1: /* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.133 2009/07/06 10:21:25 brouard
5: just nforces
6:
7: Revision 1.132 2009/07/06 08:22:05 brouard
8: Many tings
9:
10: Revision 1.131 2009/06/20 16:22:47 brouard
11: Some dimensions resccaled
12:
13: Revision 1.130 2009/05/26 06:44:34 brouard
14: (Module): Max Covariate is now set to 20 instead of 8. A
15: lot of cleaning with variables initialized to 0. Trying to make
16: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
17:
18: Revision 1.129 2007/08/31 13:49:27 lievre
19: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
20:
21: Revision 1.128 2006/06/30 13:02:05 brouard
22: (Module): Clarifications on computing e.j
23:
24: Revision 1.127 2006/04/28 18:11:50 brouard
25: (Module): Yes the sum of survivors was wrong since
26: imach-114 because nhstepm was no more computed in the age
27: loop. Now we define nhstepma in the age loop.
28: (Module): In order to speed up (in case of numerous covariates) we
29: compute health expectancies (without variances) in a first step
30: and then all the health expectancies with variances or standard
31: deviation (needs data from the Hessian matrices) which slows the
32: computation.
33: In the future we should be able to stop the program is only health
34: expectancies and graph are needed without standard deviations.
35:
36: Revision 1.126 2006/04/28 17:23:28 brouard
37: (Module): Yes the sum of survivors was wrong since
38: imach-114 because nhstepm was no more computed in the age
39: loop. Now we define nhstepma in the age loop.
40: Version 0.98h
41:
42: Revision 1.125 2006/04/04 15:20:31 lievre
43: Errors in calculation of health expectancies. Age was not initialized.
44: Forecasting file added.
45:
46: Revision 1.124 2006/03/22 17:13:53 lievre
47: Parameters are printed with %lf instead of %f (more numbers after the comma).
48: The log-likelihood is printed in the log file
49:
50: Revision 1.123 2006/03/20 10:52:43 brouard
51: * imach.c (Module): <title> changed, corresponds to .htm file
52: name. <head> headers where missing.
53:
54: * imach.c (Module): Weights can have a decimal point as for
55: English (a comma might work with a correct LC_NUMERIC environment,
56: otherwise the weight is truncated).
57: Modification of warning when the covariates values are not 0 or
58: 1.
59: Version 0.98g
60:
61: Revision 1.122 2006/03/20 09:45:41 brouard
62: (Module): Weights can have a decimal point as for
63: English (a comma might work with a correct LC_NUMERIC environment,
64: otherwise the weight is truncated).
65: Modification of warning when the covariates values are not 0 or
66: 1.
67: Version 0.98g
68:
69: Revision 1.121 2006/03/16 17:45:01 lievre
70: * imach.c (Module): Comments concerning covariates added
71:
72: * imach.c (Module): refinements in the computation of lli if
73: status=-2 in order to have more reliable computation if stepm is
74: not 1 month. Version 0.98f
75:
76: Revision 1.120 2006/03/16 15:10:38 lievre
77: (Module): refinements in the computation of lli if
78: status=-2 in order to have more reliable computation if stepm is
79: not 1 month. Version 0.98f
80:
81: Revision 1.119 2006/03/15 17:42:26 brouard
82: (Module): Bug if status = -2, the loglikelihood was
83: computed as likelihood omitting the logarithm. Version O.98e
84:
85: Revision 1.118 2006/03/14 18:20:07 brouard
86: (Module): varevsij Comments added explaining the second
87: table of variances if popbased=1 .
88: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
89: (Module): Function pstamp added
90: (Module): Version 0.98d
91:
92: Revision 1.117 2006/03/14 17:16:22 brouard
93: (Module): varevsij Comments added explaining the second
94: table of variances if popbased=1 .
95: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
96: (Module): Function pstamp added
97: (Module): Version 0.98d
98:
99: Revision 1.116 2006/03/06 10:29:27 brouard
100: (Module): Variance-covariance wrong links and
101: varian-covariance of ej. is needed (Saito).
102:
103: Revision 1.115 2006/02/27 12:17:45 brouard
104: (Module): One freematrix added in mlikeli! 0.98c
105:
106: Revision 1.114 2006/02/26 12:57:58 brouard
107: (Module): Some improvements in processing parameter
108: filename with strsep.
109:
110: Revision 1.113 2006/02/24 14:20:24 brouard
111: (Module): Memory leaks checks with valgrind and:
112: datafile was not closed, some imatrix were not freed and on matrix
113: allocation too.
114:
115: Revision 1.112 2006/01/30 09:55:26 brouard
116: (Module): Back to gnuplot.exe instead of wgnuplot.exe
117:
118: Revision 1.111 2006/01/25 20:38:18 brouard
119: (Module): Lots of cleaning and bugs added (Gompertz)
120: (Module): Comments can be added in data file. Missing date values
121: can be a simple dot '.'.
122:
123: Revision 1.110 2006/01/25 00:51:50 brouard
124: (Module): Lots of cleaning and bugs added (Gompertz)
125:
126: Revision 1.109 2006/01/24 19:37:15 brouard
127: (Module): Comments (lines starting with a #) are allowed in data.
128:
129: Revision 1.108 2006/01/19 18:05:42 lievre
130: Gnuplot problem appeared...
131: To be fixed
132:
133: Revision 1.107 2006/01/19 16:20:37 brouard
134: Test existence of gnuplot in imach path
135:
136: Revision 1.106 2006/01/19 13:24:36 brouard
137: Some cleaning and links added in html output
138:
139: Revision 1.105 2006/01/05 20:23:19 lievre
140: *** empty log message ***
141:
142: Revision 1.104 2005/09/30 16:11:43 lievre
143: (Module): sump fixed, loop imx fixed, and simplifications.
144: (Module): If the status is missing at the last wave but we know
145: that the person is alive, then we can code his/her status as -2
146: (instead of missing=-1 in earlier versions) and his/her
147: contributions to the likelihood is 1 - Prob of dying from last
148: health status (= 1-p13= p11+p12 in the easiest case of somebody in
149: the healthy state at last known wave). Version is 0.98
150:
151: Revision 1.103 2005/09/30 15:54:49 lievre
152: (Module): sump fixed, loop imx fixed, and simplifications.
153:
154: Revision 1.102 2004/09/15 17:31:30 brouard
155: Add the possibility to read data file including tab characters.
156:
157: Revision 1.101 2004/09/15 10:38:38 brouard
158: Fix on curr_time
159:
160: Revision 1.100 2004/07/12 18:29:06 brouard
161: Add version for Mac OS X. Just define UNIX in Makefile
162:
163: Revision 1.99 2004/06/05 08:57:40 brouard
164: *** empty log message ***
165:
166: Revision 1.98 2004/05/16 15:05:56 brouard
167: New version 0.97 . First attempt to estimate force of mortality
168: directly from the data i.e. without the need of knowing the health
169: state at each age, but using a Gompertz model: log u =a + b*age .
170: This is the basic analysis of mortality and should be done before any
171: other analysis, in order to test if the mortality estimated from the
172: cross-longitudinal survey is different from the mortality estimated
173: from other sources like vital statistic data.
174:
175: The same imach parameter file can be used but the option for mle should be -3.
176:
177: Agnès, who wrote this part of the code, tried to keep most of the
178: former routines in order to include the new code within the former code.
179:
180: The output is very simple: only an estimate of the intercept and of
181: the slope with 95% confident intervals.
182:
183: Current limitations:
184: A) Even if you enter covariates, i.e. with the
185: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
186: B) There is no computation of Life Expectancy nor Life Table.
187:
188: Revision 1.97 2004/02/20 13:25:42 lievre
189: Version 0.96d. Population forecasting command line is (temporarily)
190: suppressed.
191:
192: Revision 1.96 2003/07/15 15:38:55 brouard
193: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
194: rewritten within the same printf. Workaround: many printfs.
195:
196: Revision 1.95 2003/07/08 07:54:34 brouard
197: * imach.c (Repository):
198: (Repository): Using imachwizard code to output a more meaningful covariance
199: matrix (cov(a12,c31) instead of numbers.
200:
201: Revision 1.94 2003/06/27 13:00:02 brouard
202: Just cleaning
203:
204: Revision 1.93 2003/06/25 16:33:55 brouard
205: (Module): On windows (cygwin) function asctime_r doesn't
206: exist so I changed back to asctime which exists.
207: (Module): Version 0.96b
208:
209: Revision 1.92 2003/06/25 16:30:45 brouard
210: (Module): On windows (cygwin) function asctime_r doesn't
211: exist so I changed back to asctime which exists.
212:
213: Revision 1.91 2003/06/25 15:30:29 brouard
214: * imach.c (Repository): Duplicated warning errors corrected.
215: (Repository): Elapsed time after each iteration is now output. It
216: helps to forecast when convergence will be reached. Elapsed time
217: is stamped in powell. We created a new html file for the graphs
218: concerning matrix of covariance. It has extension -cov.htm.
219:
220: Revision 1.90 2003/06/24 12:34:15 brouard
221: (Module): Some bugs corrected for windows. Also, when
222: mle=-1 a template is output in file "or"mypar.txt with the design
223: of the covariance matrix to be input.
224:
225: Revision 1.89 2003/06/24 12:30:52 brouard
226: (Module): Some bugs corrected for windows. Also, when
227: mle=-1 a template is output in file "or"mypar.txt with the design
228: of the covariance matrix to be input.
229:
230: Revision 1.88 2003/06/23 17:54:56 brouard
231: * 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.
232:
233: Revision 1.87 2003/06/18 12:26:01 brouard
234: Version 0.96
235:
236: Revision 1.86 2003/06/17 20:04:08 brouard
237: (Module): Change position of html and gnuplot routines and added
238: routine fileappend.
239:
240: Revision 1.85 2003/06/17 13:12:43 brouard
241: * imach.c (Repository): Check when date of death was earlier that
242: current date of interview. It may happen when the death was just
243: prior to the death. In this case, dh was negative and likelihood
244: was wrong (infinity). We still send an "Error" but patch by
245: assuming that the date of death was just one stepm after the
246: interview.
247: (Repository): Because some people have very long ID (first column)
248: we changed int to long in num[] and we added a new lvector for
249: memory allocation. But we also truncated to 8 characters (left
250: truncation)
251: (Repository): No more line truncation errors.
252:
253: Revision 1.84 2003/06/13 21:44:43 brouard
254: * imach.c (Repository): Replace "freqsummary" at a correct
255: place. It differs from routine "prevalence" which may be called
256: many times. Probs is memory consuming and must be used with
257: parcimony.
258: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
259:
260: Revision 1.83 2003/06/10 13:39:11 lievre
261: *** empty log message ***
262:
263: Revision 1.82 2003/06/05 15:57:20 brouard
264: Add log in imach.c and fullversion number is now printed.
265:
266: */
267: /*
268: Interpolated Markov Chain
269:
270: Short summary of the programme:
271:
272: This program computes Healthy Life Expectancies from
273: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
274: first survey ("cross") where individuals from different ages are
275: interviewed on their health status or degree of disability (in the
276: case of a health survey which is our main interest) -2- at least a
277: second wave of interviews ("longitudinal") which measure each change
278: (if any) in individual health status. Health expectancies are
279: computed from the time spent in each health state according to a
280: model. More health states you consider, more time is necessary to reach the
281: Maximum Likelihood of the parameters involved in the model. The
282: simplest model is the multinomial logistic model where pij is the
283: probability to be observed in state j at the second wave
284: conditional to be observed in state i at the first wave. Therefore
285: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
286: 'age' is age and 'sex' is a covariate. If you want to have a more
287: complex model than "constant and age", you should modify the program
288: where the markup *Covariates have to be included here again* invites
289: you to do it. More covariates you add, slower the
290: convergence.
291:
292: The advantage of this computer programme, compared to a simple
293: multinomial logistic model, is clear when the delay between waves is not
294: identical for each individual. Also, if a individual missed an
295: intermediate interview, the information is lost, but taken into
296: account using an interpolation or extrapolation.
297:
298: hPijx is the probability to be observed in state i at age x+h
299: conditional to the observed state i at age x. The delay 'h' can be
300: split into an exact number (nh*stepm) of unobserved intermediate
301: states. This elementary transition (by month, quarter,
302: semester or year) is modelled as a multinomial logistic. The hPx
303: matrix is simply the matrix product of nh*stepm elementary matrices
304: and the contribution of each individual to the likelihood is simply
305: hPijx.
306:
307: Also this programme outputs the covariance matrix of the parameters but also
308: of the life expectancies. It also computes the period (stable) prevalence.
309:
310: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
311: Institut national d'études démographiques, Paris.
312: This software have been partly granted by Euro-REVES, a concerted action
313: from the European Union.
314: It is copyrighted identically to a GNU software product, ie programme and
315: software can be distributed freely for non commercial use. Latest version
316: can be accessed at http://euroreves.ined.fr/imach .
317:
318: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
319: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
320:
321: **********************************************************************/
322: /*
323: main
324: read parameterfile
325: read datafile
326: concatwav
327: freqsummary
328: if (mle >= 1)
329: mlikeli
330: print results files
331: if mle==1
332: computes hessian
333: read end of parameter file: agemin, agemax, bage, fage, estepm
334: begin-prev-date,...
335: open gnuplot file
336: open html file
337: period (stable) prevalence
338: for age prevalim()
339: h Pij x
340: variance of p varprob
341: forecasting if prevfcast==1 prevforecast call prevalence()
342: health expectancies
343: Variance-covariance of DFLE
344: prevalence()
345: movingaverage()
346: varevsij()
347: if popbased==1 varevsij(,popbased)
348: total life expectancies
349: Variance of period (stable) prevalence
350: end
351: */
352:
353:
354:
355:
356: #include <math.h>
357: #include <stdio.h>
358: #include <stdlib.h>
359: #include <string.h>
360: #include <unistd.h>
361:
362: #include <limits.h>
363: #include <sys/types.h>
364: #include <sys/stat.h>
365: #include <errno.h>
366: extern int errno;
367:
368: /* #include <sys/time.h> */
369: #include <time.h>
370: #include "timeval.h"
371:
372: /* #include <libintl.h> */
373: /* #define _(String) gettext (String) */
374:
375: #define MAXLINE 256
376:
377: #define GNUPLOTPROGRAM "gnuplot"
378: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
379: #define FILENAMELENGTH 132
380:
381: #define GLOCK_ERROR_NOPATH -1 /* empty path */
382: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
383:
384: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
385: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
386:
387: #define NINTERVMAX 8
388: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
389: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
390: #define NCOVMAX 20 /* Maximum number of covariates */
391: #define MAXN 20000
392: #define YEARM 12. /* Number of months per year */
393: #define AGESUP 130
394: #define AGEBASE 40
395: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
396: #ifdef UNIX
397: #define DIRSEPARATOR '/'
398: #define CHARSEPARATOR "/"
399: #define ODIRSEPARATOR '\\'
400: #else
401: #define DIRSEPARATOR '\\'
402: #define CHARSEPARATOR "\\"
403: #define ODIRSEPARATOR '/'
404: #endif
405:
406: /* $Id: imach.c,v 1.133 2009/07/06 10:21:25 brouard Exp $ */
407: /* $State: Exp $ */
408:
409: char version[]="Imach version 0.98k, June 2009, INED-EUROREVES-Institut de longevite ";
410: char fullversion[]="$Revision: 1.133 $ $Date: 2009/07/06 10:21:25 $";
411: char strstart[80];
412: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
413: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
414: int nvar=0, nforce=0; /* Number of variables, number of forces */
415: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
416: int npar=NPARMAX;
417: int nlstate=2; /* Number of live states */
418: int ndeath=1; /* Number of dead states */
419: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
420: int popbased=0;
421:
422: int *wav; /* Number of waves for this individuual 0 is possible */
423: int maxwav=0; /* Maxim number of waves */
424: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
425: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
426: int gipmx=0, gsw=0; /* Global variables on the number of contributions
427: to the likelihood and the sum of weights (done by funcone)*/
428: int mle=1, weightopt=0;
429: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
430: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
431: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
432: * wave mi and wave mi+1 is not an exact multiple of stepm. */
433: double jmean=1; /* Mean space between 2 waves */
434: double **oldm, **newm, **savm; /* Working pointers to matrices */
435: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
436: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
437: FILE *ficlog, *ficrespow;
438: int globpr=0; /* Global variable for printing or not */
439: double fretone; /* Only one call to likelihood */
440: long ipmx=0; /* Number of contributions */
441: double sw; /* Sum of weights */
442: char filerespow[FILENAMELENGTH];
443: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
444: FILE *ficresilk;
445: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
446: FILE *ficresprobmorprev;
447: FILE *fichtm, *fichtmcov; /* Html File */
448: FILE *ficreseij;
449: char filerese[FILENAMELENGTH];
450: FILE *ficresstdeij;
451: char fileresstde[FILENAMELENGTH];
452: FILE *ficrescveij;
453: char filerescve[FILENAMELENGTH];
454: FILE *ficresvij;
455: char fileresv[FILENAMELENGTH];
456: FILE *ficresvpl;
457: char fileresvpl[FILENAMELENGTH];
458: char title[MAXLINE];
459: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
460: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
461: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
462: char command[FILENAMELENGTH];
463: int outcmd=0;
464:
465: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
466:
467: char filelog[FILENAMELENGTH]; /* Log file */
468: char filerest[FILENAMELENGTH];
469: char fileregp[FILENAMELENGTH];
470: char popfile[FILENAMELENGTH];
471:
472: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
473:
474: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
475: struct timezone tzp;
476: extern int gettimeofday();
477: struct tm tmg, tm, tmf, *gmtime(), *localtime();
478: long time_value;
479: extern long time();
480: char strcurr[80], strfor[80];
481:
482: char *endptr;
483: long lval;
484: double dval;
485:
486: #define NR_END 1
487: #define FREE_ARG char*
488: #define FTOL 1.0e-10
489:
490: #define NRANSI
491: #define ITMAX 200
492:
493: #define TOL 2.0e-4
494:
495: #define CGOLD 0.3819660
496: #define ZEPS 1.0e-10
497: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
498:
499: #define GOLD 1.618034
500: #define GLIMIT 100.0
501: #define TINY 1.0e-20
502:
503: static double maxarg1,maxarg2;
504: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
505: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
506:
507: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
508: #define rint(a) floor(a+0.5)
509:
510: static double sqrarg;
511: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
512: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
513: int agegomp= AGEGOMP;
514:
515: int imx;
516: int stepm=1;
517: /* Stepm, step in month: minimum step interpolation*/
518:
519: int estepm;
520: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
521:
522: int m,nb;
523: long *num;
524: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
525: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
526: double **pmmij, ***probs;
527: double *ageexmed,*agecens;
528: double dateintmean=0;
529:
530: double *weight;
531: int **s; /* Status */
532: double *agedc, **covar, idx;
533: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
534: double *lsurv, *lpop, *tpop;
535:
536: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
537: double ftolhess; /* Tolerance for computing hessian */
538:
539: /**************** split *************************/
540: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
541: {
542: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
543: the name of the file (name), its extension only (ext) and its first part of the name (finame)
544: */
545: char *ss; /* pointer */
546: int l1, l2; /* length counters */
547:
548: l1 = strlen(path ); /* length of path */
549: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
550: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
551: if ( ss == NULL ) { /* no directory, so determine current directory */
552: strcpy( name, path ); /* we got the fullname name because no directory */
553: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
554: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
555: /* get current working directory */
556: /* extern char* getcwd ( char *buf , int len);*/
557: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
558: return( GLOCK_ERROR_GETCWD );
559: }
560: /* got dirc from getcwd*/
561: printf(" DIRC = %s \n",dirc);
562: } else { /* strip direcotry from path */
563: ss++; /* after this, the filename */
564: l2 = strlen( ss ); /* length of filename */
565: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
566: strcpy( name, ss ); /* save file name */
567: strncpy( dirc, path, l1 - l2 ); /* now the directory */
568: dirc[l1-l2] = 0; /* add zero */
569: printf(" DIRC2 = %s \n",dirc);
570: }
571: /* We add a separator at the end of dirc if not exists */
572: l1 = strlen( dirc ); /* length of directory */
573: if( dirc[l1-1] != DIRSEPARATOR ){
574: dirc[l1] = DIRSEPARATOR;
575: dirc[l1+1] = 0;
576: printf(" DIRC3 = %s \n",dirc);
577: }
578: ss = strrchr( name, '.' ); /* find last / */
579: if (ss >0){
580: ss++;
581: strcpy(ext,ss); /* save extension */
582: l1= strlen( name);
583: l2= strlen(ss)+1;
584: strncpy( finame, name, l1-l2);
585: finame[l1-l2]= 0;
586: }
587:
588: return( 0 ); /* we're done */
589: }
590:
591:
592: /******************************************/
593:
594: void replace_back_to_slash(char *s, char*t)
595: {
596: int i;
597: int lg=0;
598: i=0;
599: lg=strlen(t);
600: for(i=0; i<= lg; i++) {
601: (s[i] = t[i]);
602: if (t[i]== '\\') s[i]='/';
603: }
604: }
605:
606: char *trimbb(char *out, char *in)
607: { /* Trim multiple blanks in line */
608: char *s;
609: s=out;
610: while (*in != '\0'){
611: while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
612: in++;
613: }
614: *out++ = *in++;
615: }
616: *out='\0';
617: return s;
618: }
619:
620: int nbocc(char *s, char occ)
621: {
622: int i,j=0;
623: int lg=20;
624: i=0;
625: lg=strlen(s);
626: for(i=0; i<= lg; i++) {
627: if (s[i] == occ ) j++;
628: }
629: return j;
630: }
631:
632: void cutv(char *u,char *v, char*t, char occ)
633: {
634: /* cuts string t into u and v where u ends before first occurence of char 'occ'
635: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
636: gives u="abcedf" and v="ghi2j" */
637: int i,lg,j,p=0;
638: i=0;
639: for(j=0; j<=strlen(t)-1; j++) {
640: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
641: }
642:
643: lg=strlen(t);
644: for(j=0; j<p; j++) {
645: (u[j] = t[j]);
646: }
647: u[p]='\0';
648:
649: for(j=0; j<= lg; j++) {
