Annotation of imach/src/imach.c, revision 1.129
1.129 ! lievre 1: /* $Id: imach.c,v 1.128 2006/06/30 13:02:05 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.129 ! lievre 4: Revision 1.128 2006/06/30 13:02:05 brouard
! 5: (Module): Clarifications on computing e.j
! 6:
1.128 brouard 7: Revision 1.127 2006/04/28 18:11:50 brouard
8: (Module): Yes the sum of survivors was wrong since
9: imach-114 because nhstepm was no more computed in the age
10: loop. Now we define nhstepma in the age loop.
11: (Module): In order to speed up (in case of numerous covariates) we
12: compute health expectancies (without variances) in a first step
13: and then all the health expectancies with variances or standard
14: deviation (needs data from the Hessian matrices) which slows the
15: computation.
16: In the future we should be able to stop the program is only health
17: expectancies and graph are needed without standard deviations.
18:
1.127 brouard 19: Revision 1.126 2006/04/28 17:23:28 brouard
20: (Module): Yes the sum of survivors was wrong since
21: imach-114 because nhstepm was no more computed in the age
22: loop. Now we define nhstepma in the age loop.
23: Version 0.98h
24:
1.126 brouard 25: Revision 1.125 2006/04/04 15:20:31 lievre
26: Errors in calculation of health expectancies. Age was not initialized.
27: Forecasting file added.
28:
29: Revision 1.124 2006/03/22 17:13:53 lievre
30: Parameters are printed with %lf instead of %f (more numbers after the comma).
31: The log-likelihood is printed in the log file
32:
33: Revision 1.123 2006/03/20 10:52:43 brouard
34: * imach.c (Module): <title> changed, corresponds to .htm file
35: name. <head> headers where missing.
36:
37: * imach.c (Module): Weights can have a decimal point as for
38: English (a comma might work with a correct LC_NUMERIC environment,
39: otherwise the weight is truncated).
40: Modification of warning when the covariates values are not 0 or
41: 1.
42: Version 0.98g
43:
44: Revision 1.122 2006/03/20 09:45:41 brouard
45: (Module): Weights can have a decimal point as for
46: English (a comma might work with a correct LC_NUMERIC environment,
47: otherwise the weight is truncated).
48: Modification of warning when the covariates values are not 0 or
49: 1.
50: Version 0.98g
51:
52: Revision 1.121 2006/03/16 17:45:01 lievre
53: * imach.c (Module): Comments concerning covariates added
54:
55: * imach.c (Module): refinements in the computation of lli if
56: status=-2 in order to have more reliable computation if stepm is
57: not 1 month. Version 0.98f
58:
59: Revision 1.120 2006/03/16 15:10:38 lievre
60: (Module): refinements in the computation of lli if
61: status=-2 in order to have more reliable computation if stepm is
62: not 1 month. Version 0.98f
63:
64: Revision 1.119 2006/03/15 17:42:26 brouard
65: (Module): Bug if status = -2, the loglikelihood was
66: computed as likelihood omitting the logarithm. Version O.98e
67:
68: Revision 1.118 2006/03/14 18:20:07 brouard
69: (Module): varevsij Comments added explaining the second
70: table of variances if popbased=1 .
71: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
72: (Module): Function pstamp added
73: (Module): Version 0.98d
74:
75: Revision 1.117 2006/03/14 17:16:22 brouard
76: (Module): varevsij Comments added explaining the second
77: table of variances if popbased=1 .
78: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
79: (Module): Function pstamp added
80: (Module): Version 0.98d
81:
82: Revision 1.116 2006/03/06 10:29:27 brouard
83: (Module): Variance-covariance wrong links and
84: varian-covariance of ej. is needed (Saito).
85:
86: Revision 1.115 2006/02/27 12:17:45 brouard
87: (Module): One freematrix added in mlikeli! 0.98c
88:
89: Revision 1.114 2006/02/26 12:57:58 brouard
90: (Module): Some improvements in processing parameter
91: filename with strsep.
92:
93: Revision 1.113 2006/02/24 14:20:24 brouard
94: (Module): Memory leaks checks with valgrind and:
95: datafile was not closed, some imatrix were not freed and on matrix
96: allocation too.
97:
98: Revision 1.112 2006/01/30 09:55:26 brouard
99: (Module): Back to gnuplot.exe instead of wgnuplot.exe
100:
101: Revision 1.111 2006/01/25 20:38:18 brouard
102: (Module): Lots of cleaning and bugs added (Gompertz)
103: (Module): Comments can be added in data file. Missing date values
104: can be a simple dot '.'.
105:
106: Revision 1.110 2006/01/25 00:51:50 brouard
107: (Module): Lots of cleaning and bugs added (Gompertz)
108:
109: Revision 1.109 2006/01/24 19:37:15 brouard
110: (Module): Comments (lines starting with a #) are allowed in data.
111:
112: Revision 1.108 2006/01/19 18:05:42 lievre
113: Gnuplot problem appeared...
114: To be fixed
115:
116: Revision 1.107 2006/01/19 16:20:37 brouard
117: Test existence of gnuplot in imach path
118:
119: Revision 1.106 2006/01/19 13:24:36 brouard
120: Some cleaning and links added in html output
121:
122: Revision 1.105 2006/01/05 20:23:19 lievre
123: *** empty log message ***
124:
125: Revision 1.104 2005/09/30 16:11:43 lievre
126: (Module): sump fixed, loop imx fixed, and simplifications.
127: (Module): If the status is missing at the last wave but we know
128: that the person is alive, then we can code his/her status as -2
129: (instead of missing=-1 in earlier versions) and his/her
130: contributions to the likelihood is 1 - Prob of dying from last
131: health status (= 1-p13= p11+p12 in the easiest case of somebody in
132: the healthy state at last known wave). Version is 0.98
133:
134: Revision 1.103 2005/09/30 15:54:49 lievre
135: (Module): sump fixed, loop imx fixed, and simplifications.
136:
137: Revision 1.102 2004/09/15 17:31:30 brouard
138: Add the possibility to read data file including tab characters.
139:
140: Revision 1.101 2004/09/15 10:38:38 brouard
141: Fix on curr_time
142:
143: Revision 1.100 2004/07/12 18:29:06 brouard
144: Add version for Mac OS X. Just define UNIX in Makefile
145:
146: Revision 1.99 2004/06/05 08:57:40 brouard
147: *** empty log message ***
148:
149: Revision 1.98 2004/05/16 15:05:56 brouard
150: New version 0.97 . First attempt to estimate force of mortality
151: directly from the data i.e. without the need of knowing the health
152: state at each age, but using a Gompertz model: log u =a + b*age .
153: This is the basic analysis of mortality and should be done before any
154: other analysis, in order to test if the mortality estimated from the
155: cross-longitudinal survey is different from the mortality estimated
156: from other sources like vital statistic data.
157:
158: The same imach parameter file can be used but the option for mle should be -3.
159:
160: Agnès, who wrote this part of the code, tried to keep most of the
161: former routines in order to include the new code within the former code.
162:
163: The output is very simple: only an estimate of the intercept and of
164: the slope with 95% confident intervals.
165:
166: Current limitations:
167: A) Even if you enter covariates, i.e. with the
168: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
169: B) There is no computation of Life Expectancy nor Life Table.
170:
171: Revision 1.97 2004/02/20 13:25:42 lievre
172: Version 0.96d. Population forecasting command line is (temporarily)
173: suppressed.
174:
175: Revision 1.96 2003/07/15 15:38:55 brouard
176: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
177: rewritten within the same printf. Workaround: many printfs.
178:
179: Revision 1.95 2003/07/08 07:54:34 brouard
180: * imach.c (Repository):
181: (Repository): Using imachwizard code to output a more meaningful covariance
182: matrix (cov(a12,c31) instead of numbers.
183:
184: Revision 1.94 2003/06/27 13:00:02 brouard
185: Just cleaning
186:
187: Revision 1.93 2003/06/25 16:33:55 brouard
188: (Module): On windows (cygwin) function asctime_r doesn't
189: exist so I changed back to asctime which exists.
190: (Module): Version 0.96b
191:
192: Revision 1.92 2003/06/25 16:30:45 brouard
193: (Module): On windows (cygwin) function asctime_r doesn't
194: exist so I changed back to asctime which exists.
195:
196: Revision 1.91 2003/06/25 15:30:29 brouard
197: * imach.c (Repository): Duplicated warning errors corrected.
198: (Repository): Elapsed time after each iteration is now output. It
199: helps to forecast when convergence will be reached. Elapsed time
200: is stamped in powell. We created a new html file for the graphs
201: concerning matrix of covariance. It has extension -cov.htm.
202:
203: Revision 1.90 2003/06/24 12:34:15 brouard
204: (Module): Some bugs corrected for windows. Also, when
205: mle=-1 a template is output in file "or"mypar.txt with the design
206: of the covariance matrix to be input.
207:
208: Revision 1.89 2003/06/24 12:30:52 brouard
209: (Module): Some bugs corrected for windows. Also, when
210: mle=-1 a template is output in file "or"mypar.txt with the design
211: of the covariance matrix to be input.
212:
213: Revision 1.88 2003/06/23 17:54:56 brouard
214: * 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.
215:
216: Revision 1.87 2003/06/18 12:26:01 brouard
217: Version 0.96
218:
219: Revision 1.86 2003/06/17 20:04:08 brouard
220: (Module): Change position of html and gnuplot routines and added
221: routine fileappend.
222:
223: Revision 1.85 2003/06/17 13:12:43 brouard
224: * imach.c (Repository): Check when date of death was earlier that
225: current date of interview. It may happen when the death was just
226: prior to the death. In this case, dh was negative and likelihood
227: was wrong (infinity). We still send an "Error" but patch by
228: assuming that the date of death was just one stepm after the
229: interview.
230: (Repository): Because some people have very long ID (first column)
231: we changed int to long in num[] and we added a new lvector for
232: memory allocation. But we also truncated to 8 characters (left
233: truncation)
234: (Repository): No more line truncation errors.
235:
236: Revision 1.84 2003/06/13 21:44:43 brouard
237: * imach.c (Repository): Replace "freqsummary" at a correct
238: place. It differs from routine "prevalence" which may be called
239: many times. Probs is memory consuming and must be used with
240: parcimony.
241: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
242:
243: Revision 1.83 2003/06/10 13:39:11 lievre
244: *** empty log message ***
245:
246: Revision 1.82 2003/06/05 15:57:20 brouard
247: Add log in imach.c and fullversion number is now printed.
248:
249: */
250: /*
251: Interpolated Markov Chain
252:
253: Short summary of the programme:
254:
255: This program computes Healthy Life Expectancies from
256: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
257: first survey ("cross") where individuals from different ages are
258: interviewed on their health status or degree of disability (in the
259: case of a health survey which is our main interest) -2- at least a
260: second wave of interviews ("longitudinal") which measure each change
261: (if any) in individual health status. Health expectancies are
262: computed from the time spent in each health state according to a
263: model. More health states you consider, more time is necessary to reach the
264: Maximum Likelihood of the parameters involved in the model. The
265: simplest model is the multinomial logistic model where pij is the
266: probability to be observed in state j at the second wave
267: conditional to be observed in state i at the first wave. Therefore
268: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
269: 'age' is age and 'sex' is a covariate. If you want to have a more
270: complex model than "constant and age", you should modify the program
271: where the markup *Covariates have to be included here again* invites
272: you to do it. More covariates you add, slower the
273: convergence.
274:
275: The advantage of this computer programme, compared to a simple
276: multinomial logistic model, is clear when the delay between waves is not
277: identical for each individual. Also, if a individual missed an
278: intermediate interview, the information is lost, but taken into
279: account using an interpolation or extrapolation.
280:
281: hPijx is the probability to be observed in state i at age x+h
282: conditional to the observed state i at age x. The delay 'h' can be
283: split into an exact number (nh*stepm) of unobserved intermediate
284: states. This elementary transition (by month, quarter,
285: semester or year) is modelled as a multinomial logistic. The hPx
286: matrix is simply the matrix product of nh*stepm elementary matrices
287: and the contribution of each individual to the likelihood is simply
288: hPijx.
289:
290: Also this programme outputs the covariance matrix of the parameters but also
291: of the life expectancies. It also computes the period (stable) prevalence.
292:
293: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
294: Institut national d'études démographiques, Paris.
295: This software have been partly granted by Euro-REVES, a concerted action
296: from the European Union.
297: It is copyrighted identically to a GNU software product, ie programme and
298: software can be distributed freely for non commercial use. Latest version
299: can be accessed at http://euroreves.ined.fr/imach .
300:
301: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
302: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
303:
304: **********************************************************************/
305: /*
306: main
307: read parameterfile
308: read datafile
309: concatwav
310: freqsummary
311: if (mle >= 1)
312: mlikeli
313: print results files
314: if mle==1
315: computes hessian
316: read end of parameter file: agemin, agemax, bage, fage, estepm
317: begin-prev-date,...
318: open gnuplot file
319: open html file
320: period (stable) prevalence
321: for age prevalim()
322: h Pij x
323: variance of p varprob
324: forecasting if prevfcast==1 prevforecast call prevalence()
325: health expectancies
326: Variance-covariance of DFLE
327: prevalence()
328: movingaverage()
329: varevsij()
330: if popbased==1 varevsij(,popbased)
331: total life expectancies
332: Variance of period (stable) prevalence
333: end
334: */
335:
336:
337:
338:
339: #include <math.h>
340: #include <stdio.h>
341: #include <stdlib.h>
342: #include <string.h>
343: #include <unistd.h>
344:
345: #include <limits.h>
346: #include <sys/types.h>
347: #include <sys/stat.h>
348: #include <errno.h>
349: extern int errno;
350:
351: /* #include <sys/time.h> */
352: #include <time.h>
353: #include "timeval.h"
354:
355: /* #include <libintl.h> */
356: /* #define _(String) gettext (String) */
357:
358: #define MAXLINE 256
359:
360: #define GNUPLOTPROGRAM "gnuplot"
361: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
362: #define FILENAMELENGTH 132
363:
364: #define GLOCK_ERROR_NOPATH -1 /* empty path */
365: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
366:
367: #define MAXPARM 30 /* Maximum number of parameters for the optimization */
368: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
369:
370: #define NINTERVMAX 8
371: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
372: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
373: #define NCOVMAX 8 /* Maximum number of covariates */
374: #define MAXN 20000
375: #define YEARM 12. /* Number of months per year */
376: #define AGESUP 130
377: #define AGEBASE 40
378: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
379: #ifdef UNIX
380: #define DIRSEPARATOR '/'
381: #define CHARSEPARATOR "/"
382: #define ODIRSEPARATOR '\\'
383: #else
384: #define DIRSEPARATOR '\\'
385: #define CHARSEPARATOR "\\"
386: #define ODIRSEPARATOR '/'
387: #endif
388:
1.129 ! lievre 389: /* $Id: imach.c,v 1.128 2006/06/30 13:02:05 brouard Exp $ */
1.126 brouard 390: /* $State: Exp $ */
391:
1.128 brouard 392: char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
1.129 ! lievre 393: char fullversion[]="$Revision: 1.128 $ $Date: 2006/06/30 13:02:05 $";
1.126 brouard 394: char strstart[80];
395: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
396: int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
397: int nvar;
398: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
399: int npar=NPARMAX;
400: int nlstate=2; /* Number of live states */
401: int ndeath=1; /* Number of dead states */
402: int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
403: int popbased=0;
404:
405: int *wav; /* Number of waves for this individuual 0 is possible */
406: int maxwav; /* Maxim number of waves */
407: int jmin, jmax; /* min, max spacing between 2 waves */
408: int ijmin, ijmax; /* Individuals having jmin and jmax */
409: int gipmx, gsw; /* Global variables on the number of contributions
410: to the likelihood and the sum of weights (done by funcone)*/
411: int mle, weightopt;
412: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
413: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
414: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
415: * wave mi and wave mi+1 is not an exact multiple of stepm. */
416: double jmean; /* Mean space between 2 waves */
417: double **oldm, **newm, **savm; /* Working pointers to matrices */
418: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
419: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
420: FILE *ficlog, *ficrespow;
421: int globpr; /* Global variable for printing or not */
422: double fretone; /* Only one call to likelihood */
423: long ipmx; /* Number of contributions */
424: double sw; /* Sum of weights */
425: char filerespow[FILENAMELENGTH];
426: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
427: FILE *ficresilk;
428: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
429: FILE *ficresprobmorprev;
430: FILE *fichtm, *fichtmcov; /* Html File */
431: FILE *ficreseij;
432: char filerese[FILENAMELENGTH];
433: FILE *ficresstdeij;
434: char fileresstde[FILENAMELENGTH];
435: FILE *ficrescveij;
436: char filerescve[FILENAMELENGTH];
437: FILE *ficresvij;
438: char fileresv[FILENAMELENGTH];
439: FILE *ficresvpl;
440: char fileresvpl[FILENAMELENGTH];
441: char title[MAXLINE];
442: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
443: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
444: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
445: char command[FILENAMELENGTH];
446: int outcmd=0;
447:
448: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
449:
450: char filelog[FILENAMELENGTH]; /* Log file */
451: char filerest[FILENAMELENGTH];
452: char fileregp[FILENAMELENGTH];
453: char popfile[FILENAMELENGTH];
454:
455: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
456:
457: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
458: struct timezone tzp;
459: extern int gettimeofday();
460: struct tm tmg, tm, tmf, *gmtime(), *localtime();
461: long time_value;
462: extern long time();
463: char strcurr[80], strfor[80];
464:
465: char *endptr;
466: long lval;
467: double dval;
468:
469: #define NR_END 1
470: #define FREE_ARG char*
471: #define FTOL 1.0e-10
472:
473: #define NRANSI
474: #define ITMAX 200
475:
476: #define TOL 2.0e-4
477:
478: #define CGOLD 0.3819660
479: #define ZEPS 1.0e-10
480: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
481:
482: #define GOLD 1.618034
483: #define GLIMIT 100.0
484: #define TINY 1.0e-20
485:
486: static double maxarg1,maxarg2;
487: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
488: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
489:
490: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
491: #define rint(a) floor(a+0.5)
492:
493: static double sqrarg;
494: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
495: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
496: int agegomp= AGEGOMP;
497:
498: int imx;
499: int stepm=1;
500: /* Stepm, step in month: minimum step interpolation*/
501:
502: int estepm;
503: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
504:
505: int m,nb;
506: long *num;
507: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
508: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
509: double **pmmij, ***probs;
510: double *ageexmed,*agecens;
511: double dateintmean=0;
512:
513: double *weight;
514: int **s; /* Status */
515: double *agedc, **covar, idx;
516: int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
517: double *lsurv, *lpop, *tpop;
518:
519: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
520: double ftolhess; /* Tolerance for computing hessian */
521:
522: /**************** split *************************/
523: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
524: {
525: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
526: the name of the file (name), its extension only (ext) and its first part of the name (finame)
527: */
528: char *ss; /* pointer */
529: int l1, l2; /* length counters */
530:
531: l1 = strlen(path ); /* length of path */
532: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
533: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
534: if ( ss == NULL ) { /* no directory, so determine current directory */
535: strcpy( name, path ); /* we got the fullname name because no directory */
536: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
537: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
538: /* get current working directory */
539: /* extern char* getcwd ( char *buf , int len);*/
540: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
541: return( GLOCK_ERROR_GETCWD );
542: }
543: /* got dirc from getcwd*/
544: printf(" DIRC = %s \n",dirc);
545: } else { /* strip direcotry from path */
546: ss++; /* after this, the filename */
547: l2 = strlen( ss ); /* length of filename */
548: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
549: strcpy( name, ss ); /* save file name */
550: strncpy( dirc, path, l1 - l2 ); /* now the directory */
551: dirc[l1-l2] = 0; /* add zero */
552: printf(" DIRC2 = %s \n",dirc);
553: }
554: /* We add a separator at the end of dirc if not exists */
555: l1 = strlen( dirc ); /* length of directory */
556: if( dirc[l1-1] != DIRSEPARATOR ){
557: dirc[l1] = DIRSEPARATOR;
558: dirc[l1+1] = 0;
559: printf(" DIRC3 = %s \n",dirc);
560: }
561: ss = strrchr( name, '.' ); /* find last / */
562: if (ss >0){
563: ss++;
564: strcpy(ext,ss); /* save extension */
565: l1= strlen( name);
566: l2= strlen(ss)+1;
567: strncpy( finame, name, l1-l2);
568: finame[l1-l2]= 0;
569: }
570:
571: return( 0 ); /* we're done */
572: }
573:
574:
575: /******************************************/
576:
577: void replace_back_to_slash(char *s, char*t)
578: {
579: int i;
580: int lg=0;
581: i=0;
582: lg=strlen(t);
583: for(i=0; i<= lg; i++) {
584: (s[i] = t[i]);
585: if (t[i]== '\\') s[i]='/';
586: }
587: }
588:
589: int nbocc(char *s, char occ)
590: {
591: int i,j=0;
592: int lg=20;
593: i=0;
594: lg=strlen(s);
595: for(i=0; i<= lg; i++) {
596: if (s[i] == occ ) j++;
597: }
598: return j;
599: }
600:
601: void cutv(char *u,char *v, char*t, char occ)
602: {
603: /* cuts string t into u and v where u ends before first occurence of char 'occ'
604: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
605: gives u="abcedf" and v="ghi2j" */
606: int i,lg,j,p=0;
607: i=0;
608: for(j=0; j<=strlen(t)-1; j++) {
609: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
610: }
611:
612: lg=strlen(t);
613: for(j=0; j<p; j++) {
614: (u[j] = t[j]);
615: }
616: u[p]='\0';
617:
618: for(j=0; j<= lg; j++) {
619: if (j>=(p+1))(v[j-p-1] = t[j]);
620: }
621: }
622:
623: /********************** nrerror ********************/
624:
625: void nrerror(char error_text[])
626: {
627: fprintf(stderr,"ERREUR ...\n");
628: fprintf(stderr,"%s\n",error_text);
629: exit(EXIT_FAILURE);
630: }
631: /*********************** vector *******************/
632: double *vector(int nl, int nh)
