1: /* $Id: imach.c,v 1.135 2009/10/29 15:33:14 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.135 2009/10/29 15:33:14 brouard
5: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
6:
7: Revision 1.134 2009/10/29 13:18:53 brouard
8: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
9:
10: Revision 1.133 2009/07/06 10:21:25 brouard
11: just nforces
12:
13: Revision 1.132 2009/07/06 08:22:05 brouard
14: Many tings
15:
16: Revision 1.131 2009/06/20 16:22:47 brouard
17: Some dimensions resccaled
18:
19: Revision 1.130 2009/05/26 06:44:34 brouard
20: (Module): Max Covariate is now set to 20 instead of 8. A
21: lot of cleaning with variables initialized to 0. Trying to make
22: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
23:
24: Revision 1.129 2007/08/31 13:49:27 lievre
25: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
26:
27: Revision 1.128 2006/06/30 13:02:05 brouard
28: (Module): Clarifications on computing e.j
29:
30: Revision 1.127 2006/04/28 18:11:50 brouard
31: (Module): Yes the sum of survivors was wrong since
32: imach-114 because nhstepm was no more computed in the age
33: loop. Now we define nhstepma in the age loop.
34: (Module): In order to speed up (in case of numerous covariates) we
35: compute health expectancies (without variances) in a first step
36: and then all the health expectancies with variances or standard
37: deviation (needs data from the Hessian matrices) which slows the
38: computation.
39: In the future we should be able to stop the program is only health
40: expectancies and graph are needed without standard deviations.
41:
42: Revision 1.126 2006/04/28 17:23:28 brouard
43: (Module): Yes the sum of survivors was wrong since
44: imach-114 because nhstepm was no more computed in the age
45: loop. Now we define nhstepma in the age loop.
46: Version 0.98h
47:
48: Revision 1.125 2006/04/04 15:20:31 lievre
49: Errors in calculation of health expectancies. Age was not initialized.
50: Forecasting file added.
51:
52: Revision 1.124 2006/03/22 17:13:53 lievre
53: Parameters are printed with %lf instead of %f (more numbers after the comma).
54: The log-likelihood is printed in the log file
55:
56: Revision 1.123 2006/03/20 10:52:43 brouard
57: * imach.c (Module): <title> changed, corresponds to .htm file
58: name. <head> headers where missing.
59:
60: * imach.c (Module): Weights can have a decimal point as for
61: English (a comma might work with a correct LC_NUMERIC environment,
62: otherwise the weight is truncated).
63: Modification of warning when the covariates values are not 0 or
64: 1.
65: Version 0.98g
66:
67: Revision 1.122 2006/03/20 09:45:41 brouard
68: (Module): Weights can have a decimal point as for
69: English (a comma might work with a correct LC_NUMERIC environment,
70: otherwise the weight is truncated).
71: Modification of warning when the covariates values are not 0 or
72: 1.
73: Version 0.98g
74:
75: Revision 1.121 2006/03/16 17:45:01 lievre
76: * imach.c (Module): Comments concerning covariates added
77:
78: * imach.c (Module): refinements in the computation of lli if
79: status=-2 in order to have more reliable computation if stepm is
80: not 1 month. Version 0.98f
81:
82: Revision 1.120 2006/03/16 15:10:38 lievre
83: (Module): refinements in the computation of lli if
84: status=-2 in order to have more reliable computation if stepm is
85: not 1 month. Version 0.98f
86:
87: Revision 1.119 2006/03/15 17:42:26 brouard
88: (Module): Bug if status = -2, the loglikelihood was
89: computed as likelihood omitting the logarithm. Version O.98e
90:
91: Revision 1.118 2006/03/14 18:20:07 brouard
92: (Module): varevsij Comments added explaining the second
93: table of variances if popbased=1 .
94: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
95: (Module): Function pstamp added
96: (Module): Version 0.98d
97:
98: Revision 1.117 2006/03/14 17:16:22 brouard
99: (Module): varevsij Comments added explaining the second
100: table of variances if popbased=1 .
101: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
102: (Module): Function pstamp added
103: (Module): Version 0.98d
104:
105: Revision 1.116 2006/03/06 10:29:27 brouard
106: (Module): Variance-covariance wrong links and
107: varian-covariance of ej. is needed (Saito).
108:
109: Revision 1.115 2006/02/27 12:17:45 brouard
110: (Module): One freematrix added in mlikeli! 0.98c
111:
112: Revision 1.114 2006/02/26 12:57:58 brouard
113: (Module): Some improvements in processing parameter
114: filename with strsep.
115:
116: Revision 1.113 2006/02/24 14:20:24 brouard
117: (Module): Memory leaks checks with valgrind and:
118: datafile was not closed, some imatrix were not freed and on matrix
119: allocation too.
120:
121: Revision 1.112 2006/01/30 09:55:26 brouard
122: (Module): Back to gnuplot.exe instead of wgnuplot.exe
123:
124: Revision 1.111 2006/01/25 20:38:18 brouard
125: (Module): Lots of cleaning and bugs added (Gompertz)
126: (Module): Comments can be added in data file. Missing date values
127: can be a simple dot '.'.
128:
129: Revision 1.110 2006/01/25 00:51:50 brouard
130: (Module): Lots of cleaning and bugs added (Gompertz)
131:
132: Revision 1.109 2006/01/24 19:37:15 brouard
133: (Module): Comments (lines starting with a #) are allowed in data.
134:
135: Revision 1.108 2006/01/19 18:05:42 lievre
136: Gnuplot problem appeared...
137: To be fixed
138:
139: Revision 1.107 2006/01/19 16:20:37 brouard
140: Test existence of gnuplot in imach path
141:
142: Revision 1.106 2006/01/19 13:24:36 brouard
143: Some cleaning and links added in html output
144:
145: Revision 1.105 2006/01/05 20:23:19 lievre
146: *** empty log message ***
147:
148: Revision 1.104 2005/09/30 16:11:43 lievre
149: (Module): sump fixed, loop imx fixed, and simplifications.
150: (Module): If the status is missing at the last wave but we know
151: that the person is alive, then we can code his/her status as -2
152: (instead of missing=-1 in earlier versions) and his/her
153: contributions to the likelihood is 1 - Prob of dying from last
154: health status (= 1-p13= p11+p12 in the easiest case of somebody in
155: the healthy state at last known wave). Version is 0.98
156:
157: Revision 1.103 2005/09/30 15:54:49 lievre
158: (Module): sump fixed, loop imx fixed, and simplifications.
159:
160: Revision 1.102 2004/09/15 17:31:30 brouard
161: Add the possibility to read data file including tab characters.
162:
163: Revision 1.101 2004/09/15 10:38:38 brouard
164: Fix on curr_time
165:
166: Revision 1.100 2004/07/12 18:29:06 brouard
167: Add version for Mac OS X. Just define UNIX in Makefile
168:
169: Revision 1.99 2004/06/05 08:57:40 brouard
170: *** empty log message ***
171:
172: Revision 1.98 2004/05/16 15:05:56 brouard
173: New version 0.97 . First attempt to estimate force of mortality
174: directly from the data i.e. without the need of knowing the health
175: state at each age, but using a Gompertz model: log u =a + b*age .
176: This is the basic analysis of mortality and should be done before any
177: other analysis, in order to test if the mortality estimated from the
178: cross-longitudinal survey is different from the mortality estimated
179: from other sources like vital statistic data.
180:
181: The same imach parameter file can be used but the option for mle should be -3.