650: if (j>=(p+1))(v[j-p-1] = t[j]);
651: }
652: }
653:
654: /********************** nrerror ********************/
655:
656: void nrerror(char error_text[])
657: {
658: fprintf(stderr,"ERREUR ...\n");
659: fprintf(stderr,"%s\n",error_text);
660: exit(EXIT_FAILURE);
661: }
662: /*********************** vector *******************/
663: double *vector(int nl, int nh)
664: {
665: double *v;
666: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
667: if (!v) nrerror("allocation failure in vector");
668: return v-nl+NR_END;
669: }
670:
671: /************************ free vector ******************/
672: void free_vector(double*v, int nl, int nh)
673: {
674: free((FREE_ARG)(v+nl-NR_END));
675: }
676:
677: /************************ivector *******************************/
678: int *ivector(long nl,long nh)
679: {
680: int *v;
681: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
682: if (!v) nrerror("allocation failure in ivector");
683: return v-nl+NR_END;
684: }
685:
686: /******************free ivector **************************/
687: void free_ivector(int *v, long nl, long nh)
688: {
689: free((FREE_ARG)(v+nl-NR_END));
690: }
691:
692: /************************lvector *******************************/
693: long *lvector(long nl,long nh)
694: {
695: long *v;
696: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
697: if (!v) nrerror("allocation failure in ivector");
698: return v-nl+NR_END;
699: }
700:
701: /******************free lvector **************************/
702: void free_lvector(long *v, long nl, long nh)
703: {
704: free((FREE_ARG)(v+nl-NR_END));
705: }
706:
707: /******************* imatrix *******************************/
708: int **imatrix(long nrl, long nrh, long ncl, long nch)
709: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
710: {
711: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
712: int **m;
713:
714: /* allocate pointers to rows */
715: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
716: if (!m) nrerror("allocation failure 1 in matrix()");
717: m += NR_END;
718: m -= nrl;
719:
720:
721: /* allocate rows and set pointers to them */
722: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
723: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
724: m[nrl] += NR_END;
725: m[nrl] -= ncl;
726:
727: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
728:
729: /* return pointer to array of pointers to rows */
730: return m;
731: }
732:
733: /****************** free_imatrix *************************/
734: void free_imatrix(m,nrl,nrh,ncl,nch)
735: int **m;
736: long nch,ncl,nrh,nrl;
737: /* free an int matrix allocated by imatrix() */
738: {
739: free((FREE_ARG) (m[nrl]+ncl-NR_END));
740: free((FREE_ARG) (m+nrl-NR_END));
741: }
742:
743: /******************* matrix *******************************/
744: double **matrix(long nrl, long nrh, long ncl, long nch)
745: {
746: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
747: double **m;
748:
749: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
750: if (!m) nrerror("allocation failure 1 in matrix()");
751: m += NR_END;
752: m -= nrl;
753:
754: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
755: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
756: m[nrl] += NR_END;
757: m[nrl] -= ncl;
758:
759: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
760: return m;
761: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
762: */
763: }
764:
765: /*************************free matrix ************************/
766: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
767: {
768: free((FREE_ARG)(m[nrl]+ncl-NR_END));
769: free((FREE_ARG)(m+nrl-NR_END));
770: }
771:
772: /******************* ma3x *******************************/
773: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
774: {
775: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
776: double ***m;
777:
778: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
779: if (!m) nrerror("allocation failure 1 in matrix()");
780: m += NR_END;
781: m -= nrl;
782:
783: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
784: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
785: m[nrl] += NR_END;
786: m[nrl] -= ncl;
787:
788: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
789:
790: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
791: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
792: m[nrl][ncl] += NR_END;
793: m[nrl][ncl] -= nll;
794: for (j=ncl+1; j<=nch; j++)
795: m[nrl][j]=m[nrl][j-1]+nlay;
796:
797: for (i=nrl+1; i<=nrh; i++) {
798: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
799: for (j=ncl+1; j<=nch; j++)
800: m[i][j]=m[i][j-1]+nlay;
801: }
802: return m;
803: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
804: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
805: */
806: }
807:
808: /*************************free ma3x ************************/
809: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
810: {
811: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
812: free((FREE_ARG)(m[nrl]+ncl-NR_END));
813: free((FREE_ARG)(m+nrl-NR_END));
814: }
815:
816: /*************** function subdirf ***********/
817: char *subdirf(char fileres[])
818: {
819: /* Caution optionfilefiname is hidden */
820: strcpy(tmpout,optionfilefiname);
821: strcat(tmpout,"/"); /* Add to the right */
822: strcat(tmpout,fileres);
823: return tmpout;
824: }
825:
826: /*************** function subdirf2 ***********/
827: char *subdirf2(char fileres[], char *preop)
828: {
829:
830: /* Caution optionfilefiname is hidden */
831: strcpy(tmpout,optionfilefiname);
832: strcat(tmpout,"/");
833: strcat(tmpout,preop);
834: strcat(tmpout,fileres);
835: return tmpout;
836: }
837:
838: /*************** function subdirf3 ***********/
839: char *subdirf3(char fileres[], char *preop, char *preop2)
840: {
841:
842: /* Caution optionfilefiname is hidden */
843: strcpy(tmpout,optionfilefiname);
844: strcat(tmpout,"/");
845: strcat(tmpout,preop);
846: strcat(tmpout,preop2);
847: strcat(tmpout,fileres);
848: return tmpout;
849: }
850:
851: /***************** f1dim *************************/
852: extern int ncom;
853: extern double *pcom,*xicom;
854: extern double (*nrfunc)(double []);
855:
856: double f1dim(double x)
857: {
858: int j;
859: double f;
860: double *xt;
861:
862: xt=vector(1,ncom);
863: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
864: f=(*nrfunc)(xt);
865: free_vector(xt,1,ncom);
866: return f;
867: }
868:
869: /*****************brent *************************/
870: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
871: {
872: int iter;
873: double a,b,d,etemp;
874: double fu,fv,fw,fx;
875: double ftemp;
876: double p,q,r,tol1,tol2,u,v,w,x,xm;
877: double e=0.0;
878:
879: a=(ax < cx ? ax : cx);
880: b=(ax > cx ? ax : cx);
881: x=w=v=bx;
882: fw=fv=fx=(*f)(x);
883: for (iter=1;iter<=ITMAX;iter++) {
884: xm=0.5*(a+b);
885: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
886: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
887: printf(".");fflush(stdout);
888: fprintf(ficlog,".");fflush(ficlog);
889: #ifdef DEBUG
890: 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);
891: 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);
892: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
893: #endif
894: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
895: *xmin=x;
896: return fx;
897: }
898: ftemp=fu;
899: if (fabs(e) > tol1) {
900: r=(x-w)*(fx-fv);
901: q=(x-v)*(fx-fw);
902: p=(x-v)*q-(x-w)*r;
903: q=2.0*(q-r);
904: if (q > 0.0) p = -p;
905: q=fabs(q);
906: etemp=e;
907: e=d;
908: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
909: d=CGOLD*(e=(x >= xm ? a-x : b-x));
910: else {
911: d=p/q;
912: u=x+d;
913: if (u-a < tol2 || b-u < tol2)
914: d=SIGN(tol1,xm-x);
915: }
916: } else {
917: d=CGOLD*(e=(x >= xm ? a-x : b-x));
918: }
919: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
920: fu=(*f)(u);
921: if (fu <= fx) {
922: if (u >= x) a=x; else b=x;
923: SHFT(v,w,x,u)
924: SHFT(fv,fw,fx,fu)
925: } else {
926: if (u < x) a=u; else b=u;
927: if (fu <= fw || w == x) {
928: v=w;
929: w=u;
930: fv=fw;
931: fw=fu;
932: } else if (fu <= fv || v == x || v == w) {
933: v=u;
934: fv=fu;
935: }
936: }
937: }
938: nrerror("Too many iterations in brent");
939: *xmin=x;
940: return fx;
941: }
942:
943: /****************** mnbrak ***********************/
944:
945: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
946: double (*func)(double))
947: {
948: double ulim,u,r,q, dum;
949: double fu;
950:
951: *fa=(*func)(*ax);
952: *fb=(*func)(*bx);
953: if (*fb > *fa) {
954: SHFT(dum,*ax,*bx,dum)
955: SHFT(dum,*fb,*fa,dum)
956: }
957: *cx=(*bx)+GOLD*(*bx-*ax);
958: *fc=(*func)(*cx);
959: while (*fb > *fc) {
960: r=(*bx-*ax)*(*fb-*fc);
961: q=(*bx-*cx)*(*fb-*fa);
962: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
963: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
964: ulim=(*bx)+GLIMIT*(*cx-*bx);
965: if ((*bx-u)*(u-*cx) > 0.0) {
966: fu=(*func)(u);
967: } else if ((*cx-u)*(u-ulim) > 0.0) {
968: fu=(*func)(u);
969: if (fu < *fc) {
970: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
971: SHFT(*fb,*fc,fu,(*func)(u))
972: }
973: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
974: u=ulim;
975: fu=(*func)(u);
976: } else {
977: u=(*cx)+GOLD*(*cx-*bx);
978: fu=(*func)(u);
979: }
980: SHFT(*ax,*bx,*cx,u)
981: SHFT(*fa,*fb,*fc,fu)
982: }
983: }
984:
985: /*************** linmin ************************/
986:
987: int ncom;
988: double *pcom,*xicom;
989: double (*nrfunc)(double []);
990:
991: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
992: {
993: double brent(double ax, double bx, double cx,
994: double (*f)(double), double tol, double *xmin);
995: double f1dim(double x);
996: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
997: double *fc, double (*func)(double));
998: int j;
999: double xx,xmin,bx,ax;
1000: double fx,fb,fa;
1001:
1002: ncom=n;
1003: pcom=vector(1,n);
1004: xicom=vector(1,n);
1005: nrfunc=func;
1006: for (j=1;j<=n;j++) {
1007: pcom[j]=p[j];
1008: xicom[j]=xi[j];
1009: }
1010: ax=0.0;
1011: xx=1.0;
1012: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1013: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1014: #ifdef DEBUG
1015: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1016: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1017: #endif
1018: for (j=1;j<=n;j++) {
1019: xi[j] *= xmin;
1020: p[j] += xi[j];
1021: }
1022: free_vector(xicom,1,n);
1023: free_vector(pcom,1,n);
1024: }
1025:
1026: char *asc_diff_time(long time_sec, char ascdiff[])
1027: {
1028: long sec_left, days, hours, minutes;
1029: days = (time_sec) / (60*60*24);
1030: sec_left = (time_sec) % (60*60*24);
1031: hours = (sec_left) / (60*60) ;
1032: sec_left = (sec_left) %(60*60);
1033: minutes = (sec_left) /60;
1034: sec_left = (sec_left) % (60);
1035: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1036: return ascdiff;
1037: }
1038:
1039: /*************** powell ************************/
1040: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1041: double (*func)(double []))
1042: {
1043: void linmin(double p[], double xi[], int n, double *fret,
1044: double (*func)(double []));
1045: int i,ibig,j;
1046: double del,t,*pt,*ptt,*xit;
1047: double fp,fptt;
1048: double *xits;
1049: int niterf, itmp;
1050:
1051: pt=vector(1,n);
1052: ptt=vector(1,n);
1053: xit=vector(1,n);
1054: xits=vector(1,n);
1055: *fret=(*func)(p);
1056: for (j=1;j<=n;j++) pt[j]=p[j];
1057: for (*iter=1;;++(*iter)) {
1058: fp=(*fret);
1059: ibig=0;
1060: del=0.0;
1061: last_time=curr_time;
1062: (void) gettimeofday(&curr_time,&tzp);
1063: 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);
1064: 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);
1065: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1066: for (i=1;i<=n;i++) {
1067: printf(" %d %.12f",i, p[i]);
1068: fprintf(ficlog," %d %.12lf",i, p[i]);
1069: fprintf(ficrespow," %.12lf", p[i]);
1070: }
1071: printf("\n");
1072: fprintf(ficlog,"\n");
1073: fprintf(ficrespow,"\n");fflush(ficrespow);
1074: if(*iter <=3){
1075: tm = *localtime(&curr_time.tv_sec);
1076: strcpy(strcurr,asctime(&tm));
1077: /* asctime_r(&tm,strcurr); */
1078: forecast_time=curr_time;
1079: itmp = strlen(strcurr);
1080: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1081: strcurr[itmp-1]='\0';
1082: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1083: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1084: for(niterf=10;niterf<=30;niterf+=10){
1085: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1086: tmf = *localtime(&forecast_time.tv_sec);
1087: /* asctime_r(&tmf,strfor); */
1088: strcpy(strfor,asctime(&tmf));
1089: itmp = strlen(strfor);
1090: if(strfor[itmp-1]=='\n')
1091: strfor[itmp-1]='\0';
1092: 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);
1093: 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);
1094: }
1095: }
1096: for (i=1;i<=n;i++) {
1097: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1098: fptt=(*fret);
1099: #ifdef DEBUG
1100: printf("fret=%lf \n",*fret);
1101: fprintf(ficlog,"fret=%lf \n",*fret);
1102: #endif
1103: printf("%d",i);fflush(stdout);
1104: fprintf(ficlog,"%d",i);fflush(ficlog);
1105: linmin(p,xit,n,fret,func);
1106: if (fabs(fptt-(*fret)) > del) {
1107: del=fabs(fptt-(*fret));
1108: ibig=i;
1109: }
1110: #ifdef DEBUG
1111: printf("%d %.12e",i,(*fret));
1112: fprintf(ficlog,"%d %.12e",i,(*fret));
1113: for (j=1;j<=n;j++) {
1114: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1115: printf(" x(%d)=%.12e",j,xit[j]);
1116: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1117: }
1118: for(j=1;j<=n;j++) {
1119: printf(" p=%.12e",p[j]);
1120: fprintf(ficlog," p=%.12e",p[j]);
1121: }
1122: printf("\n");
1123: fprintf(ficlog,"\n");
1124: #endif
1125: }
1126: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1127: #ifdef DEBUG
1128: int k[2],l;
1129: k[0]=1;
1130: k[1]=-1;
1131: printf("Max: %.12e",(*func)(p));
1132: fprintf(ficlog,"Max: %.12e",(*func)(p));
1133: for (j=1;j<=n;j++) {
1134: printf(" %.12e",p[j]);
1135: fprintf(ficlog," %.12e",p[j]);
1136: }
1137: printf("\n");
1138: fprintf(ficlog,"\n");
1139: for(l=0;l<=1;l++) {
1140: for (j=1;j<=n;j++) {
1141: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1142: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1143: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1144: }
1145: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1146: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1147: }
1148: #endif
1149:
1150:
1151: free_vector(xit,1,n);
1152: free_vector(xits,1,n);
1153: free_vector(ptt,1,n);
1154: free_vector(pt,1,n);
1155: return;
1156: }
1157: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1158: for (j=1;j<=n;j++) {
1159: ptt[j]=2.0*p[j]-pt[j];
1160: xit[j]=p[j]-pt[j];
1161: pt[j]=p[j];
1162: }
1163: fptt=(*func)(ptt);
1164: if (fptt < fp) {
1165: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1166: if (t < 0.0) {
1167: linmin(p,xit,n,fret,func);
1168: for (j=1;j<=n;j++) {
1169: xi[j][ibig]=xi[j][n];
1170: xi[j][n]=xit[j];
1171: }
1172: #ifdef DEBUG
1173: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1174: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1175: for(j=1;j<=n;j++){
1176: printf(" %.12e",xit[j]);
1177: fprintf(ficlog," %.12e",xit[j]);
1178: }
1179: printf("\n");
1180: fprintf(ficlog,"\n");
1181: #endif
1182: }
1183: }
1184: }
1185: }
1186:
1187: /**** Prevalence limit (stable or period prevalence) ****************/
1188:
1189: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1190: {
1191: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1192: matrix by transitions matrix until convergence is reached */
1193:
1194: int i, ii,j,k;
1195: double min, max, maxmin, maxmax,sumnew=0.;
1196: double **matprod2();
1197: double **out, cov[NCOVMAX+1], **pmij();
1198: double **newm;
1199: double agefin, delaymax=50 ; /* Max number of years to converge */
1200:
1201: for (ii=1;ii<=nlstate+ndeath;ii++)
1202: for (j=1;j<=nlstate+ndeath;j++){
1203: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1204: }
1205:
1206: cov[1]=1.;
1207:
1208: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1209: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1210: newm=savm;
1211: /* Covariates have to be included here again */
1212: cov[2]=agefin;
1213:
1214: for (k=1; k<=cptcovn;k++) {
1215: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1216: /* 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]]);*/
1217: }
1218: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1219: for (k=1; k<=cptcovprod;k++)
1220: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1221:
1222: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1223: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1224: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1225: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1226:
1227: savm=oldm;
1228: oldm=newm;
1229: maxmax=0.;
1230: for(j=1;j<=nlstate;j++){
1231: min=1.;
1232: max=0.;
1233: for(i=1; i<=nlstate; i++) {
1234: sumnew=0;
1235: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1236: prlim[i][j]= newm[i][j]/(1-sumnew);
1237: max=FMAX(max,prlim[i][j]);
1238: min=FMIN(min,prlim[i][j]);
1239: }
1240: maxmin=max-min;
1241: maxmax=FMAX(maxmax,maxmin);
1242: }
1243: if(maxmax < ftolpl){
1244: return prlim;
1245: }
1246: }
1247: }
1248:
1249: /*************** transition probabilities ***************/
1250:
1251: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1252: {
1253: double s1, s2;
1254: /*double t34;*/
1255: int i,j,j1, nc, ii, jj;
1256:
1257: for(i=1; i<= nlstate; i++){
1258: for(j=1; j<i;j++){
1259: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1260: /*s2 += param[i][j][nc]*cov[nc];*/
1261: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1262: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1263: }
1264: ps[i][j]=s2;
1265: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1266: }
1267: for(j=i+1; j<=nlstate+ndeath;j++){
1268: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1269: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1270: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1271: }
1272: ps[i][j]=s2;
1273: }
1274: }
1275: /*ps[3][2]=1;*/
1276:
1277: for(i=1; i<= nlstate; i++){
1278: s1=0;
1279: for(j=1; j<i; j++){
1280: s1+=exp(ps[i][j]);
1281: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1282: }
1283: for(j=i+1; j<=nlstate+ndeath; j++){
1284: s1+=exp(ps[i][j]);
1285: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1286: }
1287: ps[i][i]=1./(s1+1.);
1288: for(j=1; j<i; j++)
1289: ps[i][j]= exp(ps[i][j])*ps[i][i];
1290: for(j=i+1; j<=nlstate+ndeath; j++)
1291: ps[i][j]= exp(ps[i][j])*ps[i][i];
1292: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1293: } /* end i */
1294:
1295: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1296: for(jj=1; jj<= nlstate+ndeath; jj++){
1297: ps[ii][jj]=0;
1298: ps[ii][ii]=1;
1299: }
1300: }
1301:
1302:
1303: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1304: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1305: /* printf("ddd %lf ",ps[ii][jj]); */
1306: /* } */
1307: /* printf("\n "); */
1308: /* } */
1309: /* printf("\n ");printf("%lf ",cov[2]); */
1310: /*
1311: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1312: goto end;*/
1313: return ps;
1314: }
1315:
1316: /**************** Product of 2 matrices ******************/
1317:
1318: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1319: {
1320: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1321: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1322: /* in, b, out are matrice of pointers which should have been initialized
1323: before: only the contents of out is modified. The function returns
1324: a pointer to pointers identical to out */
1325: long i, j, k;
1326: for(i=nrl; i<= nrh; i++)
1327: for(k=ncolol; k<=ncoloh; k++)
1328: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1329: out[i][k] +=in[i][j]*b[j][k];
1330:
1331: return out;
1332: }
1333:
1334:
1335: /************* Higher Matrix Product ***************/
1336:
1337: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1338: {
1339: /* Computes the transition matrix starting at age 'age' over
1340: 'nhstepm*hstepm*stepm' months (i.e. until
1341: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1342: nhstepm*hstepm matrices.
1343: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1344: (typically every 2 years instead of every month which is too big
1345: for the memory).
1346: Model is determined by parameters x and covariates have to be
1347: included manually here.
1348:
1349: */
1350:
1351: int i, j, d, h, k;
1352: double **out, cov[NCOVMAX+1];
1353: double **newm;
1354:
1355: /* Hstepm could be zero and should return the unit matrix */
1356: for (i=1;i<=nlstate+ndeath;i++)
1357: for (j=1;j<=nlstate+ndeath;j++){
1358: oldm[i][j]=(i==j ? 1.0 : 0.0);
1359: po[i][j][0]=(i==j ? 1.0 : 0.0);
1360: }
1361: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1362: for(h=1; h <=nhstepm; h++){
1363: for(d=1; d <=hstepm; d++){
1364: newm=savm;
1365: /* Covariates have to be included here again */
1366: cov[1]=1.;
1367: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1368: for (k=1; k<=cptcovn;k++)
1369: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1370: for (k=1; k<=cptcovage;k++)
1371: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1372: for (k=1; k<=cptcovprod;k++)
1373: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1374:
1375:
1376: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1377: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1378: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1379: pmij(pmmij,cov,ncovmodel,x,nlstate));
1380: savm=oldm;
1381: oldm=newm;
1382: }
1383: for(i=1; i<=nlstate+ndeath; i++)
1384: for(j=1;j<=nlstate+ndeath;j++) {
1385: po[i][j][h]=newm[i][j];
1386: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1387: }
1388: /*printf("h=%d ",h);*/
1389: } /* end h */
1390: /* printf("\n H=%d \n",h); */
1391: return po;
1392: }
1393:
1394:
1395: /*************** log-likelihood *************/
1396: double func( double *x)
1397: {
1398: int i, ii, j, k, mi, d, kk;
1399: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1400: double **out;
1401: double sw; /* Sum of weights */
1402: double lli; /* Individual log likelihood */
1403: int s1, s2;
1404: double bbh, survp;
1405: long ipmx;
1406: /*extern weight */
1407: /* We are differentiating ll according to initial status */
1408: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1409: /*for(i=1;i<imx;i++)
1410: printf(" %d\n",s[4][i]);
1411: */
1412: cov[1]=1.;
1413:
1414: for(k=1; k<=nlstate; k++) ll[k]=0.;
1415:
1416: if(mle==1){
1417: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1418: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1419: for(mi=1; mi<= wav[i]-1; mi++){
1420: for (ii=1;ii<=nlstate+ndeath;ii++)
1421: for (j=1;j<=nlstate+ndeath;j++){
1422: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1423: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1424: }
1425: for(d=0; d<dh[mi][i]; d++){
1426: newm=savm;
1427: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1428: for (kk=1; kk<=cptcovage;kk++) {
1429: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1430: }
1431: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1432: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1433: savm=oldm;
1434: oldm=newm;
1435: } /* end mult */
1436:
1437: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1438: /* But now since version 0.9 we anticipate for bias at large stepm.
1439: * If stepm is larger than one month (smallest stepm) and if the exact delay
1440: * (in months) between two waves is not a multiple of stepm, we rounded to
1441: * the nearest (and in case of equal distance, to the lowest) interval but now
1442: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1443: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1444: * probability in order to take into account the bias as a fraction of the way
1445: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1446: * -stepm/2 to stepm/2 .
