1,nlstate*nlstate,1,npar);
2555: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2556:
2557: pstamp(ficresstdeij);
2558: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2559: fprintf(ficresstdeij,"# Age");
2560: for(i=1; i<=nlstate;i++){
2561: for(j=1; j<=nlstate;j++)
2562: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2563: fprintf(ficresstdeij," e%1d. ",i);
2564: }
2565: fprintf(ficresstdeij,"\n");
2566:
2567: pstamp(ficrescveij);
2568: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2569: fprintf(ficrescveij,"# Age");
2570: for(i=1; i<=nlstate;i++)
2571: for(j=1; j<=nlstate;j++){
2572: cptj= (j-1)*nlstate+i;
2573: for(i2=1; i2<=nlstate;i2++)
2574: for(j2=1; j2<=nlstate;j2++){
2575: cptj2= (j2-1)*nlstate+i2;
2576: if(cptj2 <= cptj)
2577: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2578: }
2579: }
2580: fprintf(ficrescveij,"\n");
2581:
2582: if(estepm < stepm){
2583: printf ("Problem %d lower than %d\n",estepm, stepm);
2584: }
2585: else hstepm=estepm;
2586: /* We compute the life expectancy from trapezoids spaced every estepm months
2587: * This is mainly to measure the difference between two models: for example
2588: * if stepm=24 months pijx are given only every 2 years and by summing them
2589: * we are calculating an estimate of the Life Expectancy assuming a linear
2590: * progression in between and thus overestimating or underestimating according
2591: * to the curvature of the survival function. If, for the same date, we
2592: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2593: * to compare the new estimate of Life expectancy with the same linear
2594: * hypothesis. A more precise result, taking into account a more precise
2595: * curvature will be obtained if estepm is as small as stepm. */
2596:
2597: /* For example we decided to compute the life expectancy with the smallest unit */
2598: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2599: nhstepm is the number of hstepm from age to agelim
2600: nstepm is the number of stepm from age to agelin.
2601: Look at hpijx to understand the reason of that which relies in memory size
2602: and note for a fixed period like estepm months */
2603: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2604: survival function given by stepm (the optimization length). Unfortunately it
2605: means that if the survival funtion is printed only each two years of age and if
2606: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2607: results. So we changed our mind and took the option of the best precision.
2608: */
2609: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2610:
2611: /* If stepm=6 months */
2612: /* nhstepm age range expressed in number of stepm */
2613: agelim=AGESUP;
2614: nstepm=(int) rint((agelim-age)*YEARM/stepm);
2615: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2616: /* if (stepm >= YEARM) hstepm=1;*/
2617: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2618:
2619: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2620: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2621: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2622: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2623: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2624: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2625:
2626: for (age=bage; age<=fage; age ++){
2627:
2628: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2629: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2630:
2631: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2632:
2633: /* Computing Variances of health expectancies */
2634: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2635: decrease memory allocation */
2636: for(theta=1; theta <=npar; theta++){
2637: for(i=1; i<=npar; i++){
2638: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2639: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2640: }
2641: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2642: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2643:
2644: for(j=1; j<= nlstate; j++){
2645: for(i=1; i<=nlstate; i++){
2646: for(h=0; h<=nhstepm-1; h++){
2647: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2648: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2649: }
2650: }
2651: }
2652:
2653: for(ij=1; ij<= nlstate*nlstate; ij++)
2654: for(h=0; h<=nhstepm-1; h++){
2655: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2656: }
2657: }/* End theta */
2658:
2659:
2660: for(h=0; h<=nhstepm-1; h++)
2661: for(j=1; j<=nlstate*nlstate;j++)
2662: for(theta=1; theta <=npar; theta++)
2663: trgradg[h][j][theta]=gradg[h][theta][j];
2664:
2665:
2666: for(ij=1;ij<=nlstate*nlstate;ij++)
2667: for(ji=1;ji<=nlstate*nlstate;ji++)
2668: varhe[ij][ji][(int)age] =0.;
2669:
2670: printf("%d|",(int)age);fflush(stdout);
2671: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2672: for(h=0;h<=nhstepm-1;h++){
2673: for(k=0;k<=nhstepm-1;k++){
2674: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2675: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2676: for(ij=1;ij<=nlstate*nlstate;ij++)
2677: for(ji=1;ji<=nlstate*nlstate;ji++)
2678: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2679: }
2680: }
2681: /* Computing expectancies */
2682: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2683: for(i=1; i<=nlstate;i++)
2684: for(j=1; j<=nlstate;j++)
2685: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2686: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2687:
2688: /* 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]);*/
2689:
2690: }
2691:
2692: fprintf(ficresstdeij,"%3.0f",age );
2693: for(i=1; i<=nlstate;i++){
2694: eip=0.;
2695: vip=0.;
2696: for(j=1; j<=nlstate;j++){
2697: eip += eij[i][j][(int)age];
2698: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2699: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2700: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2701: }
2702: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2703: }
2704: fprintf(ficresstdeij,"\n");
2705:
2706: fprintf(ficrescveij,"%3.0f",age );
2707: for(i=1; i<=nlstate;i++)
2708: for(j=1; j<=nlstate;j++){
2709: cptj= (j-1)*nlstate+i;
2710: for(i2=1; i2<=nlstate;i2++)
2711: for(j2=1; j2<=nlstate;j2++){
2712: cptj2= (j2-1)*nlstate+i2;
2713: if(cptj2 <= cptj)
2714: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2715: }
2716: }
2717: fprintf(ficrescveij,"\n");
2718:
2719: }
2720: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2721: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2722: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2723: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2724: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2725: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2726: printf("\n");
2727: fprintf(ficlog,"\n");
2728:
2729: free_vector(xm,1,npar);
2730: free_vector(xp,1,npar);
2731: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2732: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2733: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2734: }
2735:
2736: /************ Variance ******************/
2737: 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[])
2738: {
2739: /* Variance of health expectancies */
2740: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2741: /* double **newm;*/
2742: double **dnewm,**doldm;
2743: double **dnewmp,**doldmp;
2744: int i, j, nhstepm, hstepm, h, nstepm ;
2745: int k, cptcode;
2746: double *xp;
2747: double **gp, **gm; /* for var eij */
2748: double ***gradg, ***trgradg; /*for var eij */
2749: double **gradgp, **trgradgp; /* for var p point j */
2750: double *gpp, *gmp; /* for var p point j */
2751: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2752: double ***p3mat;
2753: double age,agelim, hf;
2754: double ***mobaverage;
2755: int theta;
2756: char digit[4];
2757: char digitp[25];
2758:
2759: char fileresprobmorprev[FILENAMELENGTH];
2760:
2761: if(popbased==1){
2762: if(mobilav!=0)
2763: strcpy(digitp,"-populbased-mobilav-");
2764: else strcpy(digitp,"-populbased-nomobil-");
2765: }
2766: else
2767: strcpy(digitp,"-stablbased-");
2768:
2769: if (mobilav!=0) {
2770: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2771: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2772: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2773: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2774: }
2775: }
2776:
2777: strcpy(fileresprobmorprev,"prmorprev");
2778: sprintf(digit,"%-d",ij);
2779: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2780: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2781: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2782: strcat(fileresprobmorprev,fileres);
2783: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2784: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2785: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2786: }
2787: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2788:
2789: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2790: pstamp(ficresprobmorprev);
2791: 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);
2792: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2793: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2794: fprintf(ficresprobmorprev," p.%-d SE",j);
2795: for(i=1; i<=nlstate;i++)
2796: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2797: }
2798: fprintf(ficresprobmorprev,"\n");
2799: fprintf(ficgp,"\n# Routine varevsij");
2800: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2801: 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");
2802: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2803: /* } */
2804: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2805: pstamp(ficresvij);
2806: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2807: if(popbased==1)
2808: fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
2809: else
2810: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2811: fprintf(ficresvij,"# Age");
2812: for(i=1; i<=nlstate;i++)
2813: for(j=1; j<=nlstate;j++)
2814: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2815: fprintf(ficresvij,"\n");
2816:
2817: xp=vector(1,npar);
2818: dnewm=matrix(1,nlstate,1,npar);
2819: doldm=matrix(1,nlstate,1,nlstate);
2820: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2821: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2822:
2823: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2824: gpp=vector(nlstate+1,nlstate+ndeath);
2825: gmp=vector(nlstate+1,nlstate+ndeath);
2826: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2827:
2828: if(estepm < stepm){
2829: printf ("Problem %d lower than %d\n",estepm, stepm);
2830: }
2831: else hstepm=estepm;
2832: /* For example we decided to compute the life expectancy with the smallest unit */
2833: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2834: nhstepm is the number of hstepm from age to agelim
2835: nstepm is the number of stepm from age to agelin.
2836: Look at hpijx to understand the reason of that which relies in memory size
2837: and note for a fixed period like k years */
2838: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2839: survival function given by stepm (the optimization length). Unfortunately it
2840: means that if the survival funtion is printed every two years of age and if
2841: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2842: results. So we changed our mind and took the option of the best precision.
2843: */
2844: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2845: agelim = AGESUP;
2846: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2847: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2848: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2849: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2850: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2851: gp=matrix(0,nhstepm,1,nlstate);
2852: gm=matrix(0,nhstepm,1,nlstate);
2853:
2854:
2855: for(theta=1; theta <=npar; theta++){
2856: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2857: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2858: }
2859: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2860: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2861:
2862: if (popbased==1) {
2863: if(mobilav ==0){
2864: for(i=1; i<=nlstate;i++)
2865: prlim[i][i]=probs[(int)age][i][ij];
2866: }else{ /* mobilav */
2867: for(i=1; i<=nlstate;i++)
2868: prlim[i][i]=mobaverage[(int)age][i][ij];
2869: }
2870: }
2871:
2872: for(j=1; j<= nlstate; j++){
2873: for(h=0; h<=nhstepm; h++){
2874: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2875: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2876: }
2877: }
2878: /* This for computing probability of death (h=1 means
2879: computed over hstepm matrices product = hstepm*stepm months)
2880: as a weighted average of prlim.
2881: */
2882: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2883: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2884: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2885: }
2886: /* end probability of death */
2887:
2888: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2889: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2890: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2891: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2892:
2893: if (popbased==1) {
2894: if(mobilav ==0){
2895: for(i=1; i<=nlstate;i++)
2896: prlim[i][i]=probs[(int)age][i][ij];
2897: }else{ /* mobilav */
2898: for(i=1; i<=nlstate;i++)
2899: prlim[i][i]=mobaverage[(int)age][i][ij];
2900: }
2901: }
2902:
2903: for(j=1; j<= nlstate; j++){
2904: for(h=0; h<=nhstepm; h++){
2905: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2906: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2907: }
2908: }
2909: /* This for computing probability of death (h=1 means
2910: computed over hstepm matrices product = hstepm*stepm months)
2911: as a weighted average of prlim.
2912: */
2913: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2914: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2915: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2916: }
2917: /* end probability of death */
2918:
2919: for(j=1; j<= nlstate; j++) /* vareij */
2920: for(h=0; h<=nhstepm; h++){
2921: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2922: }
2923:
2924: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2925: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2926: }
2927:
2928: } /* End theta */
2929:
2930: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2931:
2932: for(h=0; h<=nhstepm; h++) /* veij */
2933: for(j=1; j<=nlstate;j++)
2934: for(theta=1; theta <=npar; theta++)
2935: trgradg[h][j][theta]=gradg[h][theta][j];
2936:
2937: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
2938: for(theta=1; theta <=npar; theta++)
2939: trgradgp[j][theta]=gradgp[theta][j];
2940:
2941:
2942: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2943: for(i=1;i<=nlstate;i++)
2944: for(j=1;j<=nlstate;j++)
2945: vareij[i][j][(int)age] =0.;
2946:
2947: for(h=0;h<=nhstepm;h++){
2948: for(k=0;k<=nhstepm;k++){
2949: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
2950: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
2951: for(i=1;i<=nlstate;i++)
2952: for(j=1;j<=nlstate;j++)
2953: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
2954: }
2955: }
2956:
2957: /* pptj */
2958: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
2959: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
2960: for(j=nlstate+1;j<=nlstate+ndeath;j++)
2961: for(i=nlstate+1;i<=nlstate+ndeath;i++)
2962: varppt[j][i]=doldmp[j][i];
2963: /* end ppptj */
2964: /* x centered again */
2965: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
2966: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
2967:
2968: if (popbased==1) {
2969: if(mobilav ==0){
2970: for(i=1; i<=nlstate;i++)
2971: prlim[i][i]=probs[(int)age][i][ij];
2972: }else{ /* mobilav */
2973: for(i=1; i<=nlstate;i++)
2974: prlim[i][i]=mobaverage[(int)age][i][ij];
2975: }
2976: }
2977:
2978: /* This for computing probability of death (h=1 means
2979: computed over hstepm (estepm) matrices product = hstepm*stepm months)
2980: as a weighted average of prlim.