182:
183: Agnès, who wrote this part of the code, tried to keep most of the
184: former routines in order to include the new code within the former code.
185:
186: The output is very simple: only an estimate of the intercept and of
187: the slope with 95% confident intervals.
188:
189: Current limitations:
190: A) Even if you enter covariates, i.e. with the
191: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
192: B) There is no computation of Life Expectancy nor Life Table.
193:
194: Revision 1.97 2004/02/20 13:25:42 lievre
195: Version 0.96d. Population forecasting command line is (temporarily)
196: suppressed.
197:
198: Revision 1.96 2003/07/15 15:38:55 brouard
199: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
200: rewritten within the same printf. Workaround: many printfs.
201:
202: Revision 1.95 2003/07/08 07:54:34 brouard
203: * imach.c (Repository):
204: (Repository): Using imachwizard code to output a more meaningful covariance
205: matrix (cov(a12,c31) instead of numbers.
206:
207: Revision 1.94 2003/06/27 13:00:02 brouard
208: Just cleaning
209:
210: Revision 1.93 2003/06/25 16:33:55 brouard
211: (Module): On windows (cygwin) function asctime_r doesn't
212: exist so I changed back to asctime which exists.
213: (Module): Version 0.96b
214:
215: Revision 1.92 2003/06/25 16:30:45 brouard
216: (Module): On windows (cygwin) function asctime_r doesn't
217: exist so I changed back to asctime which exists.
218:
219: Revision 1.91 2003/06/25 15:30:29 brouard
220: * imach.c (Repository): Duplicated warning errors corrected.
221: (Repository): Elapsed time after each iteration is now output. It
222: helps to forecast when convergence will be reached. Elapsed time
223: is stamped in powell. We created a new html file for the graphs
224: concerning matrix of covariance. It has extension -cov.htm.
225:
226: Revision 1.90 2003/06/24 12:34:15 brouard
227: (Module): Some bugs corrected for windows. Also, when
228: mle=-1 a template is output in file "or"mypar.txt with the design
229: of the covariance matrix to be input.
230:
231: Revision 1.89 2003/06/24 12:30:52 brouard
232: (Module): Some bugs corrected for windows. Also, when
233: mle=-1 a template is output in file "or"mypar.txt with the design
234: of the covariance matrix to be input.
235:
236: Revision 1.88 2003/06/23 17:54:56 brouard
237: * 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.
238:
239: Revision 1.87 2003/06/18 12:26:01 brouard
240: Version 0.96
241:
242: Revision 1.86 2003/06/17 20:04:08 brouard
243: (Module): Change position of html and gnuplot routines and added
244: routine fileappend.
245:
246: Revision 1.85 2003/06/17 13:12:43 brouard
247: * imach.c (Repository): Check when date of death was earlier that
248: current date of interview. It may happen when the death was just
249: prior to the death. In this case, dh was negative and likelihood
250: was wrong (infinity). We still send an "Error" but patch by
251: assuming that the date of death was just one stepm after the
252: interview.
253: (Repository): Because some people have very long ID (first column)
254: we changed int to long in num[] and we added a new lvector for
255: memory allocation. But we also truncated to 8 characters (left
256: truncation)
257: (Repository): No more line truncation errors.
258:
259: Revision 1.84 2003/06/13 21:44:43 brouard
260: * imach.c (Repository): Replace "freqsummary" at a correct
261: place. It differs from routine "prevalence" which may be called
262: many times. Probs is memory consuming and must be used with
263: parcimony.
264: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
265:
266: Revision 1.83 2003/06/10 13:39:11 lievre
267: *** empty log message ***
268:
269: Revision 1.82 2003/06/05 15:57:20 brouard
270: Add log in imach.c and fullversion number is now printed.
271:
272: */
273: /*
274: Interpolated Markov Chain
275:
276: Short summary of the programme:
277:
278: This program computes Healthy Life Expectancies from
279: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
280: first survey ("cross") where individuals from different ages are
281: interviewed on their health status or degree of disability (in the
282: case of a health survey which is our main interest) -2- at least a
283: second wave of interviews ("longitudinal") which measure each change
284: (if any) in individual health status. Health expectancies are
285: computed from the time spent in each health state according to a
286: model. More health states you consider, more time is necessary to reach the
287: Maximum Likelihood of the parameters involved in the model. The
288: simplest model is the multinomial logistic model where pij is the
289: probability to be observed in state j at the second wave
290: conditional to be observed in state i at the first wave. Therefore
291: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
292: 'age' is age and 'sex' is a covariate. If you want to have a more
293: complex model than "constant and age", you should modify the program
294: where the markup *Covariates have to be included here again* invites
295: you to do it. More covariates you add, slower the
296: convergence.
297:
298: The advantage of this computer programme, compared to a simple
299: multinomial logistic model, is clear when the delay between waves is not
300: identical for each individual. Also, if a individual missed an
301: intermediate interview, the information is lost, but taken into
302: account using an interpolation or extrapolation.
303:
304: hPijx is the probability to be observed in state i at age x+h
305: conditional to the observed state i at age x. The delay 'h' can be
306: split into an exact number (nh*stepm) of unobserved intermediate
307: states. This elementary transition (by month, quarter,
308: semester or year) is modelled as a multinomial logistic. The hPx
309: matrix is simply the matrix product of nh*stepm elementary matrices
310: and the contribution of each individual to the likelihood is simply
311: hPijx.
312:
313: Also this programme outputs the covariance matrix of the parameters but also
314: of the life expectancies. It also computes the period (stable) prevalence.
315:
316: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
317: Institut national d'études démographiques, Paris.
318: This software have been partly granted by Euro-REVES, a concerted action
319: from the European Union.
320: It is copyrighted identically to a GNU software product, ie programme and
321: software can be distributed freely for non commercial use. Latest version
322: can be accessed at http://euroreves.ined.fr/imach .
323:
324: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
325: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
326:
327: **********************************************************************/
328: /*
329: main
330: read parameterfile
331: read datafile
332: concatwav
333: freqsummary
334: if (mle >= 1)
335: mlikeli
336: print results files
337: if mle==1
338: computes hessian
339: read end of parameter file: agemin, agemax, bage, fage, estepm
340: begin-prev-date,...