1447: * For stepm=1 the results are the same as for previous versions of Imach.
1448: * For stepm > 1 the results are less biased than in previous versions.
1449: */
1450: s1=s[mw[mi][i]][i];
1451: s2=s[mw[mi+1][i]][i];
1452: bbh=(double)bh[mi][i]/(double)stepm;
1453: /* bias bh is positive if real duration
1454: * is higher than the multiple of stepm and negative otherwise.
1455: */
1456: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1457: if( s2 > nlstate){
1458: /* i.e. if s2 is a death state and if the date of death is known
1459: then the contribution to the likelihood is the probability to
1460: die between last step unit time and current step unit time,
1461: which is also equal to probability to die before dh
1462: minus probability to die before dh-stepm .
1463: In version up to 0.92 likelihood was computed
1464: as if date of death was unknown. Death was treated as any other
1465: health state: the date of the interview describes the actual state
1466: and not the date of a change in health state. The former idea was
1467: to consider that at each interview the state was recorded
1468: (healthy, disable or death) and IMaCh was corrected; but when we
1469: introduced the exact date of death then we should have modified
1470: the contribution of an exact death to the likelihood. This new
1471: contribution is smaller and very dependent of the step unit
1472: stepm. It is no more the probability to die between last interview
1473: and month of death but the probability to survive from last
1474: interview up to one month before death multiplied by the
1475: probability to die within a month. Thanks to Chris
1476: Jackson for correcting this bug. Former versions increased
1477: mortality artificially. The bad side is that we add another loop
1478: which slows down the processing. The difference can be up to 10%
1479: lower mortality.
1480: */
1481: lli=log(out[s1][s2] - savm[s1][s2]);
1482:
1483:
1484: } else if (s2==-2) {
1485: for (j=1,survp=0. ; j<=nlstate; j++)
1486: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1487: /*survp += out[s1][j]; */
1488: lli= log(survp);
1489: }
1490:
1491: else if (s2==-4) {
1492: for (j=3,survp=0. ; j<=nlstate; j++)
1493: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1494: lli= log(survp);
1495: }
1496:
1497: else if (s2==-5) {
1498: for (j=1,survp=0. ; j<=2; j++)
1499: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1500: lli= log(survp);
1501: }
1502:
1503: else{
1504: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1505: /* 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 */
1506: }
1507: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1508: /*if(lli ==000.0)*/
1509: /*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); */
1510: ipmx +=1;
1511: sw += weight[i];
1512: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1513: } /* end of wave */
1514: } /* end of individual */
1515: } else if(mle==2){
1516: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1517: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1518: for(mi=1; mi<= wav[i]-1; mi++){
1519: for (ii=1;ii<=nlstate+ndeath;ii++)
1520: for (j=1;j<=nlstate+ndeath;j++){
1521: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1522: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1523: }
1524: for(d=0; d<=dh[mi][i]; d++){
1525: newm=savm;
1526: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1527: for (kk=1; kk<=cptcovage;kk++) {
1528: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1529: }
1530: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1531: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1532: savm=oldm;
1533: oldm=newm;
1534: } /* end mult */
1535:
1536: s1=s[mw[mi][i]][i];
1537: s2=s[mw[mi+1][i]][i];
1538: bbh=(double)bh[mi][i]/(double)stepm;
1539: 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 */
1540: ipmx +=1;
1541: sw += weight[i];
1542: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1543: } /* end of wave */
1544: } /* end of individual */
1545: } else if(mle==3){ /* exponential inter-extrapolation */
1546: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1547: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1548: for(mi=1; mi<= wav[i]-1; mi++){
1549: for (ii=1;ii<=nlstate+ndeath;ii++)
1550: for (j=1;j<=nlstate+ndeath;j++){
1551: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1552: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1553: }
1554: for(d=0; d<dh[mi][i]; d++){
1555: newm=savm;
1556: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1557: for (kk=1; kk<=cptcovage;kk++) {
1558: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1559: }
1560: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1561: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1562: savm=oldm;
1563: oldm=newm;
1564: } /* end mult */
1565:
1566: s1=s[mw[mi][i]][i];
1567: s2=s[mw[mi+1][i]][i];
1568: bbh=(double)bh[mi][i]/(double)stepm;
1569: 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 */
1570: ipmx +=1;
1571: sw += weight[i];
1572: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1573: } /* end of wave */
1574: } /* end of individual */
1575: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1576: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1577: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1578: for(mi=1; mi<= wav[i]-1; mi++){
1579: for (ii=1;ii<=nlstate+ndeath;ii++)
1580: for (j=1;j<=nlstate+ndeath;j++){
1581: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1582: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1583: }
1584: for(d=0; d<dh[mi][i]; d++){
1585: newm=savm;
1586: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1587: for (kk=1; kk<=cptcovage;kk++) {
1588: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1589: }
1590:
1591: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1592: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1593: savm=oldm;
1594: oldm=newm;
1595: } /* end mult */
1596:
1597: s1=s[mw[mi][i]][i];
1598: s2=s[mw[mi+1][i]][i];
1599: if( s2 > nlstate){
1600: lli=log(out[s1][s2] - savm[s1][s2]);
1601: }else{
1602: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1603: }
1604: ipmx +=1;
1605: sw += weight[i];
1606: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1607: /* 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]); */
1608: } /* end of wave */
1609: } /* end of individual */
1610: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1611: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1612: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1613: for(mi=1; mi<= wav[i]-1; mi++){
1614: for (ii=1;ii<=nlstate+ndeath;ii++)
1615: for (j=1;j<=nlstate+ndeath;j++){
1616: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1617: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1618: }
1619: for(d=0; d<dh[mi][i]; d++){
1620: newm=savm;
1621: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1622: for (kk=1; kk<=cptcovage;kk++) {
1623: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1624: }
1625:
1626: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1627: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1628: savm=oldm;
1629: oldm=newm;
1630: } /* end mult */
1631:
1632: s1=s[mw[mi][i]][i];
1633: s2=s[mw[mi+1][i]][i];
1634: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1635: ipmx +=1;
1636: sw += weight[i];
1637: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1638: /*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]);*/
1639: } /* end of wave */
1640: } /* end of individual */
1641: } /* End of if */
1642: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1643: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1644: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1645: return -l;
1646: }
1647:
1648: /*************** log-likelihood *************/
1649: double funcone( double *x)
1650: {
1651: /* Same as likeli but slower because of a lot of printf and if */
1652: int i, ii, j, k, mi, d, kk;
1653: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1654: double **out;
1655: double lli; /* Individual log likelihood */
1656: double llt;
1657: int s1, s2;
1658: double bbh, survp;
1659: /*extern weight */
1660: /* We are differentiating ll according to initial status */
1661: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1662: /*for(i=1;i<imx;i++)
1663: printf(" %d\n",s[4][i]);
1664: */
1665: cov[1]=1.;
1666:
1667: for(k=1; k<=nlstate; k++) ll[k]=0.;
1668:
1669: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1670: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1671: for(mi=1; mi<= wav[i]-1; mi++){
1672: for (ii=1;ii<=nlstate+ndeath;ii++)
1673: for (j=1;j<=nlstate+ndeath;j++){
1674: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1675: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1676: }
1677: for(d=0; d<dh[mi][i]; d++){
1678: newm=savm;
1679: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1680: for (kk=1; kk<=cptcovage;kk++) {
1681: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1682: }
1683: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1684: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1685: savm=oldm;
1686: oldm=newm;
1687: } /* end mult */
1688:
1689: s1=s[mw[mi][i]][i];
1690: s2=s[mw[mi+1][i]][i];
1691: bbh=(double)bh[mi][i]/(double)stepm;
1692: /* bias is positive if real duration
1693: * is higher than the multiple of stepm and negative otherwise.
1694: */
1695: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1696: lli=log(out[s1][s2] - savm[s1][s2]);
1697: } else if (s2==-2) {
1698: for (j=1,survp=0. ; j<=nlstate; j++)
1699: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1700: lli= log(survp);
1701: }else if (mle==1){
1702: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1703: } else if(mle==2){
1704: 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 */
1705: } else if(mle==3){ /* exponential inter-extrapolation */
1706: 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 */
1707: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1708: lli=log(out[s1][s2]); /* Original formula */
1709: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1710: lli=log(out[s1][s2]); /* Original formula */
1711: } /* End of if */
1712: ipmx +=1;
1713: sw += weight[i];
1714: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1715: /*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]); */
1716: if(globpr){
1717: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1718: %11.6f %11.6f %11.6f ", \
1719: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1720: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1721: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1722: llt +=ll[k]*gipmx/gsw;
1723: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1724: }
1725: fprintf(ficresilk," %10.6f\n", -llt);
1726: }
1727: } /* end of wave */
1728: } /* end of individual */
1729: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1730: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1731: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1732: if(globpr==0){ /* First time we count the contributions and weights */
1733: gipmx=ipmx;
1734: gsw=sw;
1735: }
1736: return -l;
1737: }
1738:
1739:
1740: /*************** function likelione ***********/
1741: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1742: {
1743: /* This routine should help understanding what is done with
1744: the selection of individuals/waves and
1745: to check the exact contribution to the likelihood.
1746: Plotting could be done.
1747: */
1748: int k;
1749:
1750: if(*globpri !=0){ /* Just counts and sums, no printings */
1751: strcpy(fileresilk,"ilk");
1752: strcat(fileresilk,fileres);
1753: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1754: printf("Problem with resultfile: %s\n", fileresilk);
1755: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1756: }
1757: 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");
1758: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1759: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1760: for(k=1; k<=nlstate; k++)
1761: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1762: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1763: }
1764:
1765: *fretone=(*funcone)(p);
1766: if(*globpri !=0){
1767: fclose(ficresilk);
1768: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1769: fflush(fichtm);
1770: }
1771: return;
1772: }
1773:
1774:
1775: /*********** Maximum Likelihood Estimation ***************/
1776:
1777: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1778: {
1779: int i,j, iter;
1780: double **xi;
1781: double fret;
1782: double fretone; /* Only one call to likelihood */
1783: /* char filerespow[FILENAMELENGTH];*/
1784: xi=matrix(1,npar,1,npar);
1785: for (i=1;i<=npar;i++)
1786: for (j=1;j<=npar;j++)
1787: xi[i][j]=(i==j ? 1.0 : 0.0);
1788: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1789: strcpy(filerespow,"pow");
1790: strcat(filerespow,fileres);
1791: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1792: printf("Problem with resultfile: %s\n", filerespow);
1793: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1794: }
1795: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1796: for (i=1;i<=nlstate;i++)
1797: for(j=1;j<=nlstate+ndeath;j++)
1798: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1799: fprintf(ficrespow,"\n");
1800:
1801: powell(p,xi,npar,ftol,&iter,&fret,func);
1802:
1803: free_matrix(xi,1,npar,1,npar);
1804: fclose(ficrespow);
1805: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1806: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1807: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1808:
1809: }
1810:
1811: /**** Computes Hessian and covariance matrix ***/
1812: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1813: {
1814: double **a,**y,*x,pd;
1815: double **hess;
1816: int i, j,jk;
1817: int *indx;
1818:
1819: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1820: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1821: void lubksb(double **a, int npar, int *indx, double b[]) ;
1822: void ludcmp(double **a, int npar, int *indx, double *d) ;
1823: double gompertz(double p[]);
1824: hess=matrix(1,npar,1,npar);
1825:
1826: printf("\nCalculation of the hessian matrix. Wait...\n");
1827: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1828: for (i=1;i<=npar;i++){
1829: printf("%d",i);fflush(stdout);
1830: fprintf(ficlog,"%d",i);fflush(ficlog);
1831:
1832: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1833:
1834: /* printf(" %f ",p[i]);
1835: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1836: }
1837:
1838: for (i=1;i<=npar;i++) {
1839: for (j=1;j<=npar;j++) {
1840: if (j>i) {
1841: printf(".%d%d",i,j);fflush(stdout);
1842: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1843: hess[i][j]=hessij(p,delti,i,j,func,npar);
1844:
1845: hess[j][i]=hess[i][j];
1846: /*printf(" %lf ",hess[i][j]);*/
1847: }
1848: }
1849: }
1850: printf("\n");
1851: fprintf(ficlog,"\n");
1852:
1853: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1854: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1855:
1856: a=matrix(1,npar,1,npar);
1857: y=matrix(1,npar,1,npar);
1858: x=vector(1,npar);
1859: indx=ivector(1,npar);
1860: for (i=1;i<=npar;i++)
1861: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1862: ludcmp(a,npar,indx,&pd);
1863:
1864: for (j=1;j<=npar;j++) {
1865: for (i=1;i<=npar;i++) x[i]=0;
1866: x[j]=1;
1867: lubksb(a,npar,indx,x);
1868: for (i=1;i<=npar;i++){
1869: matcov[i][j]=x[i];
1870: }
1871: }
1872:
1873: printf("\n#Hessian matrix#\n");
1874: fprintf(ficlog,"\n#Hessian matrix#\n");
1875: for (i=1;i<=npar;i++) {
1876: for (j=1;j<=npar;j++) {
1877: printf("%.3e ",hess[i][j]);
1878: fprintf(ficlog,"%.3e ",hess[i][j]);
1879: }
1880: printf("\n");
1881: fprintf(ficlog,"\n");
1882: }
1883:
1884: /* Recompute Inverse */
1885: for (i=1;i<=npar;i++)
1886: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1887: ludcmp(a,npar,indx,&pd);
1888:
1889: /* printf("\n#Hessian matrix recomputed#\n");
1890:
1891: for (j=1;j<=npar;j++) {
1892: for (i=1;i<=npar;i++) x[i]=0;
1893: x[j]=1;
1894: lubksb(a,npar,indx,x);
1895: for (i=1;i<=npar;i++){
1896: y[i][j]=x[i];
1897: printf("%.3e ",y[i][j]);
1898: fprintf(ficlog,"%.3e ",y[i][j]);
1899: }
1900: printf("\n");
1901: fprintf(ficlog,"\n");
1902: }
1903: */
1904:
1905: free_matrix(a,1,npar,1,npar);
1906: free_matrix(y,1,npar,1,npar);
1907: free_vector(x,1,npar);
1908: free_ivector(indx,1,npar);
1909: free_matrix(hess,1,npar,1,npar);
1910:
1911:
1912: }
1913:
1914: /*************** hessian matrix ****************/
1915: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1916: {
1917: int i;
1918: int l=1, lmax=20;
1919: double k1,k2;
1920: double p2[MAXPARM+1]; /* identical to x */
1921: double res;
1922: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1923: double fx;
1924: int k=0,kmax=10;
1925: double l1;
1926:
1927: fx=func(x);
1928: for (i=1;i<=npar;i++) p2[i]=x[i];
1929: for(l=0 ; l <=lmax; l++){
1930: l1=pow(10,l);
1931: delts=delt;
1932: for(k=1 ; k <kmax; k=k+1){
1933: delt = delta*(l1*k);
1934: p2[theta]=x[theta] +delt;
1935: k1=func(p2)-fx;
1936: p2[theta]=x[theta]-delt;
1937: k2=func(p2)-fx;
1938: /*res= (k1-2.0*fx+k2)/delt/delt; */
1939: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1940:
1941: #ifdef DEBUGHESS
1942: 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);
1943: 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);
1944: #endif
1945: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1946: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1947: k=kmax;
1948: }
1949: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1950: k=kmax; l=lmax*10.;
1951: }
1952: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1953: delts=delt;
1954: }
1955: }
1956: }
1957: delti[theta]=delts;
1958: return res;
1959:
1960: }
1961:
1962: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1963: {
1964: int i;
1965: int l=1, l1, lmax=20;
1966: double k1,k2,k3,k4,res,fx;
1967: double p2[MAXPARM+1];
1968: int k;
1969:
1970: fx=func(x);
1971: for (k=1; k<=2; k++) {
1972: for (i=1;i<=npar;i++) p2[i]=x[i];
1973: p2[thetai]=x[thetai]+delti[thetai]/k;
1974: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1975: k1=func(p2)-fx;
1976:
1977: p2[thetai]=x[thetai]+delti[thetai]/k;
1978: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1979: k2=func(p2)-fx;
1980:
1981: p2[thetai]=x[thetai]-delti[thetai]/k;
1982: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1983: k3=func(p2)-fx;
1984:
1985: p2[thetai]=x[thetai]-delti[thetai]/k;
1986: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1987: k4=func(p2)-fx;
1988: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1989: #ifdef DEBUG
1990: 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);
1991: 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);
1992: #endif
1993: }
1994: return res;
1995: }
1996:
1997: /************** Inverse of matrix **************/
1998: void ludcmp(double **a, int n, int *indx, double *d)
1999: {
2000: int i,imax,j,k;
2001: double big,dum,sum,temp;
2002: double *vv;
2003:
2004: vv=vector(1,n);
2005: *d=1.0;
2006: for (i=1;i<=n;i++) {
2007: big=0.0;
2008: for (j=1;j<=n;j++)
2009: if ((temp=fabs(a[i][j])) > big) big=temp;
2010: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2011: vv[i]=1.0/big;
2012: }
2013: for (j=1;j<=n;j++) {
2014: for (i=1;i<j;i++) {
2015: sum=a[i][j];
2016: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2017: a[i][j]=sum;
2018: }
2019: big=0.0;
2020: for (i=j;i<=n;i++) {
2021: sum=a[i][j];
2022: for (k=1;k<j;k++)
2023: sum -= a[i][k]*a[k][j];
2024: a[i][j]=sum;
2025: if ( (dum=vv[i]*fabs(sum)) >= big) {
2026: big=dum;
2027: imax=i;
2028: }
2029: }
2030: if (j != imax) {
2031: for (k=1;k<=n;k++) {
2032: dum=a[imax][k];
2033: a[imax][k]=a[j][k];
2034: a[j][k]=dum;
2035: }
2036: *d = -(*d);
2037: vv[imax]=vv[j];
2038: }
2039: indx[j]=imax;
2040: if (a[j][j] == 0.0) a[j][j]=TINY;
2041: if (j != n) {
2042: dum=1.0/(a[j][j]);
2043: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2044: }
2045: }
2046: free_vector(vv,1,n); /* Doesn't work */
2047: ;
2048: }
2049:
2050: void lubksb(double **a, int n, int *indx, double b[])
2051: {
2052: int i,ii=0,ip,j;
2053: double sum;
2054:
2055: for (i=1;i<=n;i++) {
2056: ip=indx[i];
2057: sum=b[ip];
2058: b[ip]=b[i];
2059: if (ii)
2060: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2061: else if (sum) ii=i;
2062: b[i]=sum;
2063: }
2064: for (i=n;i>=1;i--) {
2065: sum=b[i];
2066: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2067: b[i]=sum/a[i][i];
2068: }
2069: }
2070:
2071: void pstamp(FILE *fichier)
2072: {
2073: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2074: }
2075:
2076: /************ Frequencies ********************/
2077: 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[])
2078: { /* Some frequencies */
2079:
2080: int i, m, jk, k1,i1, j1, bool, z1,j;
2081: int first;
2082: double ***freq; /* Frequencies */
2083: double *pp, **prop;
2084: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2085: char fileresp[FILENAMELENGTH];
2086:
2087: pp=vector(1,nlstate);
2088: prop=matrix(1,nlstate,iagemin,iagemax+3);
2089: strcpy(fileresp,"p");
2090: strcat(fileresp,fileres);
2091: if((ficresp=fopen(fileresp,"w"))==NULL) {
2092: printf("Problem with prevalence resultfile: %s\n", fileresp);
2093: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2094: exit(0);
2095: }
2096: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2097: j1=0;
2098:
2099: j=cptcoveff;
2100: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2101:
2102: first=1;
2103:
2104: for(k1=1; k1<=j;k1++){
2105: for(i1=1; i1<=ncodemax[k1];i1++){
2106: j1++;
2107: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2108: scanf("%d", i);*/
2109: for (i=-5; i<=nlstate+ndeath; i++)
2110: for (jk=-5; jk<=nlstate+ndeath; jk++)
2111: for(m=iagemin; m <= iagemax+3; m++)
2112: freq[i][jk][m]=0;
2113:
2114: for (i=1; i<=nlstate; i++)
2115: for(m=iagemin; m <= iagemax+3; m++)
2116: prop[i][m]=0;
2117:
2118: dateintsum=0;
2119: k2cpt=0;
2120: for (i=1; i<=imx; i++) {
2121: bool=1;
2122: if (cptcovn>0) {
2123: for (z1=1; z1<=cptcoveff; z1++)
2124: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2125: bool=0;
2126: }
2127: if (bool==1){
2128: for(m=firstpass; m<=lastpass; m++){
2129: k2=anint[m][i]+(mint[m][i]/12.);
2130: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2131: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2132: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2133: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2134: if (m<lastpass) {
2135: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2136: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2137: }
2138:
2139: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2140: dateintsum=dateintsum+k2;
2141: k2cpt++;
2142: }
2143: /*}*/
2144: }
2145: }
2146: }
2147:
2148: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2149: pstamp(ficresp);
2150: if (cptcovn>0) {
2151: fprintf(ficresp, "\n#********** Variable ");
2152: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2153: fprintf(ficresp, "**********\n#");
2154: }
2155: for(i=1; i<=nlstate;i++)
2156: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2157: fprintf(ficresp, "\n");
2158:
2159: for(i=iagemin; i <= iagemax+3; i++){
2160: if(i==iagemax+3){
2161: fprintf(ficlog,"Total");
2162: }else{
2163: if(first==1){
2164: first=0;
2165: printf("See log file for details...\n");
2166: }
2167: fprintf(ficlog,"Age %d", i);
2168: }
2169: for(jk=1; jk <=nlstate ; jk++){
2170: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2171: pp[jk] += freq[jk][m][i];
2172: }
2173: for(jk=1; jk <=nlstate ; jk++){
2174: for(m=-1, pos=0; m <=0 ; m++)
2175: pos += freq[jk][m][i];
2176: if(pp[jk]>=1.e-10){
2177: if(first==1){
2178: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2179: }
2180: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2181: }else{
2182: if(first==1)
2183: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2184: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2185: }
2186: }
2187:
2188: for(jk=1; jk <=nlstate ; jk++){
2189: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2190: pp[jk] += freq[jk][m][i];
2191: }
2192: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2193: pos += pp[jk];
2194: posprop += prop[jk][i];
2195: }
2196: for(jk=1; jk <=nlstate ; jk++){
2197: if(pos>=1.e-5){
2198: if(first==1)
2199: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2200: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2201: }else{
2202: if(first==1)
2203: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2204: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2205: }
2206: if( i <= iagemax){
2207: if(pos>=1.e-5){
2208: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2209: /*probs[i][jk][j1]= pp[jk]/pos;*/
2210: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2211: }
2212: else
2213: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2214: }
2215: }
2216:
2217: for(jk=-1; jk <=nlstate+ndeath; jk++)
2218: for(m=-1; m <=nlstate+ndeath; m++)
2219: if(freq[jk][m][i] !=0 ) {
2220: if(first==1)
2221: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2222: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2223: }
2224: if(i <= iagemax)
2225: fprintf(ficresp,"\n");
2226: if(first==1)
2227: printf("Others in log...\n");
2228: fprintf(ficlog,"\n");
2229: }
2230: }
2231: }
2232: dateintmean=dateintsum/k2cpt;
2233:
2234: fclose(ficresp);
2235: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2236: free_vector(pp,1,nlstate);
2237: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2238: /* End of Freq */
2239: }
2240:
2241: /************ Prevalence ********************/
2242: 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)
2243: {
2244: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2245: in each health status at the date of interview (if between dateprev1 and dateprev2).