2981: */
2982: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2983: for(i=1,gmp[j]=0.;i<= nlstate; i++)
2984: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2985: }
2986: /* end probability of death */
2987:
2988: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
2989: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2990: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
2991: for(i=1; i<=nlstate;i++){
2992: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
2993: }
2994: }
2995: fprintf(ficresprobmorprev,"\n");
2996:
2997: fprintf(ficresvij,"%.0f ",age );
2998: for(i=1; i<=nlstate;i++)
2999: for(j=1; j<=nlstate;j++){
3000: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3001: }
3002: fprintf(ficresvij,"\n");
3003: free_matrix(gp,0,nhstepm,1,nlstate);
3004: free_matrix(gm,0,nhstepm,1,nlstate);
3005: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3006: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3007: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3008: } /* End age */
3009: free_vector(gpp,nlstate+1,nlstate+ndeath);
3010: free_vector(gmp,nlstate+1,nlstate+ndeath);
3011: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3012: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3013: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3014: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3015: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3016: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3017: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3018: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3019: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3020: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3021: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3022: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3023: 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);
3024: /* 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);
3025: */
3026: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3027: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3028:
3029: free_vector(xp,1,npar);
3030: free_matrix(doldm,1,nlstate,1,nlstate);
3031: free_matrix(dnewm,1,nlstate,1,npar);
3032: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3033: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3034: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3035: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3036: fclose(ficresprobmorprev);
3037: fflush(ficgp);
3038: fflush(fichtm);
3039: } /* end varevsij */
3040:
3041: /************ Variance of prevlim ******************/
3042: 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[])
3043: {
3044: /* Variance of prevalence limit */
3045: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3046: double **newm;
3047: double **dnewm,**doldm;
3048: int i, j, nhstepm, hstepm;
3049: int k, cptcode;
3050: double *xp;
3051: double *gp, *gm;
3052: double **gradg, **trgradg;
3053: double age,agelim;
3054: int theta;
3055:
3056: pstamp(ficresvpl);
3057: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3058: fprintf(ficresvpl,"# Age");
3059: for(i=1; i<=nlstate;i++)
3060: fprintf(ficresvpl," %1d-%1d",i,i);
3061: fprintf(ficresvpl,"\n");
3062:
3063: xp=vector(1,npar);
3064: dnewm=matrix(1,nlstate,1,npar);
3065: doldm=matrix(1,nlstate,1,nlstate);
3066:
3067: hstepm=1*YEARM; /* Every year of age */
3068: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3069: agelim = AGESUP;
3070: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3071: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3072: if (stepm >= YEARM) hstepm=1;
3073: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3074: gradg=matrix(1,npar,1,nlstate);
3075: gp=vector(1,nlstate);
3076: gm=vector(1,nlstate);
3077:
3078: for(theta=1; theta <=npar; theta++){
3079: for(i=1; i<=npar; i++){ /* Computes gradient */
3080: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3081: }
3082: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3083: for(i=1;i<=nlstate;i++)
3084: gp[i] = prlim[i][i];
3085:
3086: for(i=1; i<=npar; i++) /* Computes gradient */
3087: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3088: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3089: for(i=1;i<=nlstate;i++)
3090: gm[i] = prlim[i][i];
3091:
3092: for(i=1;i<=nlstate;i++)
3093: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3094: } /* End theta */
3095:
3096: trgradg =matrix(1,nlstate,1,npar);
3097:
3098: for(j=1; j<=nlstate;j++)
3099: for(theta=1; theta <=npar; theta++)
3100: trgradg[j][theta]=gradg[theta][j];
3101:
3102: for(i=1;i<=nlstate;i++)
3103: varpl[i][(int)age] =0.;
3104: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3105: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3106: for(i=1;i<=nlstate;i++)
3107: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3108:
3109: fprintf(ficresvpl,"%.0f ",age );
3110: for(i=1; i<=nlstate;i++)
3111: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3112: fprintf(ficresvpl,"\n");
3113: free_vector(gp,1,nlstate);
3114: free_vector(gm,1,nlstate);
3115: free_matrix(gradg,1,npar,1,nlstate);
3116: free_matrix(trgradg,1,nlstate,1,npar);
3117: } /* End age */
3118:
3119: free_vector(xp,1,npar);
3120: free_matrix(doldm,1,nlstate,1,npar);
3121: free_matrix(dnewm,1,nlstate,1,nlstate);
3122:
3123: }
3124:
3125: /************ Variance of one-step probabilities ******************/
3126: 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[])
3127: {
3128: int i, j=0, i1, k1, l1, t, tj;
3129: int k2, l2, j1, z1;
3130: int k=0,l, cptcode;
3131: int first=1, first1;
3132: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3133: double **dnewm,**doldm;
3134: double *xp;
3135: double *gp, *gm;
3136: double **gradg, **trgradg;
3137: double **mu;
3138: double age,agelim, cov[NCOVMAX];
3139: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3140: int theta;
3141: char fileresprob[FILENAMELENGTH];
3142: char fileresprobcov[FILENAMELENGTH];
3143: char fileresprobcor[FILENAMELENGTH];
3144:
3145: double ***varpij;
3146:
3147: strcpy(fileresprob,"prob");
3148: strcat(fileresprob,fileres);
3149: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3150: printf("Problem with resultfile: %s\n", fileresprob);
3151: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3152: }
3153: strcpy(fileresprobcov,"probcov");
3154: strcat(fileresprobcov,fileres);
3155: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3156: printf("Problem with resultfile: %s\n", fileresprobcov);
3157: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3158: }
3159: strcpy(fileresprobcor,"probcor");
3160: strcat(fileresprobcor,fileres);
3161: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3162: printf("Problem with resultfile: %s\n", fileresprobcor);
3163: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3164: }
3165: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3166: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3167: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3168: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3169: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3170: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3171: pstamp(ficresprob);
3172: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3173: fprintf(ficresprob,"# Age");
3174: pstamp(ficresprobcov);
3175: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3176: fprintf(ficresprobcov,"# Age");
3177: pstamp(ficresprobcor);
3178: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3179: fprintf(ficresprobcor,"# Age");
3180:
3181:
3182: for(i=1; i<=nlstate;i++)
3183: for(j=1; j<=(nlstate+ndeath);j++){
3184: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3185: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3186: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3187: }
3188: /* fprintf(ficresprob,"\n");
3189: fprintf(ficresprobcov,"\n");
3190: fprintf(ficresprobcor,"\n");
3191: */
3192: xp=vector(1,npar);
3193: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3194: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3195: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3196: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3197: first=1;
3198: fprintf(ficgp,"\n# Routine varprob");
3199: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3200: fprintf(fichtm,"\n");
3201:
3202: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3203: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3204: file %s<br>\n",optionfilehtmcov);
3205: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3206: and drawn. It helps understanding how is the covariance between two incidences.\
3207: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3208: 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. \
3209: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3210: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3211: standard deviations wide on each axis. <br>\
3212: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3213: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3214: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3215:
3216: cov[1]=1;
3217: tj=cptcoveff;
3218: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3219: j1=0;
3220: for(t=1; t<=tj;t++){
3221: for(i1=1; i1<=ncodemax[t];i1++){
3222: j1++;
3223: if (cptcovn>0) {
3224: fprintf(ficresprob, "\n#********** Variable ");
3225: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3226: fprintf(ficresprob, "**********\n#\n");
3227: fprintf(ficresprobcov, "\n#********** Variable ");
3228: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3229: fprintf(ficresprobcov, "**********\n#\n");
3230:
3231: fprintf(ficgp, "\n#********** Variable ");
3232: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3233: fprintf(ficgp, "**********\n#\n");
3234:
3235:
3236: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3237: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3238: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3239:
3240: fprintf(ficresprobcor, "\n#********** Variable ");
3241: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3242: fprintf(ficresprobcor, "**********\n#");
3243: }
3244:
3245: for (age=bage; age<=fage; age ++){
3246: cov[2]=age;
3247: for (k=1; k<=cptcovn;k++) {
3248: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3249: }
3250: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3251: for (k=1; k<=cptcovprod;k++)
3252: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3253:
3254: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3255: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3256: gp=vector(1,(nlstate)*(nlstate+ndeath));
3257: gm=vector(1,(nlstate)*(nlstate+ndeath));
3258:
3259: for(theta=1; theta <=npar; theta++){
3260: for(i=1; i<=npar; i++)
3261: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3262:
3263: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3264:
3265: k=0;
3266: for(i=1; i<= (nlstate); i++){
3267: for(j=1; j<=(nlstate+ndeath);j++){
3268: k=k+1;
3269: gp[k]=pmmij[i][j];
3270: }
3271: }
3272:
3273: for(i=1; i<=npar; i++)
3274: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3275:
3276: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3277: k=0;
3278: for(i=1; i<=(nlstate); i++){
3279: for(j=1; j<=(nlstate+ndeath);j++){
3280: k=k+1;
3281: gm[k]=pmmij[i][j];
3282: }
3283: }
3284:
3285: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3286: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3287: }
3288:
3289: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3290: for(theta=1; theta <=npar; theta++)
3291: trgradg[j][theta]=gradg[theta][j];
3292:
3293: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3294: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3295: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3296: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3297: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3298: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3299:
3300: pmij(pmmij,cov,ncovmodel,x,nlstate);
3301:
3302: k=0;
3303: for(i=1; i<=(nlstate); i++){
3304: for(j=1; j<=(nlstate+ndeath);j++){
3305: k=k+1;
3306: mu[k][(int) age]=pmmij[i][j];
3307: }
3308: }
3309: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3310: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3311: varpij[i][j][(int)age] = doldm[i][j];
3312:
3313: /*printf("\n%d ",(int)age);
3314: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3315: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3316: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3317: }*/
3318:
3319: fprintf(ficresprob,"\n%d ",(int)age);
3320: fprintf(ficresprobcov,"\n%d ",(int)age);
3321: fprintf(ficresprobcor,"\n%d ",(int)age);
3322:
3323: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3324: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3325: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3326: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3327: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3328: }
3329: i=0;
3330: for (k=1; k<=(nlstate);k++){
3331: for (l=1; l<=(nlstate+ndeath);l++){
3332: i=i++;
3333: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3334: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3335: for (j=1; j<=i;j++){
3336: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3337: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3338: }
3339: }
3340: }/* end of loop for state */
3341: } /* end of loop for age */
3342:
3343: /* Confidence intervalle of pij */
3344: /*
3345: fprintf(ficgp,"\nset noparametric;unset label");
3346: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3347: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3348: 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);
3349: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3350: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3351: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3352: */
3353:
3354: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3355: first1=1;
3356: for (k2=1; k2<=(nlstate);k2++){
3357: for (l2=1; l2<=(nlstate+ndeath);l2++){
3358: if(l2==k2) continue;
3359: j=(k2-1)*(nlstate+ndeath)+l2;
3360: for (k1=1; k1<=(nlstate);k1++){
3361: for (l1=1; l1<=(nlstate+ndeath);l1++){
3362: if(l1==k1) continue;
3363: i=(k1-1)*(nlstate+ndeath)+l1;
3364: if(i<=j) continue;
3365: for (age=bage; age<=fage; age ++){
3366: if ((int)age %5==0){
3367: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3368: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3369: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3370: mu1=mu[i][(int) age]/stepm*YEARM ;
3371: mu2=mu[j][(int) age]/stepm*YEARM;
3372: c12=cv12/sqrt(v1*v2);
3373: /* Computing eigen value of matrix of covariance */
3374: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3375: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3376: /* Eigen vectors */
3377: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3378: /*v21=sqrt(1.-v11*v11); *//* error */
3379: v21=(lc1-v1)/cv12*v11;
3380: v12=-v21;
3381: v22=v11;
3382: tnalp=v21/v11;
3383: if(first1==1){
3384: first1=0;
3385: 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);
3386: }
3387: 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);
3388: /*printf(fignu*/
3389: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3390: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3391: if(first==1){
3392: first=0;
3393: fprintf(ficgp,"\nset parametric;unset label");