341: open gnuplot file
342: open html file
343: period (stable) prevalence
344: for age prevalim()
345: h Pij x
346: variance of p varprob
347: forecasting if prevfcast==1 prevforecast call prevalence()
348: health expectancies
349: Variance-covariance of DFLE
350: prevalence()
351: movingaverage()
352: varevsij()
353: if popbased==1 varevsij(,popbased)
354: total life expectancies
355: Variance of period (stable) prevalence
356: end
357: */
358:
359:
360:
361:
362: #include <math.h>
363: #include <stdio.h>
364: #include <stdlib.h>
365: #include <string.h>
366: #include <unistd.h>
367:
368: #include <limits.h>
369: #include <sys/types.h>
370: #include <sys/stat.h>
371: #include <errno.h>
372: extern int errno;
373:
374: /* #include <sys/time.h> */
375: #include <time.h>
376: #include "timeval.h"
377:
378: /* #include <libintl.h> */
379: /* #define _(String) gettext (String) */
380:
381: #define MAXLINE 256
382:
383: #define GNUPLOTPROGRAM "gnuplot"
384: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
385: #define FILENAMELENGTH 132
386:
387: #define GLOCK_ERROR_NOPATH -1 /* empty path */
388: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
389:
390: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
391: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
392:
393: #define NINTERVMAX 8
394: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
395: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
396: #define NCOVMAX 20 /* Maximum number of covariates */
397: #define MAXN 20000
398: #define YEARM 12. /* Number of months per year */
399: #define AGESUP 130
400: #define AGEBASE 40
401: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
402: #ifdef UNIX
403: #define DIRSEPARATOR '/'
404: #define CHARSEPARATOR "/"
405: #define ODIRSEPARATOR '\\'
406: #else
407: #define DIRSEPARATOR '\\'
408: #define CHARSEPARATOR "\\"
409: #define ODIRSEPARATOR '/'
410: #endif
411:
412: /* $Id: imach.c,v 1.135 2009/10/29 15:33:14 brouard Exp $ */
413: /* $State: Exp $ */
414:
415: char version[]="Imach version 0.98l, October 2009, INED-EUROREVES-Institut de longevite ";
416: char fullversion[]="$Revision: 1.135 $ $Date: 2009/10/29 15:33:14 $";
417: char strstart[80];
418: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
419: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
420: int nvar=0, nforce=0; /* Number of variables, number of forces */
421: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
422: int npar=NPARMAX;
423: int nlstate=2; /* Number of live states */
424: int ndeath=1; /* Number of dead states */
425: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
426: int popbased=0;
427:
428: int *wav; /* Number of waves for this individuual 0 is possible */
429: int maxwav=0; /* Maxim number of waves */
430: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
431: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
432: int gipmx=0, gsw=0; /* Global variables on the number of contributions
433: to the likelihood and the sum of weights (done by funcone)*/
434: int mle=1, weightopt=0;
435: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
436: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
437: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
438: * wave mi and wave mi+1 is not an exact multiple of stepm. */
439: double jmean=1; /* Mean space between 2 waves */
440: double **oldm, **newm, **savm; /* Working pointers to matrices */
441: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
442: FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
443: FILE *ficlog, *ficrespow;
444: int globpr=0; /* Global variable for printing or not */
445: double fretone; /* Only one call to likelihood */
446: long ipmx=0; /* Number of contributions */
447: double sw; /* Sum of weights */
448: char filerespow[FILENAMELENGTH];
449: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
450: FILE *ficresilk;
451: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
452: FILE *ficresprobmorprev;
453: FILE *fichtm, *fichtmcov; /* Html File */
454: FILE *ficreseij;
455: char filerese[FILENAMELENGTH];
456: FILE *ficresstdeij;
457: char fileresstde[FILENAMELENGTH];
458: FILE *ficrescveij;
459: char filerescve[FILENAMELENGTH];
460: FILE *ficresvij;
461: char fileresv[FILENAMELENGTH];
462: FILE *ficresvpl;
463: char fileresvpl[FILENAMELENGTH];
464: char title[MAXLINE];
465: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
466: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
467: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
468: char command[FILENAMELENGTH];
469: int outcmd=0;
470:
471: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
472:
473: char filelog[FILENAMELENGTH]; /* Log file */
474: char filerest[FILENAMELENGTH];
475: char fileregp[FILENAMELENGTH];
476: char popfile[FILENAMELENGTH];
477:
478: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
479:
480: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
481: struct timezone tzp;
482: extern int gettimeofday();
483: struct tm tmg, tm, tmf, *gmtime(), *localtime();
484: long time_value;
485: extern long time();
486: char strcurr[80], strfor[80];
487:
488: char *endptr;
489: long lval;
490: double dval;
491:
492: #define NR_END 1
493: #define FREE_ARG char*
494: #define FTOL 1.0e-10
495:
496: #define NRANSI
497: #define ITMAX 200
498:
499: #define TOL 2.0e-4
500:
501: #define CGOLD 0.3819660
502: #define ZEPS 1.0e-10
503: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
504:
505: #define GOLD 1.618034
506: #define GLIMIT 100.0
507: #define TINY 1.0e-20
508:
509: static double maxarg1,maxarg2;
510: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
511: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
512:
513: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
514: #define rint(a) floor(a+0.5)
515:
516: static double sqrarg;
517: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
518: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
519: int agegomp= AGEGOMP;
520:
521: int imx;
522: int stepm=1;
523: /* Stepm, step in month: minimum step interpolation*/
524:
525: int estepm;
526: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
527:
528: int m,nb;
529: long *num;
530: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
531: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
532: double **pmmij, ***probs;
533: double *ageexmed,*agecens;
534: double dateintmean=0;
535:
536: double *weight;
537: int **s; /* Status */
538: double *agedc, **covar, idx;
539: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
540: double *lsurv, *lpop, *tpop;
541:
542: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
543: double ftolhess; /* Tolerance for computing hessian */
544:
545: /**************** split *************************/
546: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
547: {
548: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
549: the name of the file (name), its extension only (ext) and its first part of the name (finame)
550: */
551: char *ss; /* pointer */
552: int l1, l2; /* length counters */
553:
554: l1 = strlen(path ); /* length of path */
555: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
556: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
557: if ( ss == NULL ) { /* no directory, so determine current directory */
558: strcpy( name, path ); /* we got the fullname name because no directory */
559: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
560: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
561: /* get current working directory */
562: /* extern char* getcwd ( char *buf , int len);*/
563: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
564: return( GLOCK_ERROR_GETCWD );
565: }
566: /* got dirc from getcwd*/
567: printf(" DIRC = %s \n",dirc);
568: } else { /* strip direcotry from path */
569: ss++; /* after this, the filename */
570: l2 = strlen( ss ); /* length of filename */
571: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
572: strcpy( name, ss ); /* save file name */
573: strncpy( dirc, path, l1 - l2 ); /* now the directory */
574: dirc[l1-l2] = 0; /* add zero */
575: printf(" DIRC2 = %s \n",dirc);
576: }
577: /* We add a separator at the end of dirc if not exists */
578: l1 = strlen( dirc ); /* length of directory */
579: if( dirc[l1-1] != DIRSEPARATOR ){
580: dirc[l1] = DIRSEPARATOR;
581: dirc[l1+1] = 0;
582: printf(" DIRC3 = %s \n",dirc);