2246: We still use firstpass and lastpass as another selection.
2247: */
2248:
2249: int i, m, jk, k1, i1, j1, bool, z1,j;
2250: double ***freq; /* Frequencies */
2251: double *pp, **prop;
2252: double pos,posprop;
2253: double y2; /* in fractional years */
2254: int iagemin, iagemax;
2255:
2256: iagemin= (int) agemin;
2257: iagemax= (int) agemax;
2258: /*pp=vector(1,nlstate);*/
2259: prop=matrix(1,nlstate,iagemin,iagemax+3);
2260: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2261: j1=0;
2262:
2263: j=cptcoveff;
2264: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2265:
2266: for(k1=1; k1<=j;k1++){
2267: for(i1=1; i1<=ncodemax[k1];i1++){
2268: j1++;
2269:
2270: for (i=1; i<=nlstate; i++)
2271: for(m=iagemin; m <= iagemax+3; m++)
2272: prop[i][m]=0.0;
2273:
2274: for (i=1; i<=imx; i++) { /* Each individual */
2275: bool=1;
2276: if (cptcovn>0) {
2277: for (z1=1; z1<=cptcoveff; z1++)
2278: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2279: bool=0;
2280: }
2281: if (bool==1) {
2282: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2283: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2284: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2285: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2286: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2287: 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);
2288: if (s[m][i]>0 && s[m][i]<=nlstate) {
2289: /*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]]);*/
2290: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2291: prop[s[m][i]][iagemax+3] += weight[i];
2292: }
2293: }
2294: } /* end selection of waves */
2295: }
2296: }
2297: for(i=iagemin; i <= iagemax+3; i++){
2298:
2299: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2300: posprop += prop[jk][i];
2301: }
2302:
2303: for(jk=1; jk <=nlstate ; jk++){
2304: if( i <= iagemax){
2305: if(posprop>=1.e-5){
2306: probs[i][jk][j1]= prop[jk][i]/posprop;
2307: } else
2308: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2309: }
2310: }/* end jk */
2311: }/* end i */
2312: } /* end i1 */
2313: } /* end k1 */
2314:
2315: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2316: /*free_vector(pp,1,nlstate);*/
2317: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2318: } /* End of prevalence */
2319:
2320: /************* Waves Concatenation ***************/
2321:
2322: 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)
2323: {
2324: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2325: Death is a valid wave (if date is known).
2326: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2327: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2328: and mw[mi+1][i]. dh depends on stepm.
2329: */
2330:
2331: int i, mi, m;
2332: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2333: double sum=0., jmean=0.;*/
2334: int first;
2335: int j, k=0,jk, ju, jl;
2336: double sum=0.;
2337: first=0;
2338: jmin=1e+5;
2339: jmax=-1;
2340: jmean=0.;
2341: for(i=1; i<=imx; i++){
2342: mi=0;
2343: m=firstpass;
2344: while(s[m][i] <= nlstate){
2345: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2346: mw[++mi][i]=m;
2347: if(m >=lastpass)
2348: break;
2349: else
2350: m++;
2351: }/* end while */
2352: if (s[m][i] > nlstate){
2353: mi++; /* Death is another wave */
2354: /* if(mi==0) never been interviewed correctly before death */
2355: /* Only death is a correct wave */
2356: mw[mi][i]=m;
2357: }
2358:
2359: wav[i]=mi;
2360: if(mi==0){
2361: nbwarn++;
2362: if(first==0){
2363: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2364: first=1;
2365: }
2366: if(first==1){
2367: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2368: }
2369: } /* end mi==0 */
2370: } /* End individuals */
2371:
2372: for(i=1; i<=imx; i++){
2373: for(mi=1; mi<wav[i];mi++){
2374: if (stepm <=0)
2375: dh[mi][i]=1;
2376: else{
2377: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2378: if (agedc[i] < 2*AGESUP) {
2379: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2380: if(j==0) j=1; /* Survives at least one month after exam */
2381: else if(j<0){
2382: nberr++;
2383: 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]);
2384: j=1; /* Temporary Dangerous patch */
2385: 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);
2386: 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]);
2387: 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);
2388: }
2389: k=k+1;
2390: if (j >= jmax){
2391: jmax=j;
2392: ijmax=i;
2393: }
2394: if (j <= jmin){
2395: jmin=j;
2396: ijmin=i;
2397: }
2398: sum=sum+j;
2399: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2400: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2401: }
2402: }
2403: else{
2404: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2405: /* 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]); */
2406:
2407: k=k+1;
2408: if (j >= jmax) {
2409: jmax=j;
2410: ijmax=i;
2411: }
2412: else if (j <= jmin){
2413: jmin=j;
2414: ijmin=i;
2415: }
2416: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2417: /*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]);*/
2418: if(j<0){
2419: nberr++;
2420: 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]);
2421: 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]);
2422: }
2423: sum=sum+j;
2424: }
2425: jk= j/stepm;
2426: jl= j -jk*stepm;
2427: ju= j -(jk+1)*stepm;
2428: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2429: if(jl==0){
2430: dh[mi][i]=jk;
2431: bh[mi][i]=0;
2432: }else{ /* We want a negative bias in order to only have interpolation ie
2433: * at the price of an extra matrix product in likelihood */
2434: dh[mi][i]=jk+1;
2435: bh[mi][i]=ju;
2436: }
2437: }else{
2438: if(jl <= -ju){
2439: dh[mi][i]=jk;
2440: bh[mi][i]=jl; /* bias is positive if real duration
2441: * is higher than the multiple of stepm and negative otherwise.
2442: */
2443: }
2444: else{
2445: dh[mi][i]=jk+1;
2446: bh[mi][i]=ju;
2447: }
2448: if(dh[mi][i]==0){
2449: dh[mi][i]=1; /* At least one step */
2450: bh[mi][i]=ju; /* At least one step */
2451: /* 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);*/
2452: }
2453: } /* end if mle */
2454: }
2455: } /* end wave */
2456: }
2457: jmean=sum/k;
2458: 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);
2459: 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);
2460: }
2461:
2462: /*********** Tricode ****************************/
2463: void tricode(int *Tvar, int **nbcode, int imx)
2464: {
2465:
2466: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2467:
2468: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2469: int cptcode=0;
2470: cptcoveff=0;
2471:
2472: for (k=0; k<maxncov; k++) Ndum[k]=0;
2473: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
2474:
2475: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
2476: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2477: modality*/
2478: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
2479: Ndum[ij]++; /*counts the occurence of this modality */
2480: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2481: if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
2482: Tvar[j]. If V=sex and male is 0 and
2483: female is 1, then cptcode=1.*/
2484: }
2485:
2486: for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
2487: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
2488: th covariate. In fact
2489: ncodemax[j]=2
2490: (dichotom. variables only) but
2491: it can be more */
2492: } /* Ndum[-1] number of undefined modalities */
2493:
2494: ij=1;
2495: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
2496: for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
2497: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2498: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2499: k is a modality. If we have model=V1+V1*sex
2500: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2501: ij++;
2502: }
2503: if (ij > ncodemax[j]) break;
2504: }
2505: }
2506: }
2507:
2508: for (k=0; k< maxncov; k++) Ndum[k]=0;
2509:
2510: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2511: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2512: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2513: Ndum[ij]++;
2514: }
2515:
2516: ij=1;
2517: for (i=1; i<= maxncov; i++) {
2518: if((Ndum[i]!=0) && (i<=ncovcol)){
2519: Tvaraff[ij]=i; /*For printing */
2520: ij++;
2521: }
2522: }
2523: ij--;
2524: cptcoveff=ij; /*Number of simple covariates*/
2525: }
2526:
2527: /*********** Health Expectancies ****************/
2528:
2529: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2530:
2531: {
2532: /* Health expectancies, no variances */
2533: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2534: int nhstepma, nstepma; /* Decreasing with age */
2535: double age, agelim, hf;
2536: double ***p3mat;
2537: double eip;
2538:
2539: pstamp(ficreseij);
2540: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2541: fprintf(ficreseij,"# Age");
2542: for(i=1; i<=nlstate;i++){
2543: for(j=1; j<=nlstate;j++){
2544: fprintf(ficreseij," e%1d%1d ",i,j);
2545: }
2546: fprintf(ficreseij," e%1d. ",i);
2547: }
2548: fprintf(ficreseij,"\n");
2549:
2550:
2551: if(estepm < stepm){
2552: printf ("Problem %d lower than %d\n",estepm, stepm);
2553: }
2554: else hstepm=estepm;
2555: /* We compute the life expectancy from trapezoids spaced every estepm months
2556: * This is mainly to measure the difference between two models: for example
2557: * if stepm=24 months pijx are given only every 2 years and by summing them
2558: * we are calculating an estimate of the Life Expectancy assuming a linear
2559: * progression in between and thus overestimating or underestimating according
2560: * to the curvature of the survival function. If, for the same date, we
2561: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2562: * to compare the new estimate of Life expectancy with the same linear
2563: * hypothesis. A more precise result, taking into account a more precise
2564: * curvature will be obtained if estepm is as small as stepm. */
2565:
2566: /* For example we decided to compute the life expectancy with the smallest unit */
2567: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2568: nhstepm is the number of hstepm from age to agelim
2569: nstepm is the number of stepm from age to agelin.
2570: Look at hpijx to understand the reason of that which relies in memory size
2571: and note for a fixed period like estepm months */
2572: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2573: survival function given by stepm (the optimization length). Unfortunately it
2574: means that if the survival funtion is printed only each two years of age and if
2575: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2576: results. So we changed our mind and took the option of the best precision.
2577: */
2578: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2579:
2580: agelim=AGESUP;
2581: /* If stepm=6 months */
2582: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2583: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2584:
2585: /* nhstepm age range expressed in number of stepm */
2586: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2587: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2588: /* if (stepm >= YEARM) hstepm=1;*/
2589: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2590: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2591:
2592: for (age=bage; age<=fage; age ++){
2593: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2594: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2595: /* if (stepm >= YEARM) hstepm=1;*/
2596: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2597:
2598: /* If stepm=6 months */
2599: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2600: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2601:
2602: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2603:
2604: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2605:
2606: printf("%d|",(int)age);fflush(stdout);
2607: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2608:
2609: /* Computing expectancies */
2610: for(i=1; i<=nlstate;i++)
2611: for(j=1; j<=nlstate;j++)
2612: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2613: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2614:
2615: /* 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]);*/
2616:
2617: }
2618:
2619: fprintf(ficreseij,"%3.0f",age );
2620: for(i=1; i<=nlstate;i++){
2621: eip=0;
2622: for(j=1; j<=nlstate;j++){
2623: eip +=eij[i][j][(int)age];
2624: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2625: }
2626: fprintf(ficreseij,"%9.4f", eip );
2627: }
2628: fprintf(ficreseij,"\n");
2629:
2630: }
2631: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2632: printf("\n");
2633: fprintf(ficlog,"\n");
2634:
2635: }
2636:
2637: 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[] )
2638:
2639: {
2640: /* Covariances of health expectancies eij and of total life expectancies according
2641: to initial status i, ei. .
2642: */
2643: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2644: int nhstepma, nstepma; /* Decreasing with age */
2645: double age, agelim, hf;
2646: double ***p3matp, ***p3matm, ***varhe;
2647: double **dnewm,**doldm;
2648: double *xp, *xm;
2649: double **gp, **gm;
2650: double ***gradg, ***trgradg;
2651: int theta;
2652:
2653: double eip, vip;
2654:
2655: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2656: xp=vector(1,npar);
2657: xm=vector(1,npar);
2658: dnewm=matrix(1,nlstate*nlstate,1,npar);
2659: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2660:
2661: pstamp(ficresstdeij);
2662: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2663: fprintf(ficresstdeij,"# Age");
2664: for(i=1; i<=nlstate;i++){
2665: for(j=1; j<=nlstate;j++)
2666: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2667: fprintf(ficresstdeij," e%1d. ",i);
2668: }
2669: fprintf(ficresstdeij,"\n");
2670:
2671: pstamp(ficrescveij);
2672: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2673: fprintf(ficrescveij,"# Age");
2674: for(i=1; i<=nlstate;i++)
2675: for(j=1; j<=nlstate;j++){
2676: cptj= (j-1)*nlstate+i;
2677: for(i2=1; i2<=nlstate;i2++)
2678: for(j2=1; j2<=nlstate;j2++){
2679: cptj2= (j2-1)*nlstate+i2;
2680: if(cptj2 <= cptj)
2681: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2682: }
2683: }
2684: fprintf(ficrescveij,"\n");
2685:
2686: if(estepm < stepm){
2687: printf ("Problem %d lower than %d\n",estepm, stepm);
2688: }
2689: else hstepm=estepm;
2690: /* We compute the life expectancy from trapezoids spaced every estepm months
2691: * This is mainly to measure the difference between two models: for example
2692: * if stepm=24 months pijx are given only every 2 years and by summing them
2693: * we are calculating an estimate of the Life Expectancy assuming a linear
2694: * progression in between and thus overestimating or underestimating according
2695: * to the curvature of the survival function. If, for the same date, we
2696: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2697: * to compare the new estimate of Life expectancy with the same linear
2698: * hypothesis. A more precise result, taking into account a more precise
2699: * curvature will be obtained if estepm is as small as stepm. */
2700:
2701: /* For example we decided to compute the life expectancy with the smallest unit */
2702: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2703: nhstepm is the number of hstepm from age to agelim
2704: nstepm is the number of stepm from age to agelin.
2705: Look at hpijx to understand the reason of that which relies in memory size
2706: and note for a fixed period like estepm months */
2707: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2708: survival function given by stepm (the optimization length). Unfortunately it
2709: means that if the survival funtion is printed only each two years of age and if
2710: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2711: results. So we changed our mind and took the option of the best precision.
2712: */
2713: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2714:
2715: /* If stepm=6 months */
2716: /* nhstepm age range expressed in number of stepm */
2717: agelim=AGESUP;
2718: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2719: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2720: /* if (stepm >= YEARM) hstepm=1;*/
2721: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2722:
2723: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2724: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2725: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2726: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2727: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2728: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2729:
2730: for (age=bage; age<=fage; age ++){
2731: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2732: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2733: /* if (stepm >= YEARM) hstepm=1;*/
2734: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2735:
2736: /* If stepm=6 months */
2737: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2738: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2739:
2740: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2741:
2742: /* Computing Variances of health expectancies */
2743: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2744: decrease memory allocation */
2745: for(theta=1; theta <=npar; theta++){
2746: for(i=1; i<=npar; i++){
2747: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2748: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2749: }
2750: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2751: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2752:
2753: for(j=1; j<= nlstate; j++){
2754: for(i=1; i<=nlstate; i++){
2755: for(h=0; h<=nhstepm-1; h++){
2756: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2757: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2758: }
2759: }
2760: }
2761:
2762: for(ij=1; ij<= nlstate*nlstate; ij++)
2763: for(h=0; h<=nhstepm-1; h++){
2764: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2765: }
2766: }/* End theta */
2767:
2768:
2769: for(h=0; h<=nhstepm-1; h++)
2770: for(j=1; j<=nlstate*nlstate;j++)
2771: for(theta=1; theta <=npar; theta++)
2772: trgradg[h][j][theta]=gradg[h][theta][j];
2773:
2774:
2775: for(ij=1;ij<=nlstate*nlstate;ij++)
2776: for(ji=1;ji<=nlstate*nlstate;ji++)
2777: varhe[ij][ji][(int)age] =0.;
2778:
2779: printf("%d|",(int)age);fflush(stdout);
2780: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2781: for(h=0;h<=nhstepm-1;h++){
2782: for(k=0;k<=nhstepm-1;k++){
2783: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2784: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2785: for(ij=1;ij<=nlstate*nlstate;ij++)
2786: for(ji=1;ji<=nlstate*nlstate;ji++)
2787: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2788: }
2789: }
2790:
2791: /* Computing expectancies */
2792: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2793: for(i=1; i<=nlstate;i++)
2794: for(j=1; j<=nlstate;j++)
2795: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2796: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2797:
2798: /* 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]);*/
2799:
2800: }
2801:
2802: fprintf(ficresstdeij,"%3.0f",age );
2803: for(i=1; i<=nlstate;i++){
2804: eip=0.;
2805: vip=0.;
2806: for(j=1; j<=nlstate;j++){
2807: eip += eij[i][j][(int)age];
2808: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2809: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2810: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2811: }
2812: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2813: }
2814: fprintf(ficresstdeij,"\n");
2815:
2816: fprintf(ficrescveij,"%3.0f",age );
2817: for(i=1; i<=nlstate;i++)
2818: for(j=1; j<=nlstate;j++){
2819: cptj= (j-1)*nlstate+i;
2820: for(i2=1; i2<=nlstate;i2++)
2821: for(j2=1; j2<=nlstate;j2++){
2822: cptj2= (j2-1)*nlstate+i2;
2823: if(cptj2 <= cptj)
2824: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2825: }
2826: }
2827: fprintf(ficrescveij,"\n");
2828:
2829: }
2830: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2831: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2832: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2833: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2834: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2835: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2836: printf("\n");
2837: fprintf(ficlog,"\n");
2838:
2839: free_vector(xm,1,npar);
2840: free_vector(xp,1,npar);
2841: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2842: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2843: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2844: }
2845:
2846: /************ Variance ******************/
2847: 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[])
2848: {
2849: /* Variance of health expectancies */
2850: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2851: /* double **newm;*/
2852: double **dnewm,**doldm;
2853: double **dnewmp,**doldmp;
2854: int i, j, nhstepm, hstepm, h, nstepm ;
2855: int k, cptcode;
2856: double *xp;
2857: double **gp, **gm; /* for var eij */
2858: double ***gradg, ***trgradg; /*for var eij */
2859: double **gradgp, **trgradgp; /* for var p point j */
2860: double *gpp, *gmp; /* for var p point j */
2861: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2862: double ***p3mat;
2863: double age,agelim, hf;
2864: double ***mobaverage;
2865: int theta;
2866: char digit[4];
2867: char digitp[25];
2868:
2869: char fileresprobmorprev[FILENAMELENGTH];
2870:
2871: if(popbased==1){
2872: if(mobilav!=0)
2873: strcpy(digitp,"-populbased-mobilav-");
2874: else strcpy(digitp,"-populbased-nomobil-");
2875: }
2876: else
2877: strcpy(digitp,"-stablbased-");
2878:
2879: if (mobilav!=0) {
2880: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2881: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2882: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2883: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2884: }
2885: }
2886:
2887: strcpy(fileresprobmorprev,"prmorprev");
2888: sprintf(digit,"%-d",ij);
2889: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2890: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2891: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2892: strcat(fileresprobmorprev,fileres);
2893: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2894: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2895: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2896: }
2897: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2898:
2899: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2900: pstamp(ficresprobmorprev);
2901: 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);
2902: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2903: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2904: fprintf(ficresprobmorprev," p.%-d SE",j);
2905: for(i=1; i<=nlstate;i++)
2906: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2907: }
2908: fprintf(ficresprobmorprev,"\n");
2909: fprintf(ficgp,"\n# Routine varevsij");
2910: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2911: 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");
2912: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2913: /* } */
2914: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2915: pstamp(ficresvij);
2916: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2917: if(popbased==1)
2918: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
2919: else
2920: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2921: fprintf(ficresvij,"# Age");
2922: for(i=1; i<=nlstate;i++)
2923: for(j=1; j<=nlstate;j++)
2924: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2925: fprintf(ficresvij,"\n");
2926:
2927: xp=vector(1,npar);
2928: dnewm=matrix(1,nlstate,1,npar);
2929: doldm=matrix(1,nlstate,1,nlstate);
2930: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2931: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2932:
2933: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2934: gpp=vector(nlstate+1,nlstate+ndeath);
2935: gmp=vector(nlstate+1,nlstate+ndeath);
2936: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2937:
2938: if(estepm < stepm){
2939: printf ("Problem %d lower than %d\n",estepm, stepm);
2940: }
2941: else hstepm=estepm;
2942: /* For example we decided to compute the life expectancy with the smallest unit */
2943: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2944: nhstepm is the number of hstepm from age to agelim
2945: nstepm is the number of stepm from age to agelin.
2946: Look at function hpijx to understand why (it is linked to memory size questions) */
2947: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2948: survival function given by stepm (the optimization length). Unfortunately it
2949: means that if the survival funtion is printed every two years of age and if
2950: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2951: results. So we changed our mind and took the option of the best precision.
2952: */
2953: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2954: agelim = AGESUP;
2955: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2956: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2957: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2958: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2959: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2960: gp=matrix(0,nhstepm,1,nlstate);
2961: gm=matrix(0,nhstepm,1,nlstate);
2962:
2963:
2964: for(theta=1; theta <=npar; theta++){
2965: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2966: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2967: }
2968: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2969: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2970:
2971: if (popbased==1) {
2972: if(mobilav ==0){
2973: for(i=1; i<=nlstate;i++)
2974: prlim[i][i]=probs[(int)age][i][ij];
2975: }else{ /* mobilav */
2976: for(i=1; i<=nlstate;i++)
2977: prlim[i][i]=mobaverage[(int)age][i][ij];
2978: }
2979: }
2980:
2981: for(j=1; j<= nlstate; j++){
2982: for(h=0; h<=nhstepm; h++){
2983: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2984: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2985: }
2986: }
2987: /* This for computing probability of death (h=1 means
2988: computed over hstepm matrices product = hstepm*stepm months)
2989: as a weighted average of prlim.