3394: 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);
3395: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3396: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3397: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3398: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3399: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3400: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3401: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3402: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3403: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3404: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3405: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3406: 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",\
3407: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3408: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3409: }else{
3410: first=0;
3411: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3412: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3413: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3414: 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",\
3415: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3416: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3417: }/* if first */
3418: } /* age mod 5 */
3419: } /* end loop age */
3420: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3421: first=1;
3422: } /*l12 */
3423: } /* k12 */
3424: } /*l1 */
3425: }/* k1 */
3426: } /* loop covariates */
3427: }
3428: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3429: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3430: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3431: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3432: free_vector(xp,1,npar);
3433: fclose(ficresprob);
3434: fclose(ficresprobcov);
3435: fclose(ficresprobcor);
3436: fflush(ficgp);
3437: fflush(fichtmcov);
3438: }
3439:
3440:
3441: /******************* Printing html file ***********/
3442: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3443: int lastpass, int stepm, int weightopt, char model[],\
3444: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3445: int popforecast, int estepm ,\
3446: double jprev1, double mprev1,double anprev1, \
3447: double jprev2, double mprev2,double anprev2){
3448: int jj1, k1, i1, cpt;
3449:
3450: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3451: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3452: </ul>");
3453: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3454: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3455: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3456: fprintf(fichtm,"\
3457: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3458: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3459: fprintf(fichtm,"\
3460: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3461: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3462: fprintf(fichtm,"\
3463: - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
3464: <a href=\"%s\">%s</a> <br>\n</li>",
3465: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3466:
3467:
3468: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3469:
3470: m=cptcoveff;
3471: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3472:
3473: jj1=0;
3474: for(k1=1; k1<=m;k1++){
3475: for(i1=1; i1<=ncodemax[k1];i1++){
3476: jj1++;
3477: if (cptcovn > 0) {
3478: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3479: for (cpt=1; cpt<=cptcoveff;cpt++)
3480: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3481: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3482: }
3483: /* Pij */
3484: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
3485: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3486: /* Quasi-incidences */
3487: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3488: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
3489: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3490: /* Period (stable) prevalence in each health state */
3491: for(cpt=1; cpt<nlstate;cpt++){
3492: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3493: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3494: }
3495: for(cpt=1; cpt<=nlstate;cpt++) {
3496: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
3497: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3498: }
3499: } /* end i1 */
3500: }/* End k1 */
3501: fprintf(fichtm,"</ul>");
3502:
3503:
3504: fprintf(fichtm,"\
3505: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3506: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3507:
3508: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3509: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3510: fprintf(fichtm,"\
3511: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3512: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3513:
3514: fprintf(fichtm,"\
3515: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3516: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3517: fprintf(fichtm,"\
3518: - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
3519: <a href=\"%s\">%s</a> <br>\n</li>",
3520: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3521: fprintf(fichtm,"\
3522: - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
3523: <a href=\"%s\">%s</a> <br>\n</li>",
3524: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3525: fprintf(fichtm,"\
3526: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3527: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3528: fprintf(fichtm,"\
3529: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
3530: subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3531: fprintf(fichtm,"\
3532: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3533: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3534:
3535: /* if(popforecast==1) fprintf(fichtm,"\n */
3536: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3537: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3538: /* <br>",fileres,fileres,fileres,fileres); */
3539: /* else */
3540: /* 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); */
3541: fflush(fichtm);
3542: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3543:
3544: m=cptcoveff;
3545: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3546:
3547: jj1=0;
3548: for(k1=1; k1<=m;k1++){
3549: for(i1=1; i1<=ncodemax[k1];i1++){
3550: jj1++;
3551: if (cptcovn > 0) {
3552: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3553: for (cpt=1; cpt<=cptcoveff;cpt++)
3554: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3555: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3556: }
3557: for(cpt=1; cpt<=nlstate;cpt++) {
3558: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3559: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3560: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3561: }
3562: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3563: health expectancies in states (1) and (2): %s%d.png<br>\
3564: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3565: } /* end i1 */
3566: }/* End k1 */
3567: fprintf(fichtm,"</ul>");
3568: fflush(fichtm);
3569: }
3570:
3571: /******************* Gnuplot file **************/
3572: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3573:
3574: char dirfileres[132],optfileres[132];
3575: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3576: int ng;
3577: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3578: /* printf("Problem with file %s",optionfilegnuplot); */
3579: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3580: /* } */
3581:
3582: /*#ifdef windows */
3583: fprintf(ficgp,"cd \"%s\" \n",pathc);
3584: /*#endif */
3585: m=pow(2,cptcoveff);
3586:
3587: strcpy(dirfileres,optionfilefiname);
3588: strcpy(optfileres,"vpl");
3589: /* 1eme*/
3590: for (cpt=1; cpt<= nlstate ; cpt ++) {
3591: for (k1=1; k1<= m ; k1 ++) {
3592: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3593: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3594: fprintf(ficgp,"set xlabel \"Age\" \n\
3595: set ylabel \"Probability\" \n\
3596: set ter png small\n\
3597: set size 0.65,0.65\n\
3598: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3599:
3600: for (i=1; i<= nlstate ; i ++) {
3601: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3602: else fprintf(ficgp," \%%*lf (\%%*lf)");
3603: }
3604: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3605: for (i=1; i<= nlstate ; i ++) {
3606: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3607: else fprintf(ficgp," \%%*lf (\%%*lf)");
3608: }
3609: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3610: for (i=1; i<= nlstate ; i ++) {
3611: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3612: else fprintf(ficgp," \%%*lf (\%%*lf)");
3613: }
3614: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3615: }
3616: }
3617: /*2 eme*/
3618:
3619: for (k1=1; k1<= m ; k1 ++) {
3620: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3621: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3622:
3623: for (i=1; i<= nlstate+1 ; i ++) {
3624: k=2*i;
3625: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3626: for (j=1; j<= nlstate+1 ; j ++) {
3627: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3628: else fprintf(ficgp," \%%*lf (\%%*lf)");
3629: }
3630: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3631: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3632: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3633: for (j=1; j<= nlstate+1 ; j ++) {
3634: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3635: else fprintf(ficgp," \%%*lf (\%%*lf)");
3636: }
3637: fprintf(ficgp,"\" t\"\" w l 0,");
3638: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3639: for (j=1; j<= nlstate+1 ; j ++) {
3640: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3641: else fprintf(ficgp," \%%*lf (\%%*lf)");
3642: }
3643: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3644: else fprintf(ficgp,"\" t\"\" w l 0,");
3645: }
3646: }
3647:
3648: /*3eme*/
3649:
3650: for (k1=1; k1<= m ; k1 ++) {
3651: for (cpt=1; cpt<= nlstate ; cpt ++) {
3652: /* k=2+nlstate*(2*cpt-2); */
3653: k=2+(nlstate+1)*(cpt-1);
3654: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3655: fprintf(ficgp,"set ter png small\n\
3656: set size 0.65,0.65\n\
3657: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3658: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3659: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3660: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3661: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3662: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3663: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3664:
3665: */
3666: for (i=1; i< nlstate ; i ++) {
3667: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
3668: /* 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);*/
3669:
3670: }
3671: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3672: }
3673: }
3674:
3675: /* CV preval stable (period) */
3676: for (k1=1; k1<= m ; k1 ++) {
3677: for (cpt=1; cpt<=nlstate ; cpt ++) {
3678: k=3;
3679: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3680: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3681: set ter png small\nset size 0.65,0.65\n\
3682: unset log y\n\
3683: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3684:
3685: for (i=1; i< nlstate ; i ++)
3686: fprintf(ficgp,"+$%d",k+i+1);
3687: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3688:
3689: l=3+(nlstate+ndeath)*cpt;
3690: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3691: for (i=1; i< nlstate ; i ++) {
3692: l=3+(nlstate+ndeath)*cpt;
3693: fprintf(ficgp,"+$%d",l+i+1);
3694: }
3695: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3696: }
3697: }
3698:
3699: /* proba elementaires */
3700: for(i=1,jk=1; i <=nlstate; i++){
3701: for(k=1; k <=(nlstate+ndeath); k++){
3702: if (k != i) {
3703: for(j=1; j <=ncovmodel; j++){
3704: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3705: jk++;
3706: fprintf(ficgp,"\n");
3707: }
3708: }
3709: }
3710: }
3711:
3712: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3713: for(jk=1; jk <=m; jk++) {
3714: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3715: if (ng==2)
3716: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3717: else
3718: fprintf(ficgp,"\nset title \"Probability\"\n");
3719: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3720: i=1;
3721: for(k2=1; k2<=nlstate; k2++) {
3722: k3=i;
3723: for(k=1; k<=(nlstate+ndeath); k++) {
3724: if (k != k2){
3725: if(ng==2)
3726: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3727: else
3728: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3729: ij=1;
3730: for(j=3; j <=ncovmodel; j++) {
3731: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3732: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3733: ij++;
3734: }
3735: else
3736: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3737: }
3738: fprintf(ficgp,")/(1");
3739:
3740: for(k1=1; k1 <=nlstate; k1++){
3741: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3742: ij=1;
3743: for(j=3; j <=ncovmodel; j++){
3744: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3745: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3746: ij++;
3747: }
3748: else
3749: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3750: }
3751: fprintf(ficgp,")");
3752: }
3753: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3754: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3755: i=i+ncovmodel;
3756: }
3757: } /* end k */
3758: } /* end k2 */
3759: } /* end jk */
3760: } /* end ng */
3761: fflush(ficgp);
3762: } /* end gnuplot */
3763:
3764:
3765: /*************** Moving average **************/
3766: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3767:
3768: int i, cpt, cptcod;
3769: int modcovmax =1;
3770: int mobilavrange, mob;
3771: double age;
3772:
3773: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3774: a covariate has 2 modalities */
3775: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3776:
3777: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3778: if(mobilav==1) mobilavrange=5; /* default */
3779: else mobilavrange=mobilav;
3780: for (age=bage; age<=fage; age++)
3781: for (i=1; i<=nlstate;i++)
3782: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3783: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3784: /* We keep the original values on the extreme ages bage, fage and for
3785: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3786: we use a 5 terms etc. until the borders are no more concerned.
3787: */
3788: for (mob=3;mob <=mobilavrange;mob=mob+2){
3789: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3790: for (i=1; i<=nlstate;i++){
3791: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3792: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3793: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3794: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3795: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3796: }
3797: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3798: }
3799: }
3800: }/* end age */
3801: }/* end mob */
3802: }else return -1;
3803: return 0;
3804: }/* End movingaverage */
3805:
3806:
3807: /************** Forecasting ******************/
3808: 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){
3809: /* proj1, year, month, day of starting projection
3810: agemin, agemax range of age
3811: dateprev1 dateprev2 range of dates during which prevalence is computed
3812: anproj2 year of en of projection (same day and month as proj1).