633: {
634: double *v;
635: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
636: if (!v) nrerror("allocation failure in vector");
637: return v-nl+NR_END;
638: }
639:
640: /************************ free vector ******************/
641: void free_vector(double*v, int nl, int nh)
642: {
643: free((FREE_ARG)(v+nl-NR_END));
644: }
645:
646: /************************ivector *******************************/
647: int *ivector(long nl,long nh)
648: {
649: int *v;
650: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
651: if (!v) nrerror("allocation failure in ivector");
652: return v-nl+NR_END;
653: }
654:
655: /******************free ivector **************************/
656: void free_ivector(int *v, long nl, long nh)
657: {
658: free((FREE_ARG)(v+nl-NR_END));
659: }
660:
661: /************************lvector *******************************/
662: long *lvector(long nl,long nh)
663: {
664: long *v;
665: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
666: if (!v) nrerror("allocation failure in ivector");
667: return v-nl+NR_END;
668: }
669:
670: /******************free lvector **************************/
671: void free_lvector(long *v, long nl, long nh)
672: {
673: free((FREE_ARG)(v+nl-NR_END));
674: }
675:
676: /******************* imatrix *******************************/
677: int **imatrix(long nrl, long nrh, long ncl, long nch)
678: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
679: {
680: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
681: int **m;
682:
683: /* allocate pointers to rows */
684: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
685: if (!m) nrerror("allocation failure 1 in matrix()");
686: m += NR_END;
687: m -= nrl;
688:
689:
690: /* allocate rows and set pointers to them */
691: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
692: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
693: m[nrl] += NR_END;
694: m[nrl] -= ncl;
695:
696: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
697:
698: /* return pointer to array of pointers to rows */
699: return m;
700: }
701:
702: /****************** free_imatrix *************************/
703: void free_imatrix(m,nrl,nrh,ncl,nch)
704: int **m;
705: long nch,ncl,nrh,nrl;
706: /* free an int matrix allocated by imatrix() */
707: {
708: free((FREE_ARG) (m[nrl]+ncl-NR_END));
709: free((FREE_ARG) (m+nrl-NR_END));
710: }
711:
712: /******************* matrix *******************************/
713: double **matrix(long nrl, long nrh, long ncl, long nch)
714: {
715: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
716: double **m;
717:
718: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
719: if (!m) nrerror("allocation failure 1 in matrix()");
720: m += NR_END;
721: m -= nrl;
722:
723: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
724: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
725: m[nrl] += NR_END;
726: m[nrl] -= ncl;
727:
728: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
729: return m;
730: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
731: */
732: }
733:
734: /*************************free matrix ************************/
735: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
736: {
737: free((FREE_ARG)(m[nrl]+ncl-NR_END));
738: free((FREE_ARG)(m+nrl-NR_END));
739: }
740:
741: /******************* ma3x *******************************/
742: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
743: {
744: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
745: double ***m;
746:
747: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
748: if (!m) nrerror("allocation failure 1 in matrix()");
749: m += NR_END;
750: m -= nrl;
751:
752: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
753: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
754: m[nrl] += NR_END;
755: m[nrl] -= ncl;
756:
757: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
758:
759: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
760: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
761: m[nrl][ncl] += NR_END;
762: m[nrl][ncl] -= nll;
763: for (j=ncl+1; j<=nch; j++)
764: m[nrl][j]=m[nrl][j-1]+nlay;
765:
766: for (i=nrl+1; i<=nrh; i++) {
767: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
768: for (j=ncl+1; j<=nch; j++)
769: m[i][j]=m[i][j-1]+nlay;
770: }
771: return m;
772: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
773: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
774: */
775: }
776:
777: /*************************free ma3x ************************/
778: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
779: {
780: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
781: free((FREE_ARG)(m[nrl]+ncl-NR_END));
782: free((FREE_ARG)(m+nrl-NR_END));
783: }
784:
785: /*************** function subdirf ***********/
786: char *subdirf(char fileres[])
787: {
788: /* Caution optionfilefiname is hidden */
789: strcpy(tmpout,optionfilefiname);
790: strcat(tmpout,"/"); /* Add to the right */
791: strcat(tmpout,fileres);
792: return tmpout;
793: }
794:
795: /*************** function subdirf2 ***********/
796: char *subdirf2(char fileres[], char *preop)
797: {
798:
799: /* Caution optionfilefiname is hidden */
800: strcpy(tmpout,optionfilefiname);
801: strcat(tmpout,"/");
802: strcat(tmpout,preop);
803: strcat(tmpout,fileres);
804: return tmpout;
805: }
806:
807: /*************** function subdirf3 ***********/
808: char *subdirf3(char fileres[], char *preop, char *preop2)
809: {
810:
811: /* Caution optionfilefiname is hidden */
812: strcpy(tmpout,optionfilefiname);
813: strcat(tmpout,"/");
814: strcat(tmpout,preop);
815: strcat(tmpout,preop2);
816: strcat(tmpout,fileres);
817: return tmpout;
818: }
819:
820: /***************** f1dim *************************/
821: extern int ncom;
822: extern double *pcom,*xicom;
823: extern double (*nrfunc)(double []);
824:
825: double f1dim(double x)
826: {
827: int j;
828: double f;
829: double *xt;
830:
831: xt=vector(1,ncom);
832: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
833: f=(*nrfunc)(xt);
834: free_vector(xt,1,ncom);
835: return f;
836: }
837:
838: /*****************brent *************************/
839: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
840: {
841: int iter;
842: double a,b,d,etemp;
843: double fu,fv,fw,fx;
844: double ftemp;
845: double p,q,r,tol1,tol2,u,v,w,x,xm;
846: double e=0.0;
847:
848: a=(ax < cx ? ax : cx);
849: b=(ax > cx ? ax : cx);
850: x=w=v=bx;
851: fw=fv=fx=(*f)(x);
852: for (iter=1;iter<=ITMAX;iter++) {
853: xm=0.5*(a+b);
854: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
855: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
856: printf(".");fflush(stdout);
857: fprintf(ficlog,".");fflush(ficlog);
858: #ifdef DEBUG
859: 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);
860: 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);
861: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
862: #endif
863: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
864: *xmin=x;
865: return fx;
866: }
867: ftemp=fu;
868: if (fabs(e) > tol1) {
869: r=(x-w)*(fx-fv);
870: q=(x-v)*(fx-fw);
871: p=(x-v)*q-(x-w)*r;
872: q=2.0*(q-r);
873: if (q > 0.0) p = -p;
874: q=fabs(q);
875: etemp=e;
876: e=d;
877: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
878: d=CGOLD*(e=(x >= xm ? a-x : b-x));
879: else {
880: d=p/q;
881: u=x+d;
882: if (u-a < tol2 || b-u < tol2)
883: d=SIGN(tol1,xm-x);
884: }
885: } else {
886: d=CGOLD*(e=(x >= xm ? a-x : b-x));
887: }
888: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
889: fu=(*f)(u);
890: if (fu <= fx) {
891: if (u >= x) a=x; else b=x;
892: SHFT(v,w,x,u)
893: SHFT(fv,fw,fx,fu)
894: } else {
895: if (u < x) a=u; else b=u;
896: if (fu <= fw || w == x) {
897: v=w;
898: w=u;
899: fv=fw;
900: fw=fu;
901: } else if (fu <= fv || v == x || v == w) {
902: v=u;
903: fv=fu;
904: }
905: }
906: }
907: nrerror("Too many iterations in brent");
908: *xmin=x;
909: return fx;
910: }
911:
912: /****************** mnbrak ***********************/
913:
914: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
915: double (*func)(double))
916: {
917: double ulim,u,r,q, dum;
918: double fu;
919:
920: *fa=(*func)(*ax);
921: *fb=(*func)(*bx);
922: if (*fb > *fa) {
923: SHFT(dum,*ax,*bx,dum)
924: SHFT(dum,*fb,*fa,dum)
925: }
926: *cx=(*bx)+GOLD*(*bx-*ax);
927: *fc=(*func)(*cx);
928: while (*fb > *fc) {
929: r=(*bx-*ax)*(*fb-*fc);
930: q=(*bx-*cx)*(*fb-*fa);
931: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
932: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
933: ulim=(*bx)+GLIMIT*(*cx-*bx);
934: if ((*bx-u)*(u-*cx) > 0.0) {
935: fu=(*func)(u);
936: } else if ((*cx-u)*(u-ulim) > 0.0) {
937: fu=(*func)(u);
938: if (fu < *fc) {
939: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
940: SHFT(*fb,*fc,fu,(*func)(u))
941: }
942: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
943: u=ulim;
944: fu=(*func)(u);
945: } else {
946: u=(*cx)+GOLD*(*cx-*bx);
947: fu=(*func)(u);
948: }
949: SHFT(*ax,*bx,*cx,u)
950: SHFT(*fa,*fb,*fc,fu)
951: }
952: }
953:
954: /*************** linmin ************************/
955:
956: int ncom;
957: double *pcom,*xicom;
958: double (*nrfunc)(double []);
959:
960: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
961: {
962: double brent(double ax, double bx, double cx,
963: double (*f)(double), double tol, double *xmin);
964: double f1dim(double x);
965: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
966: double *fc, double (*func)(double));
967: int j;
968: double xx,xmin,bx,ax;
969: double fx,fb,fa;
970:
971: ncom=n;
972: pcom=vector(1,n);
973: xicom=vector(1,n);
974: nrfunc=func;
975: for (j=1;j<=n;j++) {
976: pcom[j]=p[j];
977: xicom[j]=xi[j];
978: }
979: ax=0.0;
980: xx=1.0;
981: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
982: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
983: #ifdef DEBUG
984: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
985: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
986: #endif
987: for (j=1;j<=n;j++) {
988: xi[j] *= xmin;
989: p[j] += xi[j];
990: }
991: free_vector(xicom,1,n);
992: free_vector(pcom,1,n);
993: }
994:
995: char *asc_diff_time(long time_sec, char ascdiff[])
996: {
997: long sec_left, days, hours, minutes;
998: days = (time_sec) / (60*60*24);
999: sec_left = (time_sec) % (60*60*24);
1000: hours = (sec_left) / (60*60) ;
1001: sec_left = (sec_left) %(60*60);
1002: minutes = (sec_left) /60;
1003: sec_left = (sec_left) % (60);
1004: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1005: return ascdiff;
1006: }
1007:
1008: /*************** powell ************************/
1009: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1010: double (*func)(double []))
1011: {
1012: void linmin(double p[], double xi[], int n, double *fret,
1013: double (*func)(double []));
1014: int i,ibig,j;
1015: double del,t,*pt,*ptt,*xit;
1016: double fp,fptt;
1017: double *xits;
1018: int niterf, itmp;
1019:
1020: pt=vector(1,n);
1021: ptt=vector(1,n);
1022: xit=vector(1,n);
1023: xits=vector(1,n);
1024: *fret=(*func)(p);
1025: for (j=1;j<=n;j++) pt[j]=p[j];
1026: for (*iter=1;;++(*iter)) {
1027: fp=(*fret);
1028: ibig=0;
1029: del=0.0;
1030: last_time=curr_time;
1031: (void) gettimeofday(&curr_time,&tzp);
1032: 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);
1033: 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); fflush(ficlog);
1034: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1035: for (i=1;i<=n;i++) {
1036: printf(" %d %.12f",i, p[i]);
1037: fprintf(ficlog," %d %.12lf",i, p[i]);
1038: fprintf(ficrespow," %.12lf", p[i]);
1039: }
1040: printf("\n");
1041: fprintf(ficlog,"\n");
1042: fprintf(ficrespow,"\n");fflush(ficrespow);
1043: if(*iter <=3){
1044: tm = *localtime(&curr_time.tv_sec);
1045: strcpy(strcurr,asctime(&tm));
1046: /* asctime_r(&tm,strcurr); */
1047: forecast_time=curr_time;
1048: itmp = strlen(strcurr);
1049: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1050: strcurr[itmp-1]='\0';
1051: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1052: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1053: for(niterf=10;niterf<=30;niterf+=10){
1054: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1055: tmf = *localtime(&forecast_time.tv_sec);
1056: /* asctime_r(&tmf,strfor); */
1057: strcpy(strfor,asctime(&tmf));
1058: itmp = strlen(strfor);
1059: if(strfor[itmp-1]=='\n')
1060: strfor[itmp-1]='\0';
1061: 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);
1062: 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);
1063: }
1064: }
1065: for (i=1;i<=n;i++) {
1066: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1067: fptt=(*fret);
1068: #ifdef DEBUG
1069: printf("fret=%lf \n",*fret);
1070: fprintf(ficlog,"fret=%lf \n",*fret);
1071: #endif
1072: printf("%d",i);fflush(stdout);
1073: fprintf(ficlog,"%d",i);fflush(ficlog);
1074: linmin(p,xit,n,fret,func);
1075: if (fabs(fptt-(*fret)) > del) {
1076: del=fabs(fptt-(*fret));
1077: ibig=i;
1078: }
1079: #ifdef DEBUG
1080: printf("%d %.12e",i,(*fret));
1081: fprintf(ficlog,"%d %.12e",i,(*fret));
1082: for (j=1;j<=n;j++) {
1083: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1084: printf(" x(%d)=%.12e",j,xit[j]);
1085: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1086: }
1087: for(j=1;j<=n;j++) {
1088: printf(" p=%.12e",p[j]);
1089: fprintf(ficlog," p=%.12e",p[j]);
1090: }
1091: printf("\n");
1092: fprintf(ficlog,"\n");
1093: #endif
1094: }
1095: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1096: #ifdef DEBUG
1097: int k[2],l;
1098: k[0]=1;
1099: k[1]=-1;
1100: printf("Max: %.12e",(*func)(p));
1101: fprintf(ficlog,"Max: %.12e",(*func)(p));
1102: for (j=1;j<=n;j++) {
1103: printf(" %.12e",p[j]);
1104: fprintf(ficlog," %.12e",p[j]);
1105: }
1106: printf("\n");
1107: fprintf(ficlog,"\n");
1108: for(l=0;l<=1;l++) {
1109: for (j=1;j<=n;j++) {
1110: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1111: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1112: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1113: }
1114: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1115: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1116: }
1117: #endif
1118:
1119:
1120: free_vector(xit,1,n);
1121: free_vector(xits,1,n);
1122: free_vector(ptt,1,n);
1123: free_vector(pt,1,n);
1124: return;
1125: }
1126: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1127: for (j=1;j<=n;j++) {
1128: ptt[j]=2.0*p[j]-pt[j];
1129: xit[j]=p[j]-pt[j];
1130: pt[j]=p[j];
1131: }
1132: fptt=(*func)(ptt);
1133: if (fptt < fp) {
1134: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1135: if (t < 0.0) {
1136: linmin(p,xit,n,fret,func);
1137: for (j=1;j<=n;j++) {
1138: xi[j][ibig]=xi[j][n];
1139: xi[j][n]=xit[j];
1140: }
1141: #ifdef DEBUG
1142: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1143: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1144: for(j=1;j<=n;j++){
1145: printf(" %.12e",xit[j]);
1146: fprintf(ficlog," %.12e",xit[j]);
1147: }
1148: printf("\n");
1149: fprintf(ficlog,"\n");
1150: #endif
1151: }
1152: }
1153: }
1154: }
1155:
1156: /**** Prevalence limit (stable or period prevalence) ****************/
1157:
1158: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1159: {
1160: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1161: matrix by transitions matrix until convergence is reached */
1162:
1163: int i, ii,j,k;
1164: double min, max, maxmin, maxmax,sumnew=0.;
1165: double **matprod2();
1166: double **out, cov[NCOVMAX], **pmij();
1167: double **newm;
1168: double agefin, delaymax=50 ; /* Max number of years to converge */
1169:
1170: for (ii=1;ii<=nlstate+ndeath;ii++)
1171: for (j=1;j<=nlstate+ndeath;j++){
1172: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1173: }
1174:
1175: cov[1]=1.;
1176:
1177: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1178: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1179: newm=savm;
1180: /* Covariates have to be included here again */
1181: cov[2]=agefin;
1182:
1183: for (k=1; k<=cptcovn;k++) {
1184: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1185: /* 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]]);*/
1186: }
1187: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1188: for (k=1; k<=cptcovprod;k++)
1189: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1190:
1191: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1192: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1193: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1194: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1195:
1196: savm=oldm;
1197: oldm=newm;
1198: maxmax=0.;
1199: for(j=1;j<=nlstate;j++){
1200: min=1.;
1201: max=0.;
1202: for(i=1; i<=nlstate; i++) {
1203: sumnew=0;
1204: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1205: prlim[i][j]= newm[i][j]/(1-sumnew);
1206: max=FMAX(max,prlim[i][j]);
1207: min=FMIN(min,prlim[i][j]);
1208: }
1209: maxmin=max-min;
1210: maxmax=FMAX(maxmax,maxmin);
1211: }
1212: if(maxmax < ftolpl){
1213: return prlim;
1214: }
1215: }
1216: }
1217:
1218: /*************** transition probabilities ***************/
1219:
1220: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1221: {
1222: double s1, s2;
1223: /*double t34;*/
1224: int i,j,j1, nc, ii, jj;
1225:
1226: for(i=1; i<= nlstate; i++){
1227: for(j=1; j<i;j++){
1228: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1229: /*s2 += param[i][j][nc]*cov[nc];*/
1230: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1231: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1232: }
1233: ps[i][j]=s2;
1234: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1235: }
1236: for(j=i+1; j<=nlstate+ndeath;j++){
1237: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1238: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1239: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1240: }
1241: ps[i][j]=s2;
1242: }
1243: }
1244: /*ps[3][2]=1;*/
1245:
1246: for(i=1; i<= nlstate; i++){
1247: s1=0;
1248: for(j=1; j<i; j++)
1249: s1+=exp(ps[i][j]);
1250: for(j=i+1; j<=nlstate+ndeath; j++)
1251: s1+=exp(ps[i][j]);
1252: ps[i][i]=1./(s1+1.);
1253: for(j=1; j<i; j++)
1254: ps[i][j]= exp(ps[i][j])*ps[i][i];
1255: for(j=i+1; j<=nlstate+ndeath; j++)
1256: ps[i][j]= exp(ps[i][j])*ps[i][i];
1257: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1258: } /* end i */
1259:
1260: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1261: for(jj=1; jj<= nlstate+ndeath; jj++){
1262: ps[ii][jj]=0;
1263: ps[ii][ii]=1;
1264: }
1265: }
1266:
1267:
1268: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1269: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1270: /* printf("ddd %lf ",ps[ii][jj]); */
1271: /* } */
1272: /* printf("\n "); */
1273: /* } */
1274: /* printf("\n ");printf("%lf ",cov[2]); */
1275: /*
1276: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1277: goto end;*/
1278: return ps;
1279: }
1280:
1281: /**************** Product of 2 matrices ******************/
1282:
1283: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1284: {
1285: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1286: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1287: /* in, b, out are matrice of pointers which should have been initialized
1288: before: only the contents of out is modified. The function returns
1289: a pointer to pointers identical to out */
1290: long i, j, k;
1291: for(i=nrl; i<= nrh; i++)
1292: for(k=ncolol; k<=ncoloh; k++)
1293: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1294: out[i][k] +=in[i][j]*b[j][k];
1295:
1296: return out;
1297: }
1298:
1299:
1300: /************* Higher Matrix Product ***************/
1301:
1302: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1303: {
1304: /* Computes the transition matrix starting at age 'age' over
1305: 'nhstepm*hstepm*stepm' months (i.e. until
1306: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1307: nhstepm*hstepm matrices.
1308: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1309: (typically every 2 years instead of every month which is too big
1310: for the memory).
1311: Model is determined by parameters x and covariates have to be
1312: included manually here.
1313:
1314: */
1315:
1316: int i, j, d, h, k;
1317: double **out, cov[NCOVMAX];
1318: double **newm;
1319:
1320: /* Hstepm could be zero and should return the unit matrix */
1321: for (i=1;i<=nlstate+ndeath;i++)
1322: for (j=1;j<=nlstate+ndeath;j++){
1323: oldm[i][j]=(i==j ? 1.0 : 0.0);
1324: po[i][j][0]=(i==j ? 1.0 : 0.0);
1325: }
1326: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1327: for(h=1; h <=nhstepm; h++){
1328: for(d=1; d <=hstepm; d++){
1329: newm=savm;
1330: /* Covariates have to be included here again */
1331: cov[1]=1.;
1332: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1333: for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1334: for (k=1; k<=cptcovage;k++)
1335: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1336: for (k=1; k<=cptcovprod;k++)
1337: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1338:
1339:
1340: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1341: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1342: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1343: pmij(pmmij,cov,ncovmodel,x,nlstate));
1344: savm=oldm;
1345: oldm=newm;
1346: }
1347: for(i=1; i<=nlstate+ndeath; i++)
1348: for(j=1;j<=nlstate+ndeath;j++) {
1349: po[i][j][h]=newm[i][j];
1.128 brouard 1350: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1351: }
1.128 brouard 1352: /*printf("h=%d ",h);*/
1.126 brouard 1353: } /* end h */
1.128 brouard 1354: /* printf("\n H=%d \n",h); */
1.126 brouard 1355: return po;
1356: }
1357:
1358:
1359: /*************** log-likelihood *************/
1360: double func( double *x)
1361: {
1362: int i, ii, j, k, mi, d, kk;
1363: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1364: double **out;
1365: double sw; /* Sum of weights */
1366: double lli; /* Individual log likelihood */
1367: int s1, s2;
1368: double bbh, survp;
1369: long ipmx;
1370: /*extern weight */
1371: /* We are differentiating ll according to initial status */
1372: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1373: /*for(i=1;i<imx;i++)
1374: printf(" %d\n",s[4][i]);
1375: */
1376: cov[1]=1.;
1377:
1378: for(k=1; k<=nlstate; k++) ll[k]=0.;
1379:
1380: if(mle==1){
1381: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1382: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1383: for(mi=1; mi<= wav[i]-1; mi++){
1384: for (ii=1;ii<=nlstate+ndeath;ii++)
1385: for (j=1;j<=nlstate+ndeath;j++){
1386: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1387: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1388: }
1389: for(d=0; d<dh[mi][i]; d++){
1390: newm=savm;
1391: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1392: for (kk=1; kk<=cptcovage;kk++) {
1393: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1394: }
1395: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1396: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1397: savm=oldm;
1398: oldm=newm;
1399: } /* end mult */
1400:
1401: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1402: /* But now since version 0.9 we anticipate for bias at large stepm.
1403: * If stepm is larger than one month (smallest stepm) and if the exact delay
1404: * (in months) between two waves is not a multiple of stepm, we rounded to
1405: * the nearest (and in case of equal distance, to the lowest) interval but now
1406: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1407: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1408: * probability in order to take into account the bias as a fraction of the way
1409: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1410: * -stepm/2 to stepm/2 .
1411: * For stepm=1 the results are the same as for previous versions of Imach.
1412: * For stepm > 1 the results are less biased than in previous versions.