2990: */
2991: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2992: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2993: gpp[j] += prlim[i][i]*p3mat[i][j][1];
2994: }
2995: /* end probability of death */
2996:
2997: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
2998: xp[i] = x[i] - (i==theta ?delti[theta]:0);
2999: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3000: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3001:
3002: if (popbased==1) {
3003: if(mobilav ==0){
3004: for(i=1; i<=nlstate;i++)
3005: prlim[i][i]=probs[(int)age][i][ij];
3006: }else{ /* mobilav */
3007: for(i=1; i<=nlstate;i++)
3008: prlim[i][i]=mobaverage[(int)age][i][ij];
3009: }
3010: }
3011:
3012: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3013: for(h=0; h<=nhstepm; h++){
3014: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3015: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3016: }
3017: }
3018: /* This for computing probability of death (h=1 means
3019: computed over hstepm matrices product = hstepm*stepm months)
3020: as a weighted average of prlim.
3021: */
3022: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3023: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3024: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3025: }
3026: /* end probability of death */
3027:
3028: for(j=1; j<= nlstate; j++) /* vareij */
3029: for(h=0; h<=nhstepm; h++){
3030: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3031: }
3032:
3033: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3034: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3035: }
3036:
3037: } /* End theta */
3038:
3039: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3040:
3041: for(h=0; h<=nhstepm; h++) /* veij */
3042: for(j=1; j<=nlstate;j++)
3043: for(theta=1; theta <=npar; theta++)
3044: trgradg[h][j][theta]=gradg[h][theta][j];
3045:
3046: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3047: for(theta=1; theta <=npar; theta++)
3048: trgradgp[j][theta]=gradgp[theta][j];
3049:
3050:
3051: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3052: for(i=1;i<=nlstate;i++)
3053: for(j=1;j<=nlstate;j++)
3054: vareij[i][j][(int)age] =0.;
3055:
3056: for(h=0;h<=nhstepm;h++){
3057: for(k=0;k<=nhstepm;k++){
3058: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3059: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3060: for(i=1;i<=nlstate;i++)
3061: for(j=1;j<=nlstate;j++)
3062: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3063: }
3064: }
3065:
3066: /* pptj */
3067: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3068: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3069: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3070: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3071: varppt[j][i]=doldmp[j][i];
3072: /* end ppptj */
3073: /* x centered again */
3074: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3075: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3076:
3077: if (popbased==1) {
3078: if(mobilav ==0){
3079: for(i=1; i<=nlstate;i++)
3080: prlim[i][i]=probs[(int)age][i][ij];
3081: }else{ /* mobilav */
3082: for(i=1; i<=nlstate;i++)
3083: prlim[i][i]=mobaverage[(int)age][i][ij];
3084: }
3085: }
3086:
3087: /* This for computing probability of death (h=1 means
3088: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3089: as a weighted average of prlim.
3090: */
3091: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3092: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3093: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3094: }
3095: /* end probability of death */
3096:
3097: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3098: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3099: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3100: for(i=1; i<=nlstate;i++){
3101: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3102: }
3103: }
3104: fprintf(ficresprobmorprev,"\n");
3105:
3106: fprintf(ficresvij,"%.0f ",age );
3107: for(i=1; i<=nlstate;i++)
3108: for(j=1; j<=nlstate;j++){
3109: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3110: }
3111: fprintf(ficresvij,"\n");
3112: free_matrix(gp,0,nhstepm,1,nlstate);
3113: free_matrix(gm,0,nhstepm,1,nlstate);
3114: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3115: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3116: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3117: } /* End age */
3118: free_vector(gpp,nlstate+1,nlstate+ndeath);
3119: free_vector(gmp,nlstate+1,nlstate+ndeath);
3120: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3121: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3122: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
3123: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3124: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3125: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3126: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3127: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3128: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3129: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3130: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3131: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3132: 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);
3133: /* 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);
3134: */
3135: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3136: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3137:
3138: free_vector(xp,1,npar);
3139: free_matrix(doldm,1,nlstate,1,nlstate);
3140: free_matrix(dnewm,1,nlstate,1,npar);
3141: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3142: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3143: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3144: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3145: fclose(ficresprobmorprev);
3146: fflush(ficgp);
3147: fflush(fichtm);
3148: } /* end varevsij */
3149:
3150: /************ Variance of prevlim ******************/
3151: 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[])
3152: {
3153: /* Variance of prevalence limit */
3154: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3155: double **newm;
3156: double **dnewm,**doldm;
3157: int i, j, nhstepm, hstepm;
3158: int k, cptcode;
3159: double *xp;
3160: double *gp, *gm;
3161: double **gradg, **trgradg;
3162: double age,agelim;
3163: int theta;
3164:
3165: pstamp(ficresvpl);
3166: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3167: fprintf(ficresvpl,"# Age");
3168: for(i=1; i<=nlstate;i++)
3169: fprintf(ficresvpl," %1d-%1d",i,i);
3170: fprintf(ficresvpl,"\n");
3171:
3172: xp=vector(1,npar);
3173: dnewm=matrix(1,nlstate,1,npar);
3174: doldm=matrix(1,nlstate,1,nlstate);
3175:
3176: hstepm=1*YEARM; /* Every year of age */
3177: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3178: agelim = AGESUP;
3179: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3180: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3181: if (stepm >= YEARM) hstepm=1;
3182: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3183: gradg=matrix(1,npar,1,nlstate);
3184: gp=vector(1,nlstate);
3185: gm=vector(1,nlstate);
3186:
3187: for(theta=1; theta <=npar; theta++){
3188: for(i=1; i<=npar; i++){ /* Computes gradient */
3189: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3190: }
3191: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3192: for(i=1;i<=nlstate;i++)
3193: gp[i] = prlim[i][i];
3194:
3195: for(i=1; i<=npar; i++) /* Computes gradient */
3196: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3197: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3198: for(i=1;i<=nlstate;i++)
3199: gm[i] = prlim[i][i];
3200:
3201: for(i=1;i<=nlstate;i++)
3202: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3203: } /* End theta */
3204:
3205: trgradg =matrix(1,nlstate,1,npar);
3206:
3207: for(j=1; j<=nlstate;j++)
3208: for(theta=1; theta <=npar; theta++)
3209: trgradg[j][theta]=gradg[theta][j];
3210:
3211: for(i=1;i<=nlstate;i++)
3212: varpl[i][(int)age] =0.;
3213: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3214: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3215: for(i=1;i<=nlstate;i++)
3216: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3217:
3218: fprintf(ficresvpl,"%.0f ",age );
3219: for(i=1; i<=nlstate;i++)
3220: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3221: fprintf(ficresvpl,"\n");
3222: free_vector(gp,1,nlstate);
3223: free_vector(gm,1,nlstate);
3224: free_matrix(gradg,1,npar,1,nlstate);
3225: free_matrix(trgradg,1,nlstate,1,npar);
3226: } /* End age */
3227:
3228: free_vector(xp,1,npar);
3229: free_matrix(doldm,1,nlstate,1,npar);
3230: free_matrix(dnewm,1,nlstate,1,nlstate);
3231:
3232: }
3233:
3234: /************ Variance of one-step probabilities ******************/
3235: 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[])
3236: {
3237: int i, j=0, i1, k1, l1, t, tj;
3238: int k2, l2, j1, z1;
3239: int k=0,l, cptcode;
3240: int first=1, first1;
3241: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3242: double **dnewm,**doldm;
3243: double *xp;
3244: double *gp, *gm;
3245: double **gradg, **trgradg;
3246: double **mu;
3247: double age,agelim, cov[NCOVMAX];
3248: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3249: int theta;
3250: char fileresprob[FILENAMELENGTH];
3251: char fileresprobcov[FILENAMELENGTH];
3252: char fileresprobcor[FILENAMELENGTH];
3253:
3254: double ***varpij;
3255:
3256: strcpy(fileresprob,"prob");
3257: strcat(fileresprob,fileres);
3258: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3259: printf("Problem with resultfile: %s\n", fileresprob);
3260: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3261: }
3262: strcpy(fileresprobcov,"probcov");
3263: strcat(fileresprobcov,fileres);
3264: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3265: printf("Problem with resultfile: %s\n", fileresprobcov);
3266: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3267: }
3268: strcpy(fileresprobcor,"probcor");
3269: strcat(fileresprobcor,fileres);
3270: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3271: printf("Problem with resultfile: %s\n", fileresprobcor);
3272: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3273: }
3274: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3275: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3276: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3277: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3278: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3279: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3280: pstamp(ficresprob);
3281: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3282: fprintf(ficresprob,"# Age");
3283: pstamp(ficresprobcov);
3284: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3285: fprintf(ficresprobcov,"# Age");
3286: pstamp(ficresprobcor);
3287: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3288: fprintf(ficresprobcor,"# Age");
3289:
3290:
3291: for(i=1; i<=nlstate;i++)
3292: for(j=1; j<=(nlstate+ndeath);j++){
3293: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3294: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3295: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3296: }
3297: /* fprintf(ficresprob,"\n");
3298: fprintf(ficresprobcov,"\n");
3299: fprintf(ficresprobcor,"\n");
3300: */
3301: xp=vector(1,npar);
3302: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3303: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3304: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3305: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3306: first=1;
3307: fprintf(ficgp,"\n# Routine varprob");
3308: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3309: fprintf(fichtm,"\n");
3310:
3311: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3312: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3313: file %s<br>\n",optionfilehtmcov);
3314: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3315: and drawn. It helps understanding how is the covariance between two incidences.\
3316: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3317: 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. \
3318: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3319: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3320: standard deviations wide on each axis. <br>\
3321: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3322: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3323: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3324:
3325: cov[1]=1;
3326: tj=cptcoveff;
3327: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3328: j1=0;
3329: for(t=1; t<=tj;t++){
3330: for(i1=1; i1<=ncodemax[t];i1++){
3331: j1++;
3332: if (cptcovn>0) {
3333: fprintf(ficresprob, "\n#********** Variable ");
3334: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3335: fprintf(ficresprob, "**********\n#\n");
3336: fprintf(ficresprobcov, "\n#********** Variable ");
3337: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3338: fprintf(ficresprobcov, "**********\n#\n");
3339:
3340: fprintf(ficgp, "\n#********** Variable ");
3341: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3342: fprintf(ficgp, "**********\n#\n");
3343:
3344:
3345: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3346: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3347: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3348:
3349: fprintf(ficresprobcor, "\n#********** Variable ");
3350: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3351: fprintf(ficresprobcor, "**********\n#");
3352: }
3353:
3354: for (age=bage; age<=fage; age ++){
3355: cov[2]=age;
3356: for (k=1; k<=cptcovn;k++) {
3357: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3358: }
3359: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3360: for (k=1; k<=cptcovprod;k++)
3361: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3362:
3363: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3364: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3365: gp=vector(1,(nlstate)*(nlstate+ndeath));
3366: gm=vector(1,(nlstate)*(nlstate+ndeath));
3367:
3368: for(theta=1; theta <=npar; theta++){
3369: for(i=1; i<=npar; i++)
3370: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3371:
3372: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3373:
3374: k=0;
3375: for(i=1; i<= (nlstate); i++){
3376: for(j=1; j<=(nlstate+ndeath);j++){
3377: k=k+1;
3378: gp[k]=pmmij[i][j];
3379: }
3380: }
3381:
3382: for(i=1; i<=npar; i++)
3383: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3384:
3385: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3386: k=0;
3387: for(i=1; i<=(nlstate); i++){
3388: for(j=1; j<=(nlstate+ndeath);j++){
3389: k=k+1;
3390: gm[k]=pmmij[i][j];
3391: }
3392: }
3393:
3394: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3395: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3396: }
3397:
3398: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3399: for(theta=1; theta <=npar; theta++)
3400: trgradg[j][theta]=gradg[theta][j];
3401:
3402: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3403: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3404: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3405: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3406: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3407: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3408:
3409: pmij(pmmij,cov,ncovmodel,x,nlstate);
3410:
3411: k=0;
3412: for(i=1; i<=(nlstate); i++){
3413: for(j=1; j<=(nlstate+ndeath);j++){
3414: k=k+1;
3415: mu[k][(int) age]=pmmij[i][j];
3416: }
3417: }
3418: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3419: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3420: varpij[i][j][(int)age] = doldm[i][j];
3421:
3422: /*printf("\n%d ",(int)age);
3423: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3424: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3425: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3426: }*/
3427:
3428: fprintf(ficresprob,"\n%d ",(int)age);
3429: fprintf(ficresprobcov,"\n%d ",(int)age);
3430: fprintf(ficresprobcor,"\n%d ",(int)age);
3431:
3432: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3433: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3434: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3435: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3436: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3437: }
3438: i=0;
3439: for (k=1; k<=(nlstate);k++){
3440: for (l=1; l<=(nlstate+ndeath);l++){
3441: i=i++;
3442: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3443: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3444: for (j=1; j<=i;j++){
3445: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3446: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3447: }
3448: }
3449: }/* end of loop for state */
3450: } /* end of loop for age */
3451:
3452: /* Confidence intervalle of pij */
3453: /*
3454: fprintf(ficgp,"\nunset parametric;unset label");
3455: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3456: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3457: 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);
3458: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3459: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3460: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3461: */
3462:
3463: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3464: first1=1;
3465: for (k2=1; k2<=(nlstate);k2++){
3466: for (l2=1; l2<=(nlstate+ndeath);l2++){
3467: if(l2==k2) continue;
3468: j=(k2-1)*(nlstate+ndeath)+l2;
3469: for (k1=1; k1<=(nlstate);k1++){
3470: for (l1=1; l1<=(nlstate+ndeath);l1++){
3471: if(l1==k1) continue;
3472: i=(k1-1)*(nlstate+ndeath)+l1;
3473: if(i<=j) continue;
3474: for (age=bage; age<=fage; age ++){
3475: if ((int)age %5==0){
3476: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3477: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3478: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3479: mu1=mu[i][(int) age]/stepm*YEARM ;
3480: mu2=mu[j][(int) age]/stepm*YEARM;
3481: c12=cv12/sqrt(v1*v2);
3482: /* Computing eigen value of matrix of covariance */
3483: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3484: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3485: /* Eigen vectors */
3486: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3487: /*v21=sqrt(1.-v11*v11); *//* error */
3488: v21=(lc1-v1)/cv12*v11;
3489: v12=-v21;
3490: v22=v11;
3491: tnalp=v21/v11;
3492: if(first1==1){
3493: first1=0;
3494: 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);
3495: }
3496: 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);
3497: /*printf(fignu*/
3498: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3499: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3500: if(first==1){
3501: first=0;
3502: fprintf(ficgp,"\nset parametric;unset label");
3503: 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);
3504: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3505: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3506: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3507: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3508: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3509: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3510: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3511: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3512: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3513: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3514: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3515: 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",\
3516: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3517: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3518: }else{
3519: first=0;
3520: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3521: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3522: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3523: 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",\
3524: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3525: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3526: }/* if first */
3527: } /* age mod 5 */
3528: } /* end loop age */
3529: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3530: first=1;
3531: } /*l12 */
3532: } /* k12 */
3533: } /*l1 */
3534: }/* k1 */
3535: } /* loop covariates */
3536: }
3537: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3538: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3539: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3540: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3541: free_vector(xp,1,npar);
3542: fclose(ficresprob);
3543: fclose(ficresprobcov);
3544: fclose(ficresprobcor);
3545: fflush(ficgp);
3546: fflush(fichtmcov);
3547: }
3548:
3549:
3550: /******************* Printing html file ***********/
3551: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3552: int lastpass, int stepm, int weightopt, char model[],\
3553: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3554: int popforecast, int estepm ,\
3555: double jprev1, double mprev1,double anprev1, \
3556: double jprev2, double mprev2,double anprev2){
3557: int jj1, k1, i1, cpt;
3558:
3559: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3560: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3561: </ul>");
3562: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3563: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3564: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3565: fprintf(fichtm,"\
3566: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3567: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3568: fprintf(fichtm,"\
3569: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3570: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3571: fprintf(fichtm,"\
3572: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
3573: <a href=\"%s\">%s</a> <br>\n",
3574: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3575: fprintf(fichtm,"\
3576: - Population projections by age and states: \
3577: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3578:
3579: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3580:
3581: m=cptcoveff;
3582: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3583:
3584: jj1=0;
3585: for(k1=1; k1<=m;k1++){
3586: for(i1=1; i1<=ncodemax[k1];i1++){
3587: jj1++;
3588: if (cptcovn > 0) {
3589: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3590: for (cpt=1; cpt<=cptcoveff;cpt++)
3591: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3592: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3593: }
3594: /* Pij */
3595: 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> \
3596: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3597: /* Quasi-incidences */
3598: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3599: 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> \
3600: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3601: /* Period (stable) prevalence in each health state */
3602: for(cpt=1; cpt<nlstate;cpt++){
3603: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3604: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3605: }
3606: for(cpt=1; cpt<=nlstate;cpt++) {
3607: 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> \
3608: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3609: }
3610: } /* end i1 */
3611: }/* End k1 */
3612: fprintf(fichtm,"</ul>");
3613:
3614:
3615: fprintf(fichtm,"\
3616: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3617: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3618:
3619: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3620: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3621: fprintf(fichtm,"\
3622: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3623: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3624:
3625: fprintf(fichtm,"\
3626: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3627: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3628: fprintf(fichtm,"\
3629: - 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): \
3630: <a href=\"%s\">%s</a> <br>\n</li>",
3631: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3632: fprintf(fichtm,"\
3633: - (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): \
3634: <a href=\"%s\">%s</a> <br>\n</li>",
3635: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3636: fprintf(fichtm,"\
3637: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
3638: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3639: fprintf(fichtm,"\
3640: - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
3641: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3642: fprintf(fichtm,"\
3643: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3644: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3645:
3646: /* if(popforecast==1) fprintf(fichtm,"\n */
3647: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3648: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3649: /* <br>",fileres,fileres,fileres,fileres); */
3650: /* else */
3651: /* 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); */
3652: fflush(fichtm);
3653: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3654:
3655: m=cptcoveff;
3656: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3657:
3658: jj1=0;
3659: for(k1=1; k1<=m;k1++){
3660: for(i1=1; i1<=ncodemax[k1];i1++){
3661: jj1++;
3662: if (cptcovn > 0) {
3663: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3664: for (cpt=1; cpt<=cptcoveff;cpt++)
3665: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3666: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3667: }
3668: for(cpt=1; cpt<=nlstate;cpt++) {
3669: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3670: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3671: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3672: }
3673: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3674: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3675: true period expectancies (those weighted with period prevalences are also\
3676: drawn in addition to the population based expectancies computed using\
3677: observed and cahotic prevalences: %s%d.png<br>\
3678: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3679: } /* end i1 */
3680: }/* End k1 */
3681: fprintf(fichtm,"</ul>");
3682: fflush(fichtm);
3683: }
3684:
3685: /******************* Gnuplot file **************/
3686: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3687:
3688: char dirfileres[132],optfileres[132];
3689: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3690: int ng=0;
3691: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3692: /* printf("Problem with file %s",optionfilegnuplot); */
3693: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3694: /* } */
3695:
3696: /*#ifdef windows */
3697: fprintf(ficgp,"cd \"%s\" \n",pathc);
3698: /*#endif */
3699: m=pow(2,cptcoveff);
3700:
3701: strcpy(dirfileres,optionfilefiname);
3702: strcpy(optfileres,"vpl");
3703: /* 1eme*/
3704: for (cpt=1; cpt<= nlstate ; cpt ++) {
3705: for (k1=1; k1<= m ; k1 ++) {
3706: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3707: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3708: fprintf(ficgp,"set xlabel \"Age\" \n\
3709: set ylabel \"Probability\" \n\
3710: set ter png small\n\
3711: set size 0.65,0.65\n\
3712: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3713:
3714: for (i=1; i<= nlstate ; i ++) {
3715: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3716: else fprintf(ficgp," \%%*lf (\%%*lf)");
3717: }
3718: 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);
3719: for (i=1; i<= nlstate ; i ++) {
3720: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3721: else fprintf(ficgp," \%%*lf (\%%*lf)");
3722: }
3723: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3724: for (i=1; i<= nlstate ; i ++) {
3725: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3726: else fprintf(ficgp," \%%*lf (\%%*lf)");
3727: }
3728: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3729: }
3730: }
3731: /*2 eme*/
3732:
3733: for (k1=1; k1<= m ; k1 ++) {
3734: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3735: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3736:
3737: for (i=1; i<= nlstate+1 ; i ++) {
3738: k=2*i;
3739: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3740: for (j=1; j<= nlstate+1 ; j ++) {
3741: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3742: else fprintf(ficgp," \%%*lf (\%%*lf)");
3743: }
3744: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3745: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3746: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3747: for (j=1; j<= nlstate+1 ; j ++) {
3748: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3749: else fprintf(ficgp," \%%*lf (\%%*lf)");
3750: }
3751: fprintf(ficgp,"\" t\"\" w l 0,");
3752: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3753: for (j=1; j<= nlstate+1 ; j ++) {
3754: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3755: else fprintf(ficgp," \%%*lf (\%%*lf)");
3756: }
3757: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3758: else fprintf(ficgp,"\" t\"\" w l 0,");
3759: }
3760: }
3761:
3762: /*3eme*/
3763:
3764: for (k1=1; k1<= m ; k1 ++) {
3765: for (cpt=1; cpt<= nlstate ; cpt ++) {
3766: /* k=2+nlstate*(2*cpt-2); */
3767: k=2+(nlstate+1)*(cpt-1);
3768: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3769: fprintf(ficgp,"set ter png small\n\
3770: set size 0.65,0.65\n\
3771: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3772: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3773: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3774: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3775: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3776: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3777: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3778:
3779: */
3780: for (i=1; i< nlstate ; i ++) {
3781: 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);
3782: /* 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);*/
3783:
3784: }
3785: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3786: }
3787: }
3788:
3789: /* CV preval stable (period) */
3790: for (k1=1; k1<= m ; k1 ++) {
3791: for (cpt=1; cpt<=nlstate ; cpt ++) {
3792: k=3;
3793: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3794: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3795: set ter png small\nset size 0.65,0.65\n\
3796: unset log y\n\
3797: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3798:
3799: for (i=1; i< nlstate ; i ++)
3800: fprintf(ficgp,"+$%d",k+i+1);
3801: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3802:
3803: l=3+(nlstate+ndeath)*cpt;
3804: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3805: for (i=1; i< nlstate ; i ++) {
3806: l=3+(nlstate+ndeath)*cpt;
3807: fprintf(ficgp,"+$%d",l+i+1);
3808: }
3809: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3810: }
3811: }
3812:
3813: /* proba elementaires */
3814: for(i=1,jk=1; i <=nlstate; i++){
3815: for(k=1; k <=(nlstate+ndeath); k++){
3816: if (k != i) {
3817: for(j=1; j <=ncovmodel; j++){
3818: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3819: jk++;
3820: fprintf(ficgp,"\n");
3821: }
3822: }
3823: }
3824: }
3825:
3826: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3827: for(jk=1; jk <=m; jk++) {
3828: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3829: if (ng==2)
3830: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3831: else
3832: fprintf(ficgp,"\nset title \"Probability\"\n");
3833: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3834: i=1;
3835: for(k2=1; k2<=nlstate; k2++) {
3836: k3=i;
3837: for(k=1; k<=(nlstate+ndeath); k++) {
3838: if (k != k2){
3839: if(ng==2)
3840: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3841: else
3842: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3843: ij=1;
3844: for(j=3; j <=ncovmodel; j++) {
3845: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3846: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3847: ij++;
3848: }
3849: else
3850: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3851: }
3852: fprintf(ficgp,")/(1");
3853:
3854: for(k1=1; k1 <=nlstate; k1++){
3855: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3856: ij=1;
3857: for(j=3; j <=ncovmodel; j++){
3858: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3859: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3860: ij++;
3861: }
3862: else
3863: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3864: }
3865: fprintf(ficgp,")");
3866: }
3867: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3868: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3869: i=i+ncovmodel;
3870: }
3871: } /* end k */
3872: } /* end k2 */
3873: } /* end jk */
3874: } /* end ng */
3875: fflush(ficgp);
3876: } /* end gnuplot */
3877:
3878:
3879: /*************** Moving average **************/
3880: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3881:
3882: int i, cpt, cptcod;
3883: int modcovmax =1;
3884: int mobilavrange, mob;
3885: double age;
3886:
3887: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3888: a covariate has 2 modalities */
3889: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3890:
3891: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3892: if(mobilav==1) mobilavrange=5; /* default */
3893: else mobilavrange=mobilav;
3894: for (age=bage; age<=fage; age++)
3895: for (i=1; i<=nlstate;i++)
3896: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3897: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3898: /* We keep the original values on the extreme ages bage, fage and for
3899: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3900: we use a 5 terms etc. until the borders are no more concerned.