3813: */
3814: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3815: int *popage;
3816: double agec; /* generic age */
3817: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3818: double *popeffectif,*popcount;
3819: double ***p3mat;
3820: double ***mobaverage;
3821: char fileresf[FILENAMELENGTH];
3822:
3823: agelim=AGESUP;
3824: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3825:
3826: strcpy(fileresf,"f");
3827: strcat(fileresf,fileres);
3828: if((ficresf=fopen(fileresf,"w"))==NULL) {
3829: printf("Problem with forecast resultfile: %s\n", fileresf);
3830: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3831: }
3832: printf("Computing forecasting: result on file '%s' \n", fileresf);
3833: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3834:
3835: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3836:
3837: if (mobilav!=0) {
3838: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3839: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3840: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3841: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3842: }
3843: }
3844:
3845: stepsize=(int) (stepm+YEARM-1)/YEARM;
3846: if (stepm<=12) stepsize=1;
3847: if(estepm < stepm){
3848: printf ("Problem %d lower than %d\n",estepm, stepm);
3849: }
3850: else hstepm=estepm;
3851:
3852: hstepm=hstepm/stepm;
3853: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3854: fractional in yp1 */
3855: anprojmean=yp;
3856: yp2=modf((yp1*12),&yp);
3857: mprojmean=yp;
3858: yp1=modf((yp2*30.5),&yp);
3859: jprojmean=yp;
3860: if(jprojmean==0) jprojmean=1;
3861: if(mprojmean==0) jprojmean=1;
3862:
3863: i1=cptcoveff;
3864: if (cptcovn < 1){i1=1;}
3865:
3866: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3867:
3868: fprintf(ficresf,"#****** Routine prevforecast **\n");
3869:
3870: /* if (h==(int)(YEARM*yearp)){ */
3871: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3872: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3873: k=k+1;
3874: fprintf(ficresf,"\n#******");
3875: for(j=1;j<=cptcoveff;j++) {
3876: 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]]);
3877: }
3878: fprintf(ficresf,"******\n");
3879: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3880: for(j=1; j<=nlstate+ndeath;j++){
3881: for(i=1; i<=nlstate;i++)
3882: fprintf(ficresf," p%d%d",i,j);
3883: fprintf(ficresf," p.%d",j);
3884: }
3885: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3886: fprintf(ficresf,"\n");
3887: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3888:
3889: for (agec=fage; agec>=(ageminpar-1); agec--){
3890: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3891: nhstepm = nhstepm/hstepm;
3892: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3893: oldm=oldms;savm=savms;
3894: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3895:
3896: for (h=0; h<=nhstepm; h++){
3897: if (h*hstepm/YEARM*stepm ==yearp) {
3898: fprintf(ficresf,"\n");
3899: for(j=1;j<=cptcoveff;j++)
3900: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3901: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3902: }
3903: for(j=1; j<=nlstate+ndeath;j++) {
3904: ppij=0.;
3905: for(i=1; i<=nlstate;i++) {
3906: if (mobilav==1)
3907: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3908: else {
3909: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3910: }
3911: if (h*hstepm/YEARM*stepm== yearp) {
3912: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3913: }
3914: } /* end i */
3915: if (h*hstepm/YEARM*stepm==yearp) {
3916: fprintf(ficresf," %.3f", ppij);
3917: }
3918: }/* end j */
3919: } /* end h */
3920: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3921: } /* end agec */
3922: } /* end yearp */
3923: } /* end cptcod */
3924: } /* end cptcov */
3925:
3926: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3927:
3928: fclose(ficresf);
3929: }
3930:
3931: /************** Forecasting *****not tested NB*************/
3932: 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){
3933:
3934: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
3935: int *popage;
3936: double calagedatem, agelim, kk1, kk2;
3937: double *popeffectif,*popcount;
3938: double ***p3mat,***tabpop,***tabpopprev;
3939: double ***mobaverage;
3940: char filerespop[FILENAMELENGTH];
3941:
3942: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3943: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3944: agelim=AGESUP;
3945: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
3946:
3947: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3948:
3949:
3950: strcpy(filerespop,"pop");
3951: strcat(filerespop,fileres);
3952: if((ficrespop=fopen(filerespop,"w"))==NULL) {
3953: printf("Problem with forecast resultfile: %s\n", filerespop);
3954: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
3955: }
3956: printf("Computing forecasting: result on file '%s' \n", filerespop);
3957: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
3958:
3959: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3960:
3961: if (mobilav!=0) {
3962: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3963: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3964: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3965: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3966: }
3967: }
3968:
3969: stepsize=(int) (stepm+YEARM-1)/YEARM;
3970: if (stepm<=12) stepsize=1;
3971:
3972: agelim=AGESUP;
3973:
3974: hstepm=1;
3975: hstepm=hstepm/stepm;
3976:
3977: if (popforecast==1) {
3978: if((ficpop=fopen(popfile,"r"))==NULL) {
3979: printf("Problem with population file : %s\n",popfile);exit(0);
3980: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
3981: }
3982: popage=ivector(0,AGESUP);
3983: popeffectif=vector(0,AGESUP);
3984: popcount=vector(0,AGESUP);
3985:
3986: i=1;
3987: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
3988:
3989: imx=i;
3990: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
3991: }
3992:
3993: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
3994: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3995: k=k+1;
3996: fprintf(ficrespop,"\n#******");
3997: for(j=1;j<=cptcoveff;j++) {
3998: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3999: }
4000: fprintf(ficrespop,"******\n");
4001: fprintf(ficrespop,"# Age");
4002: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4003: if (popforecast==1) fprintf(ficrespop," [Population]");
4004:
4005: for (cpt=0; cpt<=0;cpt++) {
4006: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4007:
4008: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4009: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4010: nhstepm = nhstepm/hstepm;
4011:
4012: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4013: oldm=oldms;savm=savms;
4014: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4015:
4016: for (h=0; h<=nhstepm; h++){
4017: if (h==(int) (calagedatem+YEARM*cpt)) {
4018: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4019: }
4020: for(j=1; j<=nlstate+ndeath;j++) {
4021: kk1=0.;kk2=0;
4022: for(i=1; i<=nlstate;i++) {
4023: if (mobilav==1)
4024: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4025: else {
4026: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4027: }
4028: }
4029: if (h==(int)(calagedatem+12*cpt)){
4030: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4031: /*fprintf(ficrespop," %.3f", kk1);
4032: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4033: }
4034: }
4035: for(i=1; i<=nlstate;i++){
4036: kk1=0.;
4037: for(j=1; j<=nlstate;j++){
4038: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4039: }
4040: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4041: }
4042:
4043: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4044: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4045: }
4046: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4047: }
4048: }
4049:
4050: /******/
4051:
4052: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4053: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4054: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4055: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4056: nhstepm = nhstepm/hstepm;
4057:
4058: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4059: oldm=oldms;savm=savms;
4060: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4061: for (h=0; h<=nhstepm; h++){
4062: if (h==(int) (calagedatem+YEARM*cpt)) {
4063: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4064: }
4065: for(j=1; j<=nlstate+ndeath;j++) {
4066: kk1=0.;kk2=0;
4067: for(i=1; i<=nlstate;i++) {
4068: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4069: }
4070: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4071: }
4072: }
4073: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4074: }
4075: }
4076: }
4077: }
4078:
4079: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4080:
4081: if (popforecast==1) {
4082: free_ivector(popage,0,AGESUP);
4083: free_vector(popeffectif,0,AGESUP);
4084: free_vector(popcount,0,AGESUP);
4085: }
4086: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4087: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4088: fclose(ficrespop);
4089: } /* End of popforecast */
4090:
4091: int fileappend(FILE *fichier, char *optionfich)
4092: {
4093: if((fichier=fopen(optionfich,"a"))==NULL) {
4094: printf("Problem with file: %s\n", optionfich);
4095: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4096: return (0);
4097: }
4098: fflush(fichier);
4099: return (1);
4100: }
4101:
4102:
4103: /**************** function prwizard **********************/
4104: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4105: {
4106:
4107: /* Wizard to print covariance matrix template */
4108:
4109: char ca[32], cb[32], cc[32];
4110: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4111: int numlinepar;
4112:
4113: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4114: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4115: for(i=1; i <=nlstate; i++){
4116: jj=0;
4117: for(j=1; j <=nlstate+ndeath; j++){
4118: if(j==i) continue;
4119: jj++;
4120: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4121: printf("%1d%1d",i,j);
4122: fprintf(ficparo,"%1d%1d",i,j);
4123: for(k=1; k<=ncovmodel;k++){
4124: /* printf(" %lf",param[i][j][k]); */
4125: /* fprintf(ficparo," %lf",param[i][j][k]); */
4126: printf(" 0.");
4127: fprintf(ficparo," 0.");
4128: }
4129: printf("\n");
4130: fprintf(ficparo,"\n");
4131: }
4132: }
4133: printf("# Scales (for hessian or gradient estimation)\n");
4134: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4135: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4136: for(i=1; i <=nlstate; i++){
4137: jj=0;
4138: for(j=1; j <=nlstate+ndeath; j++){
4139: if(j==i) continue;
4140: jj++;
4141: fprintf(ficparo,"%1d%1d",i,j);
4142: printf("%1d%1d",i,j);
4143: fflush(stdout);
4144: for(k=1; k<=ncovmodel;k++){
4145: /* printf(" %le",delti3[i][j][k]); */
4146: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4147: printf(" 0.");
4148: fprintf(ficparo," 0.");
4149: }
4150: numlinepar++;
4151: printf("\n");
4152: fprintf(ficparo,"\n");
4153: }
4154: }
4155: printf("# Covariance matrix\n");
4156: /* # 121 Var(a12)\n\ */
4157: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4158: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4159: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4160: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4161: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4162: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4163: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4164: fflush(stdout);
4165: fprintf(ficparo,"# Covariance matrix\n");
4166: /* # 121 Var(a12)\n\ */
4167: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4168: /* # ...\n\ */
4169: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4170:
4171: for(itimes=1;itimes<=2;itimes++){
4172: jj=0;
4173: for(i=1; i <=nlstate; i++){
4174: for(j=1; j <=nlstate+ndeath; j++){
4175: if(j==i) continue;
4176: for(k=1; k<=ncovmodel;k++){
4177: jj++;
4178: ca[0]= k+'a'-1;ca[1]='\0';
4179: if(itimes==1){
4180: printf("#%1d%1d%d",i,j,k);
4181: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4182: }else{
4183: printf("%1d%1d%d",i,j,k);
4184: fprintf(ficparo,"%1d%1d%d",i,j,k);
4185: /* printf(" %.5le",matcov[i][j]); */
4186: }
4187: ll=0;
4188: for(li=1;li <=nlstate; li++){
4189: for(lj=1;lj <=nlstate+ndeath; lj++){
4190: if(lj==li) continue;
4191: for(lk=1;lk<=ncovmodel;lk++){
4192: ll++;
4193: if(ll<=jj){
4194: cb[0]= lk +'a'-1;cb[1]='\0';
4195: if(ll<jj){
4196: if(itimes==1){
4197: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4198: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4199: }else{
4200: printf(" 0.");
4201: fprintf(ficparo," 0.");
4202: }
4203: }else{
4204: if(itimes==1){
4205: printf(" Var(%s%1d%1d)",ca,i,j);
4206: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4207: }else{
4208: printf(" 0.");
4209: fprintf(ficparo," 0.");
4210: }
4211: }
4212: }
4213: } /* end lk */
4214: } /* end lj */
4215: } /* end li */
4216: printf("\n");
4217: fprintf(ficparo,"\n");
4218: numlinepar++;
4219: } /* end k*/
4220: } /*end j */
4221: } /* end i */
4222: } /* end itimes */
4223:
4224: } /* end of prwizard */
4225: /******************* Gompertz Likelihood ******************************/
4226: double gompertz(double x[])
4227: {
4228: double A,B,L=0.0,sump=0.,num=0.;
4229: int i,n=0; /* n is the size of the sample */
4230:
4231: for (i=0;i<=imx-1 ; i++) {
4232: sump=sump+weight[i];
4233: /* sump=sump+1;*/
4234: num=num+1;
4235: }
4236:
4237:
4238: /* for (i=0; i<=imx; i++)
4239: 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]);*/
4240:
4241: for (i=1;i<=imx ; i++)
4242: {
4243: if (cens[i] == 1 && wav[i]>1)
4244: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4245:
4246: if (cens[i] == 0 && wav[i]>1)
4247: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4248: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4249:
4250: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4251: if (wav[i] > 1 ) { /* ??? */
4252: L=L+A*weight[i];