583: }
584: ss = strrchr( name, '.' ); /* find last / */
585: if (ss >0){
586: ss++;
587: strcpy(ext,ss); /* save extension */
588: l1= strlen( name);
589: l2= strlen(ss)+1;
590: strncpy( finame, name, l1-l2);
591: finame[l1-l2]= 0;
592: }
593:
594: return( 0 ); /* we're done */
595: }
596:
597:
598: /******************************************/
599:
600: void replace_back_to_slash(char *s, char*t)
601: {
602: int i;
603: int lg=0;
604: i=0;
605: lg=strlen(t);
606: for(i=0; i<= lg; i++) {
607: (s[i] = t[i]);
608: if (t[i]== '\\') s[i]='/';
609: }
610: }
611:
612: char *trimbb(char *out, char *in)
613: { /* Trim multiple blanks in line */
614: char *s;
615: s=out;
616: while (*in != '\0'){
617: while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
618: in++;
619: }
620: *out++ = *in++;
621: }
622: *out='\0';
623: return s;
624: }
625:
626: int nbocc(char *s, char occ)
627: {
628: int i,j=0;
629: int lg=20;
630: i=0;
631: lg=strlen(s);
632: for(i=0; i<= lg; i++) {
633: if (s[i] == occ ) j++;
634: }
635: return j;
636: }
637:
638: void cutv(char *u,char *v, char*t, char occ)
639: {
640: /* cuts string t into u and v where u ends before first occurence of char 'occ'
641: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
642: gives u="abcedf" and v="ghi2j" */
643: int i,lg,j,p=0;
644: i=0;
645: for(j=0; j<=strlen(t)-1; j++) {
646: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
647: }
648:
649: lg=strlen(t);
650: for(j=0; j<p; j++) {
651: (u[j] = t[j]);
652: }
653: u[p]='\0';
654:
655: for(j=0; j<= lg; j++) {
656: if (j>=(p+1))(v[j-p-1] = t[j]);
657: }
658: }
659:
660: /********************** nrerror ********************/
661:
662: void nrerror(char error_text[])
663: {
664: fprintf(stderr,"ERREUR ...\n");
665: fprintf(stderr,"%s\n",error_text);
666: exit(EXIT_FAILURE);
667: }
668: /*********************** vector *******************/
669: double *vector(int nl, int nh)
670: {
671: double *v;
672: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
673: if (!v) nrerror("allocation failure in vector");
674: return v-nl+NR_END;
675: }
676:
677: /************************ free vector ******************/
678: void free_vector(double*v, int nl, int nh)
679: {
680: free((FREE_ARG)(v+nl-NR_END));
681: }
682:
683: /************************ivector *******************************/
684: int *ivector(long nl,long nh)
685: {
686: int *v;
687: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
688: if (!v) nrerror("allocation failure in ivector");
689: return v-nl+NR_END;
690: }
691:
692: /******************free ivector **************************/
693: void free_ivector(int *v, long nl, long nh)
694: {
695: free((FREE_ARG)(v+nl-NR_END));
696: }
697:
698: /************************lvector *******************************/
699: long *lvector(long nl,long nh)
700: {
701: long *v;
702: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
703: if (!v) nrerror("allocation failure in ivector");
704: return v-nl+NR_END;
705: }
706:
707: /******************free lvector **************************/
708: void free_lvector(long *v, long nl, long nh)
709: {
710: free((FREE_ARG)(v+nl-NR_END));
711: }
712:
713: /******************* imatrix *******************************/
714: int **imatrix(long nrl, long nrh, long ncl, long nch)
715: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
716: {
717: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
718: int **m;
719:
720: /* allocate pointers to rows */
721: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
722: if (!m) nrerror("allocation failure 1 in matrix()");
723: m += NR_END;
724: m -= nrl;
725:
726:
727: /* allocate rows and set pointers to them */
728: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
729: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
730: m[nrl] += NR_END;
731: m[nrl] -= ncl;
732:
733: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
734:
735: /* return pointer to array of pointers to rows */
736: return m;
737: }
738:
739: /****************** free_imatrix *************************/
740: void free_imatrix(m,nrl,nrh,ncl,nch)
741: int **m;
742: long nch,ncl,nrh,nrl;
743: /* free an int matrix allocated by imatrix() */
744: {
745: free((FREE_ARG) (m[nrl]+ncl-NR_END));
746: free((FREE_ARG) (m+nrl-NR_END));
747: }
748:
749: /******************* matrix *******************************/
750: double **matrix(long nrl, long nrh, long ncl, long nch)
751: {
752: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
753: double **m;
754:
755: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
756: if (!m) nrerror("allocation failure 1 in matrix()");
757: m += NR_END;
758: m -= nrl;
759:
760: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
761: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
762: m[nrl] += NR_END;
763: m[nrl] -= ncl;
764:
765: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
766: return m;
767: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
768: */
769: }
770:
771: /*************************free matrix ************************/
772: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
773: {
774: free((FREE_ARG)(m[nrl]+ncl-NR_END));
775: free((FREE_ARG)(m+nrl-NR_END));
776: }
777:
778: /******************* ma3x *******************************/
779: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
780: {
781: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
782: double ***m;
783:
784: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
785: if (!m) nrerror("allocation failure 1 in matrix()");
786: m += NR_END;
787: m -= nrl;
788:
789: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
790: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
791: m[nrl] += NR_END;
792: m[nrl] -= ncl;
793:
794: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
795:
796: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
797: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
798: m[nrl][ncl] += NR_END;
799: m[nrl][ncl] -= nll;
800: for (j=ncl+1; j<=nch; j++)
801: m[nrl][j]=m[nrl][j-1]+nlay;
802:
803: for (i=nrl+1; i<=nrh; i++) {
804: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
805: for (j=ncl+1; j<=nch; j++)
806: m[i][j]=m[i][j-1]+nlay;
807: }
808: return m;
809: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
810: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
811: */
812: }
813:
814: /*************************free ma3x ************************/
815: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
816: {
817: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
818: free((FREE_ARG)(m[nrl]+ncl-NR_END));
819: free((FREE_ARG)(m+nrl-NR_END));
820: }
821:
822: /*************** function subdirf ***********/
823: char *subdirf(char fileres[])
824: {
825: /* Caution optionfilefiname is hidden */
826: strcpy(tmpout,optionfilefiname);
827: strcat(tmpout,"/"); /* Add to the right */
828: strcat(tmpout,fileres);
829: return tmpout;
830: }
831:
832: /*************** function subdirf2 ***********/
833: char *subdirf2(char fileres[], char *preop)
834: {
835:
836: /* Caution optionfilefiname is hidden */
837: strcpy(tmpout,optionfilefiname);
838: strcat(tmpout,"/");
839: strcat(tmpout,preop);
840: strcat(tmpout,fileres);
841: return tmpout;
842: }
843:
844: /*************** function subdirf3 ***********/
845: char *subdirf3(char fileres[], char *preop, char *preop2)
846: {
847:
848: /* Caution optionfilefiname is hidden */
849: strcpy(tmpout,optionfilefiname);
850: strcat(tmpout,"/");
851: strcat(tmpout,preop);
852: strcat(tmpout,preop2);
853: strcat(tmpout,fileres);
854: return tmpout;
855: }
856:
857: /***************** f1dim *************************/
858: extern int ncom;
859: extern double *pcom,*xicom;
860: extern double (*nrfunc)(double []);
861:
862: double f1dim(double x)
863: {
864: int j;
865: double f;
866: double *xt;
867:
868: xt=vector(1,ncom);
869: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
870: f=(*nrfunc)(xt);
871: free_vector(xt,1,ncom);
872: return f;
873: }
874:
875: /*****************brent *************************/
876: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
877: {
878: int iter;
879: double a,b,d,etemp;
880: double fu,fv,fw,fx;
881: double ftemp;
882: double p,q,r,tol1,tol2,u,v,w,x,xm;
883: double e=0.0;
884:
885: a=(ax < cx ? ax : cx);
886: b=(ax > cx ? ax : cx);
887: x=w=v=bx;
888: fw=fv=fx=(*f)(x);
889: for (iter=1;iter<=ITMAX;iter++) {