1413: */
1414: s1=s[mw[mi][i]][i];
1415: s2=s[mw[mi+1][i]][i];
1416: bbh=(double)bh[mi][i]/(double)stepm;
1417: /* bias bh is positive if real duration
1418: * is higher than the multiple of stepm and negative otherwise.
1419: */
1420: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1421: if( s2 > nlstate){
1422: /* i.e. if s2 is a death state and if the date of death is known
1423: then the contribution to the likelihood is the probability to
1424: die between last step unit time and current step unit time,
1425: which is also equal to probability to die before dh
1426: minus probability to die before dh-stepm .
1427: In version up to 0.92 likelihood was computed
1428: as if date of death was unknown. Death was treated as any other
1429: health state: the date of the interview describes the actual state
1430: and not the date of a change in health state. The former idea was
1431: to consider that at each interview the state was recorded
1432: (healthy, disable or death) and IMaCh was corrected; but when we
1433: introduced the exact date of death then we should have modified
1434: the contribution of an exact death to the likelihood. This new
1435: contribution is smaller and very dependent of the step unit
1436: stepm. It is no more the probability to die between last interview
1437: and month of death but the probability to survive from last
1438: interview up to one month before death multiplied by the
1439: probability to die within a month. Thanks to Chris
1440: Jackson for correcting this bug. Former versions increased
1441: mortality artificially. The bad side is that we add another loop
1442: which slows down the processing. The difference can be up to 10%
1443: lower mortality.
1444: */
1445: lli=log(out[s1][s2] - savm[s1][s2]);
1446:
1447:
1448: } else if (s2==-2) {
1449: for (j=1,survp=0. ; j<=nlstate; j++)
1450: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1451: /*survp += out[s1][j]; */
1452: lli= log(survp);
1453: }
1454:
1455: else if (s2==-4) {
1456: for (j=3,survp=0. ; j<=nlstate; j++)
1457: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1458: lli= log(survp);
1459: }
1460:
1461: else if (s2==-5) {
1462: for (j=1,survp=0. ; j<=2; j++)
1463: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1464: lli= log(survp);
1465: }
1466:
1467: else{
1468: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1469: /* 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 */
1470: }
1471: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1472: /*if(lli ==000.0)*/
1473: /*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); */
1474: ipmx +=1;
1475: sw += weight[i];
1476: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1477: } /* end of wave */
1478: } /* end of individual */
1479: } else if(mle==2){
1480: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1481: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1482: for(mi=1; mi<= wav[i]-1; mi++){
1483: for (ii=1;ii<=nlstate+ndeath;ii++)
1484: for (j=1;j<=nlstate+ndeath;j++){
1485: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1486: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1487: }
1488: for(d=0; d<=dh[mi][i]; d++){
1489: newm=savm;
1490: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1491: for (kk=1; kk<=cptcovage;kk++) {
1492: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1493: }
1494: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1495: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1496: savm=oldm;
1497: oldm=newm;
1498: } /* end mult */
1499:
1500: s1=s[mw[mi][i]][i];
1501: s2=s[mw[mi+1][i]][i];
1502: bbh=(double)bh[mi][i]/(double)stepm;
1503: 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 */
1504: ipmx +=1;
1505: sw += weight[i];
1506: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1507: } /* end of wave */
1508: } /* end of individual */
1509: } else if(mle==3){ /* exponential inter-extrapolation */
1510: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1511: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1512: for(mi=1; mi<= wav[i]-1; mi++){
1513: for (ii=1;ii<=nlstate+ndeath;ii++)
1514: for (j=1;j<=nlstate+ndeath;j++){
1515: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1516: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1517: }
1518: for(d=0; d<dh[mi][i]; d++){
1519: newm=savm;
1520: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1521: for (kk=1; kk<=cptcovage;kk++) {
1522: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1523: }
1524: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1525: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1526: savm=oldm;
1527: oldm=newm;
1528: } /* end mult */
1529:
1530: s1=s[mw[mi][i]][i];
1531: s2=s[mw[mi+1][i]][i];
1532: bbh=(double)bh[mi][i]/(double)stepm;
1533: 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 */
1534: ipmx +=1;
1535: sw += weight[i];
1536: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1537: } /* end of wave */
1538: } /* end of individual */
1539: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1540: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1541: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1542: for(mi=1; mi<= wav[i]-1; mi++){
1543: for (ii=1;ii<=nlstate+ndeath;ii++)
1544: for (j=1;j<=nlstate+ndeath;j++){
1545: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1546: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1547: }
1548: for(d=0; d<dh[mi][i]; d++){
1549: newm=savm;
1550: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1551: for (kk=1; kk<=cptcovage;kk++) {
1552: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1553: }
1554:
1555: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1556: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1557: savm=oldm;
1558: oldm=newm;
1559: } /* end mult */
1560:
1561: s1=s[mw[mi][i]][i];
1562: s2=s[mw[mi+1][i]][i];
1563: if( s2 > nlstate){
1564: lli=log(out[s1][s2] - savm[s1][s2]);
1565: }else{
1566: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1567: }
1568: ipmx +=1;
1569: sw += weight[i];
1570: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1571: /* 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]); */
1572: } /* end of wave */
1573: } /* end of individual */
1574: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1575: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1576: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1577: for(mi=1; mi<= wav[i]-1; mi++){
1578: for (ii=1;ii<=nlstate+ndeath;ii++)
1579: for (j=1;j<=nlstate+ndeath;j++){
1580: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1581: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1582: }
1583: for(d=0; d<dh[mi][i]; d++){
1584: newm=savm;
1585: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1586: for (kk=1; kk<=cptcovage;kk++) {
1587: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1588: }
1589:
1590: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1591: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1592: savm=oldm;
1593: oldm=newm;
1594: } /* end mult */
1595:
1596: s1=s[mw[mi][i]][i];
1597: s2=s[mw[mi+1][i]][i];
1598: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1599: ipmx +=1;
1600: sw += weight[i];
1601: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1602: /*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]);*/
1603: } /* end of wave */
1604: } /* end of individual */
1605: } /* End of if */
1606: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1607: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1608: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1609: return -l;
1610: }
1611:
1612: /*************** log-likelihood *************/
1613: double funcone( double *x)
1614: {
1615: /* Same as likeli but slower because of a lot of printf and if */
1616: int i, ii, j, k, mi, d, kk;
1617: double l, ll[NLSTATEMAX], cov[NCOVMAX];
1618: double **out;
1619: double lli; /* Individual log likelihood */
1620: double llt;
1621: int s1, s2;
1622: double bbh, survp;
1623: /*extern weight */
1624: /* We are differentiating ll according to initial status */
1625: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1626: /*for(i=1;i<imx;i++)
1627: printf(" %d\n",s[4][i]);
1628: */
1629: cov[1]=1.;
1630:
1631: for(k=1; k<=nlstate; k++) ll[k]=0.;
1632:
1633: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1634: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1635: for(mi=1; mi<= wav[i]-1; mi++){
1636: for (ii=1;ii<=nlstate+ndeath;ii++)
1637: for (j=1;j<=nlstate+ndeath;j++){
1638: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1639: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1640: }
1641: for(d=0; d<dh[mi][i]; d++){
1642: newm=savm;
1643: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1644: for (kk=1; kk<=cptcovage;kk++) {
1645: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1646: }
1647: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1648: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1649: savm=oldm;
1650: oldm=newm;
1651: } /* end mult */
1652:
1653: s1=s[mw[mi][i]][i];
1654: s2=s[mw[mi+1][i]][i];
1655: bbh=(double)bh[mi][i]/(double)stepm;
1656: /* bias is positive if real duration
1657: * is higher than the multiple of stepm and negative otherwise.
1658: */
1659: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1660: lli=log(out[s1][s2] - savm[s1][s2]);
1661: } else if (s2==-2) {
1662: for (j=1,survp=0. ; j<=nlstate; j++)
1663: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1664: lli= log(survp);
1665: }else if (mle==1){
1666: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1667: } else if(mle==2){
1668: 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 */
1669: } else if(mle==3){ /* exponential inter-extrapolation */
1670: 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 */
1671: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1672: lli=log(out[s1][s2]); /* Original formula */
1673: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1674: lli=log(out[s1][s2]); /* Original formula */
1675: } /* End of if */
1676: ipmx +=1;
1677: sw += weight[i];
1678: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1679: /* 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]); */
1680: if(globpr){
1681: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1682: %11.6f %11.6f %11.6f ", \
1683: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1684: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1685: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1686: llt +=ll[k]*gipmx/gsw;
1687: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1688: }
1689: fprintf(ficresilk," %10.6f\n", -llt);
1690: }
1691: } /* end of wave */
1692: } /* end of individual */
1693: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1694: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1695: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1696: if(globpr==0){ /* First time we count the contributions and weights */
1697: gipmx=ipmx;
1698: gsw=sw;
1699: }
1700: return -l;
1701: }
1702:
1703:
1704: /*************** function likelione ***********/
1705: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1706: {
1707: /* This routine should help understanding what is done with
1708: the selection of individuals/waves and
1709: to check the exact contribution to the likelihood.
1710: Plotting could be done.
1711: */
1712: int k;
1713:
1714: if(*globpri !=0){ /* Just counts and sums, no printings */
1715: strcpy(fileresilk,"ilk");
1716: strcat(fileresilk,fileres);
1717: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1718: printf("Problem with resultfile: %s\n", fileresilk);
1719: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1720: }
1721: 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");
1722: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1723: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1724: for(k=1; k<=nlstate; k++)
1725: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1726: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1727: }
1728:
1729: *fretone=(*funcone)(p);
1730: if(*globpri !=0){
1731: fclose(ficresilk);
1732: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1733: fflush(fichtm);
1734: }
1735: return;
1736: }
1737:
1738:
1739: /*********** Maximum Likelihood Estimation ***************/
1740:
1741: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1742: {
1743: int i,j, iter;
1744: double **xi;
1745: double fret;
1746: double fretone; /* Only one call to likelihood */
1747: /* char filerespow[FILENAMELENGTH];*/
1748: xi=matrix(1,npar,1,npar);
1749: for (i=1;i<=npar;i++)
1750: for (j=1;j<=npar;j++)
1751: xi[i][j]=(i==j ? 1.0 : 0.0);
1752: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1753: strcpy(filerespow,"pow");
1754: strcat(filerespow,fileres);
1755: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1756: printf("Problem with resultfile: %s\n", filerespow);
1757: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1758: }
1759: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1760: for (i=1;i<=nlstate;i++)
1761: for(j=1;j<=nlstate+ndeath;j++)
1762: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1763: fprintf(ficrespow,"\n");
1764:
1765: powell(p,xi,npar,ftol,&iter,&fret,func);
1766:
1767: free_matrix(xi,1,npar,1,npar);
1768: fclose(ficrespow);
1769: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1770: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1771: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1772:
1773: }
1774:
1775: /**** Computes Hessian and covariance matrix ***/
1776: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1777: {
1778: double **a,**y,*x,pd;
1779: double **hess;
1780: int i, j,jk;
1781: int *indx;
1782:
1783: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1784: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1785: void lubksb(double **a, int npar, int *indx, double b[]) ;
1786: void ludcmp(double **a, int npar, int *indx, double *d) ;
1787: double gompertz(double p[]);
1788: hess=matrix(1,npar,1,npar);
1789:
1790: printf("\nCalculation of the hessian matrix. Wait...\n");
1791: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1792: for (i=1;i<=npar;i++){
1793: printf("%d",i);fflush(stdout);
1794: fprintf(ficlog,"%d",i);fflush(ficlog);
1795:
1796: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1797:
1798: /* printf(" %f ",p[i]);
1799: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1800: }
1801:
1802: for (i=1;i<=npar;i++) {
1803: for (j=1;j<=npar;j++) {
1804: if (j>i) {
1805: printf(".%d%d",i,j);fflush(stdout);
1806: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1807: hess[i][j]=hessij(p,delti,i,j,func,npar);
1808:
1809: hess[j][i]=hess[i][j];
1810: /*printf(" %lf ",hess[i][j]);*/
1811: }
1812: }
1813: }
1814: printf("\n");
1815: fprintf(ficlog,"\n");
1816:
1817: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1818: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1819:
1820: a=matrix(1,npar,1,npar);
1821: y=matrix(1,npar,1,npar);
1822: x=vector(1,npar);
1823: indx=ivector(1,npar);
1824: for (i=1;i<=npar;i++)
1825: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1826: ludcmp(a,npar,indx,&pd);
1827:
1828: for (j=1;j<=npar;j++) {
1829: for (i=1;i<=npar;i++) x[i]=0;
1830: x[j]=1;
1831: lubksb(a,npar,indx,x);
1832: for (i=1;i<=npar;i++){
1833: matcov[i][j]=x[i];
1834: }
1835: }
1836:
1837: printf("\n#Hessian matrix#\n");
1838: fprintf(ficlog,"\n#Hessian matrix#\n");
1839: for (i=1;i<=npar;i++) {
1840: for (j=1;j<=npar;j++) {
1841: printf("%.3e ",hess[i][j]);
1842: fprintf(ficlog,"%.3e ",hess[i][j]);
1843: }
1844: printf("\n");
1845: fprintf(ficlog,"\n");
1846: }
1847:
1848: /* Recompute Inverse */
1849: for (i=1;i<=npar;i++)
1850: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1851: ludcmp(a,npar,indx,&pd);
1852:
1853: /* printf("\n#Hessian matrix recomputed#\n");
1854:
1855: for (j=1;j<=npar;j++) {
1856: for (i=1;i<=npar;i++) x[i]=0;
1857: x[j]=1;
1858: lubksb(a,npar,indx,x);
1859: for (i=1;i<=npar;i++){
1860: y[i][j]=x[i];
1861: printf("%.3e ",y[i][j]);
1862: fprintf(ficlog,"%.3e ",y[i][j]);
1863: }
1864: printf("\n");
1865: fprintf(ficlog,"\n");
1866: }
1867: */
1868:
1869: free_matrix(a,1,npar,1,npar);
1870: free_matrix(y,1,npar,1,npar);
1871: free_vector(x,1,npar);
1872: free_ivector(indx,1,npar);
1873: free_matrix(hess,1,npar,1,npar);
1874:
1875:
1876: }
1877:
1878: /*************** hessian matrix ****************/
1879: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1880: {
1881: int i;
1882: int l=1, lmax=20;
1883: double k1,k2;
1884: double p2[NPARMAX+1];
1885: double res;
1886: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1887: double fx;
1888: int k=0,kmax=10;
1889: double l1;
1890:
1891: fx=func(x);
1892: for (i=1;i<=npar;i++) p2[i]=x[i];
1893: for(l=0 ; l <=lmax; l++){
1894: l1=pow(10,l);
1895: delts=delt;
1896: for(k=1 ; k <kmax; k=k+1){
1897: delt = delta*(l1*k);
1898: p2[theta]=x[theta] +delt;
1899: k1=func(p2)-fx;
1900: p2[theta]=x[theta]-delt;
1901: k2=func(p2)-fx;
1902: /*res= (k1-2.0*fx+k2)/delt/delt; */
1903: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1904:
1905: #ifdef DEBUG
1906: 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);
1907: 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);
1908: #endif
1909: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1910: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1911: k=kmax;
1912: }
1913: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1914: k=kmax; l=lmax*10.;
1915: }
1916: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1917: delts=delt;
1918: }
1919: }
1920: }
1921: delti[theta]=delts;
1922: return res;
1923:
1924: }
1925:
1926: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1927: {
1928: int i;
1929: int l=1, l1, lmax=20;
1930: double k1,k2,k3,k4,res,fx;
1931: double p2[NPARMAX+1];
1932: int k;
1933:
1934: fx=func(x);
1935: for (k=1; k<=2; k++) {
1936: for (i=1;i<=npar;i++) p2[i]=x[i];
1937: p2[thetai]=x[thetai]+delti[thetai]/k;
1938: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1939: k1=func(p2)-fx;
1940:
1941: p2[thetai]=x[thetai]+delti[thetai]/k;
1942: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1943: k2=func(p2)-fx;
1944:
1945: p2[thetai]=x[thetai]-delti[thetai]/k;
1946: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1947: k3=func(p2)-fx;
1948:
1949: p2[thetai]=x[thetai]-delti[thetai]/k;
1950: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1951: k4=func(p2)-fx;
1952: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1953: #ifdef DEBUG
1954: 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);
1955: 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);
1956: #endif
1957: }
1958: return res;
1959: }
1960:
1961: /************** Inverse of matrix **************/
1962: void ludcmp(double **a, int n, int *indx, double *d)
1963: {
1964: int i,imax,j,k;
1965: double big,dum,sum,temp;
1966: double *vv;
1967:
1968: vv=vector(1,n);
1969: *d=1.0;
1970: for (i=1;i<=n;i++) {
1971: big=0.0;
1972: for (j=1;j<=n;j++)
1973: if ((temp=fabs(a[i][j])) > big) big=temp;
1974: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
1975: vv[i]=1.0/big;
1976: }
1977: for (j=1;j<=n;j++) {
1978: for (i=1;i<j;i++) {
1979: sum=a[i][j];
1980: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
1981: a[i][j]=sum;
1982: }
1983: big=0.0;
1984: for (i=j;i<=n;i++) {
1985: sum=a[i][j];
1986: for (k=1;k<j;k++)
1987: sum -= a[i][k]*a[k][j];
1988: a[i][j]=sum;
1989: if ( (dum=vv[i]*fabs(sum)) >= big) {
1990: big=dum;
1991: imax=i;
1992: }
1993: }
1994: if (j != imax) {
1995: for (k=1;k<=n;k++) {
1996: dum=a[imax][k];
1997: a[imax][k]=a[j][k];
1998: a[j][k]=dum;
1999: }
2000: *d = -(*d);
2001: vv[imax]=vv[j];
2002: }
2003: indx[j]=imax;
2004: if (a[j][j] == 0.0) a[j][j]=TINY;
2005: if (j != n) {
2006: dum=1.0/(a[j][j]);
2007: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2008: }
2009: }
2010: free_vector(vv,1,n); /* Doesn't work */
2011: ;
2012: }
2013:
2014: void lubksb(double **a, int n, int *indx, double b[])
2015: {
2016: int i,ii=0,ip,j;
2017: double sum;
2018:
2019: for (i=1;i<=n;i++) {
2020: ip=indx[i];
2021: sum=b[ip];
2022: b[ip]=b[i];
2023: if (ii)
2024: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2025: else if (sum) ii=i;
2026: b[i]=sum;
2027: }
2028: for (i=n;i>=1;i--) {
2029: sum=b[i];
2030: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2031: b[i]=sum/a[i][i];
2032: }
2033: }
2034:
2035: void pstamp(FILE *fichier)
2036: {
2037: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2038: }
2039:
2040: /************ Frequencies ********************/
2041: 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[])
2042: { /* Some frequencies */
2043:
2044: int i, m, jk, k1,i1, j1, bool, z1,z2,j;
2045: int first;
2046: double ***freq; /* Frequencies */
2047: double *pp, **prop;
2048: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2049: char fileresp[FILENAMELENGTH];
2050:
2051: pp=vector(1,nlstate);
2052: prop=matrix(1,nlstate,iagemin,iagemax+3);
2053: strcpy(fileresp,"p");
2054: strcat(fileresp,fileres);
2055: if((ficresp=fopen(fileresp,"w"))==NULL) {
2056: printf("Problem with prevalence resultfile: %s\n", fileresp);
2057: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2058: exit(0);
2059: }
2060: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2061: j1=0;
2062:
2063: j=cptcoveff;
2064: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2065:
2066: first=1;
2067:
2068: for(k1=1; k1<=j;k1++){
2069: for(i1=1; i1<=ncodemax[k1];i1++){
2070: j1++;
2071: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2072: scanf("%d", i);*/
2073: for (i=-5; i<=nlstate+ndeath; i++)
2074: for (jk=-5; jk<=nlstate+ndeath; jk++)
2075: for(m=iagemin; m <= iagemax+3; m++)
2076: freq[i][jk][m]=0;
2077:
2078: for (i=1; i<=nlstate; i++)
2079: for(m=iagemin; m <= iagemax+3; m++)
2080: prop[i][m]=0;
2081:
2082: dateintsum=0;
2083: k2cpt=0;
2084: for (i=1; i<=imx; i++) {
2085: bool=1;
2086: if (cptcovn>0) {
2087: for (z1=1; z1<=cptcoveff; z1++)
2088: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2089: bool=0;
2090: }
2091: if (bool==1){
2092: for(m=firstpass; m<=lastpass; m++){
2093: k2=anint[m][i]+(mint[m][i]/12.);
2094: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2095: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2096: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2097: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2098: if (m<lastpass) {
2099: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2100: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2101: }
2102:
2103: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2104: dateintsum=dateintsum+k2;
2105: k2cpt++;
2106: }
2107: /*}*/
2108: }
2109: }
2110: }
2111:
2112: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2113: pstamp(ficresp);
2114: if (cptcovn>0) {
2115: fprintf(ficresp, "\n#********** Variable ");
2116: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2117: fprintf(ficresp, "**********\n#");
2118: }
2119: for(i=1; i<=nlstate;i++)
2120: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2121: fprintf(ficresp, "\n");
2122:
2123: for(i=iagemin; i <= iagemax+3; i++){
2124: if(i==iagemax+3){
2125: fprintf(ficlog,"Total");
2126: }else{
2127: if(first==1){
2128: first=0;
2129: printf("See log file for details...\n");
2130: }
2131: fprintf(ficlog,"Age %d", i);
2132: }
2133: for(jk=1; jk <=nlstate ; jk++){
2134: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2135: pp[jk] += freq[jk][m][i];
2136: }
2137: for(jk=1; jk <=nlstate ; jk++){
2138: for(m=-1, pos=0; m <=0 ; m++)
2139: pos += freq[jk][m][i];
2140: if(pp[jk]>=1.e-10){
2141: if(first==1){
2142: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2143: }
2144: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2145: }else{
2146: if(first==1)
2147: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2148: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2149: }
2150: }
2151:
2152: for(jk=1; jk <=nlstate ; jk++){
2153: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2154: pp[jk] += freq[jk][m][i];
2155: }
2156: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2157: pos += pp[jk];
2158: posprop += prop[jk][i];
2159: }
2160: for(jk=1; jk <=nlstate ; jk++){
2161: if(pos>=1.e-5){
2162: if(first==1)
2163: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2164: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2165: }else{
2166: if(first==1)
2167: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2168: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2169: }
2170: if( i <= iagemax){
2171: if(pos>=1.e-5){
2172: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2173: /*probs[i][jk][j1]= pp[jk]/pos;*/
2174: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2175: }
2176: else
2177: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2178: }
2179: }
2180:
2181: for(jk=-1; jk <=nlstate+ndeath; jk++)
2182: for(m=-1; m <=nlstate+ndeath; m++)
2183: if(freq[jk][m][i] !=0 ) {
2184: if(first==1)
2185: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2186: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2187: }
2188: if(i <= iagemax)
2189: fprintf(ficresp,"\n");
2190: if(first==1)
2191: printf("Others in log...\n");
2192: fprintf(ficlog,"\n");
2193: }
2194: }
2195: }
2196: dateintmean=dateintsum/k2cpt;
2197:
2198: fclose(ficresp);
2199: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2200: free_vector(pp,1,nlstate);
2201: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2202: /* End of Freq */
2203: }
2204:
2205: /************ Prevalence ********************/
2206: 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)
2207: {
2208: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2209: in each health status at the date of interview (if between dateprev1 and dateprev2).
