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