4253: /* 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]);*/
4254: }
4255: }
4256:
4257: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4258:
4259: return -2*L*num/sump;
4260: }
4261:
4262: /******************* Printing html file ***********/
4263: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4264: int lastpass, int stepm, int weightopt, char model[],\
4265: int imx, double p[],double **matcov,double agemortsup){
4266: int i,k;
4267:
4268: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4269: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4270: for (i=1;i<=2;i++)
4271: 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]));
4272: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4273: fprintf(fichtm,"</ul>");
4274:
4275: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4276:
4277: 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>");
4278:
4279: for (k=agegomp;k<(agemortsup-2);k++)
4280: 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]);
4281:
4282:
4283: fflush(fichtm);
4284: }
4285:
4286: /******************* Gnuplot file **************/
4287: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4288:
4289: char dirfileres[132],optfileres[132];
4290: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4291: int ng;
4292:
4293:
4294: /*#ifdef windows */
4295: fprintf(ficgp,"cd \"%s\" \n",pathc);
4296: /*#endif */
4297:
4298:
4299: strcpy(dirfileres,optionfilefiname);
4300: strcpy(optfileres,"vpl");
4301: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4302: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4303: fprintf(ficgp, "set ter png small\n set log y\n");
4304: fprintf(ficgp, "set size 0.65,0.65\n");
4305: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4306:
4307: }
4308:
4309:
4310:
4311:
4312:
4313: /***********************************************/
4314: /**************** Main Program *****************/
4315: /***********************************************/
4316:
4317: int main(int argc, char *argv[])
4318: {
4319: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4320: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4321: int linei, month, year,iout;
4322: int jj, ll, li, lj, lk, imk;
4323: int numlinepar=0; /* Current linenumber of parameter file */
4324: int itimes;
4325: int NDIM=2;
4326:
4327: char ca[32], cb[32], cc[32];
4328: char dummy[]=" ";
4329: /* FILE *fichtm; *//* Html File */
4330: /* FILE *ficgp;*/ /*Gnuplot File */
4331: struct stat info;
4332: double agedeb, agefin,hf;
4333: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4334:
4335: double fret;
4336: double **xi,tmp,delta;
4337:
4338: double dum; /* Dummy variable */
4339: double ***p3mat;
4340: double ***mobaverage;
4341: int *indx;
4342: char line[MAXLINE], linepar[MAXLINE];
4343: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4344: char pathr[MAXLINE], pathimach[MAXLINE];
4345: char **bp, *tok, *val; /* pathtot */
4346: int firstobs=1, lastobs=10;
4347: int sdeb, sfin; /* Status at beginning and end */
4348: int c, h , cpt,l;
4349: int ju,jl, mi;
4350: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4351: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4352: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4353: int mobilav=0,popforecast=0;
4354: int hstepm, nhstepm;
4355: int agemortsup;
4356: float sumlpop=0.;
4357: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4358: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4359:
4360: double bage, fage, age, agelim, agebase;
4361: double ftolpl=FTOL;
4362: double **prlim;
4363: double *severity;
4364: double ***param; /* Matrix of parameters */
4365: double *p;
4366: double **matcov; /* Matrix of covariance */
4367: double ***delti3; /* Scale */
4368: double *delti; /* Scale */
4369: double ***eij, ***vareij;
4370: double **varpl; /* Variances of prevalence limits by age */
4371: double *epj, vepp;
4372: double kk1, kk2;
4373: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4374: double **ximort;
4375: char *alph[]={"a","a","b","c","d","e"}, str[4];
4376: int *dcwave;
4377:
4378: char z[1]="c", occ;
4379:
4380: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4381: char *strt, strtend[80];
4382: char *stratrunc;
4383: int lstra;
4384:
4385: long total_usecs;
4386:
4387: /* setlocale (LC_ALL, ""); */
4388: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4389: /* textdomain (PACKAGE); */
4390: /* setlocale (LC_CTYPE, ""); */
4391: /* setlocale (LC_MESSAGES, ""); */
4392:
4393: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4394: (void) gettimeofday(&start_time,&tzp);
4395: curr_time=start_time;
4396: tm = *localtime(&start_time.tv_sec);
4397: tmg = *gmtime(&start_time.tv_sec);
4398: strcpy(strstart,asctime(&tm));
4399:
4400: /* printf("Localtime (at start)=%s",strstart); */
4401: /* tp.tv_sec = tp.tv_sec +86400; */
4402: /* tm = *localtime(&start_time.tv_sec); */
4403: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4404: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4405: /* tmg.tm_hour=tmg.tm_hour + 1; */
4406: /* tp.tv_sec = mktime(&tmg); */
4407: /* strt=asctime(&tmg); */
4408: /* printf("Time(after) =%s",strstart); */
4409: /* (void) time (&time_value);
4410: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4411: * tm = *localtime(&time_value);
4412: * strstart=asctime(&tm);
4413: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4414: */
4415:
4416: nberr=0; /* Number of errors and warnings */
4417: nbwarn=0;
4418: getcwd(pathcd, size);
4419:
4420: printf("\n%s\n%s",version,fullversion);
4421: if(argc <=1){
4422: printf("\nEnter the parameter file name: ");
4423: fgets(pathr,FILENAMELENGTH,stdin);
4424: i=strlen(pathr);
4425: if(pathr[i-1]=='\n')
4426: pathr[i-1]='\0';
4427: for (tok = pathr; tok != NULL; ){
4428: printf("Pathr |%s|\n",pathr);
4429: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4430: printf("val= |%s| pathr=%s\n",val,pathr);
4431: strcpy (pathtot, val);
4432: if(pathr[0] == '\0') break; /* Dirty */
4433: }
4434: }
4435: else{
4436: strcpy(pathtot,argv[1]);
4437: }
4438: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4439: /*cygwin_split_path(pathtot,path,optionfile);
4440: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4441: /* cutv(path,optionfile,pathtot,'\\');*/
4442:
4443: /* Split argv[0], imach program to get pathimach */
4444: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4445: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4446: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4447: /* strcpy(pathimach,argv[0]); */
4448: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4449: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4450: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4451: chdir(path); /* Can be a relative path */
4452: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4453: printf("Current directory %s!\n",pathcd);
4454: strcpy(command,"mkdir ");
4455: strcat(command,optionfilefiname);
4456: if((outcmd=system(command)) != 0){
4457: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4458: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4459: /* fclose(ficlog); */
4460: /* exit(1); */
4461: }
4462: /* if((imk=mkdir(optionfilefiname))<0){ */
4463: /* perror("mkdir"); */
4464: /* } */
4465:
4466: /*-------- arguments in the command line --------*/
4467:
4468: /* Log file */
4469: strcat(filelog, optionfilefiname);
4470: strcat(filelog,".log"); /* */
4471: if((ficlog=fopen(filelog,"w"))==NULL) {
4472: printf("Problem with logfile %s\n",filelog);
4473: goto end;
4474: }
4475: fprintf(ficlog,"Log filename:%s\n",filelog);
4476: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4477: fprintf(ficlog,"\nEnter the parameter file name: \n");
4478: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4479: path=%s \n\
4480: optionfile=%s\n\
4481: optionfilext=%s\n\
4482: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4483:
4484: printf("Local time (at start):%s",strstart);
4485: fprintf(ficlog,"Local time (at start): %s",strstart);
4486: fflush(ficlog);
4487: /* (void) gettimeofday(&curr_time,&tzp); */
4488: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4489:
4490: /* */
4491: strcpy(fileres,"r");
4492: strcat(fileres, optionfilefiname);
4493: strcat(fileres,".txt"); /* Other files have txt extension */
4494:
4495: /*---------arguments file --------*/
4496:
4497: if((ficpar=fopen(optionfile,"r"))==NULL) {
4498: printf("Problem with optionfile %s\n",optionfile);
4499: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4500: fflush(ficlog);
4501: goto end;
4502: }
4503:
4504:
4505:
4506: strcpy(filereso,"o");
4507: strcat(filereso,fileres);
4508: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4509: printf("Problem with Output resultfile: %s\n", filereso);
4510: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4511: fflush(ficlog);
4512: goto end;
4513: }
4514:
4515: /* Reads comments: lines beginning with '#' */
4516: numlinepar=0;
4517: while((c=getc(ficpar))=='#' && c!= EOF){
4518: ungetc(c,ficpar);
4519: fgets(line, MAXLINE, ficpar);
4520: numlinepar++;
4521: puts(line);
4522: fputs(line,ficparo);
4523: fputs(line,ficlog);
4524: }
4525: ungetc(c,ficpar);
4526:
4527: 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);
4528: numlinepar++;
4529: 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);
4530: 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);
4531: 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);
4532: fflush(ficlog);
4533: while((c=getc(ficpar))=='#' && c!= EOF){
4534: ungetc(c,ficpar);
4535: fgets(line, MAXLINE, ficpar);
4536: numlinepar++;
4537: puts(line);
4538: fputs(line,ficparo);
4539: fputs(line,ficlog);
4540: }
4541: ungetc(c,ficpar);
4542:
4543:
4544: covar=matrix(0,NCOVMAX,1,n);
4545: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4546: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4547:
4548: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4549: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4550: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4551:
4552: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4553: delti=delti3[1][1];
4554: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4555: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4556: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4557: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4558: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4559: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4560: fclose (ficparo);
4561: fclose (ficlog);
4562: exit(0);
4563: }
4564: else if(mle==-3) {
4565: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4566: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4567: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4568: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4569: matcov=matrix(1,npar,1,npar);
4570: }
4571: else{
4572: /* Read guess parameters */
4573: /* Reads comments: lines beginning with '#' */
4574: while((c=getc(ficpar))=='#' && c!= EOF){
4575: ungetc(c,ficpar);
4576: fgets(line, MAXLINE, ficpar);
4577: numlinepar++;
4578: puts(line);
4579: fputs(line,ficparo);
4580: fputs(line,ficlog);
4581: }
4582: ungetc(c,ficpar);
4583:
4584: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4585: for(i=1; i <=nlstate; i++){
4586: j=0;
4587: for(jj=1; jj <=nlstate+ndeath; jj++){
4588: if(jj==i) continue;
4589: j++;
4590: fscanf(ficpar,"%1d%1d",&i1,&j1);
4591: if ((i1 != i) && (j1 != j)){
4592: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4593: exit(1);
4594: }
4595: fprintf(ficparo,"%1d%1d",i1,j1);
4596: if(mle==1)
4597: printf("%1d%1d",i,j);
4598: fprintf(ficlog,"%1d%1d",i,j);
4599: for(k=1; k<=ncovmodel;k++){
4600: fscanf(ficpar," %lf",¶m[i][j][k]);
4601: if(mle==1){
4602: printf(" %lf",param[i][j][k]);
4603: fprintf(ficlog," %lf",param[i][j][k]);
4604: }
4605: else
4606: fprintf(ficlog," %lf",param[i][j][k]);
4607: fprintf(ficparo," %lf",param[i][j][k]);
4608: }
4609: fscanf(ficpar,"\n");
4610: numlinepar++;
4611: if(mle==1)
4612: printf("\n");
4613: fprintf(ficlog,"\n");
4614: fprintf(ficparo,"\n");
4615: }
4616: }
4617: fflush(ficlog);
4618:
4619: p=param[1][1];
4620:
4621: /* Reads comments: lines beginning with '#' */
4622: while((c=getc(ficpar))=='#' && c!= EOF){
4623: ungetc(c,ficpar);
4624: fgets(line, MAXLINE, ficpar);
4625: numlinepar++;
4626: puts(line);
4627: fputs(line,ficparo);
4628: fputs(line,ficlog);
4629: }
4630: ungetc(c,ficpar);
4631:
4632: for(i=1; i <=nlstate; i++){
4633: for(j=1; j <=nlstate+ndeath-1; j++){
4634: fscanf(ficpar,"%1d%1d",&i1,&j1);
4635: if ((i1-i)*(j1-j)!=0){
4636: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4637: exit(1);
4638: }
4639: printf("%1d%1d",i,j);
4640: fprintf(ficparo,"%1d%1d",i1,j1);
4641: fprintf(ficlog,"%1d%1d",i1,j1);
4642: for(k=1; k<=ncovmodel;k++){
4643: fscanf(ficpar,"%le",&delti3[i][j][k]);
4644: printf(" %le",delti3[i][j][k]);
4645: fprintf(ficparo," %le",delti3[i][j][k]);
4646: fprintf(ficlog," %le",delti3[i][j][k]);
4647: }
4648: fscanf(ficpar,"\n");
4649: numlinepar++;
4650: printf("\n");
4651: fprintf(ficparo,"\n");
4652: fprintf(ficlog,"\n");
4653: }
4654: }
4655: fflush(ficlog);
4656:
4657: delti=delti3[1][1];
4658:
4659:
4660: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4661:
4662: /* Reads comments: lines beginning with '#' */
4663: while((c=getc(ficpar))=='#' && c!= EOF){
4664: ungetc(c,ficpar);
4665: fgets(line, MAXLINE, ficpar);
4666: numlinepar++;
4667: puts(line);
4668: fputs(line,ficparo);
4669: fputs(line,ficlog);
4670: }
4671: ungetc(c,ficpar);
4672:
4673: matcov=matrix(1,npar,1,npar);
4674: for(i=1; i <=npar; i++){
4675: fscanf(ficpar,"%s",&str);
4676: if(mle==1)
4677: printf("%s",str);
4678: fprintf(ficlog,"%s",str);
4679: fprintf(ficparo,"%s",str);
4680: for(j=1; j <=i; j++){
4681: fscanf(ficpar," %le",&matcov[i][j]);
4682: if(mle==1){
4683: printf(" %.5le",matcov[i][j]);
4684: }
4685: fprintf(ficlog," %.5le",matcov[i][j]);
4686: fprintf(ficparo," %.5le",matcov[i][j]);
4687: }
4688: fscanf(ficpar,"\n");
4689: numlinepar++;
4690: if(mle==1)
4691: printf("\n");