890: xm=0.5*(a+b);
891: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
892: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
893: printf(".");fflush(stdout);
894: fprintf(ficlog,".");fflush(ficlog);
895: #ifdef DEBUG
896: 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);
897: 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);
898: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
899: #endif
900: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
901: *xmin=x;
902: return fx;
903: }
904: ftemp=fu;
905: if (fabs(e) > tol1) {
906: r=(x-w)*(fx-fv);
907: q=(x-v)*(fx-fw);
908: p=(x-v)*q-(x-w)*r;
909: q=2.0*(q-r);
910: if (q > 0.0) p = -p;
911: q=fabs(q);
912: etemp=e;
913: e=d;
914: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
915: d=CGOLD*(e=(x >= xm ? a-x : b-x));
916: else {
917: d=p/q;
918: u=x+d;
919: if (u-a < tol2 || b-u < tol2)
920: d=SIGN(tol1,xm-x);
921: }
922: } else {
923: d=CGOLD*(e=(x >= xm ? a-x : b-x));
924: }
925: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
926: fu=(*f)(u);
927: if (fu <= fx) {
928: if (u >= x) a=x; else b=x;
929: SHFT(v,w,x,u)
930: SHFT(fv,fw,fx,fu)
931: } else {
932: if (u < x) a=u; else b=u;
933: if (fu <= fw || w == x) {
934: v=w;
935: w=u;
936: fv=fw;
937: fw=fu;
938: } else if (fu <= fv || v == x || v == w) {
939: v=u;
940: fv=fu;
941: }
942: }
943: }
944: nrerror("Too many iterations in brent");
945: *xmin=x;
946: return fx;
947: }
948:
949: /****************** mnbrak ***********************/
950:
951: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
952: double (*func)(double))
953: {
954: double ulim,u,r,q, dum;
955: double fu;
956:
957: *fa=(*func)(*ax);
958: *fb=(*func)(*bx);
959: if (*fb > *fa) {
960: SHFT(dum,*ax,*bx,dum)
961: SHFT(dum,*fb,*fa,dum)
962: }
963: *cx=(*bx)+GOLD*(*bx-*ax);
964: *fc=(*func)(*cx);
965: while (*fb > *fc) {
966: r=(*bx-*ax)*(*fb-*fc);
967: q=(*bx-*cx)*(*fb-*fa);
968: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
969: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
970: ulim=(*bx)+GLIMIT*(*cx-*bx);
971: if ((*bx-u)*(u-*cx) > 0.0) {
972: fu=(*func)(u);
973: } else if ((*cx-u)*(u-ulim) > 0.0) {
974: fu=(*func)(u);
975: if (fu < *fc) {
976: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
977: SHFT(*fb,*fc,fu,(*func)(u))
978: }
979: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
980: u=ulim;
981: fu=(*func)(u);
982: } else {
983: u=(*cx)+GOLD*(*cx-*bx);
984: fu=(*func)(u);
985: }
986: SHFT(*ax,*bx,*cx,u)
987: SHFT(*fa,*fb,*fc,fu)
988: }
989: }
990:
991: /*************** linmin ************************/
992:
993: int ncom;
994: double *pcom,*xicom;
995: double (*nrfunc)(double []);
996:
997: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
998: {
999: double brent(double ax, double bx, double cx,
1000: double (*f)(double), double tol, double *xmin);
1001: double f1dim(double x);
1002: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1003: double *fc, double (*func)(double));
1004: int j;
1005: double xx,xmin,bx,ax;
1006: double fx,fb,fa;
1007:
1008: ncom=n;
1009: pcom=vector(1,n);
1010: xicom=vector(1,n);
1011: nrfunc=func;
1012: for (j=1;j<=n;j++) {
1013: pcom[j]=p[j];
1014: xicom[j]=xi[j];
1015: }
1016: ax=0.0;
1017: xx=1.0;
1018: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1019: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1020: #ifdef DEBUG
1021: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1022: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1023: #endif
1024: for (j=1;j<=n;j++) {
1025: xi[j] *= xmin;
1026: p[j] += xi[j];
1027: }
1028: free_vector(xicom,1,n);
1029: free_vector(pcom,1,n);
1030: }
1031:
1032: char *asc_diff_time(long time_sec, char ascdiff[])
1033: {
1034: long sec_left, days, hours, minutes;
1035: days = (time_sec) / (60*60*24);
1036: sec_left = (time_sec) % (60*60*24);
1037: hours = (sec_left) / (60*60) ;
1038: sec_left = (sec_left) %(60*60);
1039: minutes = (sec_left) /60;
1040: sec_left = (sec_left) % (60);
1041: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1042: return ascdiff;
1043: }
1044:
1045: /*************** powell ************************/
1046: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1047: double (*func)(double []))
1048: {
1049: void linmin(double p[], double xi[], int n, double *fret,
1050: double (*func)(double []));
1051: int i,ibig,j;
1052: double del,t,*pt,*ptt,*xit;
1053: double fp,fptt;
1054: double *xits;
1055: int niterf, itmp;
1056:
1057: pt=vector(1,n);
1058: ptt=vector(1,n);
1059: xit=vector(1,n);
1060: xits=vector(1,n);
1061: *fret=(*func)(p);
1062: for (j=1;j<=n;j++) pt[j]=p[j];
1063: for (*iter=1;;++(*iter)) {
1064: fp=(*fret);
1065: ibig=0;
1066: del=0.0;
1067: last_time=curr_time;
1068: (void) gettimeofday(&curr_time,&tzp);
1069: 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);
1070: 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);
1071: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1072: for (i=1;i<=n;i++) {
1073: printf(" %d %.12f",i, p[i]);
1074: fprintf(ficlog," %d %.12lf",i, p[i]);
1075: fprintf(ficrespow," %.12lf", p[i]);
1076: }
1077: printf("\n");
1078: fprintf(ficlog,"\n");
1079: fprintf(ficrespow,"\n");fflush(ficrespow);
1080: if(*iter <=3){
1081: tm = *localtime(&curr_time.tv_sec);
1082: strcpy(strcurr,asctime(&tm));
1083: /* asctime_r(&tm,strcurr); */
1084: forecast_time=curr_time;
1085: itmp = strlen(strcurr);
1086: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1087: strcurr[itmp-1]='\0';
1088: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1089: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1090: for(niterf=10;niterf<=30;niterf+=10){
1091: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1092: tmf = *localtime(&forecast_time.tv_sec);
1093: /* asctime_r(&tmf,strfor); */
1094: strcpy(strfor,asctime(&tmf));
1095: itmp = strlen(strfor);
1096: if(strfor[itmp-1]=='\n')
1097: strfor[itmp-1]='\0';
1098: 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);
1099: 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);
1100: }
1101: }
1102: for (i=1;i<=n;i++) {
1103: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1104: fptt=(*fret);
1105: #ifdef DEBUG
1106: printf("fret=%lf \n",*fret);
1107: fprintf(ficlog,"fret=%lf \n",*fret);
1108: #endif
1109: printf("%d",i);fflush(stdout);
1110: fprintf(ficlog,"%d",i);fflush(ficlog);
1111: linmin(p,xit,n,fret,func);
1112: if (fabs(fptt-(*fret)) > del) {
1113: del=fabs(fptt-(*fret));
1114: ibig=i;
1115: }
1116: #ifdef DEBUG
1117: printf("%d %.12e",i,(*fret));
1118: fprintf(ficlog,"%d %.12e",i,(*fret));
1119: for (j=1;j<=n;j++) {
1120: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1121: printf(" x(%d)=%.12e",j,xit[j]);
1122: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1123: }
1124: for(j=1;j<=n;j++) {
1125: printf(" p=%.12e",p[j]);
1126: fprintf(ficlog," p=%.12e",p[j]);
1127: }
1128: printf("\n");
1129: fprintf(ficlog,"\n");
1130: #endif
1131: }
1132: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1133: #ifdef DEBUG
1134: int k[2],l;
1135: k[0]=1;
1136: k[1]=-1;
1137: printf("Max: %.12e",(*func)(p));
1138: fprintf(ficlog,"Max: %.12e",(*func)(p));
1139: for (j=1;j<=n;j++) {
1140: printf(" %.12e",p[j]);
1141: fprintf(ficlog," %.12e",p[j]);
1142: }
1143: printf("\n");
1144: fprintf(ficlog,"\n");
1145: for(l=0;l<=1;l++) {
1146: for (j=1;j<=n;j++) {
1147: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1148: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1149: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1150: }
1151: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1152: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1153: }
1154: #endif
1155:
1156:
1157: free_vector(xit,1,n);
1158: free_vector(xits,1,n);
1159: free_vector(ptt,1,n);
1160: free_vector(pt,1,n);
1161: return;
1162: }
1163: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1164: for (j=1;j<=n;j++) {
1165: ptt[j]=2.0*p[j]-pt[j];
1166: xit[j]=p[j]-pt[j];
1167: pt[j]=p[j];
1168: }
1169: fptt=(*func)(ptt);
1170: if (fptt < fp) {
1171: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1172: if (t < 0.0) {
1173: linmin(p,xit,n,fret,func);
1174: for (j=1;j<=n;j++) {
1175: xi[j][ibig]=xi[j][n];
1176: xi[j][n]=xit[j];
1177: }
1178: #ifdef DEBUG
1179: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1180: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1181: for(j=1;j<=n;j++){