2210: We still use firstpass and lastpass as another selection.
2211: */
2212:
2213: int i, m, jk, k1, i1, j1, bool, z1,z2,j;
2214: double ***freq; /* Frequencies */
2215: double *pp, **prop;
2216: double pos,posprop;
2217: double y2; /* in fractional years */
2218: int iagemin, iagemax;
2219:
2220: iagemin= (int) agemin;
2221: iagemax= (int) agemax;
2222: /*pp=vector(1,nlstate);*/
2223: prop=matrix(1,nlstate,iagemin,iagemax+3);
2224: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2225: j1=0;
2226:
2227: j=cptcoveff;
2228: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2229:
2230: for(k1=1; k1<=j;k1++){
2231: for(i1=1; i1<=ncodemax[k1];i1++){
2232: j1++;
2233:
2234: for (i=1; i<=nlstate; i++)
2235: for(m=iagemin; m <= iagemax+3; m++)
2236: prop[i][m]=0.0;
2237:
2238: for (i=1; i<=imx; i++) { /* Each individual */
2239: bool=1;
2240: if (cptcovn>0) {
2241: for (z1=1; z1<=cptcoveff; z1++)
2242: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2243: bool=0;
2244: }
2245: if (bool==1) {
2246: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2247: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2248: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2249: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2250: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2251: 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);
2252: if (s[m][i]>0 && s[m][i]<=nlstate) {
2253: /*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]]);*/
2254: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2255: prop[s[m][i]][iagemax+3] += weight[i];
2256: }
2257: }
2258: } /* end selection of waves */
2259: }
2260: }
2261: for(i=iagemin; i <= iagemax+3; i++){
2262:
2263: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2264: posprop += prop[jk][i];
2265: }
2266:
2267: for(jk=1; jk <=nlstate ; jk++){
2268: if( i <= iagemax){
2269: if(posprop>=1.e-5){
2270: probs[i][jk][j1]= prop[jk][i]/posprop;
1.128 brouard 2271: } else
2272: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
1.126 brouard 2273: }
2274: }/* end jk */
2275: }/* end i */
2276: } /* end i1 */
2277: } /* end k1 */
2278:
2279: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2280: /*free_vector(pp,1,nlstate);*/
2281: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2282: } /* End of prevalence */
2283:
2284: /************* Waves Concatenation ***************/
2285:
2286: 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)
2287: {
2288: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2289: Death is a valid wave (if date is known).
2290: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2291: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2292: and mw[mi+1][i]. dh depends on stepm.
2293: */
2294:
2295: int i, mi, m;
2296: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2297: double sum=0., jmean=0.;*/
2298: int first;
2299: int j, k=0,jk, ju, jl;
2300: double sum=0.;
2301: first=0;
2302: jmin=1e+5;
2303: jmax=-1;
2304: jmean=0.;
2305: for(i=1; i<=imx; i++){
2306: mi=0;
2307: m=firstpass;
2308: while(s[m][i] <= nlstate){
2309: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2310: mw[++mi][i]=m;
2311: if(m >=lastpass)
2312: break;
2313: else
2314: m++;
2315: }/* end while */
2316: if (s[m][i] > nlstate){
2317: mi++; /* Death is another wave */
2318: /* if(mi==0) never been interviewed correctly before death */
2319: /* Only death is a correct wave */
2320: mw[mi][i]=m;
2321: }
2322:
2323: wav[i]=mi;
2324: if(mi==0){
2325: nbwarn++;
2326: if(first==0){
2327: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2328: first=1;
2329: }
2330: if(first==1){
2331: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2332: }
2333: } /* end mi==0 */
2334: } /* End individuals */
2335:
2336: for(i=1; i<=imx; i++){
2337: for(mi=1; mi<wav[i];mi++){
2338: if (stepm <=0)
2339: dh[mi][i]=1;
2340: else{
2341: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2342: if (agedc[i] < 2*AGESUP) {
2343: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2344: if(j==0) j=1; /* Survives at least one month after exam */
2345: else if(j<0){
2346: nberr++;
2347: 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]);
2348: j=1; /* Temporary Dangerous patch */
2349: 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);
2350: 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]);
2351: 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);
2352: }
2353: k=k+1;
2354: if (j >= jmax){
2355: jmax=j;
2356: ijmax=i;
2357: }
2358: if (j <= jmin){
2359: jmin=j;
2360: ijmin=i;
2361: }
2362: sum=sum+j;
2363: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2364: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2365: }
2366: }
2367: else{
2368: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2369: /* 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]); */
2370:
2371: k=k+1;
2372: if (j >= jmax) {
2373: jmax=j;
2374: ijmax=i;
2375: }
2376: else if (j <= jmin){
2377: jmin=j;
2378: ijmin=i;
2379: }
2380: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2381: /*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]);*/
2382: if(j<0){
2383: nberr++;
2384: 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]);
2385: 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]);
2386: }
2387: sum=sum+j;
2388: }
2389: jk= j/stepm;
2390: jl= j -jk*stepm;
2391: ju= j -(jk+1)*stepm;
2392: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2393: if(jl==0){
2394: dh[mi][i]=jk;
2395: bh[mi][i]=0;
2396: }else{ /* We want a negative bias in order to only have interpolation ie
2397: * at the price of an extra matrix product in likelihood */
2398: dh[mi][i]=jk+1;
2399: bh[mi][i]=ju;
2400: }
2401: }else{
2402: if(jl <= -ju){
2403: dh[mi][i]=jk;
2404: bh[mi][i]=jl; /* bias is positive if real duration
2405: * is higher than the multiple of stepm and negative otherwise.
2406: */
2407: }
2408: else{
2409: dh[mi][i]=jk+1;
2410: bh[mi][i]=ju;
2411: }
2412: if(dh[mi][i]==0){
2413: dh[mi][i]=1; /* At least one step */
2414: bh[mi][i]=ju; /* At least one step */
2415: /* 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);*/
2416: }
2417: } /* end if mle */
2418: }
2419: } /* end wave */
2420: }
2421: jmean=sum/k;
2422: 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);
2423: 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);
2424: }
2425:
2426: /*********** Tricode ****************************/
2427: void tricode(int *Tvar, int **nbcode, int imx)
2428: {
2429:
2430: int Ndum[20],ij=1, k, j, i, maxncov=19;
2431: int cptcode=0;
2432: cptcoveff=0;
2433:
2434: for (k=0; k<maxncov; k++) Ndum[k]=0;
2435: for (k=1; k<=7; k++) ncodemax[k]=0;
2436:
2437: for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
2438: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2439: modality*/
2440: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
2441: Ndum[ij]++; /*store the modality */
2442: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2443: if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
2444: Tvar[j]. If V=sex and male is 0 and
2445: female is 1, then cptcode=1.*/
2446: }
2447:
2448: for (i=0; i<=cptcode; i++) {
2449: 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 */
2450: }
2451:
2452: ij=1;
2453: for (i=1; i<=ncodemax[j]; i++) {
2454: for (k=0; k<= maxncov; k++) {
2455: if (Ndum[k] != 0) {
2456: nbcode[Tvar[j]][ij]=k;
2457: /* 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; */
2458:
2459: ij++;
2460: }
2461: if (ij > ncodemax[j]) break;
2462: }
2463: }
2464: }
2465:
2466: for (k=0; k< maxncov; k++) Ndum[k]=0;
2467:
2468: for (i=1; i<=ncovmodel-2; i++) {
2469: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2470: ij=Tvar[i];
2471: Ndum[ij]++;
2472: }
2473:
2474: ij=1;
2475: for (i=1; i<= maxncov; i++) {
2476: if((Ndum[i]!=0) && (i<=ncovcol)){
2477: Tvaraff[ij]=i; /*For printing */
2478: ij++;
2479: }
2480: }
2481:
2482: cptcoveff=ij-1; /*Number of simple covariates*/
2483: }
2484:
2485: /*********** Health Expectancies ****************/
2486:
1.127 brouard 2487: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 2488:
2489: {
2490: /* Health expectancies, no variances */
2491: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2492: int nhstepma, nstepma; /* Decreasing with age */
2493: double age, agelim, hf;
2494: double ***p3mat;
2495: double eip;
2496:
2497: pstamp(ficreseij);
2498: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2499: fprintf(ficreseij,"# Age");
2500: for(i=1; i<=nlstate;i++){
2501: for(j=1; j<=nlstate;j++){
2502: fprintf(ficreseij," e%1d%1d ",i,j);
2503: }
2504: fprintf(ficreseij," e%1d. ",i);
2505: }
2506: fprintf(ficreseij,"\n");
2507:
2508:
2509: if(estepm < stepm){
2510: printf ("Problem %d lower than %d\n",estepm, stepm);
2511: }
2512: else hstepm=estepm;
2513: /* We compute the life expectancy from trapezoids spaced every estepm months
2514: * This is mainly to measure the difference between two models: for example
2515: * if stepm=24 months pijx are given only every 2 years and by summing them
2516: * we are calculating an estimate of the Life Expectancy assuming a linear
2517: * progression in between and thus overestimating or underestimating according
2518: * to the curvature of the survival function. If, for the same date, we
2519: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2520: * to compare the new estimate of Life expectancy with the same linear
2521: * hypothesis. A more precise result, taking into account a more precise
2522: * curvature will be obtained if estepm is as small as stepm. */
2523:
2524: /* For example we decided to compute the life expectancy with the smallest unit */
2525: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2526: nhstepm is the number of hstepm from age to agelim
2527: nstepm is the number of stepm from age to agelin.
2528: Look at hpijx to understand the reason of that which relies in memory size
2529: and note for a fixed period like estepm months */
2530: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2531: survival function given by stepm (the optimization length). Unfortunately it
2532: means that if the survival funtion is printed only each two years of age and if
2533: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2534: results. So we changed our mind and took the option of the best precision.
2535: */
2536: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2537:
2538: agelim=AGESUP;
2539: /* If stepm=6 months */
2540: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2541: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2542:
2543: /* nhstepm age range expressed in number of stepm */
2544: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2545: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2546: /* if (stepm >= YEARM) hstepm=1;*/
2547: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2548: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2549:
2550: for (age=bage; age<=fage; age ++){
2551: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2552: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2553: /* if (stepm >= YEARM) hstepm=1;*/
2554: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2555:
2556: /* If stepm=6 months */
2557: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2558: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2559:
2560: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2561:
2562: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2563:
2564: printf("%d|",(int)age);fflush(stdout);
2565: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2566:
2567: /* Computing expectancies */
2568: for(i=1; i<=nlstate;i++)
2569: for(j=1; j<=nlstate;j++)
2570: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2571: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2572:
2573: /* 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]);*/
2574:
2575: }
2576:
2577: fprintf(ficreseij,"%3.0f",age );
2578: for(i=1; i<=nlstate;i++){
2579: eip=0;
2580: for(j=1; j<=nlstate;j++){
2581: eip +=eij[i][j][(int)age];
2582: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2583: }
2584: fprintf(ficreseij,"%9.4f", eip );
2585: }
2586: fprintf(ficreseij,"\n");
2587:
2588: }
2589: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2590: printf("\n");
2591: fprintf(ficlog,"\n");
2592:
2593: }
2594:
1.127 brouard 2595: void cvevsij(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[] )
1.126 brouard 2596:
2597: {
2598: /* Covariances of health expectancies eij and of total life expectancies according
2599: to initial status i, ei. .
2600: */
2601: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2602: int nhstepma, nstepma; /* Decreasing with age */
2603: double age, agelim, hf;
2604: double ***p3matp, ***p3matm, ***varhe;
2605: double **dnewm,**doldm;
2606: double *xp, *xm;
2607: double **gp, **gm;
2608: double ***gradg, ***trgradg;
2609: int theta;
2610:
2611: double eip, vip;
2612:
2613: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2614: xp=vector(1,npar);
2615: xm=vector(1,npar);
2616: dnewm=matrix(1,nlstate*nlstate,1,npar);
2617: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2618:
2619: pstamp(ficresstdeij);
2620: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2621: fprintf(ficresstdeij,"# Age");
2622: for(i=1; i<=nlstate;i++){
2623: for(j=1; j<=nlstate;j++)
2624: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2625: fprintf(ficresstdeij," e%1d. ",i);
2626: }
2627: fprintf(ficresstdeij,"\n");
2628:
2629: pstamp(ficrescveij);
2630: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2631: fprintf(ficrescveij,"# Age");
2632: for(i=1; i<=nlstate;i++)
2633: for(j=1; j<=nlstate;j++){
2634: cptj= (j-1)*nlstate+i;
2635: for(i2=1; i2<=nlstate;i2++)
2636: for(j2=1; j2<=nlstate;j2++){
2637: cptj2= (j2-1)*nlstate+i2;
2638: if(cptj2 <= cptj)
2639: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2640: }
2641: }
2642: fprintf(ficrescveij,"\n");
2643:
2644: if(estepm < stepm){
2645: printf ("Problem %d lower than %d\n",estepm, stepm);
2646: }
2647: else hstepm=estepm;
2648: /* We compute the life expectancy from trapezoids spaced every estepm months
2649: * This is mainly to measure the difference between two models: for example
2650: * if stepm=24 months pijx are given only every 2 years and by summing them
2651: * we are calculating an estimate of the Life Expectancy assuming a linear
2652: * progression in between and thus overestimating or underestimating according
2653: * to the curvature of the survival function. If, for the same date, we
2654: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2655: * to compare the new estimate of Life expectancy with the same linear
2656: * hypothesis. A more precise result, taking into account a more precise
2657: * curvature will be obtained if estepm is as small as stepm. */
2658:
2659: /* For example we decided to compute the life expectancy with the smallest unit */
2660: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2661: nhstepm is the number of hstepm from age to agelim
2662: nstepm is the number of stepm from age to agelin.
2663: Look at hpijx to understand the reason of that which relies in memory size
2664: and note for a fixed period like estepm months */
2665: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2666: survival function given by stepm (the optimization length). Unfortunately it
2667: means that if the survival funtion is printed only each two years of age and if
2668: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2669: results. So we changed our mind and took the option of the best precision.
2670: */
2671: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2672:
2673: /* If stepm=6 months */
2674: /* nhstepm age range expressed in number of stepm */
2675: agelim=AGESUP;
2676: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2677: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2678: /* if (stepm >= YEARM) hstepm=1;*/
2679: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2680:
2681: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2682: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2683: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2684: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2685: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2686: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2687:
2688: for (age=bage; age<=fage; age ++){
2689: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2690: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2691: /* if (stepm >= YEARM) hstepm=1;*/
2692: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2693:
2694: /* If stepm=6 months */
2695: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2696: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2697:
2698: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2699:
2700: /* Computing Variances of health expectancies */
2701: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2702: decrease memory allocation */
2703: for(theta=1; theta <=npar; theta++){
2704: for(i=1; i<=npar; i++){
2705: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2706: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2707: }
2708: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2709: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2710:
2711: for(j=1; j<= nlstate; j++){
2712: for(i=1; i<=nlstate; i++){
2713: for(h=0; h<=nhstepm-1; h++){
2714: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2715: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2716: }
2717: }
2718: }
2719:
2720: for(ij=1; ij<= nlstate*nlstate; ij++)
2721: for(h=0; h<=nhstepm-1; h++){
2722: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2723: }
2724: }/* End theta */
2725:
2726:
2727: for(h=0; h<=nhstepm-1; h++)
2728: for(j=1; j<=nlstate*nlstate;j++)
2729: for(theta=1; theta <=npar; theta++)
2730: trgradg[h][j][theta]=gradg[h][theta][j];
2731:
2732:
2733: for(ij=1;ij<=nlstate*nlstate;ij++)
2734: for(ji=1;ji<=nlstate*nlstate;ji++)
2735: varhe[ij][ji][(int)age] =0.;
2736:
2737: printf("%d|",(int)age);fflush(stdout);
2738: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2739: for(h=0;h<=nhstepm-1;h++){
2740: for(k=0;k<=nhstepm-1;k++){
2741: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2742: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2743: for(ij=1;ij<=nlstate*nlstate;ij++)
2744: for(ji=1;ji<=nlstate*nlstate;ji++)
2745: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2746: }
2747: }
2748:
2749: /* Computing expectancies */
2750: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2751: for(i=1; i<=nlstate;i++)
2752: for(j=1; j<=nlstate;j++)
2753: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2754: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2755:
2756: /* 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]);*/
2757:
2758: }
2759:
2760: fprintf(ficresstdeij,"%3.0f",age );
2761: for(i=1; i<=nlstate;i++){
2762: eip=0.;
2763: vip=0.;
2764: for(j=1; j<=nlstate;j++){
2765: eip += eij[i][j][(int)age];
2766: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2767: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2768: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2769: }
2770: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2771: }
2772: fprintf(ficresstdeij,"\n");
2773:
2774: fprintf(ficrescveij,"%3.0f",age );
2775: for(i=1; i<=nlstate;i++)
2776: for(j=1; j<=nlstate;j++){
2777: cptj= (j-1)*nlstate+i;
2778: for(i2=1; i2<=nlstate;i2++)
2779: for(j2=1; j2<=nlstate;j2++){
2780: cptj2= (j2-1)*nlstate+i2;
2781: if(cptj2 <= cptj)
2782: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2783: }
2784: }
2785: fprintf(ficrescveij,"\n");
2786:
2787: }
2788: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2789: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2790: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2791: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2792: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2793: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2794: printf("\n");
2795: fprintf(ficlog,"\n");
2796:
2797: free_vector(xm,1,npar);
2798: free_vector(xp,1,npar);
2799: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2800: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2801: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2802: }
2803:
2804: /************ Variance ******************/
2805: 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[])
2806: {
2807: /* Variance of health expectancies */
2808: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2809: /* double **newm;*/
2810: double **dnewm,**doldm;
2811: double **dnewmp,**doldmp;
2812: int i, j, nhstepm, hstepm, h, nstepm ;
2813: int k, cptcode;
2814: double *xp;
2815: double **gp, **gm; /* for var eij */
2816: double ***gradg, ***trgradg; /*for var eij */
2817: double **gradgp, **trgradgp; /* for var p point j */
2818: double *gpp, *gmp; /* for var p point j */
2819: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2820: double ***p3mat;
2821: double age,agelim, hf;
2822: double ***mobaverage;
2823: int theta;
2824: char digit[4];
2825: char digitp[25];
2826:
2827: char fileresprobmorprev[FILENAMELENGTH];
2828:
2829: if(popbased==1){
2830: if(mobilav!=0)
2831: strcpy(digitp,"-populbased-mobilav-");
2832: else strcpy(digitp,"-populbased-nomobil-");
2833: }
2834: else
2835: strcpy(digitp,"-stablbased-");
2836:
2837: if (mobilav!=0) {
2838: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2839: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2840: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2841: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2842: }
2843: }
2844:
2845: strcpy(fileresprobmorprev,"prmorprev");
2846: sprintf(digit,"%-d",ij);
2847: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2848: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2849: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2850: strcat(fileresprobmorprev,fileres);
2851: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2852: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2853: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2854: }
2855: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2856:
2857: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2858: pstamp(ficresprobmorprev);
2859: 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);
2860: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2861: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2862: fprintf(ficresprobmorprev," p.%-d SE",j);
2863: for(i=1; i<=nlstate;i++)
2864: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2865: }
2866: fprintf(ficresprobmorprev,"\n");
2867: fprintf(ficgp,"\n# Routine varevsij");
2868: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2869: 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");
2870: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2871: /* } */
2872: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2873: pstamp(ficresvij);
2874: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2875: if(popbased==1)
1.128 brouard 2876: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 2877: else
2878: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2879: fprintf(ficresvij,"# Age");
2880: for(i=1; i<=nlstate;i++)
2881: for(j=1; j<=nlstate;j++)
2882: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2883: fprintf(ficresvij,"\n");
2884:
2885: xp=vector(1,npar);
2886: dnewm=matrix(1,nlstate,1,npar);
2887: doldm=matrix(1,nlstate,1,nlstate);
2888: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2889: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2890:
2891: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2892: gpp=vector(nlstate+1,nlstate+ndeath);
2893: gmp=vector(nlstate+1,nlstate+ndeath);
2894: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2895:
2896: if(estepm < stepm){
2897: printf ("Problem %d lower than %d\n",estepm, stepm);
2898: }
2899: else hstepm=estepm;
2900: /* For example we decided to compute the life expectancy with the smallest unit */
2901: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2902: nhstepm is the number of hstepm from age to agelim
2903: nstepm is the number of stepm from age to agelin.
1.128 brouard 2904: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 2905: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2906: survival function given by stepm (the optimization length). Unfortunately it
2907: means that if the survival funtion is printed every two years of age and if
2908: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2909: results. So we changed our mind and took the option of the best precision.
2910: */
2911: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2912: agelim = AGESUP;
2913: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2914: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2915: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2916: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2917: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2918: gp=matrix(0,nhstepm,1,nlstate);
2919: gm=matrix(0,nhstepm,1,nlstate);
2920:
2921:
2922: for(theta=1; theta <=npar; theta++){
2923: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2924: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2925: }
2926: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2927: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2928:
2929: if (popbased==1) {
2930: if(mobilav ==0){
2931: for(i=1; i<=nlstate;i++)
2932: prlim[i][i]=probs[(int)age][i][ij];
2933: }else{ /* mobilav */
2934: for(i=1; i<=nlstate;i++)
2935: prlim[i][i]=mobaverage[(int)age][i][ij];
2936: }
2937: }
2938:
2939: for(j=1; j<= nlstate; j++){
2940: for(h=0; h<=nhstepm; h++){
2941: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2942: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2943: }
2944: }
2945: /* This for computing probability of death (h=1 means
2946: computed over hstepm matrices product = hstepm*stepm months)
2947: as a weighted average of prlim.