3901: */
3902: for (mob=3;mob <=mobilavrange;mob=mob+2){
3903: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3904: for (i=1; i<=nlstate;i++){
3905: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3906: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3907: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3908: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3909: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3910: }
3911: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3912: }
3913: }
3914: }/* end age */
3915: }/* end mob */
3916: }else return -1;
3917: return 0;
3918: }/* End movingaverage */
3919:
3920:
3921: /************** Forecasting ******************/
3922: 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){
3923: /* proj1, year, month, day of starting projection
3924: agemin, agemax range of age
3925: dateprev1 dateprev2 range of dates during which prevalence is computed
3926: anproj2 year of en of projection (same day and month as proj1).
3927: */
3928: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3929: int *popage;
3930: double agec; /* generic age */
3931: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3932: double *popeffectif,*popcount;
3933: double ***p3mat;
3934: double ***mobaverage;
3935: char fileresf[FILENAMELENGTH];
3936:
3937: agelim=AGESUP;
3938: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3939:
3940: strcpy(fileresf,"f");
3941: strcat(fileresf,fileres);
3942: if((ficresf=fopen(fileresf,"w"))==NULL) {
3943: printf("Problem with forecast resultfile: %s\n", fileresf);
3944: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3945: }
3946: printf("Computing forecasting: result on file '%s' \n", fileresf);
3947: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3948:
3949: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3950:
3951: if (mobilav!=0) {
3952: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3953: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3954: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3955: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3956: }
3957: }
3958:
3959: stepsize=(int) (stepm+YEARM-1)/YEARM;
3960: if (stepm<=12) stepsize=1;
3961: if(estepm < stepm){
3962: printf ("Problem %d lower than %d\n",estepm, stepm);
3963: }
3964: else hstepm=estepm;
3965:
3966: hstepm=hstepm/stepm;
3967: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3968: fractional in yp1 */
3969: anprojmean=yp;
3970: yp2=modf((yp1*12),&yp);
3971: mprojmean=yp;
3972: yp1=modf((yp2*30.5),&yp);
3973: jprojmean=yp;
3974: if(jprojmean==0) jprojmean=1;
3975: if(mprojmean==0) jprojmean=1;
3976:
3977: i1=cptcoveff;
3978: if (cptcovn < 1){i1=1;}
3979:
3980: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3981:
3982: fprintf(ficresf,"#****** Routine prevforecast **\n");
3983:
3984: /* if (h==(int)(YEARM*yearp)){ */
3985: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3986: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
3987: k=k+1;
3988: fprintf(ficresf,"\n#******");
3989: for(j=1;j<=cptcoveff;j++) {
3990: 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]]);
3991: }
3992: fprintf(ficresf,"******\n");
3993: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
3994: for(j=1; j<=nlstate+ndeath;j++){
3995: for(i=1; i<=nlstate;i++)
3996: fprintf(ficresf," p%d%d",i,j);
3997: fprintf(ficresf," p.%d",j);
3998: }
3999: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4000: fprintf(ficresf,"\n");
4001: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4002:
4003: for (agec=fage; agec>=(ageminpar-1); agec--){
4004: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4005: nhstepm = nhstepm/hstepm;
4006: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4007: oldm=oldms;savm=savms;
4008: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4009:
4010: for (h=0; h<=nhstepm; h++){
4011: if (h*hstepm/YEARM*stepm ==yearp) {
4012: fprintf(ficresf,"\n");
4013: for(j=1;j<=cptcoveff;j++)
4014: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4015: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4016: }
4017: for(j=1; j<=nlstate+ndeath;j++) {
4018: ppij=0.;
4019: for(i=1; i<=nlstate;i++) {
4020: if (mobilav==1)
4021: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4022: else {
4023: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4024: }
4025: if (h*hstepm/YEARM*stepm== yearp) {
4026: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4027: }
4028: } /* end i */
4029: if (h*hstepm/YEARM*stepm==yearp) {
4030: fprintf(ficresf," %.3f", ppij);
4031: }
4032: }/* end j */
4033: } /* end h */
4034: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4035: } /* end agec */
4036: } /* end yearp */
4037: } /* end cptcod */
4038: } /* end cptcov */
4039:
4040: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4041:
4042: fclose(ficresf);
4043: }
4044:
4045: /************** Forecasting *****not tested NB*************/
4046: 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){
4047:
4048: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4049: int *popage;
4050: double calagedatem, agelim, kk1, kk2;
4051: double *popeffectif,*popcount;
4052: double ***p3mat,***tabpop,***tabpopprev;
4053: double ***mobaverage;
4054: char filerespop[FILENAMELENGTH];
4055:
4056: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4057: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4058: agelim=AGESUP;
4059: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4060:
4061: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4062:
4063:
4064: strcpy(filerespop,"pop");
4065: strcat(filerespop,fileres);
4066: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4067: printf("Problem with forecast resultfile: %s\n", filerespop);
4068: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4069: }
4070: printf("Computing forecasting: result on file '%s' \n", filerespop);
4071: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4072:
4073: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4074:
4075: if (mobilav!=0) {
4076: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4077: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4078: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4079: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4080: }
4081: }
4082:
4083: stepsize=(int) (stepm+YEARM-1)/YEARM;
4084: if (stepm<=12) stepsize=1;
4085:
4086: agelim=AGESUP;
4087:
4088: hstepm=1;
4089: hstepm=hstepm/stepm;
4090:
4091: if (popforecast==1) {
4092: if((ficpop=fopen(popfile,"r"))==NULL) {
4093: printf("Problem with population file : %s\n",popfile);exit(0);
4094: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4095: }
4096: popage=ivector(0,AGESUP);
4097: popeffectif=vector(0,AGESUP);
4098: popcount=vector(0,AGESUP);
4099:
4100: i=1;
4101: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4102:
4103: imx=i;
4104: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4105: }
4106:
4107: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4108: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4109: k=k+1;
4110: fprintf(ficrespop,"\n#******");
4111: for(j=1;j<=cptcoveff;j++) {
4112: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4113: }
4114: fprintf(ficrespop,"******\n");
4115: fprintf(ficrespop,"# Age");
4116: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4117: if (popforecast==1) fprintf(ficrespop," [Population]");
4118:
4119: for (cpt=0; cpt<=0;cpt++) {
4120: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4121:
4122: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4123: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4124: nhstepm = nhstepm/hstepm;
4125:
4126: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4127: oldm=oldms;savm=savms;
4128: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4129:
4130: for (h=0; h<=nhstepm; h++){
4131: if (h==(int) (calagedatem+YEARM*cpt)) {
4132: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4133: }
4134: for(j=1; j<=nlstate+ndeath;j++) {
4135: kk1=0.;kk2=0;
4136: for(i=1; i<=nlstate;i++) {
4137: if (mobilav==1)
4138: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4139: else {
4140: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4141: }
4142: }
4143: if (h==(int)(calagedatem+12*cpt)){
4144: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4145: /*fprintf(ficrespop," %.3f", kk1);
4146: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4147: }
4148: }
4149: for(i=1; i<=nlstate;i++){
4150: kk1=0.;
4151: for(j=1; j<=nlstate;j++){
4152: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4153: }
4154: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4155: }
4156:
4157: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4158: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4159: }
4160: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4161: }
4162: }
4163:
4164: /******/
4165:
4166: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4167: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4168: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4169: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4170: nhstepm = nhstepm/hstepm;
4171:
4172: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4173: oldm=oldms;savm=savms;
4174: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4175: for (h=0; h<=nhstepm; h++){
4176: if (h==(int) (calagedatem+YEARM*cpt)) {
4177: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4178: }
4179: for(j=1; j<=nlstate+ndeath;j++) {
4180: kk1=0.;kk2=0;
4181: for(i=1; i<=nlstate;i++) {
4182: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4183: }
4184: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4185: }
4186: }
4187: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4188: }
4189: }
4190: }
4191: }
4192:
4193: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4194:
4195: if (popforecast==1) {
4196: free_ivector(popage,0,AGESUP);
4197: free_vector(popeffectif,0,AGESUP);
4198: free_vector(popcount,0,AGESUP);
4199: }
4200: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4201: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4202: fclose(ficrespop);
4203: } /* End of popforecast */
4204:
4205: int fileappend(FILE *fichier, char *optionfich)
4206: {
4207: if((fichier=fopen(optionfich,"a"))==NULL) {
4208: printf("Problem with file: %s\n", optionfich);
4209: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4210: return (0);
4211: }
4212: fflush(fichier);
4213: return (1);
4214: }
4215:
4216:
4217: /**************** function prwizard **********************/
4218: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4219: {
4220:
4221: /* Wizard to print covariance matrix template */
4222:
4223: char ca[32], cb[32], cc[32];
4224: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4225: int numlinepar;
4226:
4227: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4228: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4229: for(i=1; i <=nlstate; i++){
4230: jj=0;
4231: for(j=1; j <=nlstate+ndeath; j++){
4232: if(j==i) continue;
4233: jj++;
4234: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4235: printf("%1d%1d",i,j);
4236: fprintf(ficparo,"%1d%1d",i,j);
4237: for(k=1; k<=ncovmodel;k++){
4238: /* printf(" %lf",param[i][j][k]); */
4239: /* fprintf(ficparo," %lf",param[i][j][k]); */
4240: printf(" 0.");
4241: fprintf(ficparo," 0.");
4242: }
4243: printf("\n");
4244: fprintf(ficparo,"\n");
4245: }
4246: }
4247: printf("# Scales (for hessian or gradient estimation)\n");
4248: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4249: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4250: for(i=1; i <=nlstate; i++){
4251: jj=0;
4252: for(j=1; j <=nlstate+ndeath; j++){
4253: if(j==i) continue;
4254: jj++;
4255: fprintf(ficparo,"%1d%1d",i,j);
4256: printf("%1d%1d",i,j);
4257: fflush(stdout);
4258: for(k=1; k<=ncovmodel;k++){
4259: /* printf(" %le",delti3[i][j][k]); */
4260: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4261: printf(" 0.");
4262: fprintf(ficparo," 0.");
4263: }
4264: numlinepar++;
4265: printf("\n");
4266: fprintf(ficparo,"\n");
4267: }
4268: }
4269: printf("# Covariance matrix\n");
4270: /* # 121 Var(a12)\n\ */
4271: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4272: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4273: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4274: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4275: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4276: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4277: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4278: fflush(stdout);
4279: fprintf(ficparo,"# Covariance matrix\n");
4280: /* # 121 Var(a12)\n\ */
4281: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4282: /* # ...\n\ */
4283: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4284:
4285: for(itimes=1;itimes<=2;itimes++){
4286: jj=0;
4287: for(i=1; i <=nlstate; i++){
4288: for(j=1; j <=nlstate+ndeath; j++){
4289: if(j==i) continue;
4290: for(k=1; k<=ncovmodel;k++){
4291: jj++;
4292: ca[0]= k+'a'-1;ca[1]='\0';
4293: if(itimes==1){
4294: printf("#%1d%1d%d",i,j,k);
4295: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4296: }else{
4297: printf("%1d%1d%d",i,j,k);
4298: fprintf(ficparo,"%1d%1d%d",i,j,k);
4299: /* printf(" %.5le",matcov[i][j]); */
4300: }
4301: ll=0;
4302: for(li=1;li <=nlstate; li++){
4303: for(lj=1;lj <=nlstate+ndeath; lj++){
4304: if(lj==li) continue;
4305: for(lk=1;lk<=ncovmodel;lk++){
4306: ll++;
4307: if(ll<=jj){
4308: cb[0]= lk +'a'-1;cb[1]='\0';
4309: if(ll<jj){
4310: if(itimes==1){
4311: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4312: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4313: }else{
4314: printf(" 0.");
4315: fprintf(ficparo," 0.");
4316: }
4317: }else{
4318: if(itimes==1){
4319: printf(" Var(%s%1d%1d)",ca,i,j);
4320: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4321: }else{
4322: printf(" 0.");
4323: fprintf(ficparo," 0.");
4324: }
4325: }
4326: }
4327: } /* end lk */
4328: } /* end lj */
4329: } /* end li */
4330: printf("\n");
4331: fprintf(ficparo,"\n");
4332: numlinepar++;
4333: } /* end k*/
4334: } /*end j */
4335: } /* end i */
4336: } /* end itimes */
4337:
4338: } /* end of prwizard */
4339: /******************* Gompertz Likelihood ******************************/
4340: double gompertz(double x[])
4341: {
4342: double A,B,L=0.0,sump=0.,num=0.;
4343: int i,n=0; /* n is the size of the sample */
4344:
4345: for (i=0;i<=imx-1 ; i++) {
4346: sump=sump+weight[i];
4347: /* sump=sump+1;*/
4348: num=num+1;
4349: }
4350:
4351:
4352: /* for (i=0; i<=imx; i++)
4353: 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]);*/
4354:
4355: for (i=1;i<=imx ; i++)
4356: {
4357: if (cens[i] == 1 && wav[i]>1)
4358: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4359:
4360: if (cens[i] == 0 && wav[i]>1)
4361: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4362: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4363:
4364: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4365: if (wav[i] > 1 ) { /* ??? */
4366: L=L+A*weight[i];
4367: /* 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]);*/
4368: }
4369: }
4370:
4371: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4372:
4373: return -2*L*num/sump;
4374: }
4375:
4376: /******************* Printing html file ***********/
4377: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4378: int lastpass, int stepm, int weightopt, char model[],\
4379: int imx, double p[],double **matcov,double agemortsup){
4380: int i,k;
4381:
4382: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4383: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4384: for (i=1;i<=2;i++)
4385: 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]));
4386: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4387: fprintf(fichtm,"</ul>");
4388:
4389: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4390:
4391: 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>");
4392:
4393: for (k=agegomp;k<(agemortsup-2);k++)
4394: 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]);
4395:
4396:
4397: fflush(fichtm);
4398: }
4399:
4400: /******************* Gnuplot file **************/
4401: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4402:
4403: char dirfileres[132],optfileres[132];
4404: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4405: int ng;
4406:
4407:
4408: /*#ifdef windows */
4409: fprintf(ficgp,"cd \"%s\" \n",pathc);
4410: /*#endif */
4411:
4412:
4413: strcpy(dirfileres,optionfilefiname);
4414: strcpy(optfileres,"vpl");
4415: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4416: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4417: fprintf(ficgp, "set ter png small\n set log y\n");
4418: fprintf(ficgp, "set size 0.65,0.65\n");
4419: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4420:
4421: }
4422:
4423:
4424:
4425:
4426:
4427: /***********************************************/
4428: /**************** Main Program *****************/
4429: /***********************************************/
4430:
4431: int main(int argc, char *argv[])
4432: {
4433: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4434: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4435: int linei, month, year,iout;
4436: int jj, ll, li, lj, lk, imk;
4437: int numlinepar=0; /* Current linenumber of parameter file */
4438: int itimes;
4439: int NDIM=2;
4440: int vpopbased=0;
4441:
4442: char ca[32], cb[32], cc[32];
4443: char dummy[]=" ";
4444: /* FILE *fichtm; *//* Html File */
4445: /* FILE *ficgp;*/ /*Gnuplot File */
4446: struct stat info;
4447: double agedeb, agefin,hf;
4448: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4449:
4450: double fret;
4451: double **xi,tmp,delta;
4452:
4453: double dum; /* Dummy variable */
4454: double ***p3mat;
4455: double ***mobaverage;
4456: int *indx;
4457: char line[MAXLINE], linepar[MAXLINE];
4458: char linetmp[MAXLINE];
4459: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4460: char pathr[MAXLINE], pathimach[MAXLINE];
4461: char **bp, *tok, *val; /* pathtot */
4462: int firstobs=1, lastobs=10;
4463: int sdeb, sfin; /* Status at beginning and end */
4464: int c, h , cpt,l;
4465: int ju,jl, mi;
4466: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4467: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4468: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4469: int mobilav=0,popforecast=0;
4470: int hstepm, nhstepm;
4471: int agemortsup;
4472: float sumlpop=0.;
4473: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4474: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4475:
4476: double bage, fage, age, agelim, agebase;
4477: double ftolpl=FTOL;
4478: double **prlim;
4479: double *severity;
4480: double ***param; /* Matrix of parameters */
4481: double *p;
4482: double **matcov; /* Matrix of covariance */
4483: double ***delti3; /* Scale */
4484: double *delti; /* Scale */
4485: double ***eij, ***vareij;
4486: double **varpl; /* Variances of prevalence limits by age */
4487: double *epj, vepp;
4488: double kk1, kk2;
4489: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4490: double **ximort;
4491: char *alph[]={"a","a","b","c","d","e"}, str[4];
4492: int *dcwave;
4493:
4494: char z[1]="c", occ;
4495:
4496: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4497: char *strt, strtend[80];
4498: char *stratrunc;
4499: int lstra;
4500:
4501: long total_usecs;
4502:
4503: /* setlocale (LC_ALL, ""); */
4504: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4505: /* textdomain (PACKAGE); */
4506: /* setlocale (LC_CTYPE, ""); */
4507: /* setlocale (LC_MESSAGES, ""); */
4508:
4509: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4510: (void) gettimeofday(&start_time,&tzp);
4511: curr_time=start_time;
4512: tm = *localtime(&start_time.tv_sec);
4513: tmg = *gmtime(&start_time.tv_sec);
4514: strcpy(strstart,asctime(&tm));
4515:
4516: /* printf("Localtime (at start)=%s",strstart); */
4517: /* tp.tv_sec = tp.tv_sec +86400; */
4518: /* tm = *localtime(&start_time.tv_sec); */
4519: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4520: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4521: /* tmg.tm_hour=tmg.tm_hour + 1; */
4522: /* tp.tv_sec = mktime(&tmg); */
4523: /* strt=asctime(&tmg); */
4524: /* printf("Time(after) =%s",strstart); */
4525: /* (void) time (&time_value);
4526: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4527: * tm = *localtime(&time_value);
4528: * strstart=asctime(&tm);
4529: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4530: */
4531:
4532: nberr=0; /* Number of errors and warnings */
4533: nbwarn=0;
4534: getcwd(pathcd, size);
4535:
4536: printf("\n%s\n%s",version,fullversion);
4537: if(argc <=1){
4538: printf("\nEnter the parameter file name: ");
4539: fgets(pathr,FILENAMELENGTH,stdin);
4540: i=strlen(pathr);
4541: if(pathr[i-1]=='\n')
4542: pathr[i-1]='\0';
4543: for (tok = pathr; tok != NULL; ){
4544: printf("Pathr |%s|\n",pathr);
4545: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4546: printf("val= |%s| pathr=%s\n",val,pathr);
4547: strcpy (pathtot, val);
4548: if(pathr[0] == '\0') break; /* Dirty */
4549: }
4550: }
4551: else{
4552: strcpy(pathtot,argv[1]);
4553: }
4554: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4555: /*cygwin_split_path(pathtot,path,optionfile);
4556: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4557: /* cutv(path,optionfile,pathtot,'\\');*/
4558:
4559: /* Split argv[0], imach program to get pathimach */
4560: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4561: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4562: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4563: /* strcpy(pathimach,argv[0]); */
4564: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4565: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4566: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4567: chdir(path); /* Can be a relative path */
4568: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4569: printf("Current directory %s!\n",pathcd);
4570: strcpy(command,"mkdir ");
4571: strcat(command,optionfilefiname);
4572: if((outcmd=system(command)) != 0){
4573: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4574: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4575: /* fclose(ficlog); */
4576: /* exit(1); */
4577: }
4578: /* if((imk=mkdir(optionfilefiname))<0){ */
4579: /* perror("mkdir"); */
4580: /* } */
4581:
4582: /*-------- arguments in the command line --------*/
4583:
4584: /* Log file */
4585: strcat(filelog, optionfilefiname);
4586: strcat(filelog,".log"); /* */
4587: if((ficlog=fopen(filelog,"w"))==NULL) {
4588: printf("Problem with logfile %s\n",filelog);
4589: goto end;
4590: }
4591: fprintf(ficlog,"Log filename:%s\n",filelog);
4592: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4593: fprintf(ficlog,"\nEnter the parameter file name: \n");
4594: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4595: path=%s \n\
4596: optionfile=%s\n\
4597: optionfilext=%s\n\
4598: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4599:
4600: printf("Local time (at start):%s",strstart);
4601: fprintf(ficlog,"Local time (at start): %s",strstart);
4602: fflush(ficlog);
4603: /* (void) gettimeofday(&curr_time,&tzp); */
4604: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4605:
4606: /* */
4607: strcpy(fileres,"r");
4608: strcat(fileres, optionfilefiname);
4609: strcat(fileres,".txt"); /* Other files have txt extension */
4610:
4611: /*---------arguments file --------*/
4612:
4613: if((ficpar=fopen(optionfile,"r"))==NULL) {
4614: printf("Problem with optionfile %s\n",optionfile);
4615: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4616: fflush(ficlog);
4617: goto end;
4618: }
4619:
4620:
4621:
4622: strcpy(filereso,"o");
4623: strcat(filereso,fileres);
4624: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4625: printf("Problem with Output resultfile: %s\n", filereso);
4626: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4627: fflush(ficlog);
4628: goto end;
4629: }
4630:
4631: /* Reads comments: lines beginning with '#' */
4632: numlinepar=0;
4633: while((c=getc(ficpar))=='#' && c!= EOF){
4634: ungetc(c,ficpar);
4635: fgets(line, MAXLINE, ficpar);
4636: numlinepar++;
4637: puts(line);
4638: fputs(line,ficparo);
4639: fputs(line,ficlog);
4640: }
4641: ungetc(c,ficpar);
4642:
4643: 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);
4644: numlinepar++;
4645: 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);
4646: 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);
4647: 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);
4648: fflush(ficlog);
4649: while((c=getc(ficpar))=='#' && c!= EOF){
4650: ungetc(c,ficpar);
4651: fgets(line, MAXLINE, ficpar);
4652: numlinepar++;
4653: puts(line);
4654: fputs(line,ficparo);
4655: fputs(line,ficlog);
4656: }
4657: ungetc(c,ficpar);
4658:
4659:
4660: covar=matrix(0,NCOVMAX,1,n);
4661: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4662: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4663: /* where is ncovprod ?*/