4692: fprintf(ficlog,"\n");
4693: fprintf(ficparo,"\n");
4694: }
4695: for(i=1; i <=npar; i++)
4696: for(j=i+1;j<=npar;j++)
4697: matcov[i][j]=matcov[j][i];
4698:
4699: if(mle==1)
4700: printf("\n");
4701: fprintf(ficlog,"\n");
4702:
4703: fflush(ficlog);
4704:
4705: /*-------- Rewriting parameter file ----------*/
4706: strcpy(rfileres,"r"); /* "Rparameterfile */
4707: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4708: strcat(rfileres,"."); /* */
4709: strcat(rfileres,optionfilext); /* Other files have txt extension */
4710: if((ficres =fopen(rfileres,"w"))==NULL) {
4711: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4712: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4713: }
4714: fprintf(ficres,"#%s\n",version);
4715: } /* End of mle != -3 */
4716:
4717: /*-------- data file ----------*/
4718: if((fic=fopen(datafile,"r"))==NULL) {
4719: printf("Problem while opening datafile: %s\n", datafile);goto end;
4720: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4721: }
4722:
4723: n= lastobs;
4724: severity = vector(1,maxwav);
4725: outcome=imatrix(1,maxwav+1,1,n);
4726: num=lvector(1,n);
4727: moisnais=vector(1,n);
4728: annais=vector(1,n);
4729: moisdc=vector(1,n);
4730: andc=vector(1,n);
4731: agedc=vector(1,n);
4732: cod=ivector(1,n);
4733: weight=vector(1,n);
4734: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4735: mint=matrix(1,maxwav,1,n);
4736: anint=matrix(1,maxwav,1,n);
4737: s=imatrix(1,maxwav+1,1,n);
4738: tab=ivector(1,NCOVMAX);
4739: ncodemax=ivector(1,8);
4740:
4741: i=1;
4742: linei=0;
4743: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4744: linei=linei+1;
4745: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4746: if(line[j] == '\t')
4747: line[j] = ' ';
4748: }
4749: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4750: ;
4751: };
4752: line[j+1]=0; /* Trims blanks at end of line */
4753: if(line[0]=='#'){
4754: fprintf(ficlog,"Comment line\n%s\n",line);
4755: printf("Comment line\n%s\n",line);
4756: continue;
4757: }
4758:
4759: for (j=maxwav;j>=1;j--){
4760: cutv(stra, strb,line,' ');
4761: errno=0;
4762: lval=strtol(strb,&endptr,10);
4763: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4764: if( strb[0]=='\0' || (*endptr != '\0')){
4765: 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);
4766: exit(1);
4767: }
4768: s[j][i]=lval;
4769:
4770: strcpy(line,stra);
4771: cutv(stra, strb,line,' ');
4772: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4773: }
4774: else if(iout=sscanf(strb,"%s.") != 0){
4775: month=99;
4776: year=9999;
4777: }else{
4778: 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);
4779: exit(1);
4780: }
4781: anint[j][i]= (double) year;
4782: mint[j][i]= (double)month;
4783: strcpy(line,stra);
4784: } /* ENd Waves */
4785:
4786: cutv(stra, strb,line,' ');
4787: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4788: }
4789: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4790: month=99;
4791: year=9999;
4792: }else{
4793: 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);
4794: exit(1);
4795: }
4796: andc[i]=(double) year;
4797: moisdc[i]=(double) month;
4798: strcpy(line,stra);
4799:
4800: cutv(stra, strb,line,' ');
4801: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4802: }
4803: else if(iout=sscanf(strb,"%s.") != 0){
4804: month=99;
4805: year=9999;
4806: }else{
4807: 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);
4808: exit(1);
4809: }
4810: annais[i]=(double)(year);
4811: moisnais[i]=(double)(month);
4812: strcpy(line,stra);
4813:
4814: cutv(stra, strb,line,' ');
4815: errno=0;
4816: lval=strtol(strb,&endptr,10);
4817: if( strb[0]=='\0' || (*endptr != '\0')){
4818: printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);
4819: exit(1);
4820: }
4821: weight[i]=(double)(lval);
4822: strcpy(line,stra);
4823:
4824: for (j=ncovcol;j>=1;j--){
4825: cutv(stra, strb,line,' ');
4826: errno=0;
4827: lval=strtol(strb,&endptr,10);
4828: if( strb[0]=='\0' || (*endptr != '\0')){
4829: 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);
4830: exit(1);
4831: }
4832: if(lval <-1 || lval >1){
4833: 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);
4834: exit(1);
4835: }
4836: covar[j][i]=(double)(lval);
4837: strcpy(line,stra);
4838: }
4839: lstra=strlen(stra);
4840:
4841: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4842: stratrunc = &(stra[lstra-9]);
4843: num[i]=atol(stratrunc);
4844: }
4845: else
4846: num[i]=atol(stra);
4847: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4848: 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;}*/
4849:
4850: i=i+1;
4851: } /* End loop reading data */
4852: fclose(fic);
4853: /* printf("ii=%d", ij);
4854: scanf("%d",i);*/
4855: imx=i-1; /* Number of individuals */
4856:
4857: /* for (i=1; i<=imx; i++){
4858: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4859: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4860: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4861: }*/
4862: /* for (i=1; i<=imx; i++){
4863: if (s[4][i]==9) s[4][i]=-1;
4864: 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]));}*/
4865:
4866: /* for (i=1; i<=imx; i++) */
4867:
4868: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4869: else weight[i]=1;*/
4870:
4871: /* Calculation of the number of parameters from char model */
4872: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4873: Tprod=ivector(1,15);
4874: Tvaraff=ivector(1,15);
4875: Tvard=imatrix(1,15,1,2);
4876: Tage=ivector(1,15);
4877:
4878: if (strlen(model) >1){ /* If there is at least 1 covariate */
4879: j=0, j1=0, k1=1, k2=1;
4880: j=nbocc(model,'+'); /* j=Number of '+' */
4881: j1=nbocc(model,'*'); /* j1=Number of '*' */
4882: cptcovn=j+1;
4883: cptcovprod=j1; /*Number of products */
4884:
4885: strcpy(modelsav,model);
4886: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4887: printf("Error. Non available option model=%s ",model);
4888: fprintf(ficlog,"Error. Non available option model=%s ",model);
4889: goto end;
4890: }
4891:
4892: /* This loop fills the array Tvar from the string 'model'.*/
4893:
4894: for(i=(j+1); i>=1;i--){
4895: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4896: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4897: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4898: /*scanf("%d",i);*/
4899: if (strchr(strb,'*')) { /* Model includes a product */
4900: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4901: if (strcmp(strc,"age")==0) { /* Vn*age */
4902: cptcovprod--;
4903: cutv(strb,stre,strd,'V');
4904: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4905: cptcovage++;
4906: Tage[cptcovage]=i;
4907: /*printf("stre=%s ", stre);*/
4908: }
4909: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4910: cptcovprod--;
4911: cutv(strb,stre,strc,'V');
4912: Tvar[i]=atoi(stre);
4913: cptcovage++;
4914: Tage[cptcovage]=i;
4915: }
4916: else { /* Age is not in the model */
4917: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
4918: Tvar[i]=ncovcol+k1;
4919: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
4920: Tprod[k1]=i;
4921: Tvard[k1][1]=atoi(strc); /* m*/
4922: Tvard[k1][2]=atoi(stre); /* n */
4923: Tvar[cptcovn+k2]=Tvard[k1][1];
4924: Tvar[cptcovn+k2+1]=Tvard[k1][2];
4925: for (k=1; k<=lastobs;k++)
4926: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
4927: k1++;
4928: k2=k2+2;
4929: }
4930: }
4931: else { /* no more sum */
4932: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
4933: /* scanf("%d",i);*/
4934: cutv(strd,strc,strb,'V');
4935: Tvar[i]=atoi(strc);
4936: }
4937: strcpy(modelsav,stra);
4938: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
4939: scanf("%d",i);*/
4940: } /* end of loop + */
4941: } /* end model */
4942:
4943: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
4944: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
4945:
4946: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
4947: printf("cptcovprod=%d ", cptcovprod);
4948: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
4949:
4950: scanf("%d ",i);*/
4951:
4952: /* if(mle==1){*/
4953: if (weightopt != 1) { /* Maximisation without weights*/
4954: for(i=1;i<=n;i++) weight[i]=1.0;
4955: }
4956: /*-calculation of age at interview from date of interview and age at death -*/
4957: agev=matrix(1,maxwav,1,imx);
4958:
4959: for (i=1; i<=imx; i++) {
4960: for(m=2; (m<= maxwav); m++) {
4961: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
4962: anint[m][i]=9999;
4963: s[m][i]=-1;
4964: }
4965: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
4966: nberr++;
4967: 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);
4968: 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);
4969: s[m][i]=-1;
4970: }
4971: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
4972: nberr++;
4973: 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]);
4974: 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]);
4975: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
4976: }
4977: }
4978: }
4979:
4980: for (i=1; i<=imx; i++) {
4981: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
4982: for(m=firstpass; (m<= lastpass); m++){
4983: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
4984: if (s[m][i] >= nlstate+1) {
4985: if(agedc[i]>0)
4986: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
4987: agev[m][i]=agedc[i];
4988: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
4989: else {
4990: if ((int)andc[i]!=9999){
4991: nbwarn++;
4992: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
4993: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
4994: agev[m][i]=-1;
4995: }
4996: }
4997: }
4998: else if(s[m][i] !=9){ /* Standard case, age in fractional
4999: years but with the precision of a month */
5000: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5001: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5002: agev[m][i]=1;
5003: else if(agev[m][i] <agemin){
5004: agemin=agev[m][i];
5005: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5006: }
5007: else if(agev[m][i] >agemax){
5008: agemax=agev[m][i];
5009: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5010: }
5011: /*agev[m][i]=anint[m][i]-annais[i];*/
5012: /* agev[m][i] = age[i]+2*m;*/
5013: }
5014: else { /* =9 */
5015: agev[m][i]=1;
5016: s[m][i]=-1;
5017: }
5018: }
5019: else /*= 0 Unknown */
5020: agev[m][i]=1;
5021: }
5022:
5023: }
5024: for (i=1; i<=imx; i++) {
5025: for(m=firstpass; (m<=lastpass); m++){
5026: if (s[m][i] > (nlstate+ndeath)) {
5027: nberr++;
5028: 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);
5029: 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);
5030: goto end;
5031: }
5032: }
5033: }
5034:
5035: /*for (i=1; i<=imx; i++){
5036: for (m=firstpass; (m<lastpass); m++){
5037: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5038: }
5039:
5040: }*/
5041:
5042:
5043: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5044: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5045:
5046: agegomp=(int)agemin;
5047: free_vector(severity,1,maxwav);
5048: free_imatrix(outcome,1,maxwav+1,1,n);
5049: free_vector(moisnais,1,n);
5050: free_vector(annais,1,n);
5051: /* free_matrix(mint,1,maxwav,1,n);
5052: free_matrix(anint,1,maxwav,1,n);*/
5053: free_vector(moisdc,1,n);
5054: free_vector(andc,1,n);
5055:
5056:
5057: wav=ivector(1,imx);
5058: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5059: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5060: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5061:
5062: /* Concatenates waves */
5063: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5064:
5065: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5066:
5067: Tcode=ivector(1,100);
5068: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5069: ncodemax[1]=1;
5070: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5071:
5072: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5073: the estimations*/
5074: h=0;
5075: m=pow(2,cptcoveff);
5076:
5077: for(k=1;k<=cptcoveff; k++){
5078: for(i=1; i <=(m/pow(2,k));i++){
5079: for(j=1; j <= ncodemax[k]; j++){
5080: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5081: h++;
5082: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5083: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5084: }
5085: }
5086: }
5087: }
5088: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5089: codtab[1][2]=1;codtab[2][2]=2; */
5090: /* for(i=1; i <=m ;i++){
5091: for(k=1; k <=cptcovn; k++){
5092: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5093: }
5094: printf("\n");
5095: }
5096: scanf("%d",i);*/
5097:
5098: /*------------ gnuplot -------------*/
5099: strcpy(optionfilegnuplot,optionfilefiname);
5100: if(mle==-3)
5101: strcat(optionfilegnuplot,"-mort");
5102: strcat(optionfilegnuplot,".gp");
5103:
5104: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5105: printf("Problem with file %s",optionfilegnuplot);
5106: }
5107: else{
5108: fprintf(ficgp,"\n# %s\n", version);
5109: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5110: fprintf(ficgp,"set missing 'NaNq'\n");
5111: }
5112: /* fclose(ficgp);*/
5113: /*--------- index.htm --------*/
5114:
5115: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5116: if(mle==-3)
5117: strcat(optionfilehtm,"-mort");
5118: strcat(optionfilehtm,".htm");
5119: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5120: printf("Problem with %s \n",optionfilehtm), exit(0);
5121: }
5122:
5123: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5124: strcat(optionfilehtmcov,"-cov.htm");
5125: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5126: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5127: }
5128: else{
5129: fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
5130: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5131: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5132: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5133: }
5134:
5135: fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
5136: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5137: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5138: \n\
5139: <hr size=\"2\" color=\"#EC5E5E\">\