1182: printf(" %.12e",xit[j]);
1183: fprintf(ficlog," %.12e",xit[j]);
1184: }
1185: printf("\n");
1186: fprintf(ficlog,"\n");
1187: #endif
1188: }
1189: }
1190: }
1191: }
1192:
1193: /**** Prevalence limit (stable or period prevalence) ****************/
1194:
1195: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1196: {
1197: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1198: matrix by transitions matrix until convergence is reached */
1199:
1200: int i, ii,j,k;
1201: double min, max, maxmin, maxmax,sumnew=0.;
1202: double **matprod2();
1203: double **out, cov[NCOVMAX+1], **pmij();
1204: double **newm;
1205: double agefin, delaymax=50 ; /* Max number of years to converge */
1206:
1207: for (ii=1;ii<=nlstate+ndeath;ii++)
1208: for (j=1;j<=nlstate+ndeath;j++){
1209: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1210: }
1211:
1212: cov[1]=1.;
1213:
1214: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1215: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1216: newm=savm;
1217: /* Covariates have to be included here again */
1218: cov[2]=agefin;
1219:
1220: for (k=1; k<=cptcovn;k++) {
1221: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1222: /* 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]]);*/
1223: }
1224: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1225: for (k=1; k<=cptcovprod;k++)
1226: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1227:
1228: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1229: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1230: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1231: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1232:
1233: savm=oldm;
1234: oldm=newm;
1235: maxmax=0.;
1236: for(j=1;j<=nlstate;j++){
1237: min=1.;
1238: max=0.;
1239: for(i=1; i<=nlstate; i++) {
1240: sumnew=0;
1241: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1242: prlim[i][j]= newm[i][j]/(1-sumnew);
1243: max=FMAX(max,prlim[i][j]);
1244: min=FMIN(min,prlim[i][j]);
1245: }
1246: maxmin=max-min;
1247: maxmax=FMAX(maxmax,maxmin);
1248: }
1249: if(maxmax < ftolpl){
1250: return prlim;
1251: }
1252: }
1253: }
1254:
1255: /*************** transition probabilities ***************/
1256:
1257: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1258: {
1259: double s1, s2;
1260: /*double t34;*/
1261: int i,j,j1, nc, ii, jj;
1262:
1263: for(i=1; i<= nlstate; i++){
1264: for(j=1; j<i;j++){
1265: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1266: /*s2 += param[i][j][nc]*cov[nc];*/
1267: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1268: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1269: }
1270: ps[i][j]=s2;
1271: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1272: }
1273: for(j=i+1; j<=nlstate+ndeath;j++){
1274: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1275: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1276: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1277: }
1278: ps[i][j]=s2;
1279: }
1280: }
1281: /*ps[3][2]=1;*/
1282:
1283: for(i=1; i<= nlstate; i++){
1284: s1=0;
1285: for(j=1; j<i; j++){
1286: s1+=exp(ps[i][j]);
1287: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1288: }
1289: for(j=i+1; j<=nlstate+ndeath; j++){
1290: s1+=exp(ps[i][j]);
1291: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1292: }
1293: ps[i][i]=1./(s1+1.);
1294: for(j=1; j<i; j++)
1295: ps[i][j]= exp(ps[i][j])*ps[i][i];
1296: for(j=i+1; j<=nlstate+ndeath; j++)
1297: ps[i][j]= exp(ps[i][j])*ps[i][i];
1298: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1299: } /* end i */
1300:
1301: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1302: for(jj=1; jj<= nlstate+ndeath; jj++){
1303: ps[ii][jj]=0;
1304: ps[ii][ii]=1;
1305: }
1306: }
1307:
1308:
1309: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1310: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1311: /* printf("ddd %lf ",ps[ii][jj]); */
1312: /* } */
1313: /* printf("\n "); */
1314: /* } */
1315: /* printf("\n ");printf("%lf ",cov[2]); */
1316: /*
1317: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1318: goto end;*/
1319: return ps;
1320: }
1321:
1322: /**************** Product of 2 matrices ******************/
1323:
1324: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1325: {
1326: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1327: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1328: /* in, b, out are matrice of pointers which should have been initialized
1329: before: only the contents of out is modified. The function returns
1330: a pointer to pointers identical to out */
1331: long i, j, k;
1332: for(i=nrl; i<= nrh; i++)
1333: for(k=ncolol; k<=ncoloh; k++)
1334: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1335: out[i][k] +=in[i][j]*b[j][k];
1336:
1337: return out;
1338: }
1339:
1340:
1341: /************* Higher Matrix Product ***************/
1342:
1343: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1344: {
1345: /* Computes the transition matrix starting at age 'age' over
1346: 'nhstepm*hstepm*stepm' months (i.e. until
1347: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1348: nhstepm*hstepm matrices.
1349: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1350: (typically every 2 years instead of every month which is too big
1351: for the memory).
1352: Model is determined by parameters x and covariates have to be
1353: included manually here.
1354:
1355: */
1356:
1357: int i, j, d, h, k;
1358: double **out, cov[NCOVMAX+1];
1359: double **newm;
1360:
1361: /* Hstepm could be zero and should return the unit matrix */
1362: for (i=1;i<=nlstate+ndeath;i++)
1363: for (j=1;j<=nlstate+ndeath;j++){
1364: oldm[i][j]=(i==j ? 1.0 : 0.0);
1365: po[i][j][0]=(i==j ? 1.0 : 0.0);
1366: }
1367: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1368: for(h=1; h <=nhstepm; h++){
1369: for(d=1; d <=hstepm; d++){
1370: newm=savm;
1371: /* Covariates have to be included here again */
1372: cov[1]=1.;
1373: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1374: for (k=1; k<=cptcovn;k++)
1375: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1376: for (k=1; k<=cptcovage;k++)
1377: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1378: for (k=1; k<=cptcovprod;k++)
1379: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1380:
1381:
1382: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1383: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1384: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1385: pmij(pmmij,cov,ncovmodel,x,nlstate));
1386: savm=oldm;
1387: oldm=newm;
1388: }
1389: for(i=1; i<=nlstate+ndeath; i++)
1390: for(j=1;j<=nlstate+ndeath;j++) {
1391: po[i][j][h]=newm[i][j];
1392: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1393: }
1394: /*printf("h=%d ",h);*/
1395: } /* end h */
1396: /* printf("\n H=%d \n",h); */
1397: return po;
1398: }
1399:
1400:
1401: /*************** log-likelihood *************/
1402: double func( double *x)
1403: {
1404: int i, ii, j, k, mi, d, kk;
1405: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1406: double **out;
1407: double sw; /* Sum of weights */
1408: double lli; /* Individual log likelihood */
1409: int s1, s2;
1410: double bbh, survp;
1411: long ipmx;
1412: /*extern weight */
1413: /* We are differentiating ll according to initial status */
1414: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1415: /*for(i=1;i<imx;i++)
1416: printf(" %d\n",s[4][i]);
1417: */
1418: cov[1]=1.;
1419:
1420: for(k=1; k<=nlstate; k++) ll[k]=0.;
1421:
1422: if(mle==1){
1423: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1424: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1425: for(mi=1; mi<= wav[i]-1; mi++){
1426: for (ii=1;ii<=nlstate+ndeath;ii++)
1427: for (j=1;j<=nlstate+ndeath;j++){
1428: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1429: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1430: }
1431: for(d=0; d<dh[mi][i]; d++){
1432: newm=savm;
1433: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1434: for (kk=1; kk<=cptcovage;kk++) {
1435: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1436: }
1437: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1438: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1439: savm=oldm;
1440: oldm=newm;
1441: } /* end mult */
1442:
1443: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1444: /* But now since version 0.9 we anticipate for bias at large stepm.