4664: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
4665: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4666: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
4667: npar= nforce*ncovmodel; /* Number of parameters like aij*/
4668: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
4669: printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)*nlstate*ncovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
4670: fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
4671: fflush(stdout);
4672: fclose (ficlog);
4673: goto end;
4674: }
4675: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4676: delti=delti3[1][1];
4677: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4678: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4679: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4680: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4681: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4682: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4683: fclose (ficparo);
4684: fclose (ficlog);
4685: goto end;
4686: exit(0);
4687: }
4688: else if(mle==-3) {
4689: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4690: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4691: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4692: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4693: matcov=matrix(1,npar,1,npar);
4694: }
4695: else{
4696: /* Read guess parameters */
4697: /* Reads comments: lines beginning with '#' */
4698: while((c=getc(ficpar))=='#' && c!= EOF){
4699: ungetc(c,ficpar);
4700: fgets(line, MAXLINE, ficpar);
4701: numlinepar++;
4702: puts(line);
4703: fputs(line,ficparo);
4704: fputs(line,ficlog);
4705: }
4706: ungetc(c,ficpar);
4707:
4708: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4709: for(i=1; i <=nlstate; i++){
4710: j=0;
4711: for(jj=1; jj <=nlstate+ndeath; jj++){
4712: if(jj==i) continue;
4713: j++;
4714: fscanf(ficpar,"%1d%1d",&i1,&j1);
4715: if ((i1 != i) && (j1 != j)){
4716: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4717: It might be a problem of design; if ncovcol and the model are correct\n \
4718: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4719: exit(1);
4720: }
4721: fprintf(ficparo,"%1d%1d",i1,j1);
4722: if(mle==1)
4723: printf("%1d%1d",i,j);
4724: fprintf(ficlog,"%1d%1d",i,j);
4725: for(k=1; k<=ncovmodel;k++){
4726: fscanf(ficpar," %lf",¶m[i][j][k]);
4727: if(mle==1){
4728: printf(" %lf",param[i][j][k]);
4729: fprintf(ficlog," %lf",param[i][j][k]);
4730: }
4731: else
4732: fprintf(ficlog," %lf",param[i][j][k]);
4733: fprintf(ficparo," %lf",param[i][j][k]);
4734: }
4735: fscanf(ficpar,"\n");
4736: numlinepar++;
4737: if(mle==1)
4738: printf("\n");
4739: fprintf(ficlog,"\n");
4740: fprintf(ficparo,"\n");
4741: }
4742: }
4743: fflush(ficlog);
4744:
4745: p=param[1][1];
4746:
4747: /* Reads comments: lines beginning with '#' */
4748: while((c=getc(ficpar))=='#' && c!= EOF){
4749: ungetc(c,ficpar);
4750: fgets(line, MAXLINE, ficpar);
4751: numlinepar++;
4752: puts(line);
4753: fputs(line,ficparo);
4754: fputs(line,ficlog);
4755: }
4756: ungetc(c,ficpar);
4757:
4758: for(i=1; i <=nlstate; i++){
4759: for(j=1; j <=nlstate+ndeath-1; j++){
4760: fscanf(ficpar,"%1d%1d",&i1,&j1);
4761: if ((i1-i)*(j1-j)!=0){
4762: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4763: exit(1);
4764: }
4765: printf("%1d%1d",i,j);
4766: fprintf(ficparo,"%1d%1d",i1,j1);
4767: fprintf(ficlog,"%1d%1d",i1,j1);
4768: for(k=1; k<=ncovmodel;k++){
4769: fscanf(ficpar,"%le",&delti3[i][j][k]);
4770: printf(" %le",delti3[i][j][k]);
4771: fprintf(ficparo," %le",delti3[i][j][k]);
4772: fprintf(ficlog," %le",delti3[i][j][k]);
4773: }
4774: fscanf(ficpar,"\n");
4775: numlinepar++;
4776: printf("\n");
4777: fprintf(ficparo,"\n");
4778: fprintf(ficlog,"\n");
4779: }
4780: }
4781: fflush(ficlog);
4782:
4783: delti=delti3[1][1];
4784:
4785:
4786: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4787:
4788: /* Reads comments: lines beginning with '#' */
4789: while((c=getc(ficpar))=='#' && c!= EOF){
4790: ungetc(c,ficpar);
4791: fgets(line, MAXLINE, ficpar);
4792: numlinepar++;
4793: puts(line);
4794: fputs(line,ficparo);
4795: fputs(line,ficlog);
4796: }
4797: ungetc(c,ficpar);
4798:
4799: matcov=matrix(1,npar,1,npar);
4800: for(i=1; i <=npar; i++)
4801: for(j=1; j <=npar; j++) matcov[i][j]=0.;
4802:
4803: for(i=1; i <=npar; i++){
4804: fscanf(ficpar,"%s",&str);
4805: if(mle==1)
4806: printf("%s",str);
4807: fprintf(ficlog,"%s",str);
4808: fprintf(ficparo,"%s",str);
4809: for(j=1; j <=i; j++){
4810: fscanf(ficpar," %le",&matcov[i][j]);
4811: if(mle==1){
4812: printf(" %.5le",matcov[i][j]);
4813: }
4814: fprintf(ficlog," %.5le",matcov[i][j]);
4815: fprintf(ficparo," %.5le",matcov[i][j]);
4816: }
4817: fscanf(ficpar,"\n");
4818: numlinepar++;
4819: if(mle==1)
4820: printf("\n");
4821: fprintf(ficlog,"\n");
4822: fprintf(ficparo,"\n");
4823: }
4824: for(i=1; i <=npar; i++)
4825: for(j=i+1;j<=npar;j++)
4826: matcov[i][j]=matcov[j][i];
4827:
4828: if(mle==1)
4829: printf("\n");
4830: fprintf(ficlog,"\n");
4831:
4832: fflush(ficlog);
4833:
4834: /*-------- Rewriting parameter file ----------*/
4835: strcpy(rfileres,"r"); /* "Rparameterfile */
4836: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4837: strcat(rfileres,"."); /* */
4838: strcat(rfileres,optionfilext); /* Other files have txt extension */
4839: if((ficres =fopen(rfileres,"w"))==NULL) {
4840: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4841: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4842: }
4843: fprintf(ficres,"#%s\n",version);
4844: } /* End of mle != -3 */
4845:
4846: /*-------- data file ----------*/
4847: if((fic=fopen(datafile,"r"))==NULL) {
4848: printf("Problem while opening datafile: %s\n", datafile);goto end;
4849: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4850: }
4851:
4852: n= lastobs;
4853: severity = vector(1,maxwav);
4854: outcome=imatrix(1,maxwav+1,1,n);
4855: num=lvector(1,n);
4856: moisnais=vector(1,n);
4857: annais=vector(1,n);
4858: moisdc=vector(1,n);
4859: andc=vector(1,n);
4860: agedc=vector(1,n);
4861: cod=ivector(1,n);
4862: weight=vector(1,n);
4863: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4864: mint=matrix(1,maxwav,1,n);
4865: anint=matrix(1,maxwav,1,n);
4866: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
4867: tab=ivector(1,NCOVMAX);
4868: ncodemax=ivector(1,8);
4869:
4870: i=1;
4871: linei=0;
4872: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4873: linei=linei+1;
4874: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4875: if(line[j] == '\t')
4876: line[j] = ' ';
4877: }
4878: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4879: ;
4880: };
4881: line[j+1]=0; /* Trims blanks at end of line */
4882: if(line[0]=='#'){
4883: fprintf(ficlog,"Comment line\n%s\n",line);
4884: printf("Comment line\n%s\n",line);
4885: continue;
4886: }
4887: trimbb(linetmp,line); /* Trims multiple blanks in line */
4888: for (j=0; line[j]!='\0';j++){
4889: line[j]=linetmp[j];
4890: }
4891:
4892:
4893: for (j=maxwav;j>=1;j--){
4894: cutv(stra, strb,line,' ');
4895: if(strb[0]=='.') { /* Missing status */
4896: lval=-1;
4897: }else{
4898: errno=0;
4899: lval=strtol(strb,&endptr,10);
4900: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4901: if( strb[0]=='\0' || (*endptr != '\0')){
4902: printf("Error reading data around '%s' at line number %ld 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);
4903: fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);fflush(ficlog);
4904: goto end;
4905: }
4906: }
4907: s[j][i]=lval;
4908:
4909: strcpy(line,stra);
4910: cutv(stra, strb,line,' ');
4911: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4912: }
4913: else if(iout=sscanf(strb,"%s.") != 0){
4914: month=99;
4915: year=9999;
4916: }else{
4917: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4918: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
4919: goto end;
4920: }
4921: anint[j][i]= (double) year;
4922: mint[j][i]= (double)month;
4923: strcpy(line,stra);
4924: } /* ENd Waves */
4925:
4926: cutv(stra, strb,line,' ');
4927: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4928: }
4929: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4930: month=99;
4931: year=9999;
4932: }else{
4933: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4934: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4935: goto end;
4936: }
4937: andc[i]=(double) year;
4938: moisdc[i]=(double) month;
4939: strcpy(line,stra);
4940:
4941: cutv(stra, strb,line,' ');
4942: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4943: }
4944: else if(iout=sscanf(strb,"%s.") != 0){
4945: month=99;
4946: year=9999;
4947: }else{
4948: 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);
4949: fprintf(ficlog,"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);fflush(ficlog);
4950: goto end;
4951: }
4952: annais[i]=(double)(year);
4953: moisnais[i]=(double)(month);
4954: strcpy(line,stra);
4955:
4956: cutv(stra, strb,line,' ');
4957: errno=0;
4958: dval=strtod(strb,&endptr);
4959: if( strb[0]=='\0' || (*endptr != '\0')){
4960: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4961: fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4962: fflush(ficlog);
4963: goto end;
4964: }
4965: weight[i]=dval;
4966: strcpy(line,stra);
4967:
4968: for (j=ncovcol;j>=1;j--){
4969: cutv(stra, strb,line,' ');
4970: if(strb[0]=='.') { /* Missing status */
4971: lval=-1;
4972: }else{
4973: errno=0;
4974: lval=strtol(strb,&endptr,10);
4975: if( strb[0]=='\0' || (*endptr != '\0')){
4976: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
4977: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
4978: goto end;
4979: }
4980: }
4981: if(lval <-1 || lval >1){
4982: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4983: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4984: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4985: For example, for multinomial values like 1, 2 and 3,\n \
4986: build V1=0 V2=0 for the reference value (1),\n \
4987: V1=1 V2=0 for (2) \n \
4988: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4989: output of IMaCh is often meaningless.\n \
4990: Exiting.\n",lval,linei, i,line,j);
4991: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
4992: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4993: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4994: For example, for multinomial values like 1, 2 and 3,\n \
4995: build V1=0 V2=0 for the reference value (1),\n \
4996: V1=1 V2=0 for (2) \n \
4997: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4998: output of IMaCh is often meaningless.\n \
4999: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5000: goto end;
5001: }
5002: covar[j][i]=(double)(lval);
5003: strcpy(line,stra);
5004: }
5005: lstra=strlen(stra);
5006:
5007: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5008: stratrunc = &(stra[lstra-9]);
5009: num[i]=atol(stratrunc);
5010: }
5011: else
5012: num[i]=atol(stra);
5013: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5014: 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;}*/
5015:
5016: i=i+1;
5017: } /* End loop reading data */
5018: fclose(fic);
5019: /* printf("ii=%d", ij);
5020: scanf("%d",i);*/
5021: imx=i-1; /* Number of individuals */
5022:
5023: /* for (i=1; i<=imx; i++){
5024: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
5025: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
5026: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
5027: }*/
5028: /* for (i=1; i<=imx; i++){
5029: if (s[4][i]==9) s[4][i]=-1;
5030: 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]));}*/
5031:
5032: /* for (i=1; i<=imx; i++) */
5033:
5034: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
5035: else weight[i]=1;*/
5036:
5037: /* Calculation of the number of parameters from char model */
5038: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
5039: Tprod=ivector(1,15);
5040: Tvaraff=ivector(1,15);
5041: Tvard=imatrix(1,15,1,2);
5042: Tage=ivector(1,15);
5043:
5044: if (strlen(model) >1){ /* If there is at least 1 covariate */
5045: j=0, j1=0, k1=1, k2=1;
5046: j=nbocc(model,'+'); /* j=Number of '+' */
5047: j1=nbocc(model,'*'); /* j1=Number of '*' */
5048: cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
5049: cptcovprod=j1; /*Number of products V1*V2 =1 */
5050:
5051: strcpy(modelsav,model);
5052: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
5053: printf("Error. Non available option model=%s ",model);
5054: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
5055: goto end;
5056: }
5057:
5058: /* This loop fills the array Tvar from the string 'model'.*/
5059: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5060: for(i=(j+1); i>=1;i--){
5061: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5062: modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
5063: stra=V2
5064: */
5065: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5066: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5067: /*scanf("%d",i);*/
5068: if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/
5069: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5070: if (strcmp(strc,"age")==0) { /* Vn*age */
5071: cptcovprod--;
5072: cutv(strb,stre,strd,'V');
5073: Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
5074: cptcovage++; /* Sums the number of covariates including age as a product */
5075: Tage[cptcovage]=i; /* Tage[1] =2 */
5076: /*printf("stre=%s ", stre);*/
5077: }
5078: else if (strcmp(strd,"age")==0) { /* or age*Vn */
5079: cptcovprod--;
5080: cutv(strb,stre,strc,'V');
5081: Tvar[i]=atoi(stre);
5082: cptcovage++;
5083: Tage[cptcovage]=i;
5084: }
5085: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
5086: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5087: Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
5088: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
5089: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
5090: Tprod[k1]=i; /* Tprod[1] */
5091: Tvard[k1][1]=atoi(strc); /* m*/
5092: Tvard[k1][2]=atoi(stre); /* n */
5093: Tvar[cptcovn+k2]=Tvard[k1][1];
5094: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5095: for (k=1; k<=lastobs;k++)
5096: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5097: k1++;
5098: k2=k2+2;
5099: }
5100: }
5101: else { /* no more sum */
5102: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5103: /* scanf("%d",i);*/
5104: cutv(strd,strc,strb,'V');
5105: Tvar[i]=atoi(strc);
5106: }
5107: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
5108: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5109: scanf("%d",i);*/
5110: } /* end of loop + */
5111: } /* end model */
5112:
5113: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5114: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5115:
5116: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5117: printf("cptcovprod=%d ", cptcovprod);
5118: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5119:
5120: scanf("%d ",i);*/
5121:
5122: /* if(mle==1){*/
5123: if (weightopt != 1) { /* Maximisation without weights*/
5124: for(i=1;i<=n;i++) weight[i]=1.0;
5125: }
5126: /*-calculation of age at interview from date of interview and age at death -*/
5127: agev=matrix(1,maxwav,1,imx);
5128:
5129: for (i=1; i<=imx; i++) {
5130: for(m=2; (m<= maxwav); m++) {
5131: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5132: anint[m][i]=9999;
5133: s[m][i]=-1;
5134: }
5135: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5136: nberr++;
5137: 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);
5138: 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);
5139: s[m][i]=-1;
5140: }
5141: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5142: nberr++;
5143: 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]);
5144: 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]);
5145: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5146: }
5147: }
5148: }
5149:
5150: for (i=1; i<=imx; i++) {
5151: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5152: for(m=firstpass; (m<= lastpass); m++){
5153: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5154: if (s[m][i] >= nlstate+1) {
5155: if(agedc[i]>0)
5156: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5157: agev[m][i]=agedc[i];
5158: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5159: else {
5160: if ((int)andc[i]!=9999){
5161: nbwarn++;
5162: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5163: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5164: agev[m][i]=-1;
5165: }
5166: }
5167: }
5168: else if(s[m][i] !=9){ /* Standard case, age in fractional
5169: years but with the precision of a month */
5170: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5171: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5172: agev[m][i]=1;
5173: else if(agev[m][i] <agemin){
5174: agemin=agev[m][i];
5175: /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
5176: }
5177: else if(agev[m][i] >agemax){
5178: agemax=agev[m][i];
5179: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5180: }
5181: /*agev[m][i]=anint[m][i]-annais[i];*/
5182: /* agev[m][i] = age[i]+2*m;*/
5183: }
5184: else { /* =9 */
5185: agev[m][i]=1;
5186: s[m][i]=-1;
5187: }
5188: }
5189: else /*= 0 Unknown */
5190: agev[m][i]=1;
5191: }
5192:
5193: }
5194: for (i=1; i<=imx; i++) {
5195: for(m=firstpass; (m<=lastpass); m++){
5196: if (s[m][i] > (nlstate+ndeath)) {
5197: nberr++;
5198: 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);
5199: 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);
5200: goto end;
5201: }
5202: }
5203: }
5204:
5205: /*for (i=1; i<=imx; i++){
5206: for (m=firstpass; (m<lastpass); m++){
5207: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5208: }
5209:
5210: }*/
5211:
5212:
5213: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5214: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5215:
5216: agegomp=(int)agemin;
5217: free_vector(severity,1,maxwav);
5218: free_imatrix(outcome,1,maxwav+1,1,n);
5219: free_vector(moisnais,1,n);
5220: free_vector(annais,1,n);
5221: /* free_matrix(mint,1,maxwav,1,n);
5222: free_matrix(anint,1,maxwav,1,n);*/
5223: free_vector(moisdc,1,n);
5224: free_vector(andc,1,n);
5225:
5226:
5227: wav=ivector(1,imx);
5228: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5229: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5230: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5231:
5232: /* Concatenates waves */
5233: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5234:
5235: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5236:
5237: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5238: ncodemax[1]=1;
5239: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5240:
5241: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5242: the estimations*/
5243: h=0;
5244: m=pow(2,cptcoveff);
5245:
5246: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5247: for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5248: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5249: for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
5250: h++;
5251: if (h>m)
5252: h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5253: printf("h=%d k=%d j=%d codtab[h][k]=%d Tvar[k]=%d codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
5254: }
5255: }
5256: }
5257: }
5258: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5259: codtab[1][2]=1;codtab[2][2]=2; */
5260: /* for(i=1; i <=m ;i++){
5261: for(k=1; k <=cptcovn; k++){
5262: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5263: }
5264: printf("\n");
5265: }
5266: scanf("%d",i);*/
5267:
5268: /*------------ gnuplot -------------*/
5269: strcpy(optionfilegnuplot,optionfilefiname);
5270: if(mle==-3)
5271: strcat(optionfilegnuplot,"-mort");
5272: strcat(optionfilegnuplot,".gp");
5273:
5274: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5275: printf("Problem with file %s",optionfilegnuplot);
5276: }
5277: else{
5278: fprintf(ficgp,"\n# %s\n", version);
5279: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5280: fprintf(ficgp,"set missing 'NaNq'\n");
5281: }
5282: /* fclose(ficgp);*/
5283: /*--------- index.htm --------*/
5284:
5285: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5286: if(mle==-3)
5287: strcat(optionfilehtm,"-mort");
5288: strcat(optionfilehtm,".htm");
5289: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5290: printf("Problem with %s \n",optionfilehtm);
5291: exit(0);
5292: }
5293:
5294: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5295: strcat(optionfilehtmcov,"-cov.htm");
5296: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5297: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5298: }
5299: else{
5300: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5301: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5302: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5303: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5304: }
5305:
5306: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5307: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5308: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5309: \n\
5310: <hr size=\"2\" color=\"#EC5E5E\">\
5311: <ul><li><h4>Parameter files</h4>\n\
5312: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5313: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5314: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5315: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5316: - Date and time at start: %s</ul>\n",\
5317: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5318: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5319: fileres,fileres,\
5320: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5321: fflush(fichtm);
5322:
5323: strcpy(pathr,path);
5324: strcat(pathr,optionfilefiname);
5325: chdir(optionfilefiname); /* Move to directory named optionfile */
5326:
5327: /* Calculates basic frequencies. Computes observed prevalence at single age
5328: and prints on file fileres'p'. */
5329: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5330:
5331: fprintf(fichtm,"\n");
5332: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5333: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5334: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5335: imx,agemin,agemax,jmin,jmax,jmean);
5336: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5337: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5338: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5339: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5340: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5341:
5342:
5343: /* For Powell, parameters are in a vector p[] starting at p[1]
5344: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5345: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5346:
5347: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5348:
5349: if (mle==-3){
5350: ximort=matrix(1,NDIM,1,NDIM);
5351: cens=ivector(1,n);
5352: ageexmed=vector(1,n);
5353: agecens=vector(1,n);
5354: dcwave=ivector(1,n);
5355:
5356: for (i=1; i<=imx; i++){
5357: dcwave[i]=-1;
5358: for (m=firstpass; m<=lastpass; m++)
5359: if (s[m][i]>nlstate) {
5360: dcwave[i]=m;
5361: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5362: break;
5363: }
5364: }
5365:
5366: for (i=1; i<=imx; i++) {
5367: if (wav[i]>0){
5368: ageexmed[i]=agev[mw[1][i]][i];
5369: j=wav[i];
5370: agecens[i]=1.;
5371:
5372: if (ageexmed[i]> 1 && wav[i] > 0){
5373: agecens[i]=agev[mw[j][i]][i];
5374: cens[i]= 1;
5375: }else if (ageexmed[i]< 1)
5376: cens[i]= -1;
5377: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5378: cens[i]=0 ;
5379: }
5380: else cens[i]=-1;
5381: }
5382:
5383: for (i=1;i<=NDIM;i++) {
5384: for (j=1;j<=NDIM;j++)
5385: ximort[i][j]=(i == j ? 1.0 : 0.0);
5386: }
5387:
5388: p[1]=0.0268; p[NDIM]=0.083;
5389: /*printf("%lf %lf", p[1], p[2]);*/
5390:
5391:
5392: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5393: strcpy(filerespow,"pow-mort");
5394: strcat(filerespow,fileres);
5395: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5396: printf("Problem with resultfile: %s\n", filerespow);
5397: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5398: }
5399: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5400: /* for (i=1;i<=nlstate;i++)
5401: for(j=1;j<=nlstate+ndeath;j++)
5402: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5403: */
5404: fprintf(ficrespow,"\n");
5405:
5406: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5407: fclose(ficrespow);
5408:
5409: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5410:
5411: for(i=1; i <=NDIM; i++)
5412: for(j=i+1;j<=NDIM;j++)
5413: matcov[i][j]=matcov[j][i];
5414:
5415: printf("\nCovariance matrix\n ");
5416: for(i=1; i <=NDIM; i++) {
5417: for(j=1;j<=NDIM;j++){
5418: printf("%f ",matcov[i][j]);
5419: }
5420: printf("\n ");
5421: }
5422:
5423: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5424: for (i=1;i<=NDIM;i++)