5140: <ul><li><h4>Parameter files</h4>\n\
5141: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5142: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5143: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5144: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5145: - Date and time at start: %s</ul>\n",\
5146: fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5147: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5148: fileres,fileres,\
5149: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5150: fflush(fichtm);
5151:
5152: strcpy(pathr,path);
5153: strcat(pathr,optionfilefiname);
5154: chdir(optionfilefiname); /* Move to directory named optionfile */
5155:
5156: /* Calculates basic frequencies. Computes observed prevalence at single age
5157: and prints on file fileres'p'. */
5158: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5159:
5160: fprintf(fichtm,"\n");
5161: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5162: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5163: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5164: imx,agemin,agemax,jmin,jmax,jmean);
5165: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5166: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5167: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5168: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5169: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5170:
5171:
5172: /* For Powell, parameters are in a vector p[] starting at p[1]
5173: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5174: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5175:
5176: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5177:
5178: if (mle==-3){
5179: ximort=matrix(1,NDIM,1,NDIM);
5180: cens=ivector(1,n);
5181: ageexmed=vector(1,n);
5182: agecens=vector(1,n);
5183: dcwave=ivector(1,n);
5184:
5185: for (i=1; i<=imx; i++){
5186: dcwave[i]=-1;
5187: for (m=firstpass; m<=lastpass; m++)
5188: if (s[m][i]>nlstate) {
5189: dcwave[i]=m;
5190: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5191: break;
5192: }
5193: }
5194:
5195: for (i=1; i<=imx; i++) {
5196: if (wav[i]>0){
5197: ageexmed[i]=agev[mw[1][i]][i];
5198: j=wav[i];
5199: agecens[i]=1.;
5200:
5201: if (ageexmed[i]> 1 && wav[i] > 0){
5202: agecens[i]=agev[mw[j][i]][i];
5203: cens[i]= 1;
5204: }else if (ageexmed[i]< 1)
5205: cens[i]= -1;
5206: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5207: cens[i]=0 ;
5208: }
5209: else cens[i]=-1;
5210: }
5211:
5212: for (i=1;i<=NDIM;i++) {
5213: for (j=1;j<=NDIM;j++)
5214: ximort[i][j]=(i == j ? 1.0 : 0.0);
5215: }
5216:
5217: p[1]=0.0268; p[NDIM]=0.083;
5218: /*printf("%lf %lf", p[1], p[2]);*/
5219:
5220:
5221: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5222: strcpy(filerespow,"pow-mort");
5223: strcat(filerespow,fileres);
5224: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5225: printf("Problem with resultfile: %s\n", filerespow);
5226: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5227: }
5228: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5229: /* for (i=1;i<=nlstate;i++)
5230: for(j=1;j<=nlstate+ndeath;j++)
5231: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5232: */
5233: fprintf(ficrespow,"\n");
5234:
5235: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5236: fclose(ficrespow);
5237:
5238: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5239:
5240: for(i=1; i <=NDIM; i++)
5241: for(j=i+1;j<=NDIM;j++)
5242: matcov[i][j]=matcov[j][i];
5243:
5244: printf("\nCovariance matrix\n ");
5245: for(i=1; i <=NDIM; i++) {
5246: for(j=1;j<=NDIM;j++){
5247: printf("%f ",matcov[i][j]);
5248: }
5249: printf("\n ");
5250: }
5251:
5252: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5253: for (i=1;i<=NDIM;i++)
5254: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5255:
5256: lsurv=vector(1,AGESUP);
5257: lpop=vector(1,AGESUP);
5258: tpop=vector(1,AGESUP);
5259: lsurv[agegomp]=100000;
5260:
5261: for (k=agegomp;k<=AGESUP;k++) {
5262: agemortsup=k;
5263: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5264: }
5265:
5266: for (k=agegomp;k<agemortsup;k++)
5267: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5268:
5269: for (k=agegomp;k<agemortsup;k++){
5270: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5271: sumlpop=sumlpop+lpop[k];
5272: }
5273:
5274: tpop[agegomp]=sumlpop;
5275: for (k=agegomp;k<(agemortsup-3);k++){
5276: /* tpop[k+1]=2;*/
5277: tpop[k+1]=tpop[k]-lpop[k];
5278: }
5279:
5280:
5281: printf("\nAge lx qx dx Lx Tx e(x)\n");
5282: for (k=agegomp;k<(agemortsup-2);k++)
5283: 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]);
5284:
5285:
5286: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5287: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5288:
5289: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5290: stepm, weightopt,\
5291: model,imx,p,matcov,agemortsup);
5292:
5293: free_vector(lsurv,1,AGESUP);
5294: free_vector(lpop,1,AGESUP);
5295: free_vector(tpop,1,AGESUP);
5296: } /* Endof if mle==-3 */
5297:
5298: else{ /* For mle >=1 */
5299:
5300: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5301: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5302: for (k=1; k<=npar;k++)
5303: printf(" %d %8.5f",k,p[k]);
5304: printf("\n");
5305: globpr=1; /* to print the contributions */
5306: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5307: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5308: for (k=1; k<=npar;k++)
5309: printf(" %d %8.5f",k,p[k]);
5310: printf("\n");
5311: if(mle>=1){ /* Could be 1 or 2 */
5312: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5313: }
5314:
5315: /*--------- results files --------------*/
5316: 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);
5317:
5318:
5319: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5320: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5321: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5322: for(i=1,jk=1; i <=nlstate; i++){
5323: for(k=1; k <=(nlstate+ndeath); k++){
5324: if (k != i) {
5325: printf("%d%d ",i,k);
5326: fprintf(ficlog,"%d%d ",i,k);
5327: fprintf(ficres,"%1d%1d ",i,k);
5328: for(j=1; j <=ncovmodel; j++){
5329: printf("%f ",p[jk]);
5330: fprintf(ficlog,"%f ",p[jk]);
5331: fprintf(ficres,"%f ",p[jk]);
5332: jk++;
5333: }
5334: printf("\n");
5335: fprintf(ficlog,"\n");
5336: fprintf(ficres,"\n");
5337: }
5338: }
5339: }
5340: if(mle!=0){
5341: /* Computing hessian and covariance matrix */
5342: ftolhess=ftol; /* Usually correct */
5343: hesscov(matcov, p, npar, delti, ftolhess, func);
5344: }
5345: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5346: printf("# Scales (for hessian or gradient estimation)\n");
5347: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5348: for(i=1,jk=1; i <=nlstate; i++){
5349: for(j=1; j <=nlstate+ndeath; j++){
5350: if (j!=i) {
5351: fprintf(ficres,"%1d%1d",i,j);
5352: printf("%1d%1d",i,j);
5353: fprintf(ficlog,"%1d%1d",i,j);
5354: for(k=1; k<=ncovmodel;k++){
5355: printf(" %.5e",delti[jk]);
5356: fprintf(ficlog," %.5e",delti[jk]);
5357: fprintf(ficres," %.5e",delti[jk]);
5358: jk++;
5359: }
5360: printf("\n");
5361: fprintf(ficlog,"\n");
5362: fprintf(ficres,"\n");
5363: }
5364: }
5365: }
5366:
5367: 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");
5368: if(mle>=1)
5369: 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");
5370: 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");
5371: /* # 121 Var(a12)\n\ */
5372: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5373: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5374: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5375: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5376: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5377: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5378: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5379:
5380:
5381: /* Just to have a covariance matrix which will be more understandable
5382: even is we still don't want to manage dictionary of variables
5383: */
5384: for(itimes=1;itimes<=2;itimes++){
5385: jj=0;
5386: for(i=1; i <=nlstate; i++){
5387: for(j=1; j <=nlstate+ndeath; j++){
5388: if(j==i) continue;
5389: for(k=1; k<=ncovmodel;k++){
5390: jj++;
5391: ca[0]= k+'a'-1;ca[1]='\0';
5392: if(itimes==1){
5393: if(mle>=1)
5394: printf("#%1d%1d%d",i,j,k);
5395: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5396: fprintf(ficres,"#%1d%1d%d",i,j,k);
5397: }else{
5398: if(mle>=1)
5399: printf("%1d%1d%d",i,j,k);
5400: fprintf(ficlog,"%1d%1d%d",i,j,k);
5401: fprintf(ficres,"%1d%1d%d",i,j,k);
5402: }
5403: ll=0;
5404: for(li=1;li <=nlstate; li++){
5405: for(lj=1;lj <=nlstate+ndeath; lj++){
5406: if(lj==li) continue;
5407: for(lk=1;lk<=ncovmodel;lk++){
5408: ll++;
5409: if(ll<=jj){
5410: cb[0]= lk +'a'-1;cb[1]='\0';
5411: if(ll<jj){
5412: if(itimes==1){
5413: if(mle>=1)
5414: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5415: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5416: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5417: }else{
5418: if(mle>=1)
5419: printf(" %.5e",matcov[jj][ll]);
5420: fprintf(ficlog," %.5e",matcov[jj][ll]);
5421: fprintf(ficres," %.5e",matcov[jj][ll]);
5422: }
5423: }else{
5424: if(itimes==1){
5425: if(mle>=1)
5426: printf(" Var(%s%1d%1d)",ca,i,j);
5427: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5428: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5429: }else{
5430: if(mle>=1)
5431: printf(" %.5e",matcov[jj][ll]);
5432: fprintf(ficlog," %.5e",matcov[jj][ll]);
5433: fprintf(ficres," %.5e",matcov[jj][ll]);
5434: }
5435: }
5436: }
5437: } /* end lk */
5438: } /* end lj */
5439: } /* end li */
5440: if(mle>=1)
5441: printf("\n");
5442: fprintf(ficlog,"\n");
5443: fprintf(ficres,"\n");
5444: numlinepar++;
5445: } /* end k*/
5446: } /*end j */
5447: } /* end i */
5448: } /* end itimes */
5449:
5450: fflush(ficlog);
5451: fflush(ficres);
5452:
5453: while((c=getc(ficpar))=='#' && c!= EOF){
5454: ungetc(c,ficpar);
5455: fgets(line, MAXLINE, ficpar);
5456: puts(line);
5457: fputs(line,ficparo);
5458: }
5459: ungetc(c,ficpar);
5460:
5461: estepm=0;
5462: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5463: if (estepm==0 || estepm < stepm) estepm=stepm;
5464: if (fage <= 2) {
5465: bage = ageminpar;
5466: fage = agemaxpar;
5467: }
5468:
5469: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5470: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5471: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5472:
5473: while((c=getc(ficpar))=='#' && c!= EOF){
5474: ungetc(c,ficpar);
5475: fgets(line, MAXLINE, ficpar);
5476: puts(line);
5477: fputs(line,ficparo);
5478: }
5479: ungetc(c,ficpar);
5480:
5481: 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);
5482: 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);
5483: 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);
5484: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5485: 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);
5486:
5487: while((c=getc(ficpar))=='#' && c!= EOF){
5488: ungetc(c,ficpar);
5489: fgets(line, MAXLINE, ficpar);
5490: puts(line);
5491: fputs(line,ficparo);
5492: }
5493: ungetc(c,ficpar);
5494:
5495:
5496: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5497: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5498:
5499: fscanf(ficpar,"pop_based=%d\n",&popbased);
5500: fprintf(ficparo,"pop_based=%d\n",popbased);
5501: fprintf(ficres,"pop_based=%d\n",popbased);
5502:
5503: while((c=getc(ficpar))=='#' && c!= EOF){
5504: ungetc(c,ficpar);
5505: fgets(line, MAXLINE, ficpar);
5506: puts(line);
5507: fputs(line,ficparo);
5508: }
5509: ungetc(c,ficpar);
5510:
5511: 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);
5512: 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);
5513: 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);
5514: 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);
5515: 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);
5516: /* day and month of proj2 are not used but only year anproj2.*/
5517:
5518:
5519:
5520: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5521: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5522:
5523: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5524: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5525:
5526: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5527: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5528: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5529:
5530: /*------------ free_vector -------------*/
5531: /* chdir(path); */
5532:
5533: free_ivector(wav,1,imx);
5534: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5535: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5536: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5537: free_lvector(num,1,n);
5538: free_vector(agedc,1,n);
5539: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5540: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5541: fclose(ficparo);
5542: fclose(ficres);
5543:
5544:
5545: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5546:
5547: strcpy(filerespl,"pl");
5548: strcat(filerespl,fileres);
5549: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5550: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5551: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5552: }
5553: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5554: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5555: pstamp(ficrespl);
5556: fprintf(ficrespl,"# Period (stable) prevalence \n");
5557: fprintf(ficrespl,"#Age ");
5558: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5559: fprintf(ficrespl,"\n");
5560:
5561: prlim=matrix(1,nlstate,1,nlstate);
5562:
5563: agebase=ageminpar;
5564: agelim=agemaxpar;
5565: ftolpl=1.e-10;
5566: i1=cptcoveff;
5567: if (cptcovn < 1){i1=1;}
5568:
5569: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5570: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5571: k=k+1;
5572: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5573: fprintf(ficrespl,"\n#******");
5574: printf("\n#******");