1445: * If stepm is larger than one month (smallest stepm) and if the exact delay
1446: * (in months) between two waves is not a multiple of stepm, we rounded to
1447: * the nearest (and in case of equal distance, to the lowest) interval but now
1448: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1449: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1450: * probability in order to take into account the bias as a fraction of the way
1451: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1452: * -stepm/2 to stepm/2 .
1453: * For stepm=1 the results are the same as for previous versions of Imach.
1454: * For stepm > 1 the results are less biased than in previous versions.
1455: */
1456: s1=s[mw[mi][i]][i];
1457: s2=s[mw[mi+1][i]][i];
1458: bbh=(double)bh[mi][i]/(double)stepm;
1459: /* bias bh is positive if real duration
1460: * is higher than the multiple of stepm and negative otherwise.
1461: */
1462: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1463: if( s2 > nlstate){
1464: /* i.e. if s2 is a death state and if the date of death is known
1465: then the contribution to the likelihood is the probability to
1466: die between last step unit time and current step unit time,
1467: which is also equal to probability to die before dh
1468: minus probability to die before dh-stepm .
1469: In version up to 0.92 likelihood was computed
1470: as if date of death was unknown. Death was treated as any other
1471: health state: the date of the interview describes the actual state
1472: and not the date of a change in health state. The former idea was
1473: to consider that at each interview the state was recorded
1474: (healthy, disable or death) and IMaCh was corrected; but when we
1475: introduced the exact date of death then we should have modified
1476: the contribution of an exact death to the likelihood. This new
1477: contribution is smaller and very dependent of the step unit
1478: stepm. It is no more the probability to die between last interview
1479: and month of death but the probability to survive from last
1480: interview up to one month before death multiplied by the
1481: probability to die within a month. Thanks to Chris
1482: Jackson for correcting this bug. Former versions increased
1483: mortality artificially. The bad side is that we add another loop
1484: which slows down the processing. The difference can be up to 10%
1485: lower mortality.
1486: */
1487: lli=log(out[s1][s2] - savm[s1][s2]);
1488:
1489:
1490: } else if (s2==-2) {
1491: for (j=1,survp=0. ; j<=nlstate; j++)
1492: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1493: /*survp += out[s1][j]; */
1494: lli= log(survp);
1495: }
1496:
1497: else if (s2==-4) {
1498: for (j=3,survp=0. ; j<=nlstate; j++)
1499: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1500: lli= log(survp);
1501: }
1502:
1503: else if (s2==-5) {
1504: for (j=1,survp=0. ; j<=2; j++)
1505: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1506: lli= log(survp);
1507: }
1508:
1509: else{
1510: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1511: /* 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 */
1512: }
1513: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1514: /*if(lli ==000.0)*/
1515: /*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); */
1516: ipmx +=1;
1517: sw += weight[i];
1518: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1519: } /* end of wave */
1520: } /* end of individual */
1521: } else if(mle==2){
1522: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1523: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1524: for(mi=1; mi<= wav[i]-1; mi++){
1525: for (ii=1;ii<=nlstate+ndeath;ii++)
1526: for (j=1;j<=nlstate+ndeath;j++){
1527: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1528: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1529: }
1530: for(d=0; d<=dh[mi][i]; d++){
1531: newm=savm;
1532: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1533: for (kk=1; kk<=cptcovage;kk++) {
1534: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1535: }
1536: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1537: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1538: savm=oldm;
1539: oldm=newm;
1540: } /* end mult */
1541:
1542: s1=s[mw[mi][i]][i];
1543: s2=s[mw[mi+1][i]][i];
1544: bbh=(double)bh[mi][i]/(double)stepm;
1545: 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 */
1546: ipmx +=1;
1547: sw += weight[i];
1548: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1549: } /* end of wave */
1550: } /* end of individual */
1551: } else if(mle==3){ /* exponential inter-extrapolation */
1552: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1553: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1554: for(mi=1; mi<= wav[i]-1; mi++){
1555: for (ii=1;ii<=nlstate+ndeath;ii++)
1556: for (j=1;j<=nlstate+ndeath;j++){
1557: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1558: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1559: }
1560: for(d=0; d<dh[mi][i]; d++){
1561: newm=savm;
1562: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1563: for (kk=1; kk<=cptcovage;kk++) {
1564: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1565: }
1566: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1567: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1568: savm=oldm;
1569: oldm=newm;
1570: } /* end mult */
1571:
1572: s1=s[mw[mi][i]][i];
1573: s2=s[mw[mi+1][i]][i];
1574: bbh=(double)bh[mi][i]/(double)stepm;
1575: 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 */
1576: ipmx +=1;
1577: sw += weight[i];
1578: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1579: } /* end of wave */
1580: } /* end of individual */
1581: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1582: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1583: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1584: for(mi=1; mi<= wav[i]-1; mi++){
1585: for (ii=1;ii<=nlstate+ndeath;ii++)
1586: for (j=1;j<=nlstate+ndeath;j++){
1587: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1588: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1589: }
1590: for(d=0; d<dh[mi][i]; d++){
1591: newm=savm;
1592: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1593: for (kk=1; kk<=cptcovage;kk++) {
1594: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1595: }
1596:
1597: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1598: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1599: savm=oldm;
1600: oldm=newm;
1601: } /* end mult */
1602:
1603: s1=s[mw[mi][i]][i];
1604: s2=s[mw[mi+1][i]][i];
1605: if( s2 > nlstate){
1606: lli=log(out[s1][s2] - savm[s1][s2]);
1607: }else{
1608: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1609: }
1610: ipmx +=1;
1611: sw += weight[i];
1612: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1613: /* 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]); */
1614: } /* end of wave */
1615: } /* end of individual */
1616: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1617: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1618: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1619: for(mi=1; mi<= wav[i]-1; mi++){
1620: for (ii=1;ii<=nlstate+ndeath;ii++)
1621: for (j=1;j<=nlstate+ndeath;j++){
1622: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1623: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1624: }
1625: for(d=0; d<dh[mi][i]; d++){
1626: newm=savm;
1627: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1628: for (kk=1; kk<=cptcovage;kk++) {
1629: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1630: }
1631:
1632: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1633: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1634: savm=oldm;
1635: oldm=newm;
1636: } /* end mult */
1637:
1638: s1=s[mw[mi][i]][i];
1639: s2=s[mw[mi+1][i]][i];
1640: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1641: ipmx +=1;
1642: sw += weight[i];
1643: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1644: /*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]);*/
1645: } /* end of wave */
1646: } /* end of individual */
1647: } /* End of if */
1648: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1649: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1650: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1651: return -l;
1652: }
1653:
1654: /*************** log-likelihood *************/
1655: double funcone( double *x)
1656: {
1657: /* Same as likeli but slower because of a lot of printf and if */
1658: int i, ii, j, k, mi, d, kk;
1659: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1660: double **out;
1661: double lli; /* Individual log likelihood */
1662: double llt;
1663: int s1, s2;
1664: double bbh, survp;
1665: /*extern weight */
1666: /* We are differentiating ll according to initial status */
1667: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1668: /*for(i=1;i<imx;i++)
1669: printf(" %d\n",s[4][i]);
1670: */
1671: cov[1]=1.;
1672:
1673: for(k=1; k<=nlstate; k++) ll[k]=0.;
1674:
1675: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1676: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1677: for(mi=1; mi<= wav[i]-1; mi++){
1678: for (ii=1;ii<=nlstate+ndeath;ii++)
1679: for (j=1;j<=nlstate+ndeath;j++){
1680: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1681: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1682: }
1683: for(d=0; d<dh[mi][i]; d++){
1684: newm=savm;
1685: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1686: for (kk=1; kk<=cptcovage;kk++) {
1687: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1688: }
1689: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1690: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1691: savm=oldm;
1692: oldm=newm;
1693: } /* end mult */
1694:
1695: s1=s[mw[mi][i]][i];
1696: s2=s[mw[mi+1][i]][i];
1697: bbh=(double)bh[mi][i]/(double)stepm;
1698: /* bias is positive if real duration
1699: * is higher than the multiple of stepm and negative otherwise.