2948: */
2949: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2950: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2951: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2952: }
2953: /* end probability of death */
2954:
2955: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2956: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2957: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2958: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2959:
2960: if (popbased==1) {
2961: if(mobilav ==0){
2962: for(i=1; i<=nlstate;i++)
2963: prlim[i][i]=probs[(int)age][i][ij];
2964: }else{ /* mobilav */
2965: for(i=1; i<=nlstate;i++)
2966: prlim[i][i]=mobaverage[(int)age][i][ij];
2967: }
2968: }
2969:
1.128 brouard 2970: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 2971: for(h=0; h<=nhstepm; h++){
2972: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
2973: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
2974: }
2975: }
2976: /* This for computing probability of death (h=1 means
2977: computed over hstepm matrices product = hstepm*stepm months)
2978: as a weighted average of prlim.
2979: */
2980: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2981: for(i=1,gmp[j]=0.; i<= nlstate; i++)
2982: gmp[j] += prlim[i][i]*p3mat[i][j][1];
2983: }
2984: /* end probability of death */
2985:
2986: for(j=1; j<= nlstate; j++) /* vareij */
2987: for(h=0; h<=nhstepm; h++){
2988: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
2989: }
2990:
2991: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
2992: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
2993: }
2994:
2995: } /* End theta */
2996:
2997: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
2998:
2999: for(h=0; h<=nhstepm; h++) /* veij */
3000: for(j=1; j<=nlstate;j++)
3001: for(theta=1; theta <=npar; theta++)
3002: trgradg[h][j][theta]=gradg[h][theta][j];
3003:
3004: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3005: for(theta=1; theta <=npar; theta++)
3006: trgradgp[j][theta]=gradgp[theta][j];
3007:
3008:
3009: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3010: for(i=1;i<=nlstate;i++)
3011: for(j=1;j<=nlstate;j++)
3012: vareij[i][j][(int)age] =0.;
3013:
3014: for(h=0;h<=nhstepm;h++){
3015: for(k=0;k<=nhstepm;k++){
3016: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3017: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3018: for(i=1;i<=nlstate;i++)
3019: for(j=1;j<=nlstate;j++)
3020: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3021: }
3022: }
3023:
3024: /* pptj */
3025: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3026: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3027: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3028: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3029: varppt[j][i]=doldmp[j][i];
3030: /* end ppptj */
3031: /* x centered again */
3032: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3033: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3034:
3035: if (popbased==1) {
3036: if(mobilav ==0){
3037: for(i=1; i<=nlstate;i++)
3038: prlim[i][i]=probs[(int)age][i][ij];
3039: }else{ /* mobilav */
3040: for(i=1; i<=nlstate;i++)
3041: prlim[i][i]=mobaverage[(int)age][i][ij];
3042: }
3043: }
3044:
3045: /* This for computing probability of death (h=1 means
3046: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3047: as a weighted average of prlim.
3048: */
3049: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3050: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3051: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3052: }
3053: /* end probability of death */
3054:
3055: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3056: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3057: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3058: for(i=1; i<=nlstate;i++){
3059: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3060: }
3061: }
3062: fprintf(ficresprobmorprev,"\n");
3063:
3064: fprintf(ficresvij,"%.0f ",age );
3065: for(i=1; i<=nlstate;i++)
3066: for(j=1; j<=nlstate;j++){
3067: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3068: }
3069: fprintf(ficresvij,"\n");
3070: free_matrix(gp,0,nhstepm,1,nlstate);
3071: free_matrix(gm,0,nhstepm,1,nlstate);
3072: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3073: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3074: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3075: } /* End age */
3076: free_vector(gpp,nlstate+1,nlstate+ndeath);
3077: free_vector(gmp,nlstate+1,nlstate+ndeath);
3078: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3079: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3080: fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
3081: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3082: fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3083: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3084: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3085: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3086: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3087: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3088: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3089: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3090: 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);
3091: /* 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);
3092: */
3093: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3094: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3095:
3096: free_vector(xp,1,npar);
3097: free_matrix(doldm,1,nlstate,1,nlstate);
3098: free_matrix(dnewm,1,nlstate,1,npar);
3099: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3100: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3101: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3102: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3103: fclose(ficresprobmorprev);
3104: fflush(ficgp);
3105: fflush(fichtm);
3106: } /* end varevsij */
3107:
3108: /************ Variance of prevlim ******************/
3109: 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[])
3110: {
3111: /* Variance of prevalence limit */
3112: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3113: double **newm;
3114: double **dnewm,**doldm;
3115: int i, j, nhstepm, hstepm;
3116: int k, cptcode;
3117: double *xp;
3118: double *gp, *gm;
3119: double **gradg, **trgradg;
3120: double age,agelim;
3121: int theta;
3122:
3123: pstamp(ficresvpl);
3124: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3125: fprintf(ficresvpl,"# Age");
3126: for(i=1; i<=nlstate;i++)
3127: fprintf(ficresvpl," %1d-%1d",i,i);
3128: fprintf(ficresvpl,"\n");
3129:
3130: xp=vector(1,npar);
3131: dnewm=matrix(1,nlstate,1,npar);
3132: doldm=matrix(1,nlstate,1,nlstate);
3133:
3134: hstepm=1*YEARM; /* Every year of age */
3135: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3136: agelim = AGESUP;
3137: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3138: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3139: if (stepm >= YEARM) hstepm=1;
3140: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3141: gradg=matrix(1,npar,1,nlstate);
3142: gp=vector(1,nlstate);
3143: gm=vector(1,nlstate);
3144:
3145: for(theta=1; theta <=npar; theta++){
3146: for(i=1; i<=npar; i++){ /* Computes gradient */
3147: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3148: }
3149: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3150: for(i=1;i<=nlstate;i++)
3151: gp[i] = prlim[i][i];
3152:
3153: for(i=1; i<=npar; i++) /* Computes gradient */
3154: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3155: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3156: for(i=1;i<=nlstate;i++)
3157: gm[i] = prlim[i][i];
3158:
3159: for(i=1;i<=nlstate;i++)
3160: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3161: } /* End theta */
3162:
3163: trgradg =matrix(1,nlstate,1,npar);
3164:
3165: for(j=1; j<=nlstate;j++)
3166: for(theta=1; theta <=npar; theta++)
3167: trgradg[j][theta]=gradg[theta][j];
3168:
3169: for(i=1;i<=nlstate;i++)
3170: varpl[i][(int)age] =0.;
3171: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3172: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3173: for(i=1;i<=nlstate;i++)
3174: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3175:
3176: fprintf(ficresvpl,"%.0f ",age );
3177: for(i=1; i<=nlstate;i++)
3178: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3179: fprintf(ficresvpl,"\n");
3180: free_vector(gp,1,nlstate);
3181: free_vector(gm,1,nlstate);
3182: free_matrix(gradg,1,npar,1,nlstate);
3183: free_matrix(trgradg,1,nlstate,1,npar);
3184: } /* End age */
3185:
3186: free_vector(xp,1,npar);
3187: free_matrix(doldm,1,nlstate,1,npar);
3188: free_matrix(dnewm,1,nlstate,1,nlstate);
3189:
3190: }
3191:
3192: /************ Variance of one-step probabilities ******************/
3193: 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[])
3194: {
3195: int i, j=0, i1, k1, l1, t, tj;
3196: int k2, l2, j1, z1;
3197: int k=0,l, cptcode;
3198: int first=1, first1;
3199: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3200: double **dnewm,**doldm;
3201: double *xp;
3202: double *gp, *gm;
3203: double **gradg, **trgradg;
3204: double **mu;
3205: double age,agelim, cov[NCOVMAX];
3206: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3207: int theta;
3208: char fileresprob[FILENAMELENGTH];
3209: char fileresprobcov[FILENAMELENGTH];
3210: char fileresprobcor[FILENAMELENGTH];
3211:
3212: double ***varpij;
3213:
3214: strcpy(fileresprob,"prob");
3215: strcat(fileresprob,fileres);
3216: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3217: printf("Problem with resultfile: %s\n", fileresprob);
3218: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3219: }
3220: strcpy(fileresprobcov,"probcov");
3221: strcat(fileresprobcov,fileres);
3222: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3223: printf("Problem with resultfile: %s\n", fileresprobcov);
3224: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3225: }
3226: strcpy(fileresprobcor,"probcor");
3227: strcat(fileresprobcor,fileres);
3228: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3229: printf("Problem with resultfile: %s\n", fileresprobcor);
3230: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3231: }
3232: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3233: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3234: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3235: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3236: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3237: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3238: pstamp(ficresprob);
3239: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3240: fprintf(ficresprob,"# Age");
3241: pstamp(ficresprobcov);
3242: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3243: fprintf(ficresprobcov,"# Age");
3244: pstamp(ficresprobcor);
3245: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3246: fprintf(ficresprobcor,"# Age");
3247:
3248:
3249: for(i=1; i<=nlstate;i++)
3250: for(j=1; j<=(nlstate+ndeath);j++){
3251: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3252: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3253: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3254: }
3255: /* fprintf(ficresprob,"\n");
3256: fprintf(ficresprobcov,"\n");
3257: fprintf(ficresprobcor,"\n");
3258: */
3259: xp=vector(1,npar);
3260: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3261: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3262: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3263: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3264: first=1;
3265: fprintf(ficgp,"\n# Routine varprob");
3266: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3267: fprintf(fichtm,"\n");
3268:
3269: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3270: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3271: file %s<br>\n",optionfilehtmcov);
3272: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3273: and drawn. It helps understanding how is the covariance between two incidences.\
3274: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3275: 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. \
3276: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3277: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3278: standard deviations wide on each axis. <br>\
3279: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3280: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3281: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3282:
3283: cov[1]=1;
3284: tj=cptcoveff;
3285: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3286: j1=0;
3287: for(t=1; t<=tj;t++){
3288: for(i1=1; i1<=ncodemax[t];i1++){
3289: j1++;
3290: if (cptcovn>0) {
3291: fprintf(ficresprob, "\n#********** Variable ");
3292: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3293: fprintf(ficresprob, "**********\n#\n");
3294: fprintf(ficresprobcov, "\n#********** Variable ");
3295: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3296: fprintf(ficresprobcov, "**********\n#\n");
3297:
3298: fprintf(ficgp, "\n#********** Variable ");
3299: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3300: fprintf(ficgp, "**********\n#\n");
3301:
3302:
3303: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3304: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3305: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3306:
3307: fprintf(ficresprobcor, "\n#********** Variable ");
3308: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3309: fprintf(ficresprobcor, "**********\n#");
3310: }
3311:
3312: for (age=bage; age<=fage; age ++){
3313: cov[2]=age;
3314: for (k=1; k<=cptcovn;k++) {
3315: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3316: }
3317: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3318: for (k=1; k<=cptcovprod;k++)
3319: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3320:
3321: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3322: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3323: gp=vector(1,(nlstate)*(nlstate+ndeath));
3324: gm=vector(1,(nlstate)*(nlstate+ndeath));
3325:
3326: for(theta=1; theta <=npar; theta++){
3327: for(i=1; i<=npar; i++)
3328: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3329:
3330: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3331:
3332: k=0;
3333: for(i=1; i<= (nlstate); i++){
3334: for(j=1; j<=(nlstate+ndeath);j++){
3335: k=k+1;
3336: gp[k]=pmmij[i][j];
3337: }
3338: }
3339:
3340: for(i=1; i<=npar; i++)
3341: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3342:
3343: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3344: k=0;
3345: for(i=1; i<=(nlstate); i++){
3346: for(j=1; j<=(nlstate+ndeath);j++){
3347: k=k+1;
3348: gm[k]=pmmij[i][j];
3349: }
3350: }
3351:
3352: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3353: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3354: }
3355:
3356: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3357: for(theta=1; theta <=npar; theta++)
3358: trgradg[j][theta]=gradg[theta][j];
3359:
3360: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3361: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3362: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3363: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3364: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3365: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3366:
3367: pmij(pmmij,cov,ncovmodel,x,nlstate);
3368:
3369: k=0;
3370: for(i=1; i<=(nlstate); i++){
3371: for(j=1; j<=(nlstate+ndeath);j++){
3372: k=k+1;
3373: mu[k][(int) age]=pmmij[i][j];
3374: }
3375: }
3376: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3377: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3378: varpij[i][j][(int)age] = doldm[i][j];
3379:
3380: /*printf("\n%d ",(int)age);
3381: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3382: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3383: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3384: }*/
3385:
3386: fprintf(ficresprob,"\n%d ",(int)age);
3387: fprintf(ficresprobcov,"\n%d ",(int)age);
3388: fprintf(ficresprobcor,"\n%d ",(int)age);
3389:
3390: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3391: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3392: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3393: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3394: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3395: }
3396: i=0;
3397: for (k=1; k<=(nlstate);k++){
3398: for (l=1; l<=(nlstate+ndeath);l++){
3399: i=i++;
3400: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3401: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3402: for (j=1; j<=i;j++){
3403: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3404: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3405: }
3406: }
3407: }/* end of loop for state */
3408: } /* end of loop for age */
3409:
3410: /* Confidence intervalle of pij */
3411: /*
3412: fprintf(ficgp,"\nset noparametric;unset label");
3413: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3414: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3415: 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);
3416: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3417: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3418: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3419: */
3420:
3421: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3422: first1=1;
3423: for (k2=1; k2<=(nlstate);k2++){
3424: for (l2=1; l2<=(nlstate+ndeath);l2++){
3425: if(l2==k2) continue;
3426: j=(k2-1)*(nlstate+ndeath)+l2;
3427: for (k1=1; k1<=(nlstate);k1++){
3428: for (l1=1; l1<=(nlstate+ndeath);l1++){
3429: if(l1==k1) continue;
3430: i=(k1-1)*(nlstate+ndeath)+l1;
3431: if(i<=j) continue;
3432: for (age=bage; age<=fage; age ++){
3433: if ((int)age %5==0){
3434: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3435: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3436: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3437: mu1=mu[i][(int) age]/stepm*YEARM ;
3438: mu2=mu[j][(int) age]/stepm*YEARM;
3439: c12=cv12/sqrt(v1*v2);
3440: /* Computing eigen value of matrix of covariance */
3441: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3442: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3443: /* Eigen vectors */
3444: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3445: /*v21=sqrt(1.-v11*v11); *//* error */
3446: v21=(lc1-v1)/cv12*v11;
3447: v12=-v21;
3448: v22=v11;
3449: tnalp=v21/v11;
3450: if(first1==1){
3451: first1=0;
3452: 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);
3453: }
3454: 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);
3455: /*printf(fignu*/
3456: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3457: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3458: if(first==1){
3459: first=0;
3460: fprintf(ficgp,"\nset parametric;unset label");
3461: 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);
3462: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3463: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3464: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3465: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3466: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3467: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3468: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3469: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3470: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3471: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3472: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3473: 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",\
3474: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3475: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3476: }else{
3477: first=0;
3478: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3479: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3480: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3481: 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",\
3482: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3483: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3484: }/* if first */
3485: } /* age mod 5 */
3486: } /* end loop age */
3487: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3488: first=1;
3489: } /*l12 */
3490: } /* k12 */
3491: } /*l1 */
3492: }/* k1 */
3493: } /* loop covariates */
3494: }
3495: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3496: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3497: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3498: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3499: free_vector(xp,1,npar);
3500: fclose(ficresprob);
3501: fclose(ficresprobcov);
3502: fclose(ficresprobcor);
3503: fflush(ficgp);
3504: fflush(fichtmcov);
3505: }
3506:
3507:
3508: /******************* Printing html file ***********/
3509: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3510: int lastpass, int stepm, int weightopt, char model[],\
3511: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3512: int popforecast, int estepm ,\
3513: double jprev1, double mprev1,double anprev1, \
3514: double jprev2, double mprev2,double anprev2){
3515: int jj1, k1, i1, cpt;
3516:
3517: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3518: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3519: </ul>");
3520: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3521: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3522: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3523: fprintf(fichtm,"\
3524: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3525: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3526: fprintf(fichtm,"\
3527: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3528: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3529: fprintf(fichtm,"\
1.128 brouard 3530: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 3531: <a href=\"%s\">%s</a> <br>\n",
3532: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3533: fprintf(fichtm,"\
3534: - Population projections by age and states: \
3535: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3536:
3537: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3538:
3539: m=cptcoveff;
3540: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3541:
3542: jj1=0;
3543: for(k1=1; k1<=m;k1++){
3544: for(i1=1; i1<=ncodemax[k1];i1++){
3545: jj1++;
3546: if (cptcovn > 0) {
3547: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3548: for (cpt=1; cpt<=cptcoveff;cpt++)
3549: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3550: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3551: }
3552: /* Pij */
3553: 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> \
3554: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3555: /* Quasi-incidences */
3556: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3557: 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> \
3558: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3559: /* Period (stable) prevalence in each health state */
3560: for(cpt=1; cpt<nlstate;cpt++){
3561: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3562: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3563: }
3564: for(cpt=1; cpt<=nlstate;cpt++) {
3565: 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> \
3566: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3567: }
3568: } /* end i1 */
3569: }/* End k1 */
3570: fprintf(fichtm,"</ul>");
3571:
3572:
3573: fprintf(fichtm,"\
3574: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3575: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3576:
3577: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3578: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3579: fprintf(fichtm,"\
3580: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3581: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3582:
3583: fprintf(fichtm,"\
3584: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3585: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3586: fprintf(fichtm,"\
3587: - 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): \
3588: <a href=\"%s\">%s</a> <br>\n</li>",
3589: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3590: fprintf(fichtm,"\
3591: - (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): \
3592: <a href=\"%s\">%s</a> <br>\n</li>",
3593: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3594: fprintf(fichtm,"\
1.128 brouard 3595: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> 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",
1.126 brouard 3596: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3597: fprintf(fichtm,"\
1.128 brouard 3598: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
3599: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3600: fprintf(fichtm,"\
3601: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3602: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3603:
3604: /* if(popforecast==1) fprintf(fichtm,"\n */
3605: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3606: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3607: /* <br>",fileres,fileres,fileres,fileres); */
3608: /* else */
3609: /* 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); */
3610: fflush(fichtm);
3611: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3612:
3613: m=cptcoveff;
3614: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3615:
3616: jj1=0;
3617: for(k1=1; k1<=m;k1++){
3618: for(i1=1; i1<=ncodemax[k1];i1++){
3619: jj1++;
3620: if (cptcovn > 0) {
3621: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3622: for (cpt=1; cpt<=cptcoveff;cpt++)
3623: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3624: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3625: }
3626: for(cpt=1; cpt<=nlstate;cpt++) {
3627: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3628: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3629: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3630: }
3631: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3632: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3633: true period expectancies (those weighted with period prevalences are also\
3634: drawn in addition to the population based expectancies computed using\
3635: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3636: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3637: } /* end i1 */
3638: }/* End k1 */
3639: fprintf(fichtm,"</ul>");
3640: fflush(fichtm);
3641: }
3642:
3643: /******************* Gnuplot file **************/
3644: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3645:
3646: char dirfileres[132],optfileres[132];
3647: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
3648: int ng;
3649: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3650: /* printf("Problem with file %s",optionfilegnuplot); */
3651: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3652: /* } */
3653:
3654: /*#ifdef windows */
3655: fprintf(ficgp,"cd \"%s\" \n",pathc);
3656: /*#endif */
3657: m=pow(2,cptcoveff);
3658:
3659: strcpy(dirfileres,optionfilefiname);
3660: strcpy(optfileres,"vpl");
3661: /* 1eme*/
3662: for (cpt=1; cpt<= nlstate ; cpt ++) {
3663: for (k1=1; k1<= m ; k1 ++) {
3664: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3665: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3666: fprintf(ficgp,"set xlabel \"Age\" \n\
3667: set ylabel \"Probability\" \n\
3668: set ter png small\n\
3669: set size 0.65,0.65\n\
3670: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3671:
3672: for (i=1; i<= nlstate ; i ++) {
3673: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3674: else fprintf(ficgp," \%%*lf (\%%*lf)");
3675: }
3676: 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);
3677: for (i=1; i<= nlstate ; i ++) {
3678: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3679: else fprintf(ficgp," \%%*lf (\%%*lf)");
3680: }
3681: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3682: for (i=1; i<= nlstate ; i ++) {
3683: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3684: else fprintf(ficgp," \%%*lf (\%%*lf)");
3685: }
3686: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3687: }
3688: }
3689: /*2 eme*/
3690:
3691: for (k1=1; k1<= m ; k1 ++) {
3692: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3693: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3694:
3695: for (i=1; i<= nlstate+1 ; i ++) {
3696: k=2*i;
3697: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3698: for (j=1; j<= nlstate+1 ; j ++) {
3699: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3700: else fprintf(ficgp," \%%*lf (\%%*lf)");
3701: }
3702: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3703: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3704: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3705: for (j=1; j<= nlstate+1 ; j ++) {
3706: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3707: else fprintf(ficgp," \%%*lf (\%%*lf)");
3708: }
3709: fprintf(ficgp,"\" t\"\" w l 0,");
3710: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3711: for (j=1; j<= nlstate+1 ; j ++) {
3712: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3713: else fprintf(ficgp," \%%*lf (\%%*lf)");
3714: }
3715: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3716: else fprintf(ficgp,"\" t\"\" w l 0,");
3717: }
3718: }
3719:
3720: /*3eme*/
3721:
3722: for (k1=1; k1<= m ; k1 ++) {
3723: for (cpt=1; cpt<= nlstate ; cpt ++) {
3724: /* k=2+nlstate*(2*cpt-2); */
3725: k=2+(nlstate+1)*(cpt-1);
3726: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3727: fprintf(ficgp,"set ter png small\n\
3728: set size 0.65,0.65\n\
3729: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3730: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3731: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3732: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3733: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3734: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3735: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3736:
3737: */
3738: for (i=1; i< nlstate ; i ++) {
3739: 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);
3740: /* 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);*/
3741:
3742: }
3743: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3744: }
3745: }
3746:
3747: /* CV preval stable (period) */
3748: for (k1=1; k1<= m ; k1 ++) {
3749: for (cpt=1; cpt<=nlstate ; cpt ++) {
3750: k=3;
3751: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3752: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3753: set ter png small\nset size 0.65,0.65\n\
3754: unset log y\n\
3755: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3756:
3757: for (i=1; i< nlstate ; i ++)
3758: fprintf(ficgp,"+$%d",k+i+1);
3759: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3760:
3761: l=3+(nlstate+ndeath)*cpt;
3762: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3763: for (i=1; i< nlstate ; i ++) {
3764: l=3+(nlstate+ndeath)*cpt;
3765: fprintf(ficgp,"+$%d",l+i+1);
3766: }
3767: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3768: }
3769: }
3770:
3771: /* proba elementaires */
3772: for(i=1,jk=1; i <=nlstate; i++){
3773: for(k=1; k <=(nlstate+ndeath); k++){
3774: if (k != i) {
3775: for(j=1; j <=ncovmodel; j++){
3776: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3777: jk++;
3778: fprintf(ficgp,"\n");
3779: }
3780: }
3781: }
3782: }
3783:
3784: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3785: for(jk=1; jk <=m; jk++) {
3786: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3787: if (ng==2)
3788: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3789: else
3790: fprintf(ficgp,"\nset title \"Probability\"\n");
3791: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3792: i=1;
3793: for(k2=1; k2<=nlstate; k2++) {
3794: k3=i;
3795: for(k=1; k<=(nlstate+ndeath); k++) {
3796: if (k != k2){
3797: if(ng==2)
3798: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3799: else
3800: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3801: ij=1;
3802: for(j=3; j <=ncovmodel; j++) {
3803: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3804: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3805: ij++;
3806: }
3807: else
3808: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3809: }
3810: fprintf(ficgp,")/(1");
3811:
3812: for(k1=1; k1 <=nlstate; k1++){
3813: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3814: ij=1;
3815: for(j=3; j <=ncovmodel; j++){
3816: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3817: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3818: ij++;
3819: }
3820: else
3821: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3822: }
3823: fprintf(ficgp,")");
3824: }
3825: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3826: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3827: i=i+ncovmodel;
3828: }
3829: } /* end k */
3830: } /* end k2 */
3831: } /* end jk */
3832: } /* end ng */
3833: fflush(ficgp);
3834: } /* end gnuplot */
3835:
3836:
3837: /*************** Moving average **************/
3838: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3839:
3840: int i, cpt, cptcod;
3841: int modcovmax =1;
3842: int mobilavrange, mob;
3843: double age;
3844:
3845: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3846: a covariate has 2 modalities */
3847: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3848:
3849: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3850: if(mobilav==1) mobilavrange=5; /* default */
3851: else mobilavrange=mobilav;
3852: for (age=bage; age<=fage; age++)
3853: for (i=1; i<=nlstate;i++)
3854: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3855: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3856: /* We keep the original values on the extreme ages bage, fage and for
3857: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3858: we use a 5 terms etc. until the borders are no more concerned.