5575: fprintf(ficlog,"\n#******");
5576: for(j=1;j<=cptcoveff;j++) {
5577: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5578: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5579: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5580: }
5581: fprintf(ficrespl,"******\n");
5582: printf("******\n");
5583: fprintf(ficlog,"******\n");
5584:
5585: for (age=agebase; age<=agelim; age++){
5586: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5587: fprintf(ficrespl,"%.0f ",age );
5588: for(j=1;j<=cptcoveff;j++)
5589: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5590: for(i=1; i<=nlstate;i++)
5591: fprintf(ficrespl," %.5f", prlim[i][i]);
5592: fprintf(ficrespl,"\n");
5593: }
5594: }
5595: }
5596: fclose(ficrespl);
5597:
5598: /*------------- h Pij x at various ages ------------*/
5599:
5600: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5601: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5602: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5603: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5604: }
5605: printf("Computing pij: result on file '%s' \n", filerespij);
5606: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5607:
5608: stepsize=(int) (stepm+YEARM-1)/YEARM;
5609: /*if (stepm<=24) stepsize=2;*/
5610:
5611: agelim=AGESUP;
5612: hstepm=stepsize*YEARM; /* Every year of age */
5613: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5614:
5615: /* hstepm=1; aff par mois*/
5616: pstamp(ficrespij);
5617: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5618: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5619: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5620: k=k+1;
5621: fprintf(ficrespij,"\n#****** ");
5622: for(j=1;j<=cptcoveff;j++)
5623: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5624: fprintf(ficrespij,"******\n");
5625:
5626: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5627: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5628: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5629:
5630: /* nhstepm=nhstepm*YEARM; aff par mois*/
5631:
5632: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5633: oldm=oldms;savm=savms;
5634: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5635: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5636: for(i=1; i<=nlstate;i++)
5637: for(j=1; j<=nlstate+ndeath;j++)
5638: fprintf(ficrespij," %1d-%1d",i,j);
5639: fprintf(ficrespij,"\n");
5640: for (h=0; h<=nhstepm; h++){
5641: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5642: for(i=1; i<=nlstate;i++)
5643: for(j=1; j<=nlstate+ndeath;j++)
5644: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5645: fprintf(ficrespij,"\n");
5646: }
5647: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5648: fprintf(ficrespij,"\n");
5649: }
5650: }
5651: }
5652:
5653: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5654:
5655: fclose(ficrespij);
5656:
5657: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5658: for(i=1;i<=AGESUP;i++)
5659: for(j=1;j<=NCOVMAX;j++)
5660: for(k=1;k<=NCOVMAX;k++)
5661: probs[i][j][k]=0.;
5662:
5663: /*---------- Forecasting ------------------*/
5664: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5665: if(prevfcast==1){
5666: /* if(stepm ==1){*/
5667: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5668: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5669: /* } */
5670: /* else{ */
5671: /* erreur=108; */
5672: /* 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); */
5673: /* 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); */
5674: /* } */
5675: }
5676:
5677:
5678: /*---------- Health expectancies and variances ------------*/
5679:
5680: strcpy(filerest,"t");
5681: strcat(filerest,fileres);
5682: if((ficrest=fopen(filerest,"w"))==NULL) {
5683: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5684: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5685: }
5686: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5687: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5688:
5689:
5690: strcpy(filerese,"e");
5691: strcat(filerese,fileres);
5692: if((ficreseij=fopen(filerese,"w"))==NULL) {
5693: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5694: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5695: }
5696: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5697: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5698:
5699: strcpy(fileresstde,"stde");
5700: strcat(fileresstde,fileres);
5701: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5702: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5703: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5704: }
5705: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5706: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5707:
5708: strcpy(filerescve,"cve");
5709: strcat(filerescve,fileres);
5710: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5711: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5712: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5713: }
5714: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5715: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5716:
5717: strcpy(fileresv,"v");
5718: strcat(fileresv,fileres);
5719: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5720: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5721: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5722: }
5723: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5724: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5725:
5726: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5727: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5728: /* 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",\
5729: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5730: */
5731:
5732: if (mobilav!=0) {
5733: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5734: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5735: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5736: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5737: }
5738: }
5739:
5740: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5741: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5742: k=k+1;
5743: fprintf(ficrest,"\n#****** ");
5744: for(j=1;j<=cptcoveff;j++)
5745: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5746: fprintf(ficrest,"******\n");
5747:
5748: fprintf(ficreseij,"\n#****** ");
5749: fprintf(ficresstdeij,"\n#****** ");
5750: fprintf(ficrescveij,"\n#****** ");
5751: for(j=1;j<=cptcoveff;j++) {
5752: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5753: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5754: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5755: }
5756: fprintf(ficreseij,"******\n");
5757: fprintf(ficresstdeij,"******\n");
5758: fprintf(ficrescveij,"******\n");
5759:
5760: fprintf(ficresvij,"\n#****** ");
5761: for(j=1;j<=cptcoveff;j++)
5762: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5763: fprintf(ficresvij,"******\n");
5764:
5765: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5766: oldm=oldms;savm=savms;
5767: evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5768: cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5769:
5770: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5771: oldm=oldms;savm=savms;
5772: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
5773: if(popbased==1){
5774: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
5775: }
5776:
5777: pstamp(ficrest);
5778: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
5779: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5780: fprintf(ficrest,"\n");
5781:
5782: epj=vector(1,nlstate+1);
5783: for(age=bage; age <=fage ;age++){
5784: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5785: if (popbased==1) {
5786: if(mobilav ==0){
5787: for(i=1; i<=nlstate;i++)
5788: prlim[i][i]=probs[(int)age][i][k];
5789: }else{ /* mobilav */
5790: for(i=1; i<=nlstate;i++)
5791: prlim[i][i]=mobaverage[(int)age][i][k];
5792: }
5793: }
5794:
5795: fprintf(ficrest," %4.0f",age);
5796: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5797: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5798: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5799: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5800: }
5801: epj[nlstate+1] +=epj[j];
5802: }
5803:
5804: for(i=1, vepp=0.;i <=nlstate;i++)
5805: for(j=1;j <=nlstate;j++)
5806: vepp += vareij[i][j][(int)age];
5807: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5808: for(j=1;j <=nlstate;j++){
5809: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5810: }
5811: fprintf(ficrest,"\n");
5812: }
5813: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5814: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5815: free_vector(epj,1,nlstate+1);
5816: }
5817: }
5818: free_vector(weight,1,n);
5819: free_imatrix(Tvard,1,15,1,2);
5820: free_imatrix(s,1,maxwav+1,1,n);
5821: free_matrix(anint,1,maxwav,1,n);
5822: free_matrix(mint,1,maxwav,1,n);
5823: free_ivector(cod,1,n);
5824: free_ivector(tab,1,NCOVMAX);
5825: fclose(ficreseij);
5826: fclose(ficresstdeij);
5827: fclose(ficrescveij);
5828: fclose(ficresvij);
5829: fclose(ficrest);
5830: fclose(ficpar);
5831:
5832: /*------- Variance of period (stable) prevalence------*/
5833:
5834: strcpy(fileresvpl,"vpl");
5835: strcat(fileresvpl,fileres);
5836: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5837: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5838: exit(0);
5839: }
5840: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5841:
5842: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5843: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5844: k=k+1;
5845: fprintf(ficresvpl,"\n#****** ");
5846: for(j=1;j<=cptcoveff;j++)
5847: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5848: fprintf(ficresvpl,"******\n");
5849:
5850: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5851: oldm=oldms;savm=savms;
5852: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5853: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5854: }
5855: }
5856:
5857: fclose(ficresvpl);
5858:
5859: /*---------- End : free ----------------*/
5860: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5861: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5862:
5863: } /* mle==-3 arrives here for freeing */
5864: free_matrix(prlim,1,nlstate,1,nlstate);
5865: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5866: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5867: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5868: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5869: free_matrix(covar,0,NCOVMAX,1,n);
5870: free_matrix(matcov,1,npar,1,npar);
5871: /*free_vector(delti,1,npar);*/
5872: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5873: free_matrix(agev,1,maxwav,1,imx);
5874: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5875:
5876: free_ivector(ncodemax,1,8);
5877: free_ivector(Tvar,1,15);
5878: free_ivector(Tprod,1,15);
5879: free_ivector(Tvaraff,1,15);
5880: free_ivector(Tage,1,15);
5881: free_ivector(Tcode,1,100);
5882:
5883: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5884: free_imatrix(codtab,1,100,1,10);
5885: fflush(fichtm);
5886: fflush(ficgp);
5887:
5888:
5889: if((nberr >0) || (nbwarn>0)){
5890: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5891: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5892: }else{
5893: printf("End of Imach\n");
5894: fprintf(ficlog,"End of Imach\n");
5895: }
5896: printf("See log file on %s\n",filelog);
5897: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
5898: (void) gettimeofday(&end_time,&tzp);
5899: tm = *localtime(&end_time.tv_sec);
5900: tmg = *gmtime(&end_time.tv_sec);
5901: strcpy(strtend,asctime(&tm));
5902: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
5903: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
5904: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5905:
5906: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5907: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
5908: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
5909: /* printf("Total time was %d uSec.\n", total_usecs);*/
5910: /* if(fileappend(fichtm,optionfilehtm)){ */
5911: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);
5912: fclose(fichtm);
5913: fclose(fichtmcov);
5914: fclose(ficgp);
5915: fclose(ficlog);
5916: /*------ End -----------*/
5917:
5918:
5919: printf("Before Current directory %s!\n",pathcd);
5920: if(chdir(pathcd) != 0)
5921: printf("Can't move to directory %s!\n",path);
5922: if(getcwd(pathcd,MAXLINE) > 0)
5923: printf("Current directory %s!\n",pathcd);
5924: /*strcat(plotcmd,CHARSEPARATOR);*/
5925: sprintf(plotcmd,"gnuplot");
5926: #ifndef UNIX
5927: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
5928: #endif
5929: if(!stat(plotcmd,&info)){
5930: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5931: if(!stat(getenv("GNUPLOTBIN"),&info)){
5932: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
5933: }else
5934: strcpy(pplotcmd,plotcmd);
5935: #ifdef UNIX
5936: strcpy(plotcmd,GNUPLOTPROGRAM);
5937: if(!stat(plotcmd,&info)){
5938: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
5939: }else
5940: strcpy(pplotcmd,plotcmd);
5941: #endif
5942: }else
5943: strcpy(pplotcmd,plotcmd);
5944:
5945: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
5946: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
5947:
5948: if((outcmd=system(plotcmd)) != 0){
5949: printf("\n Problem with gnuplot\n");
5950: }
5951: printf(" Wait...");
5952: while (z[0] != 'q') {
5953: /* chdir(path); */
5954: printf("\nType e to edit output files, g to graph again and q for exiting: ");
5955: scanf("%s",z);
5956: /* if (z[0] == 'c') system("./imach"); */
5957: if (z[0] == 'e') {
5958: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
5959: system(optionfilehtm);
5960: }
5961: else if (z[0] == 'g') system(plotcmd);
5962: else if (z[0] == 'q') exit(0);
5963: }
5964: end:
5965: while (z[0] != 'q') {
5966: printf("\nType q for exiting: ");
5967: scanf("%s",z);
5968: }
5969: }
5970:
5971:
5972:
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