5425: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5426:
5427: lsurv=vector(1,AGESUP);
5428: lpop=vector(1,AGESUP);
5429: tpop=vector(1,AGESUP);
5430: lsurv[agegomp]=100000;
5431:
5432: for (k=agegomp;k<=AGESUP;k++) {
5433: agemortsup=k;
5434: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5435: }
5436:
5437: for (k=agegomp;k<agemortsup;k++)
5438: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5439:
5440: for (k=agegomp;k<agemortsup;k++){
5441: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5442: sumlpop=sumlpop+lpop[k];
5443: }
5444:
5445: tpop[agegomp]=sumlpop;
5446: for (k=agegomp;k<(agemortsup-3);k++){
5447: /* tpop[k+1]=2;*/
5448: tpop[k+1]=tpop[k]-lpop[k];
5449: }
5450:
5451:
5452: printf("\nAge lx qx dx Lx Tx e(x)\n");
5453: for (k=agegomp;k<(agemortsup-2);k++)
5454: 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]);
5455:
5456:
5457: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5458: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5459:
5460: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5461: stepm, weightopt,\
5462: model,imx,p,matcov,agemortsup);
5463:
5464: free_vector(lsurv,1,AGESUP);
5465: free_vector(lpop,1,AGESUP);
5466: free_vector(tpop,1,AGESUP);
5467: } /* Endof if mle==-3 */
5468:
5469: else{ /* For mle >=1 */
5470: globpr=0;/* debug */
5471: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5472: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5473: for (k=1; k<=npar;k++)
5474: printf(" %d %8.5f",k,p[k]);
5475: printf("\n");
5476: globpr=1; /* to print the contributions */
5477: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5478: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5479: for (k=1; k<=npar;k++)
5480: printf(" %d %8.5f",k,p[k]);
5481: printf("\n");
5482: if(mle>=1){ /* Could be 1 or 2 */
5483: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5484: }
5485:
5486: /*--------- results files --------------*/
5487: 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);
5488:
5489:
5490: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5491: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5492: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5493: for(i=1,jk=1; i <=nlstate; i++){
5494: for(k=1; k <=(nlstate+ndeath); k++){
5495: if (k != i) {
5496: printf("%d%d ",i,k);
5497: fprintf(ficlog,"%d%d ",i,k);
5498: fprintf(ficres,"%1d%1d ",i,k);
5499: for(j=1; j <=ncovmodel; j++){
5500: printf("%lf ",p[jk]);
5501: fprintf(ficlog,"%lf ",p[jk]);
5502: fprintf(ficres,"%lf ",p[jk]);
5503: jk++;
5504: }
5505: printf("\n");
5506: fprintf(ficlog,"\n");
5507: fprintf(ficres,"\n");
5508: }
5509: }
5510: }
5511: if(mle!=0){
5512: /* Computing hessian and covariance matrix */
5513: ftolhess=ftol; /* Usually correct */
5514: hesscov(matcov, p, npar, delti, ftolhess, func);
5515: }
5516: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5517: printf("# Scales (for hessian or gradient estimation)\n");
5518: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5519: for(i=1,jk=1; i <=nlstate; i++){
5520: for(j=1; j <=nlstate+ndeath; j++){
5521: if (j!=i) {
5522: fprintf(ficres,"%1d%1d",i,j);
5523: printf("%1d%1d",i,j);
5524: fprintf(ficlog,"%1d%1d",i,j);
5525: for(k=1; k<=ncovmodel;k++){
5526: printf(" %.5e",delti[jk]);
5527: fprintf(ficlog," %.5e",delti[jk]);
5528: fprintf(ficres," %.5e",delti[jk]);
5529: jk++;
5530: }
5531: printf("\n");
5532: fprintf(ficlog,"\n");
5533: fprintf(ficres,"\n");
5534: }
5535: }
5536: }
5537:
5538: 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");
5539: if(mle>=1)
5540: 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");
5541: 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");
5542: /* # 121 Var(a12)\n\ */
5543: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5544: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5545: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5546: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5547: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5548: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5549: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5550:
5551:
5552: /* Just to have a covariance matrix which will be more understandable
5553: even is we still don't want to manage dictionary of variables
5554: */
5555: for(itimes=1;itimes<=2;itimes++){
5556: jj=0;
5557: for(i=1; i <=nlstate; i++){
5558: for(j=1; j <=nlstate+ndeath; j++){
5559: if(j==i) continue;
5560: for(k=1; k<=ncovmodel;k++){
5561: jj++;
5562: ca[0]= k+'a'-1;ca[1]='\0';
5563: if(itimes==1){
5564: if(mle>=1)
5565: printf("#%1d%1d%d",i,j,k);
5566: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5567: fprintf(ficres,"#%1d%1d%d",i,j,k);
5568: }else{
5569: if(mle>=1)
5570: printf("%1d%1d%d",i,j,k);
5571: fprintf(ficlog,"%1d%1d%d",i,j,k);
5572: fprintf(ficres,"%1d%1d%d",i,j,k);
5573: }
5574: ll=0;
5575: for(li=1;li <=nlstate; li++){
5576: for(lj=1;lj <=nlstate+ndeath; lj++){
5577: if(lj==li) continue;
5578: for(lk=1;lk<=ncovmodel;lk++){
5579: ll++;
5580: if(ll<=jj){
5581: cb[0]= lk +'a'-1;cb[1]='\0';
5582: if(ll<jj){
5583: if(itimes==1){
5584: if(mle>=1)
5585: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5586: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5587: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5588: }else{
5589: if(mle>=1)
5590: printf(" %.5e",matcov[jj][ll]);
5591: fprintf(ficlog," %.5e",matcov[jj][ll]);
5592: fprintf(ficres," %.5e",matcov[jj][ll]);
5593: }
5594: }else{
5595: if(itimes==1){
5596: if(mle>=1)
5597: printf(" Var(%s%1d%1d)",ca,i,j);
5598: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5599: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5600: }else{
5601: if(mle>=1)
5602: printf(" %.5e",matcov[jj][ll]);
5603: fprintf(ficlog," %.5e",matcov[jj][ll]);
5604: fprintf(ficres," %.5e",matcov[jj][ll]);
5605: }
5606: }
5607: }
5608: } /* end lk */
5609: } /* end lj */
5610: } /* end li */
5611: if(mle>=1)
5612: printf("\n");
5613: fprintf(ficlog,"\n");
5614: fprintf(ficres,"\n");
5615: numlinepar++;
5616: } /* end k*/
5617: } /*end j */
5618: } /* end i */
5619: } /* end itimes */
5620:
5621: fflush(ficlog);
5622: fflush(ficres);
5623:
5624: while((c=getc(ficpar))=='#' && c!= EOF){
5625: ungetc(c,ficpar);
5626: fgets(line, MAXLINE, ficpar);
5627: puts(line);
5628: fputs(line,ficparo);
5629: }
5630: ungetc(c,ficpar);
5631:
5632: estepm=0;
5633: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5634: if (estepm==0 || estepm < stepm) estepm=stepm;
5635: if (fage <= 2) {
5636: bage = ageminpar;
5637: fage = agemaxpar;
5638: }
5639:
5640: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5641: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5642: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5643:
5644: while((c=getc(ficpar))=='#' && c!= EOF){
5645: ungetc(c,ficpar);
5646: fgets(line, MAXLINE, ficpar);
5647: puts(line);
5648: fputs(line,ficparo);
5649: }
5650: ungetc(c,ficpar);
5651:
5652: 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);
5653: 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);
5654: 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);
5655: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5656: 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);
5657:
5658: while((c=getc(ficpar))=='#' && c!= EOF){
5659: ungetc(c,ficpar);
5660: fgets(line, MAXLINE, ficpar);
5661: puts(line);
5662: fputs(line,ficparo);
5663: }
5664: ungetc(c,ficpar);
5665:
5666:
5667: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5668: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5669:
5670: fscanf(ficpar,"pop_based=%d\n",&popbased);
5671: fprintf(ficparo,"pop_based=%d\n",popbased);
5672: fprintf(ficres,"pop_based=%d\n",popbased);
5673:
5674: while((c=getc(ficpar))=='#' && c!= EOF){
5675: ungetc(c,ficpar);
5676: fgets(line, MAXLINE, ficpar);
5677: puts(line);
5678: fputs(line,ficparo);
5679: }
5680: ungetc(c,ficpar);
5681:
5682: 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);
5683: 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);
5684: 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);
5685: 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);
5686: 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);
5687: /* day and month of proj2 are not used but only year anproj2.*/
5688:
5689:
5690:
5691: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5692: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5693:
5694: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5695: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5696:
5697: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5698: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5699: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5700:
5701: /*------------ free_vector -------------*/
5702: /* chdir(path); */
5703:
5704: free_ivector(wav,1,imx);
5705: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5706: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5707: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5708: free_lvector(num,1,n);
5709: free_vector(agedc,1,n);
5710: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5711: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5712: fclose(ficparo);
5713: fclose(ficres);
5714:
5715:
5716: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5717:
5718: strcpy(filerespl,"pl");
5719: strcat(filerespl,fileres);
5720: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5721: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5722: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5723: }
5724: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5725: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5726: pstamp(ficrespl);
5727: fprintf(ficrespl,"# Period (stable) prevalence \n");
5728: fprintf(ficrespl,"#Age ");
5729: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5730: fprintf(ficrespl,"\n");
5731:
5732: prlim=matrix(1,nlstate,1,nlstate);
5733:
5734: agebase=ageminpar;
5735: agelim=agemaxpar;
5736: ftolpl=1.e-10;
5737: i1=cptcoveff;
5738: if (cptcovn < 1){i1=1;}
5739:
5740: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5741: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5742: k=k+1;
5743: /* to clean */
5744: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
5745: fprintf(ficrespl,"\n#******");
5746: printf("\n#******");
5747: fprintf(ficlog,"\n#******");
5748: for(j=1;j<=cptcoveff;j++) {
5749: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5750: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5751: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5752: }
5753: fprintf(ficrespl,"******\n");
5754: printf("******\n");
5755: fprintf(ficlog,"******\n");
5756:
5757: for (age=agebase; age<=agelim; age++){
5758: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5759: fprintf(ficrespl,"%.0f ",age );
5760: for(j=1;j<=cptcoveff;j++)
5761: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5762: for(i=1; i<=nlstate;i++)
5763: fprintf(ficrespl," %.5f", prlim[i][i]);
5764: fprintf(ficrespl,"\n");
5765: }
5766: }
5767: }
5768: fclose(ficrespl);
5769:
5770: /*------------- h Pij x at various ages ------------*/
5771:
5772: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5773: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5774: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5775: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5776: }
5777: printf("Computing pij: result on file '%s' \n", filerespij);
5778: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5779:
5780: stepsize=(int) (stepm+YEARM-1)/YEARM;
5781: /*if (stepm<=24) stepsize=2;*/
5782:
5783: agelim=AGESUP;
5784: hstepm=stepsize*YEARM; /* Every year of age */
5785: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5786:
5787: /* hstepm=1; aff par mois*/
5788: pstamp(ficrespij);
5789: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5790: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5791: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5792: k=k+1;
5793: fprintf(ficrespij,"\n#****** ");
5794: for(j=1;j<=cptcoveff;j++)
5795: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5796: fprintf(ficrespij,"******\n");
5797:
5798: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5799: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5800: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5801:
5802: /* nhstepm=nhstepm*YEARM; aff par mois*/
5803:
5804: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5805: oldm=oldms;savm=savms;
5806: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5807: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5808: for(i=1; i<=nlstate;i++)
5809: for(j=1; j<=nlstate+ndeath;j++)
5810: fprintf(ficrespij," %1d-%1d",i,j);
5811: fprintf(ficrespij,"\n");
5812: for (h=0; h<=nhstepm; h++){
5813: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5814: for(i=1; i<=nlstate;i++)
5815: for(j=1; j<=nlstate+ndeath;j++)
5816: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5817: fprintf(ficrespij,"\n");
5818: }
5819: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5820: fprintf(ficrespij,"\n");
5821: }
5822: }
5823: }
5824:
5825: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5826:
5827: fclose(ficrespij);
5828:
5829: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5830: for(i=1;i<=AGESUP;i++)
5831: for(j=1;j<=NCOVMAX;j++)
5832: for(k=1;k<=NCOVMAX;k++)
5833: probs[i][j][k]=0.;
5834:
5835: /*---------- Forecasting ------------------*/
5836: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5837: if(prevfcast==1){
5838: /* if(stepm ==1){*/
5839: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5840: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5841: /* } */
5842: /* else{ */
5843: /* erreur=108; */
5844: /* 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); */
5845: /* 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); */
5846: /* } */
5847: }
5848:
5849:
5850: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5851:
5852: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5853: /* 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",\
5854: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5855: */
5856:
5857: if (mobilav!=0) {
5858: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5859: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5860: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5861: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5862: }
5863: }
5864:
5865:
5866: /*---------- Health expectancies, no variances ------------*/
5867:
5868: strcpy(filerese,"e");
5869: strcat(filerese,fileres);
5870: if((ficreseij=fopen(filerese,"w"))==NULL) {
5871: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5872: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5873: }
5874: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5875: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5876: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5877: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5878: k=k+1;
5879: fprintf(ficreseij,"\n#****** ");
5880: for(j=1;j<=cptcoveff;j++) {
5881: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5882: }
5883: fprintf(ficreseij,"******\n");
5884:
5885: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5886: oldm=oldms;savm=savms;
5887: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5888:
5889: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5890: }
5891: }
5892: fclose(ficreseij);
5893:
5894:
5895: /*---------- Health expectancies and variances ------------*/
5896:
5897:
5898: strcpy(filerest,"t");
5899: strcat(filerest,fileres);
5900: if((ficrest=fopen(filerest,"w"))==NULL) {
5901: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5902: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5903: }
5904: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5905: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5906:
5907:
5908: strcpy(fileresstde,"stde");
5909: strcat(fileresstde,fileres);
5910: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5911: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5912: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5913: }
5914: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5915: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5916:
5917: strcpy(filerescve,"cve");
5918: strcat(filerescve,fileres);
5919: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5920: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5921: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5922: }
5923: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5924: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5925:
5926: strcpy(fileresv,"v");
5927: strcat(fileresv,fileres);
5928: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5929: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5930: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5931: }
5932: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5933: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5934:
5935: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5936: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5937: k=k+1;
5938: fprintf(ficrest,"\n#****** ");
5939: for(j=1;j<=cptcoveff;j++)
5940: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5941: fprintf(ficrest,"******\n");
5942:
5943: fprintf(ficresstdeij,"\n#****** ");
5944: fprintf(ficrescveij,"\n#****** ");
5945: for(j=1;j<=cptcoveff;j++) {
5946: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5947: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5948: }
5949: fprintf(ficresstdeij,"******\n");
5950: fprintf(ficrescveij,"******\n");
5951:
5952: fprintf(ficresvij,"\n#****** ");
5953: for(j=1;j<=cptcoveff;j++)
5954: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5955: fprintf(ficresvij,"******\n");
5956:
5957: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5958: oldm=oldms;savm=savms;
5959: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5960:
5961: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5962: pstamp(ficrest);
5963: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5964: oldm=oldms;savm=savms;
5965: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
5966: if(vpopbased==1)
5967: fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
5968: else
5969: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5970: fprintf(ficrest,"# Age e.. (std) ");
5971: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5972: fprintf(ficrest,"\n");
5973:
5974: epj=vector(1,nlstate+1);
5975: for(age=bage; age <=fage ;age++){
5976: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5977: if (vpopbased==1) {
5978: if(mobilav ==0){
5979: for(i=1; i<=nlstate;i++)
5980: prlim[i][i]=probs[(int)age][i][k];
5981: }else{ /* mobilav */
5982: for(i=1; i<=nlstate;i++)
5983: prlim[i][i]=mobaverage[(int)age][i][k];
5984: }
5985: }
5986:
5987: fprintf(ficrest," %4.0f",age);
5988: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
5989: for(i=1, epj[j]=0.;i <=nlstate;i++) {
5990: epj[j] += prlim[i][i]*eij[i][j][(int)age];
5991: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
5992: }
5993: epj[nlstate+1] +=epj[j];
5994: }
5995:
5996: for(i=1, vepp=0.;i <=nlstate;i++)
5997: for(j=1;j <=nlstate;j++)
5998: vepp += vareij[i][j][(int)age];
5999: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6000: for(j=1;j <=nlstate;j++){
6001: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6002: }
6003: fprintf(ficrest,"\n");
6004: }
6005: }
6006: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6007: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6008: free_vector(epj,1,nlstate+1);
6009: }
6010: }
6011: free_vector(weight,1,n);
6012: free_imatrix(Tvard,1,15,1,2);
6013: free_imatrix(s,1,maxwav+1,1,n);
6014: free_matrix(anint,1,maxwav,1,n);
6015: free_matrix(mint,1,maxwav,1,n);
6016: free_ivector(cod,1,n);
6017: free_ivector(tab,1,NCOVMAX);
6018: fclose(ficresstdeij);
6019: fclose(ficrescveij);
6020: fclose(ficresvij);
6021: fclose(ficrest);
6022: fclose(ficpar);
6023:
6024: /*------- Variance of period (stable) prevalence------*/
6025:
6026: strcpy(fileresvpl,"vpl");
6027: strcat(fileresvpl,fileres);
6028: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6029: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6030: exit(0);
6031: }
6032: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6033:
6034: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6035: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6036: k=k+1;
6037: fprintf(ficresvpl,"\n#****** ");
6038: for(j=1;j<=cptcoveff;j++)
6039: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6040: fprintf(ficresvpl,"******\n");
6041:
6042: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6043: oldm=oldms;savm=savms;
6044: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6045: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6046: }
6047: }
6048:
6049: fclose(ficresvpl);
6050:
6051: /*---------- End : free ----------------*/
6052: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6053: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6054:
6055: } /* mle==-3 arrives here for freeing */
6056: endfree:
6057: free_matrix(prlim,1,nlstate,1,nlstate);
6058: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6059: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6060: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6061: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6062: free_matrix(covar,0,NCOVMAX,1,n);
6063: free_matrix(matcov,1,npar,1,npar);
6064: /*free_vector(delti,1,npar);*/
6065: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6066: free_matrix(agev,1,maxwav,1,imx);
6067: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6068:
6069: free_ivector(ncodemax,1,8);
6070: free_ivector(Tvar,1,15);
6071: free_ivector(Tprod,1,15);
6072: free_ivector(Tvaraff,1,15);
6073: free_ivector(Tage,1,15);
6074:
6075: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6076: free_imatrix(codtab,1,100,1,10);
6077: fflush(fichtm);
6078: fflush(ficgp);
6079:
6080:
6081: if((nberr >0) || (nbwarn>0)){
6082: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6083: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6084: }else{
6085: printf("End of Imach\n");
6086: fprintf(ficlog,"End of Imach\n");
6087: }
6088: printf("See log file on %s\n",filelog);
6089: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6090: (void) gettimeofday(&end_time,&tzp);
6091: tm = *localtime(&end_time.tv_sec);
6092: tmg = *gmtime(&end_time.tv_sec);
6093: strcpy(strtend,asctime(&tm));
6094: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6095: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6096: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6097:
6098: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6099: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6100: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6101: /* printf("Total time was %d uSec.\n", total_usecs);*/
6102: /* if(fileappend(fichtm,optionfilehtm)){ */
6103: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6104: fclose(fichtm);
6105: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6106: fclose(fichtmcov);
6107: fclose(ficgp);
6108: fclose(ficlog);
6109: /*------ End -----------*/
6110:
6111:
6112: printf("Before Current directory %s!\n",pathcd);
6113: if(chdir(pathcd) != 0)
6114: printf("Can't move to directory %s!\n",path);
6115: if(getcwd(pathcd,MAXLINE) > 0)
6116: printf("Current directory %s!\n",pathcd);
6117: /*strcat(plotcmd,CHARSEPARATOR);*/
6118: sprintf(plotcmd,"gnuplot");
6119: #ifndef UNIX
6120: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6121: #endif
6122: if(!stat(plotcmd,&info)){
6123: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6124: if(!stat(getenv("GNUPLOTBIN"),&info)){
6125: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6126: }else
6127: strcpy(pplotcmd,plotcmd);
6128: #ifdef UNIX
6129: strcpy(plotcmd,GNUPLOTPROGRAM);
6130: if(!stat(plotcmd,&info)){
6131: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6132: }else
6133: strcpy(pplotcmd,plotcmd);
6134: #endif
6135: }else
6136: strcpy(pplotcmd,plotcmd);
6137:
6138: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6139: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6140:
6141: if((outcmd=system(plotcmd)) != 0){
6142: printf("\n Problem with gnuplot\n");
6143: }
6144: printf(" Wait...");
6145: while (z[0] != 'q') {
6146: /* chdir(path); */
6147: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6148: scanf("%s",z);
6149: /* if (z[0] == 'c') system("./imach"); */
6150: if (z[0] == 'e') {
6151: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6152: system(optionfilehtm);
6153: }
6154: else if (z[0] == 'g') system(plotcmd);
6155: else if (z[0] == 'q') exit(0);
6156: }
6157: end:
6158: while (z[0] != 'q') {
6159: printf("\nType q for exiting: ");
6160: scanf("%s",z);
6161: }
6162: }
6163:
6164:
6165:
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