3859: */
3860: for (mob=3;mob <=mobilavrange;mob=mob+2){
3861: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3862: for (i=1; i<=nlstate;i++){
3863: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3864: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3865: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3866: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3867: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3868: }
3869: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3870: }
3871: }
3872: }/* end age */
3873: }/* end mob */
3874: }else return -1;
3875: return 0;
3876: }/* End movingaverage */
3877:
3878:
3879: /************** Forecasting ******************/
3880: 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){
3881: /* proj1, year, month, day of starting projection
3882: agemin, agemax range of age
3883: dateprev1 dateprev2 range of dates during which prevalence is computed
3884: anproj2 year of en of projection (same day and month as proj1).
3885: */
3886: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3887: int *popage;
3888: double agec; /* generic age */
3889: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3890: double *popeffectif,*popcount;
3891: double ***p3mat;
3892: double ***mobaverage;
3893: char fileresf[FILENAMELENGTH];
3894:
3895: agelim=AGESUP;
3896: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3897:
3898: strcpy(fileresf,"f");
3899: strcat(fileresf,fileres);
3900: if((ficresf=fopen(fileresf,"w"))==NULL) {
3901: printf("Problem with forecast resultfile: %s\n", fileresf);
3902: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3903: }
3904: printf("Computing forecasting: result on file '%s' \n", fileresf);
3905: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3906:
3907: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3908:
3909: if (mobilav!=0) {
3910: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3911: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3912: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3913: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3914: }
3915: }
3916:
3917: stepsize=(int) (stepm+YEARM-1)/YEARM;
3918: if (stepm<=12) stepsize=1;
3919: if(estepm < stepm){
3920: printf ("Problem %d lower than %d\n",estepm, stepm);
3921: }
3922: else hstepm=estepm;
3923:
3924: hstepm=hstepm/stepm;
3925: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3926: fractional in yp1 */
3927: anprojmean=yp;
3928: yp2=modf((yp1*12),&yp);
3929: mprojmean=yp;
3930: yp1=modf((yp2*30.5),&yp);
3931: jprojmean=yp;
3932: if(jprojmean==0) jprojmean=1;
3933: if(mprojmean==0) jprojmean=1;
3934:
3935: i1=cptcoveff;
3936: if (cptcovn < 1){i1=1;}
3937:
3938: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3939:
3940: fprintf(ficresf,"#****** Routine prevforecast **\n");
3941:
3942: /* if (h==(int)(YEARM*yearp)){ */
3943: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3944: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3945: k=k+1;
3946: fprintf(ficresf,"\n#******");
3947: for(j=1;j<=cptcoveff;j++) {
3948: 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]]);
3949: }
3950: fprintf(ficresf,"******\n");
3951: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3952: for(j=1; j<=nlstate+ndeath;j++){
3953: for(i=1; i<=nlstate;i++)
3954: fprintf(ficresf," p%d%d",i,j);
3955: fprintf(ficresf," p.%d",j);
3956: }
3957: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
3958: fprintf(ficresf,"\n");
3959: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
3960:
3961: for (agec=fage; agec>=(ageminpar-1); agec--){
3962: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
3963: nhstepm = nhstepm/hstepm;
3964: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3965: oldm=oldms;savm=savms;
3966: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
3967:
3968: for (h=0; h<=nhstepm; h++){
3969: if (h*hstepm/YEARM*stepm ==yearp) {
3970: fprintf(ficresf,"\n");
3971: for(j=1;j<=cptcoveff;j++)
3972: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
3973: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
3974: }
3975: for(j=1; j<=nlstate+ndeath;j++) {
3976: ppij=0.;
3977: for(i=1; i<=nlstate;i++) {
3978: if (mobilav==1)
3979: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
3980: else {
3981: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
3982: }
3983: if (h*hstepm/YEARM*stepm== yearp) {
3984: fprintf(ficresf," %.3f", p3mat[i][j][h]);
3985: }
3986: } /* end i */
3987: if (h*hstepm/YEARM*stepm==yearp) {
3988: fprintf(ficresf," %.3f", ppij);
3989: }
3990: }/* end j */
3991: } /* end h */
3992: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3993: } /* end agec */
3994: } /* end yearp */
3995: } /* end cptcod */
3996: } /* end cptcov */
3997:
3998: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3999:
4000: fclose(ficresf);
4001: }
4002:
4003: /************** Forecasting *****not tested NB*************/
4004: 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){
4005:
4006: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4007: int *popage;
4008: double calagedatem, agelim, kk1, kk2;
4009: double *popeffectif,*popcount;
4010: double ***p3mat,***tabpop,***tabpopprev;
4011: double ***mobaverage;
4012: char filerespop[FILENAMELENGTH];
4013:
4014: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4015: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4016: agelim=AGESUP;
4017: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4018:
4019: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4020:
4021:
4022: strcpy(filerespop,"pop");
4023: strcat(filerespop,fileres);
4024: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4025: printf("Problem with forecast resultfile: %s\n", filerespop);
4026: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4027: }
4028: printf("Computing forecasting: result on file '%s' \n", filerespop);
4029: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4030:
4031: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4032:
4033: if (mobilav!=0) {
4034: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4035: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4036: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4037: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4038: }
4039: }
4040:
4041: stepsize=(int) (stepm+YEARM-1)/YEARM;
4042: if (stepm<=12) stepsize=1;
4043:
4044: agelim=AGESUP;
4045:
4046: hstepm=1;
4047: hstepm=hstepm/stepm;
4048:
4049: if (popforecast==1) {
4050: if((ficpop=fopen(popfile,"r"))==NULL) {
4051: printf("Problem with population file : %s\n",popfile);exit(0);
4052: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4053: }
4054: popage=ivector(0,AGESUP);
4055: popeffectif=vector(0,AGESUP);
4056: popcount=vector(0,AGESUP);
4057:
4058: i=1;
4059: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4060:
4061: imx=i;
4062: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4063: }
4064:
4065: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4066: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4067: k=k+1;
4068: fprintf(ficrespop,"\n#******");
4069: for(j=1;j<=cptcoveff;j++) {
4070: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4071: }
4072: fprintf(ficrespop,"******\n");
4073: fprintf(ficrespop,"# Age");
4074: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4075: if (popforecast==1) fprintf(ficrespop," [Population]");
4076:
4077: for (cpt=0; cpt<=0;cpt++) {
4078: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4079:
4080: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4081: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4082: nhstepm = nhstepm/hstepm;
4083:
4084: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4085: oldm=oldms;savm=savms;
4086: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4087:
4088: for (h=0; h<=nhstepm; h++){
4089: if (h==(int) (calagedatem+YEARM*cpt)) {
4090: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4091: }
4092: for(j=1; j<=nlstate+ndeath;j++) {
4093: kk1=0.;kk2=0;
4094: for(i=1; i<=nlstate;i++) {
4095: if (mobilav==1)
4096: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4097: else {
4098: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4099: }
4100: }
4101: if (h==(int)(calagedatem+12*cpt)){
4102: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4103: /*fprintf(ficrespop," %.3f", kk1);
4104: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4105: }
4106: }
4107: for(i=1; i<=nlstate;i++){
4108: kk1=0.;
4109: for(j=1; j<=nlstate;j++){
4110: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4111: }
4112: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4113: }
4114:
4115: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4116: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4117: }
4118: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4119: }
4120: }
4121:
4122: /******/
4123:
4124: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4125: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4126: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4127: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4128: nhstepm = nhstepm/hstepm;
4129:
4130: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4131: oldm=oldms;savm=savms;
4132: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4133: for (h=0; h<=nhstepm; h++){
4134: if (h==(int) (calagedatem+YEARM*cpt)) {
4135: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4136: }
4137: for(j=1; j<=nlstate+ndeath;j++) {
4138: kk1=0.;kk2=0;
4139: for(i=1; i<=nlstate;i++) {
4140: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4141: }
4142: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4143: }
4144: }
4145: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4146: }
4147: }
4148: }
4149: }
4150:
4151: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4152:
4153: if (popforecast==1) {
4154: free_ivector(popage,0,AGESUP);
4155: free_vector(popeffectif,0,AGESUP);
4156: free_vector(popcount,0,AGESUP);
4157: }
4158: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4159: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4160: fclose(ficrespop);
4161: } /* End of popforecast */
4162:
4163: int fileappend(FILE *fichier, char *optionfich)
4164: {
4165: if((fichier=fopen(optionfich,"a"))==NULL) {
4166: printf("Problem with file: %s\n", optionfich);
4167: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4168: return (0);
4169: }
4170: fflush(fichier);
4171: return (1);
4172: }
4173:
4174:
4175: /**************** function prwizard **********************/
4176: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4177: {
4178:
4179: /* Wizard to print covariance matrix template */
4180:
4181: char ca[32], cb[32], cc[32];
4182: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4183: int numlinepar;
4184:
4185: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4186: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4187: for(i=1; i <=nlstate; i++){
4188: jj=0;
4189: for(j=1; j <=nlstate+ndeath; j++){
4190: if(j==i) continue;
4191: jj++;
4192: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4193: printf("%1d%1d",i,j);
4194: fprintf(ficparo,"%1d%1d",i,j);
4195: for(k=1; k<=ncovmodel;k++){
4196: /* printf(" %lf",param[i][j][k]); */
4197: /* fprintf(ficparo," %lf",param[i][j][k]); */
4198: printf(" 0.");
4199: fprintf(ficparo," 0.");
4200: }
4201: printf("\n");
4202: fprintf(ficparo,"\n");
4203: }
4204: }
4205: printf("# Scales (for hessian or gradient estimation)\n");
4206: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4207: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4208: for(i=1; i <=nlstate; i++){
4209: jj=0;
4210: for(j=1; j <=nlstate+ndeath; j++){
4211: if(j==i) continue;
4212: jj++;
4213: fprintf(ficparo,"%1d%1d",i,j);
4214: printf("%1d%1d",i,j);
4215: fflush(stdout);
4216: for(k=1; k<=ncovmodel;k++){
4217: /* printf(" %le",delti3[i][j][k]); */
4218: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4219: printf(" 0.");
4220: fprintf(ficparo," 0.");
4221: }
4222: numlinepar++;
4223: printf("\n");
4224: fprintf(ficparo,"\n");
4225: }
4226: }
4227: printf("# Covariance matrix\n");
4228: /* # 121 Var(a12)\n\ */
4229: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4230: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4231: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4232: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4233: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4234: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4235: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4236: fflush(stdout);
4237: fprintf(ficparo,"# Covariance matrix\n");
4238: /* # 121 Var(a12)\n\ */
4239: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4240: /* # ...\n\ */
4241: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4242:
4243: for(itimes=1;itimes<=2;itimes++){
4244: jj=0;
4245: for(i=1; i <=nlstate; i++){
4246: for(j=1; j <=nlstate+ndeath; j++){
4247: if(j==i) continue;
4248: for(k=1; k<=ncovmodel;k++){
4249: jj++;
4250: ca[0]= k+'a'-1;ca[1]='\0';
4251: if(itimes==1){
4252: printf("#%1d%1d%d",i,j,k);
4253: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4254: }else{
4255: printf("%1d%1d%d",i,j,k);
4256: fprintf(ficparo,"%1d%1d%d",i,j,k);
4257: /* printf(" %.5le",matcov[i][j]); */
4258: }
4259: ll=0;
4260: for(li=1;li <=nlstate; li++){
4261: for(lj=1;lj <=nlstate+ndeath; lj++){
4262: if(lj==li) continue;
4263: for(lk=1;lk<=ncovmodel;lk++){
4264: ll++;
4265: if(ll<=jj){
4266: cb[0]= lk +'a'-1;cb[1]='\0';
4267: if(ll<jj){
4268: if(itimes==1){
4269: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4270: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4271: }else{
4272: printf(" 0.");
4273: fprintf(ficparo," 0.");
4274: }
4275: }else{
4276: if(itimes==1){
4277: printf(" Var(%s%1d%1d)",ca,i,j);
4278: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4279: }else{
4280: printf(" 0.");
4281: fprintf(ficparo," 0.");
4282: }
4283: }
4284: }
4285: } /* end lk */
4286: } /* end lj */
4287: } /* end li */
4288: printf("\n");
4289: fprintf(ficparo,"\n");
4290: numlinepar++;
4291: } /* end k*/
4292: } /*end j */
4293: } /* end i */
4294: } /* end itimes */
4295:
4296: } /* end of prwizard */
4297: /******************* Gompertz Likelihood ******************************/
4298: double gompertz(double x[])
4299: {
4300: double A,B,L=0.0,sump=0.,num=0.;
4301: int i,n=0; /* n is the size of the sample */
4302:
4303: for (i=0;i<=imx-1 ; i++) {
4304: sump=sump+weight[i];
4305: /* sump=sump+1;*/
4306: num=num+1;
4307: }
4308:
4309:
4310: /* for (i=0; i<=imx; i++)
4311: 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]);*/
4312:
4313: for (i=1;i<=imx ; i++)
4314: {
4315: if (cens[i] == 1 && wav[i]>1)
4316: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4317:
4318: if (cens[i] == 0 && wav[i]>1)
4319: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4320: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4321:
4322: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4323: if (wav[i] > 1 ) { /* ??? */
4324: L=L+A*weight[i];
4325: /* 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]);*/
4326: }
4327: }
4328:
4329: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4330:
4331: return -2*L*num/sump;
4332: }
4333:
4334: /******************* Printing html file ***********/
4335: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4336: int lastpass, int stepm, int weightopt, char model[],\
4337: int imx, double p[],double **matcov,double agemortsup){
4338: int i,k;
4339:
4340: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4341: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4342: for (i=1;i<=2;i++)
4343: 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]));
4344: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4345: fprintf(fichtm,"</ul>");
4346:
4347: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4348:
4349: 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>");
4350:
4351: for (k=agegomp;k<(agemortsup-2);k++)
4352: 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]);
4353:
4354:
4355: fflush(fichtm);
4356: }
4357:
4358: /******************* Gnuplot file **************/
4359: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4360:
4361: char dirfileres[132],optfileres[132];
4362: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4363: int ng;
4364:
4365:
4366: /*#ifdef windows */
4367: fprintf(ficgp,"cd \"%s\" \n",pathc);
4368: /*#endif */
4369:
4370:
4371: strcpy(dirfileres,optionfilefiname);
4372: strcpy(optfileres,"vpl");
4373: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4374: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4375: fprintf(ficgp, "set ter png small\n set log y\n");
4376: fprintf(ficgp, "set size 0.65,0.65\n");
4377: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4378:
4379: }
4380:
4381:
4382:
4383:
4384:
4385: /***********************************************/
4386: /**************** Main Program *****************/
4387: /***********************************************/
4388:
4389: int main(int argc, char *argv[])
4390: {
4391: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4392: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4393: int linei, month, year,iout;
4394: int jj, ll, li, lj, lk, imk;
4395: int numlinepar=0; /* Current linenumber of parameter file */
4396: int itimes;
4397: int NDIM=2;
1.128 brouard 4398: int vpopbased=0;
1.126 brouard 4399:
4400: char ca[32], cb[32], cc[32];
4401: char dummy[]=" ";
4402: /* FILE *fichtm; *//* Html File */
4403: /* FILE *ficgp;*/ /*Gnuplot File */
4404: struct stat info;
4405: double agedeb, agefin,hf;
4406: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4407:
4408: double fret;
4409: double **xi,tmp,delta;
4410:
4411: double dum; /* Dummy variable */
4412: double ***p3mat;
4413: double ***mobaverage;
4414: int *indx;
4415: char line[MAXLINE], linepar[MAXLINE];
4416: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4417: char pathr[MAXLINE], pathimach[MAXLINE];
4418: char **bp, *tok, *val; /* pathtot */
4419: int firstobs=1, lastobs=10;
4420: int sdeb, sfin; /* Status at beginning and end */
4421: int c, h , cpt,l;
4422: int ju,jl, mi;
4423: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4424: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4425: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4426: int mobilav=0,popforecast=0;
4427: int hstepm, nhstepm;
4428: int agemortsup;
4429: float sumlpop=0.;
4430: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4431: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4432:
4433: double bage, fage, age, agelim, agebase;
4434: double ftolpl=FTOL;
4435: double **prlim;
4436: double *severity;
4437: double ***param; /* Matrix of parameters */
4438: double *p;
4439: double **matcov; /* Matrix of covariance */
4440: double ***delti3; /* Scale */
4441: double *delti; /* Scale */
4442: double ***eij, ***vareij;
4443: double **varpl; /* Variances of prevalence limits by age */
4444: double *epj, vepp;
4445: double kk1, kk2;
4446: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4447: double **ximort;
4448: char *alph[]={"a","a","b","c","d","e"}, str[4];
4449: int *dcwave;
4450:
4451: char z[1]="c", occ;
4452:
4453: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4454: char *strt, strtend[80];
4455: char *stratrunc;
4456: int lstra;
4457:
4458: long total_usecs;
4459:
4460: /* setlocale (LC_ALL, ""); */
4461: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4462: /* textdomain (PACKAGE); */
4463: /* setlocale (LC_CTYPE, ""); */
4464: /* setlocale (LC_MESSAGES, ""); */
4465:
4466: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4467: (void) gettimeofday(&start_time,&tzp);
4468: curr_time=start_time;
4469: tm = *localtime(&start_time.tv_sec);
4470: tmg = *gmtime(&start_time.tv_sec);
4471: strcpy(strstart,asctime(&tm));
4472:
4473: /* printf("Localtime (at start)=%s",strstart); */
4474: /* tp.tv_sec = tp.tv_sec +86400; */
4475: /* tm = *localtime(&start_time.tv_sec); */
4476: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4477: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4478: /* tmg.tm_hour=tmg.tm_hour + 1; */
4479: /* tp.tv_sec = mktime(&tmg); */
4480: /* strt=asctime(&tmg); */
4481: /* printf("Time(after) =%s",strstart); */
4482: /* (void) time (&time_value);
4483: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4484: * tm = *localtime(&time_value);
4485: * strstart=asctime(&tm);
4486: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4487: */
4488:
4489: nberr=0; /* Number of errors and warnings */
4490: nbwarn=0;
4491: getcwd(pathcd, size);
4492:
4493: printf("\n%s\n%s",version,fullversion);
4494: if(argc <=1){
4495: printf("\nEnter the parameter file name: ");
4496: fgets(pathr,FILENAMELENGTH,stdin);
4497: i=strlen(pathr);
4498: if(pathr[i-1]=='\n')
4499: pathr[i-1]='\0';
4500: for (tok = pathr; tok != NULL; ){
4501: printf("Pathr |%s|\n",pathr);
4502: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4503: printf("val= |%s| pathr=%s\n",val,pathr);
4504: strcpy (pathtot, val);
4505: if(pathr[0] == '\0') break; /* Dirty */
4506: }
4507: }
4508: else{
4509: strcpy(pathtot,argv[1]);
4510: }
4511: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4512: /*cygwin_split_path(pathtot,path,optionfile);
4513: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4514: /* cutv(path,optionfile,pathtot,'\\');*/
4515:
4516: /* Split argv[0], imach program to get pathimach */
4517: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4518: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4519: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4520: /* strcpy(pathimach,argv[0]); */
4521: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4522: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4523: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4524: chdir(path); /* Can be a relative path */
4525: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4526: printf("Current directory %s!\n",pathcd);
4527: strcpy(command,"mkdir ");
4528: strcat(command,optionfilefiname);
4529: if((outcmd=system(command)) != 0){
4530: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4531: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4532: /* fclose(ficlog); */
4533: /* exit(1); */
4534: }
4535: /* if((imk=mkdir(optionfilefiname))<0){ */
4536: /* perror("mkdir"); */
4537: /* } */
4538:
4539: /*-------- arguments in the command line --------*/
4540:
4541: /* Log file */
4542: strcat(filelog, optionfilefiname);
4543: strcat(filelog,".log"); /* */
4544: if((ficlog=fopen(filelog,"w"))==NULL) {
4545: printf("Problem with logfile %s\n",filelog);
4546: goto end;
4547: }
4548: fprintf(ficlog,"Log filename:%s\n",filelog);
4549: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4550: fprintf(ficlog,"\nEnter the parameter file name: \n");
4551: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4552: path=%s \n\
4553: optionfile=%s\n\
4554: optionfilext=%s\n\
4555: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4556:
4557: printf("Local time (at start):%s",strstart);
4558: fprintf(ficlog,"Local time (at start): %s",strstart);
4559: fflush(ficlog);
4560: /* (void) gettimeofday(&curr_time,&tzp); */
4561: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4562:
4563: /* */
4564: strcpy(fileres,"r");
4565: strcat(fileres, optionfilefiname);
4566: strcat(fileres,".txt"); /* Other files have txt extension */
4567:
4568: /*---------arguments file --------*/
4569:
4570: if((ficpar=fopen(optionfile,"r"))==NULL) {
4571: printf("Problem with optionfile %s\n",optionfile);
4572: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4573: fflush(ficlog);
4574: goto end;
4575: }
4576:
4577:
4578:
4579: strcpy(filereso,"o");
4580: strcat(filereso,fileres);
4581: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4582: printf("Problem with Output resultfile: %s\n", filereso);
4583: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4584: fflush(ficlog);
4585: goto end;
4586: }
4587:
4588: /* Reads comments: lines beginning with '#' */
4589: numlinepar=0;
4590: while((c=getc(ficpar))=='#' && c!= EOF){
4591: ungetc(c,ficpar);
4592: fgets(line, MAXLINE, ficpar);
4593: numlinepar++;
4594: puts(line);
4595: fputs(line,ficparo);
4596: fputs(line,ficlog);
4597: }
4598: ungetc(c,ficpar);
4599:
4600: 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);
4601: numlinepar++;
4602: 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);
4603: 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);
4604: 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);
4605: fflush(ficlog);
4606: while((c=getc(ficpar))=='#' && c!= EOF){
4607: ungetc(c,ficpar);
4608: fgets(line, MAXLINE, ficpar);
4609: numlinepar++;
4610: puts(line);
4611: fputs(line,ficparo);
4612: fputs(line,ficlog);
4613: }
4614: ungetc(c,ficpar);
4615:
4616:
4617: covar=matrix(0,NCOVMAX,1,n);
4618: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4619: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4620:
4621: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
4622: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4623: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4624:
4625: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4626: delti=delti3[1][1];
4627: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4628: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4629: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4630: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4631: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4632: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4633: fclose (ficparo);
4634: fclose (ficlog);
4635: goto end;
4636: exit(0);
4637: }
4638: else if(mle==-3) {
4639: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4640: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4641: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4642: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4643: matcov=matrix(1,npar,1,npar);
4644: }
4645: else{
4646: /* Read guess parameters */
4647: /* Reads comments: lines beginning with '#' */
4648: while((c=getc(ficpar))=='#' && c!= EOF){
4649: ungetc(c,ficpar);
4650: fgets(line, MAXLINE, ficpar);
4651: numlinepar++;
4652: puts(line);
4653: fputs(line,ficparo);
4654: fputs(line,ficlog);
4655: }
4656: ungetc(c,ficpar);
4657:
4658: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4659: for(i=1; i <=nlstate; i++){
4660: j=0;
4661: for(jj=1; jj <=nlstate+ndeath; jj++){
4662: if(jj==i) continue;
4663: j++;
4664: fscanf(ficpar,"%1d%1d",&i1,&j1);
4665: if ((i1 != i) && (j1 != j)){
4666: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4667: It might be a problem of design; if ncovcol and the model are correct\n \
4668: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4669: exit(1);
4670: }
4671: fprintf(ficparo,"%1d%1d",i1,j1);
4672: if(mle==1)
4673: printf("%1d%1d",i,j);
4674: fprintf(ficlog,"%1d%1d",i,j);
4675: for(k=1; k<=ncovmodel;k++){
4676: fscanf(ficpar," %lf",¶m[i][j][k]);
4677: if(mle==1){
4678: printf(" %lf",param[i][j][k]);
4679: fprintf(ficlog," %lf",param[i][j][k]);
4680: }
4681: else
4682: fprintf(ficlog," %lf",param[i][j][k]);
4683: fprintf(ficparo," %lf",param[i][j][k]);
4684: }
4685: fscanf(ficpar,"\n");
4686: numlinepar++;
4687: if(mle==1)
4688: printf("\n");
4689: fprintf(ficlog,"\n");
4690: fprintf(ficparo,"\n");
4691: }
4692: }
4693: fflush(ficlog);
4694:
4695: p=param[1][1];
4696:
4697: /* Reads comments: lines beginning with '#' */
4698: while((c=getc(ficpar))=='#' && c!= EOF){
4699: ungetc(c,ficpar);
4700: fgets(line, MAXLINE, ficpar);
4701: numlinepar++;
4702: puts(line);
4703: fputs(line,ficparo);
4704: fputs(line,ficlog);
4705: }
4706: ungetc(c,ficpar);
4707:
4708: for(i=1; i <=nlstate; i++){
4709: for(j=1; j <=nlstate+ndeath-1; j++){
4710: fscanf(ficpar,"%1d%1d",&i1,&j1);
4711: if ((i1-i)*(j1-j)!=0){
4712: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4713: exit(1);
4714: }
4715: printf("%1d%1d",i,j);
4716: fprintf(ficparo,"%1d%1d",i1,j1);
4717: fprintf(ficlog,"%1d%1d",i1,j1);
4718: for(k=1; k<=ncovmodel;k++){
4719: fscanf(ficpar,"%le",&delti3[i][j][k]);
4720: printf(" %le",delti3[i][j][k]);
4721: fprintf(ficparo," %le",delti3[i][j][k]);
4722: fprintf(ficlog," %le",delti3[i][j][k]);
4723: }
4724: fscanf(ficpar,"\n");
4725: numlinepar++;
4726: printf("\n");
4727: fprintf(ficparo,"\n");
4728: fprintf(ficlog,"\n");
4729: }
4730: }
4731: fflush(ficlog);
4732:
4733: delti=delti3[1][1];
4734:
4735:
4736: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4737:
4738: /* Reads comments: lines beginning with '#' */
4739: while((c=getc(ficpar))=='#' && c!= EOF){
4740: ungetc(c,ficpar);
4741: fgets(line, MAXLINE, ficpar);
4742: numlinepar++;
4743: puts(line);
4744: fputs(line,ficparo);
4745: fputs(line,ficlog);
4746: }
4747: ungetc(c,ficpar);
4748:
4749: matcov=matrix(1,npar,1,npar);
4750: for(i=1; i <=npar; i++){
4751: fscanf(ficpar,"%s",&str);
4752: if(mle==1)
4753: printf("%s",str);
4754: fprintf(ficlog,"%s",str);
4755: fprintf(ficparo,"%s",str);
4756: for(j=1; j <=i; j++){
4757: fscanf(ficpar," %le",&matcov[i][j]);
4758: if(mle==1){
4759: printf(" %.5le",matcov[i][j]);
4760: }
4761: fprintf(ficlog," %.5le",matcov[i][j]);
4762: fprintf(ficparo," %.5le",matcov[i][j]);
4763: }
4764: fscanf(ficpar,"\n");
4765: numlinepar++;
4766: if(mle==1)
4767: printf("\n");
4768: fprintf(ficlog,"\n");
4769: fprintf(ficparo,"\n");
4770: }
4771: for(i=1; i <=npar; i++)
4772: for(j=i+1;j<=npar;j++)
4773: matcov[i][j]=matcov[j][i];
4774:
4775: if(mle==1)
4776: printf("\n");
4777: fprintf(ficlog,"\n");
4778:
4779: fflush(ficlog);
4780:
4781: /*-------- Rewriting parameter file ----------*/
4782: strcpy(rfileres,"r"); /* "Rparameterfile */
4783: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4784: strcat(rfileres,"."); /* */
4785: strcat(rfileres,optionfilext); /* Other files have txt extension */
4786: if((ficres =fopen(rfileres,"w"))==NULL) {
4787: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4788: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4789: }
4790: fprintf(ficres,"#%s\n",version);
4791: } /* End of mle != -3 */
4792:
4793: /*-------- data file ----------*/
4794: if((fic=fopen(datafile,"r"))==NULL) {
4795: printf("Problem while opening datafile: %s\n", datafile);goto end;
4796: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4797: }
4798:
4799: n= lastobs;
4800: severity = vector(1,maxwav);
4801: outcome=imatrix(1,maxwav+1,1,n);
4802: num=lvector(1,n);
4803: moisnais=vector(1,n);
4804: annais=vector(1,n);
4805: moisdc=vector(1,n);
4806: andc=vector(1,n);
4807: agedc=vector(1,n);
4808: cod=ivector(1,n);
4809: weight=vector(1,n);
4810: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4811: mint=matrix(1,maxwav,1,n);
4812: anint=matrix(1,maxwav,1,n);
4813: s=imatrix(1,maxwav+1,1,n);
4814: tab=ivector(1,NCOVMAX);
4815: ncodemax=ivector(1,8);
4816:
4817: i=1;
4818: linei=0;
4819: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4820: linei=linei+1;
4821: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4822: if(line[j] == '\t')
4823: line[j] = ' ';
4824: }
4825: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4826: ;
4827: };
4828: line[j+1]=0; /* Trims blanks at end of line */
4829: if(line[0]=='#'){
4830: fprintf(ficlog,"Comment line\n%s\n",line);
4831: printf("Comment line\n%s\n",line);
4832: continue;
4833: }
4834:
4835: for (j=maxwav;j>=1;j--){
4836: cutv(stra, strb,line,' ');
4837: errno=0;
4838: lval=strtol(strb,&endptr,10);
4839: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4840: if( strb[0]=='\0' || (*endptr != '\0')){
4841: 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);
4842: exit(1);
4843: }
4844: s[j][i]=lval;
4845:
4846: strcpy(line,stra);
4847: cutv(stra, strb,line,' ');
4848: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4849: }
4850: else if(iout=sscanf(strb,"%s.") != 0){
4851: month=99;
4852: year=9999;
4853: }else{
4854: 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);
4855: exit(1);
4856: }
4857: anint[j][i]= (double) year;
4858: mint[j][i]= (double)month;
4859: strcpy(line,stra);
4860: } /* ENd Waves */
4861:
4862: cutv(stra, strb,line,' ');
4863: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4864: }
4865: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4866: month=99;
4867: year=9999;
4868: }else{
4869: 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);
4870: exit(1);
4871: }
4872: andc[i]=(double) year;
4873: moisdc[i]=(double) month;
4874: strcpy(line,stra);
4875:
4876: cutv(stra, strb,line,' ');
4877: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4878: }
4879: else if(iout=sscanf(strb,"%s.") != 0){
4880: month=99;
4881: year=9999;
4882: }else{
4883: 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);
4884: exit(1);
4885: }
4886: annais[i]=(double)(year);
4887: moisnais[i]=(double)(month);
4888: strcpy(line,stra);
4889:
4890: cutv(stra, strb,line,' ');
4891: errno=0;
4892: dval=strtod(strb,&endptr);
4893: if( strb[0]=='\0' || (*endptr != '\0')){
4894: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4895: exit(1);
4896: }
4897: weight[i]=dval;
4898: strcpy(line,stra);
4899:
4900: for (j=ncovcol;j>=1;j--){
4901: cutv(stra, strb,line,' ');
4902: errno=0;
4903: lval=strtol(strb,&endptr,10);
4904: if( strb[0]=='\0' || (*endptr != '\0')){
4905: 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);
4906: exit(1);
4907: }
4908: if(lval <-1 || lval >1){
4909: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4910: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4911: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4912: For example, for multinomial values like 1, 2 and 3,\n \
4913: build V1=0 V2=0 for the reference value (1),\n \
4914: V1=1 V2=0 for (2) \n \
4915: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4916: output of IMaCh is often meaningless.\n \
4917: Exiting.\n",lval,linei, i,line,j);
1.129 ! lievre 4918: goto end;
1.126 brouard 4919: }
4920: covar[j][i]=(double)(lval);
4921: strcpy(line,stra);
1.129 ! lievre 4922: }
1.126 brouard 4923: lstra=strlen(stra);
1.129 ! lievre 4924:
1.126 brouard 4925: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4926: stratrunc = &(stra[lstra-9]);
4927: num[i]=atol(stratrunc);
4928: }
4929: else
4930: num[i]=atol(stra);
4931: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4932: 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;}*/
4933:
4934: i=i+1;
4935: } /* End loop reading data */
4936: fclose(fic);
4937: /* printf("ii=%d", ij);
4938: scanf("%d",i);*/
4939: imx=i-1; /* Number of individuals */
4940:
4941: /* for (i=1; i<=imx; i++){
4942: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
4943: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
4944: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
4945: }*/
4946: /* for (i=1; i<=imx; i++){
4947: if (s[4][i]==9) s[4][i]=-1;
4948: 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]));}*/
4949:
4950: /* for (i=1; i<=imx; i++) */
4951:
4952: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
4953: else weight[i]=1;*/
4954:
4955: /* Calculation of the number of parameters from char model */
4956: Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
4957: Tprod=ivector(1,15);
4958: Tvaraff=ivector(1,15);
4959: Tvard=imatrix(1,15,1,2);
4960: Tage=ivector(1,15);
4961:
4962: if (strlen(model) >1){ /* If there is at least 1 covariate */
4963: j=0, j1=0, k1=1, k2=1;
4964: j=nbocc(model,'+'); /* j=Number of '+' */
4965: j1=nbocc(model,'*'); /* j1=Number of '*' */
4966: cptcovn=j+1;
4967: cptcovprod=j1; /*Number of products */
4968:
4969: strcpy(modelsav,model);
4970: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
4971: printf("Error. Non available option model=%s ",model);
4972: fprintf(ficlog,"Error. Non available option model=%s ",model);
4973: goto end;
4974: }
4975:
4976: /* This loop fills the array Tvar from the string 'model'.*/
4977:
4978: for(i=(j+1); i>=1;i--){
4979: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
4980: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
4981: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
4982: /*scanf("%d",i);*/
4983: if (strchr(strb,'*')) { /* Model includes a product */
4984: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
4985: if (strcmp(strc,"age")==0) { /* Vn*age */
4986: cptcovprod--;
4987: cutv(strb,stre,strd,'V');
4988: Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
4989: cptcovage++;
4990: Tage[cptcovage]=i;
4991: /*printf("stre=%s ", stre);*/
4992: }
4993: else if (strcmp(strd,"age")==0) { /* or age*Vn */
4994: cptcovprod--;
4995: cutv(strb,stre,strc,'V');
4996: Tvar[i]=atoi(stre);
4997: cptcovage++;
4998: Tage[cptcovage]=i;
4999: }
5000: else { /* Age is not in the model */
5001: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
5002: Tvar[i]=ncovcol+k1;
5003: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
5004: Tprod[k1]=i;
5005: Tvard[k1][1]=atoi(strc); /* m*/
5006: Tvard[k1][2]=atoi(stre); /* n */
5007: Tvar[cptcovn+k2]=Tvard[k1][1];
5008: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5009: for (k=1; k<=lastobs;k++)
5010: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5011: k1++;
5012: k2=k2+2;
5013: }
5014: }
5015: else { /* no more sum */
5016: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5017: /* scanf("%d",i);*/
5018: cutv(strd,strc,strb,'V');
5019: Tvar[i]=atoi(strc);
5020: }
5021: strcpy(modelsav,stra);
5022: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5023: scanf("%d",i);*/
5024: } /* end of loop + */
5025: } /* end model */
5026:
5027: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5028: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5029:
5030: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5031: printf("cptcovprod=%d ", cptcovprod);
5032: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5033:
5034: scanf("%d ",i);*/
5035:
5036: /* if(mle==1){*/
5037: if (weightopt != 1) { /* Maximisation without weights*/
5038: for(i=1;i<=n;i++) weight[i]=1.0;
5039: }
5040: /*-calculation of age at interview from date of interview and age at death -*/
5041: agev=matrix(1,maxwav,1,imx);
5042:
5043: for (i=1; i<=imx; i++) {
5044: for(m=2; (m<= maxwav); m++) {
5045: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5046: anint[m][i]=9999;
5047: s[m][i]=-1;
5048: }
5049: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5050: nberr++;
5051: 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);
5052: 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);
5053: s[m][i]=-1;
5054: }
5055: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5056: nberr++;
5057: 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]);
5058: 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]);
5059: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5060: }
5061: }
5062: }
5063:
5064: for (i=1; i<=imx; i++) {
5065: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5066: for(m=firstpass; (m<= lastpass); m++){
5067: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5068: if (s[m][i] >= nlstate+1) {
5069: if(agedc[i]>0)
5070: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5071: agev[m][i]=agedc[i];
5072: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5073: else {
5074: if ((int)andc[i]!=9999){
5075: nbwarn++;
5076: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5077: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5078: agev[m][i]=-1;
5079: }
5080: }
5081: }
5082: else if(s[m][i] !=9){ /* Standard case, age in fractional
5083: years but with the precision of a month */
5084: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5085: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5086: agev[m][i]=1;
5087: else if(agev[m][i] <agemin){
5088: agemin=agev[m][i];
5089: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5090: }
5091: else if(agev[m][i] >agemax){
5092: agemax=agev[m][i];
5093: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5094: }
5095: /*agev[m][i]=anint[m][i]-annais[i];*/
5096: /* agev[m][i] = age[i]+2*m;*/
5097: }
5098: else { /* =9 */
5099: agev[m][i]=1;
5100: s[m][i]=-1;
5101: }
5102: }
5103: else /*= 0 Unknown */
5104: agev[m][i]=1;
5105: }
5106:
5107: }
5108: for (i=1; i<=imx; i++) {
5109: for(m=firstpass; (m<=lastpass); m++){
5110: if (s[m][i] > (nlstate+ndeath)) {
5111: nberr++;
5112: 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);
5113: 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);
5114: goto end;
5115: }
5116: }
5117: }
5118:
5119: /*for (i=1; i<=imx; i++){
5120: for (m=firstpass; (m<lastpass); m++){
5121: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5122: }
5123:
5124: }*/
5125:
5126:
5127: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5128: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5129:
5130: agegomp=(int)agemin;
5131: free_vector(severity,1,maxwav);
5132: free_imatrix(outcome,1,maxwav+1,1,n);
5133: free_vector(moisnais,1,n);
5134: free_vector(annais,1,n);
5135: /* free_matrix(mint,1,maxwav,1,n);
5136: free_matrix(anint,1,maxwav,1,n);*/
5137: free_vector(moisdc,1,n);
5138: free_vector(andc,1,n);
5139:
5140:
5141: wav=ivector(1,imx);
5142: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5143: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5144: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5145:
5146: /* Concatenates waves */
5147: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5148:
5149: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5150:
5151: Tcode=ivector(1,100);
5152: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5153: ncodemax[1]=1;
5154: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5155:
5156: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5157: the estimations*/
5158: h=0;
5159: m=pow(2,cptcoveff);
5160:
5161: for(k=1;k<=cptcoveff; k++){
5162: for(i=1; i <=(m/pow(2,k));i++){
5163: for(j=1; j <= ncodemax[k]; j++){
5164: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
5165: h++;
5166: if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5167: /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
5168: }
5169: }
5170: }
5171: }
5172: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5173: codtab[1][2]=1;codtab[2][2]=2; */
5174: /* for(i=1; i <=m ;i++){
5175: for(k=1; k <=cptcovn; k++){
5176: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5177: }
5178: printf("\n");
5179: }
5180: scanf("%d",i);*/
5181:
5182: /*------------ gnuplot -------------*/
5183: strcpy(optionfilegnuplot,optionfilefiname);
5184: if(mle==-3)
5185: strcat(optionfilegnuplot,"-mort");
5186: strcat(optionfilegnuplot,".gp");
5187:
5188: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5189: printf("Problem with file %s",optionfilegnuplot);
5190: }
5191: else{
5192: fprintf(ficgp,"\n# %s\n", version);
5193: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5194: fprintf(ficgp,"set missing 'NaNq'\n");
5195: }
5196: /* fclose(ficgp);*/
5197: /*--------- index.htm --------*/
5198:
5199: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5200: if(mle==-3)
5201: strcat(optionfilehtm,"-mort");
5202: strcat(optionfilehtm,".htm");
5203: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5204: printf("Problem with %s \n",optionfilehtm), exit(0);
5205: }
5206:
5207: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5208: strcat(optionfilehtmcov,"-cov.htm");
5209: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5210: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5211: }
5212: else{
5213: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5214: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5215: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5216: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5217: }
5218:
5219: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5220: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5221: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5222: \n\
5223: <hr size=\"2\" color=\"#EC5E5E\">\
5224: <ul><li><h4>Parameter files</h4>\n\
5225: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5226: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5227: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5228: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5229: - Date and time at start: %s</ul>\n",\
5230: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5231: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5232: fileres,fileres,\
5233: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5234: fflush(fichtm);
5235:
5236: strcpy(pathr,path);
5237: strcat(pathr,optionfilefiname);
5238: chdir(optionfilefiname); /* Move to directory named optionfile */
5239:
5240: /* Calculates basic frequencies. Computes observed prevalence at single age
5241: and prints on file fileres'p'. */
5242: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5243:
5244: fprintf(fichtm,"\n");
5245: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5246: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5247: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5248: imx,agemin,agemax,jmin,jmax,jmean);
5249: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5250: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5251: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5252: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5253: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5254:
5255:
5256: /* For Powell, parameters are in a vector p[] starting at p[1]
5257: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5258: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5259:
5260: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5261:
5262: if (mle==-3){
5263: ximort=matrix(1,NDIM,1,NDIM);
5264: cens=ivector(1,n);
5265: ageexmed=vector(1,n);
5266: agecens=vector(1,n);
5267: dcwave=ivector(1,n);
5268:
5269: for (i=1; i<=imx; i++){
5270: dcwave[i]=-1;
5271: for (m=firstpass; m<=lastpass; m++)
5272: if (s[m][i]>nlstate) {
5273: dcwave[i]=m;
5274: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5275: break;
5276: }
5277: }
5278:
5279: for (i=1; i<=imx; i++) {
5280: if (wav[i]>0){
5281: ageexmed[i]=agev[mw[1][i]][i];
5282: j=wav[i];
5283: agecens[i]=1.;
5284:
5285: if (ageexmed[i]> 1 && wav[i] > 0){
5286: agecens[i]=agev[mw[j][i]][i];
5287: cens[i]= 1;
5288: }else if (ageexmed[i]< 1)
5289: cens[i]= -1;
5290: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5291: cens[i]=0 ;
5292: }
5293: else cens[i]=-1;
5294: }
5295:
5296: for (i=1;i<=NDIM;i++) {
5297: for (j=1;j<=NDIM;j++)
5298: ximort[i][j]=(i == j ? 1.0 : 0.0);
5299: }
5300:
5301: p[1]=0.0268; p[NDIM]=0.083;
5302: /*printf("%lf %lf", p[1], p[2]);*/
5303:
5304:
5305: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5306: strcpy(filerespow,"pow-mort");
5307: strcat(filerespow,fileres);
5308: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5309: printf("Problem with resultfile: %s\n", filerespow);
5310: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5311: }
5312: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5313: /* for (i=1;i<=nlstate;i++)
5314: for(j=1;j<=nlstate+ndeath;j++)
5315: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5316: */
5317: fprintf(ficrespow,"\n");
5318:
5319: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5320: fclose(ficrespow);
5321:
5322: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5323:
5324: for(i=1; i <=NDIM; i++)
5325: for(j=i+1;j<=NDIM;j++)
5326: matcov[i][j]=matcov[j][i];
5327:
5328: printf("\nCovariance matrix\n ");
5329: for(i=1; i <=NDIM; i++) {
5330: for(j=1;j<=NDIM;j++){
5331: printf("%f ",matcov[i][j]);
5332: }
5333: printf("\n ");
5334: }
5335:
5336: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5337: for (i=1;i<=NDIM;i++)
5338: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5339:
5340: lsurv=vector(1,AGESUP);
5341: lpop=vector(1,AGESUP);
5342: tpop=vector(1,AGESUP);
5343: lsurv[agegomp]=100000;
5344:
5345: for (k=agegomp;k<=AGESUP;k++) {
5346: agemortsup=k;
5347: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5348: }
5349:
5350: for (k=agegomp;k<agemortsup;k++)
5351: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5352:
5353: for (k=agegomp;k<agemortsup;k++){
5354: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5355: sumlpop=sumlpop+lpop[k];
5356: }
5357:
5358: tpop[agegomp]=sumlpop;
5359: for (k=agegomp;k<(agemortsup-3);k++){
5360: /* tpop[k+1]=2;*/
5361: tpop[k+1]=tpop[k]-lpop[k];
5362: }
5363:
5364:
5365: printf("\nAge lx qx dx Lx Tx e(x)\n");
5366: for (k=agegomp;k<(agemortsup-2);k++)
5367: 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]);
5368:
5369:
5370: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5371: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5372:
5373: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5374: stepm, weightopt,\
5375: model,imx,p,matcov,agemortsup);
5376:
5377: free_vector(lsurv,1,AGESUP);
5378: free_vector(lpop,1,AGESUP);
5379: free_vector(tpop,1,AGESUP);
5380: } /* Endof if mle==-3 */
5381:
5382: else{ /* For mle >=1 */
5383:
5384: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5385: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5386: for (k=1; k<=npar;k++)
5387: printf(" %d %8.5f",k,p[k]);
5388: printf("\n");
5389: globpr=1; /* to print the contributions */
5390: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5391: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5392: for (k=1; k<=npar;k++)
5393: printf(" %d %8.5f",k,p[k]);
5394: printf("\n");
5395: if(mle>=1){ /* Could be 1 or 2 */
5396: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5397: }
5398:
5399: /*--------- results files --------------*/
5400: 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);
5401:
5402:
5403: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5404: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5405: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5406: for(i=1,jk=1; i <=nlstate; i++){
5407: for(k=1; k <=(nlstate+ndeath); k++){
5408: if (k != i) {
5409: printf("%d%d ",i,k);
5410: fprintf(ficlog,"%d%d ",i,k);
5411: fprintf(ficres,"%1d%1d ",i,k);
5412: for(j=1; j <=ncovmodel; j++){
5413: printf("%lf ",p[jk]);
5414: fprintf(ficlog,"%lf ",p[jk]);
5415: fprintf(ficres,"%lf ",p[jk]);
5416: jk++;
5417: }
5418: printf("\n");
5419: fprintf(ficlog,"\n");
5420: fprintf(ficres,"\n");
5421: }
5422: }
5423: }
5424: if(mle!=0){
5425: /* Computing hessian and covariance matrix */
5426: ftolhess=ftol; /* Usually correct */
5427: hesscov(matcov, p, npar, delti, ftolhess, func);
5428: }
5429: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5430: printf("# Scales (for hessian or gradient estimation)\n");
5431: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5432: for(i=1,jk=1; i <=nlstate; i++){
5433: for(j=1; j <=nlstate+ndeath; j++){
5434: if (j!=i) {
5435: fprintf(ficres,"%1d%1d",i,j);
5436: printf("%1d%1d",i,j);
5437: fprintf(ficlog,"%1d%1d",i,j);
5438: for(k=1; k<=ncovmodel;k++){
5439: printf(" %.5e",delti[jk]);
5440: fprintf(ficlog," %.5e",delti[jk]);
5441: fprintf(ficres," %.5e",delti[jk]);
5442: jk++;
5443: }
5444: printf("\n");
5445: fprintf(ficlog,"\n");
5446: fprintf(ficres,"\n");
5447: }
5448: }
5449: }
5450:
5451: 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");
5452: if(mle>=1)
5453: 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");
5454: 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");
5455: /* # 121 Var(a12)\n\ */
5456: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5457: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5458: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5459: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5460: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5461: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5462: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5463:
5464:
5465: /* Just to have a covariance matrix which will be more understandable
5466: even is we still don't want to manage dictionary of variables
5467: */
5468: for(itimes=1;itimes<=2;itimes++){
5469: jj=0;
5470: for(i=1; i <=nlstate; i++){
5471: for(j=1; j <=nlstate+ndeath; j++){
5472: if(j==i) continue;
5473: for(k=1; k<=ncovmodel;k++){
5474: jj++;
5475: ca[0]= k+'a'-1;ca[1]='\0';
5476: if(itimes==1){
5477: if(mle>=1)
5478: printf("#%1d%1d%d",i,j,k);
5479: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5480: fprintf(ficres,"#%1d%1d%d",i,j,k);
5481: }else{
5482: if(mle>=1)
5483: printf("%1d%1d%d",i,j,k);
5484: fprintf(ficlog,"%1d%1d%d",i,j,k);
5485: fprintf(ficres,"%1d%1d%d",i,j,k);
5486: }
5487: ll=0;
5488: for(li=1;li <=nlstate; li++){
5489: for(lj=1;lj <=nlstate+ndeath; lj++){
5490: if(lj==li) continue;
5491: for(lk=1;lk<=ncovmodel;lk++){
5492: ll++;
5493: if(ll<=jj){
5494: cb[0]= lk +'a'-1;cb[1]='\0';
5495: if(ll<jj){
5496: if(itimes==1){
5497: if(mle>=1)
5498: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5499: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5500: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5501: }else{
5502: if(mle>=1)
5503: printf(" %.5e",matcov[jj][ll]);
5504: fprintf(ficlog," %.5e",matcov[jj][ll]);
5505: fprintf(ficres," %.5e",matcov[jj][ll]);
5506: }
5507: }else{
5508: if(itimes==1){
5509: if(mle>=1)
5510: printf(" Var(%s%1d%1d)",ca,i,j);
5511: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5512: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5513: }else{
5514: if(mle>=1)
5515: printf(" %.5e",matcov[jj][ll]);
5516: fprintf(ficlog," %.5e",matcov[jj][ll]);
5517: fprintf(ficres," %.5e",matcov[jj][ll]);
5518: }
5519: }
5520: }
5521: } /* end lk */
5522: } /* end lj */
5523: } /* end li */
5524: if(mle>=1)
5525: printf("\n");
5526: fprintf(ficlog,"\n");
5527: fprintf(ficres,"\n");
5528: numlinepar++;
5529: } /* end k*/
5530: } /*end j */
5531: } /* end i */
5532: } /* end itimes */
5533:
5534: fflush(ficlog);
5535: fflush(ficres);
5536:
5537: while((c=getc(ficpar))=='#' && c!= EOF){
5538: ungetc(c,ficpar);
5539: fgets(line, MAXLINE, ficpar);
5540: puts(line);
5541: fputs(line,ficparo);
5542: }
5543: ungetc(c,ficpar);
5544:
5545: estepm=0;
5546: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5547: if (estepm==0 || estepm < stepm) estepm=stepm;
5548: if (fage <= 2) {
5549: bage = ageminpar;
5550: fage = agemaxpar;
5551: }
5552:
5553: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5554: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5555: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5556:
5557: while((c=getc(ficpar))=='#' && c!= EOF){
5558: ungetc(c,ficpar);
5559: fgets(line, MAXLINE, ficpar);
5560: puts(line);
5561: fputs(line,ficparo);
5562: }
5563: ungetc(c,ficpar);
5564:
5565: 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);
5566: 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);
5567: 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);
5568: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5569: 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);
5570:
5571: while((c=getc(ficpar))=='#' && c!= EOF){
5572: ungetc(c,ficpar);
5573: fgets(line, MAXLINE, ficpar);
5574: puts(line);
5575: fputs(line,ficparo);
5576: }
5577: ungetc(c,ficpar);
5578:
5579:
5580: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5581: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5582:
5583: fscanf(ficpar,"pop_based=%d\n",&popbased);
5584: fprintf(ficparo,"pop_based=%d\n",popbased);
5585: fprintf(ficres,"pop_based=%d\n",popbased);
5586:
5587: while((c=getc(ficpar))=='#' && c!= EOF){
5588: ungetc(c,ficpar);
5589: fgets(line, MAXLINE, ficpar);
5590: puts(line);
5591: fputs(line,ficparo);
5592: }
5593: ungetc(c,ficpar);
5594:
5595: 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);
5596: 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);
5597: 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);
5598: 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);
5599: 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);
5600: /* day and month of proj2 are not used but only year anproj2.*/
5601:
5602:
5603:
5604: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5605: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5606:
5607: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5608: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5609:
5610: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5611: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5612: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5613:
5614: /*------------ free_vector -------------*/
5615: /* chdir(path); */
5616:
5617: free_ivector(wav,1,imx);
5618: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5619: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5620: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5621: free_lvector(num,1,n);
5622: free_vector(agedc,1,n);
5623: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5624: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5625: fclose(ficparo);
5626: fclose(ficres);
5627:
5628:
5629: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5630:
5631: strcpy(filerespl,"pl");
5632: strcat(filerespl,fileres);
5633: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5634: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5635: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5636: }
5637: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5638: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5639: pstamp(ficrespl);
5640: fprintf(ficrespl,"# Period (stable) prevalence \n");
5641: fprintf(ficrespl,"#Age ");
5642: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5643: fprintf(ficrespl,"\n");
5644:
5645: prlim=matrix(1,nlstate,1,nlstate);
5646:
5647: agebase=ageminpar;
5648: agelim=agemaxpar;
5649: ftolpl=1.e-10;
5650: i1=cptcoveff;
5651: if (cptcovn < 1){i1=1;}
5652:
5653: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5654: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5655: k=k+1;
5656: /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
5657: fprintf(ficrespl,"\n#******");
5658: printf("\n#******");
5659: fprintf(ficlog,"\n#******");
5660: for(j=1;j<=cptcoveff;j++) {
5661: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5662: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5663: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5664: }
5665: fprintf(ficrespl,"******\n");
5666: printf("******\n");
5667: fprintf(ficlog,"******\n");
5668:
5669: for (age=agebase; age<=agelim; age++){
5670: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5671: fprintf(ficrespl,"%.0f ",age );
5672: for(j=1;j<=cptcoveff;j++)
5673: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5674: for(i=1; i<=nlstate;i++)
5675: fprintf(ficrespl," %.5f", prlim[i][i]);
5676: fprintf(ficrespl,"\n");
5677: }
5678: }
5679: }
5680: fclose(ficrespl);
5681:
5682: /*------------- h Pij x at various ages ------------*/
5683:
5684: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5685: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5686: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5687: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5688: }
5689: printf("Computing pij: result on file '%s' \n", filerespij);
5690: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5691:
5692: stepsize=(int) (stepm+YEARM-1)/YEARM;
5693: /*if (stepm<=24) stepsize=2;*/
5694:
5695: agelim=AGESUP;
5696: hstepm=stepsize*YEARM; /* Every year of age */
5697: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5698:
5699: /* hstepm=1; aff par mois*/
5700: pstamp(ficrespij);
5701: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5702: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5703: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5704: k=k+1;
5705: fprintf(ficrespij,"\n#****** ");
5706: for(j=1;j<=cptcoveff;j++)
5707: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5708: fprintf(ficrespij,"******\n");
5709:
5710: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5711: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5712: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5713:
5714: /* nhstepm=nhstepm*YEARM; aff par mois*/
5715:
5716: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5717: oldm=oldms;savm=savms;
5718: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5719: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5720: for(i=1; i<=nlstate;i++)
5721: for(j=1; j<=nlstate+ndeath;j++)
5722: fprintf(ficrespij," %1d-%1d",i,j);
5723: fprintf(ficrespij,"\n");
5724: for (h=0; h<=nhstepm; h++){
5725: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5726: for(i=1; i<=nlstate;i++)
5727: for(j=1; j<=nlstate+ndeath;j++)
5728: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5729: fprintf(ficrespij,"\n");
5730: }
5731: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5732: fprintf(ficrespij,"\n");
5733: }
5734: }
5735: }
5736:
5737: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5738:
5739: fclose(ficrespij);
5740:
5741: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5742: for(i=1;i<=AGESUP;i++)
5743: for(j=1;j<=NCOVMAX;j++)
5744: for(k=1;k<=NCOVMAX;k++)
5745: probs[i][j][k]=0.;
5746:
5747: /*---------- Forecasting ------------------*/
5748: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5749: if(prevfcast==1){
5750: /* if(stepm ==1){*/
5751: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5752: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5753: /* } */
5754: /* else{ */
5755: /* erreur=108; */
5756: /* 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); */
5757: /* 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); */
5758: /* } */
5759: }
5760:
5761:
1.127 brouard 5762: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5763:
5764: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5765: /* 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",\
5766: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5767: */
1.126 brouard 5768:
1.127 brouard 5769: if (mobilav!=0) {
5770: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5771: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5772: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5773: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5774: }
1.126 brouard 5775: }
5776:
5777:
1.127 brouard 5778: /*---------- Health expectancies, no variances ------------*/
5779:
1.126 brouard 5780: strcpy(filerese,"e");
5781: strcat(filerese,fileres);
5782: if((ficreseij=fopen(filerese,"w"))==NULL) {
5783: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5784: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5785: }
5786: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5787: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.127 brouard 5788: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5789: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5790: k=k+1;
5791: fprintf(ficreseij,"\n#****** ");
5792: for(j=1;j<=cptcoveff;j++) {
5793: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5794: }
5795: fprintf(ficreseij,"******\n");
5796:
5797: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5798: oldm=oldms;savm=savms;
5799: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5800:
5801: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5802: }
5803: }
5804: fclose(ficreseij);
5805:
5806:
5807: /*---------- Health expectancies and variances ------------*/
5808:
5809:
5810: strcpy(filerest,"t");
5811: strcat(filerest,fileres);
5812: if((ficrest=fopen(filerest,"w"))==NULL) {
5813: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5814: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5815: }
5816: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5817: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5818:
1.126 brouard 5819:
5820: strcpy(fileresstde,"stde");
5821: strcat(fileresstde,fileres);
5822: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5823: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5824: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5825: }
5826: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5827: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5828:
5829: strcpy(filerescve,"cve");
5830: strcat(filerescve,fileres);
5831: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5832: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5833: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5834: }
5835: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5836: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5837:
5838: strcpy(fileresv,"v");
5839: strcat(fileresv,fileres);
5840: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5841: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5842: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5843: }
5844: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5845: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5846:
5847: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5848: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5849: k=k+1;
5850: fprintf(ficrest,"\n#****** ");
5851: for(j=1;j<=cptcoveff;j++)
5852: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5853: fprintf(ficrest,"******\n");
5854:
5855: fprintf(ficresstdeij,"\n#****** ");
5856: fprintf(ficrescveij,"\n#****** ");
5857: for(j=1;j<=cptcoveff;j++) {
5858: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5859: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5860: }
5861: fprintf(ficresstdeij,"******\n");
5862: fprintf(ficrescveij,"******\n");
5863:
5864: fprintf(ficresvij,"\n#****** ");
5865: for(j=1;j<=cptcoveff;j++)
5866: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5867: fprintf(ficresvij,"******\n");
5868:
5869: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5870: oldm=oldms;savm=savms;
1.127 brouard 5871: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.126 brouard 5872:
5873: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5874: pstamp(ficrest);
1.128 brouard 5875: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5876: oldm=oldms;savm=savms;
5877: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
5878: if(vpopbased==1)
5879: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
5880: else
5881: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5882: fprintf(ficrest,"# Age e.. (std) ");
5883: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5884: fprintf(ficrest,"\n");
1.126 brouard 5885:
1.128 brouard 5886: epj=vector(1,nlstate+1);
5887: for(age=bage; age <=fage ;age++){
5888: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5889: if (vpopbased==1) {
5890: if(mobilav ==0){
5891: for(i=1; i<=nlstate;i++)
5892: prlim[i][i]=probs[(int)age][i][k];
5893: }else{ /* mobilav */
5894: for(i=1; i<=nlstate;i++)
5895: prlim[i][i]=mobaverage[(int)age][i][k];
5896: }
1.126 brouard 5897: }
5898:
1.128 brouard 5899: fprintf(ficrest," %4.0f",age);
5900: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5901: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5902: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5903: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5904: }
5905: epj[nlstate+1] +=epj[j];
1.126 brouard 5906: }
5907:
1.128 brouard 5908: for(i=1, vepp=0.;i <=nlstate;i++)
5909: for(j=1;j <=nlstate;j++)
5910: vepp += vareij[i][j][(int)age];
5911: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
5912: for(j=1;j <=nlstate;j++){
5913: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
5914: }
5915: fprintf(ficrest,"\n");
1.126 brouard 5916: }
5917: }
5918: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5919: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5920: free_vector(epj,1,nlstate+1);
5921: }
5922: }
5923: free_vector(weight,1,n);
5924: free_imatrix(Tvard,1,15,1,2);
5925: free_imatrix(s,1,maxwav+1,1,n);
5926: free_matrix(anint,1,maxwav,1,n);
5927: free_matrix(mint,1,maxwav,1,n);
5928: free_ivector(cod,1,n);
5929: free_ivector(tab,1,NCOVMAX);
5930: fclose(ficresstdeij);
5931: fclose(ficrescveij);
5932: fclose(ficresvij);
5933: fclose(ficrest);
5934: fclose(ficpar);
5935:
5936: /*------- Variance of period (stable) prevalence------*/
5937:
5938: strcpy(fileresvpl,"vpl");
5939: strcat(fileresvpl,fileres);
5940: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
5941: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
5942: exit(0);
5943: }
5944: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
5945:
5946: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5947: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5948: k=k+1;
5949: fprintf(ficresvpl,"\n#****** ");
5950: for(j=1;j<=cptcoveff;j++)
5951: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5952: fprintf(ficresvpl,"******\n");
5953:
5954: varpl=matrix(1,nlstate,(int) bage, (int) fage);
5955: oldm=oldms;savm=savms;
5956: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
5957: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
5958: }
5959: }
5960:
5961: fclose(ficresvpl);
5962:
5963: /*---------- End : free ----------------*/
5964: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5965: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5966:
5967: } /* mle==-3 arrives here for freeing */
5968: free_matrix(prlim,1,nlstate,1,nlstate);
5969: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
5970: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
5971: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
5972: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
5973: free_matrix(covar,0,NCOVMAX,1,n);
5974: free_matrix(matcov,1,npar,1,npar);
5975: /*free_vector(delti,1,npar);*/
5976: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5977: free_matrix(agev,1,maxwav,1,imx);
5978: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5979:
5980: free_ivector(ncodemax,1,8);
5981: free_ivector(Tvar,1,15);
5982: free_ivector(Tprod,1,15);
5983: free_ivector(Tvaraff,1,15);
5984: free_ivector(Tage,1,15);
5985: free_ivector(Tcode,1,100);
5986:
5987: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
5988: free_imatrix(codtab,1,100,1,10);
5989: fflush(fichtm);
5990: fflush(ficgp);
5991:
5992:
5993: if((nberr >0) || (nbwarn>0)){
5994: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
5995: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
5996: }else{
5997: printf("End of Imach\n");
5998: fprintf(ficlog,"End of Imach\n");
5999: }
6000: printf("See log file on %s\n",filelog);
6001: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6002: (void) gettimeofday(&end_time,&tzp);
6003: tm = *localtime(&end_time.tv_sec);
6004: tmg = *gmtime(&end_time.tv_sec);
6005: strcpy(strtend,asctime(&tm));
6006: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6007: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6008: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6009:
6010: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6011: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6012: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6013: /* printf("Total time was %d uSec.\n", total_usecs);*/
6014: /* if(fileappend(fichtm,optionfilehtm)){ */
6015: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6016: fclose(fichtm);
6017: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6018: fclose(fichtmcov);
6019: fclose(ficgp);
6020: fclose(ficlog);
6021: /*------ End -----------*/
6022:
6023:
6024: printf("Before Current directory %s!\n",pathcd);
6025: if(chdir(pathcd) != 0)
6026: printf("Can't move to directory %s!\n",path);
6027: if(getcwd(pathcd,MAXLINE) > 0)
6028: printf("Current directory %s!\n",pathcd);
6029: /*strcat(plotcmd,CHARSEPARATOR);*/
6030: sprintf(plotcmd,"gnuplot");
6031: #ifndef UNIX
6032: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6033: #endif
6034: if(!stat(plotcmd,&info)){
6035: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6036: if(!stat(getenv("GNUPLOTBIN"),&info)){
6037: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6038: }else
6039: strcpy(pplotcmd,plotcmd);
6040: #ifdef UNIX
6041: strcpy(plotcmd,GNUPLOTPROGRAM);
6042: if(!stat(plotcmd,&info)){
6043: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6044: }else
6045: strcpy(pplotcmd,plotcmd);
6046: #endif
6047: }else
6048: strcpy(pplotcmd,plotcmd);
6049:
6050: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6051: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6052:
6053: if((outcmd=system(plotcmd)) != 0){
6054: printf("\n Problem with gnuplot\n");
6055: }
6056: printf(" Wait...");
6057: while (z[0] != 'q') {
6058: /* chdir(path); */
6059: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6060: scanf("%s",z);
6061: /* if (z[0] == 'c') system("./imach"); */
6062: if (z[0] == 'e') {
6063: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6064: system(optionfilehtm);
6065: }
6066: else if (z[0] == 'g') system(plotcmd);
6067: else if (z[0] == 'q') exit(0);
6068: }
6069: end:
6070: while (z[0] != 'q') {
6071: printf("\nType q for exiting: ");
6072: scanf("%s",z);
6073: }
6074: }
6075:
6076:
6077:
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