1700: */
1701: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1702: lli=log(out[s1][s2] - savm[s1][s2]);
1703: } else if (s2==-2) {
1704: for (j=1,survp=0. ; j<=nlstate; j++)
1705: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1706: lli= log(survp);
1707: }else if (mle==1){
1708: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1709: } else if(mle==2){
1710: 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 */
1711: } else if(mle==3){ /* exponential inter-extrapolation */
1712: 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 */
1713: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1714: lli=log(out[s1][s2]); /* Original formula */
1715: } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
1716: lli=log(out[s1][s2]); /* Original formula */
1717: } /* End of if */
1718: ipmx +=1;
1719: sw += weight[i];
1720: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1721: /*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]); */
1722: if(globpr){
1723: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1724: %11.6f %11.6f %11.6f ", \
1725: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1726: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1727: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1728: llt +=ll[k]*gipmx/gsw;
1729: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1730: }
1731: fprintf(ficresilk," %10.6f\n", -llt);
1732: }
1733: } /* end of wave */
1734: } /* end of individual */
1735: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1736: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1737: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1738: if(globpr==0){ /* First time we count the contributions and weights */
1739: gipmx=ipmx;
1740: gsw=sw;
1741: }
1742: return -l;
1743: }
1744:
1745:
1746: /*************** function likelione ***********/
1747: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1748: {
1749: /* This routine should help understanding what is done with
1750: the selection of individuals/waves and
1751: to check the exact contribution to the likelihood.
1752: Plotting could be done.
1753: */
1754: int k;
1755:
1756: if(*globpri !=0){ /* Just counts and sums, no printings */
1757: strcpy(fileresilk,"ilk");
1758: strcat(fileresilk,fileres);
1759: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1760: printf("Problem with resultfile: %s\n", fileresilk);
1761: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1762: }
1763: 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");
1764: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1765: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1766: for(k=1; k<=nlstate; k++)
1767: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1768: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1769: }
1770:
1771: *fretone=(*funcone)(p);
1772: if(*globpri !=0){
1773: fclose(ficresilk);
1774: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1775: fflush(fichtm);
1776: }
1777: return;
1778: }
1779:
1780:
1781: /*********** Maximum Likelihood Estimation ***************/
1782:
1783: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1784: {
1785: int i,j, iter;
1786: double **xi;
1787: double fret;
1788: double fretone; /* Only one call to likelihood */
1789: /* char filerespow[FILENAMELENGTH];*/
1790: xi=matrix(1,npar,1,npar);
1791: for (i=1;i<=npar;i++)
1792: for (j=1;j<=npar;j++)
1793: xi[i][j]=(i==j ? 1.0 : 0.0);
1794: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1795: strcpy(filerespow,"pow");
1796: strcat(filerespow,fileres);
1797: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1798: printf("Problem with resultfile: %s\n", filerespow);
1799: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1800: }
1801: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1802: for (i=1;i<=nlstate;i++)
1803: for(j=1;j<=nlstate+ndeath;j++)
1804: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1805: fprintf(ficrespow,"\n");
1806:
1807: powell(p,xi,npar,ftol,&iter,&fret,func);
1808:
1809: free_matrix(xi,1,npar,1,npar);
1810: fclose(ficrespow);
1811: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1812: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1813: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1814:
1815: }
1816:
1817: /**** Computes Hessian and covariance matrix ***/
1818: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1819: {
1820: double **a,**y,*x,pd;
1821: double **hess;
1822: int i, j,jk;
1823: int *indx;
1824:
1825: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1826: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1827: void lubksb(double **a, int npar, int *indx, double b[]) ;
1828: void ludcmp(double **a, int npar, int *indx, double *d) ;
1829: double gompertz(double p[]);
1830: hess=matrix(1,npar,1,npar);
1831:
1832: printf("\nCalculation of the hessian matrix. Wait...\n");
1833: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1834: for (i=1;i<=npar;i++){
1835: printf("%d",i);fflush(stdout);
1836: fprintf(ficlog,"%d",i);fflush(ficlog);
1837:
1838: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1839:
1840: /* printf(" %f ",p[i]);
1841: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1842: }
1843:
1844: for (i=1;i<=npar;i++) {
1845: for (j=1;j<=npar;j++) {
1846: if (j>i) {
1847: printf(".%d%d",i,j);fflush(stdout);
1848: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1849: hess[i][j]=hessij(p,delti,i,j,func,npar);
1850:
1851: hess[j][i]=hess[i][j];
1852: /*printf(" %lf ",hess[i][j]);*/
1853: }
1854: }
1855: }
1856: printf("\n");
1857: fprintf(ficlog,"\n");
1858:
1859: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1860: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1861:
1862: a=matrix(1,npar,1,npar);
1863: y=matrix(1,npar,1,npar);
1864: x=vector(1,npar);
1865: indx=ivector(1,npar);
1866: for (i=1;i<=npar;i++)
1867: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1868: ludcmp(a,npar,indx,&pd);
1869:
1870: for (j=1;j<=npar;j++) {
1871: for (i=1;i<=npar;i++) x[i]=0;
1872: x[j]=1;
1873: lubksb(a,npar,indx,x);
1874: for (i=1;i<=npar;i++){
1875: matcov[i][j]=x[i];
1876: }
1877: }
1878:
1879: printf("\n#Hessian matrix#\n");
1880: fprintf(ficlog,"\n#Hessian matrix#\n");
1881: for (i=1;i<=npar;i++) {
1882: for (j=1;j<=npar;j++) {
1883: printf("%.3e ",hess[i][j]);
1884: fprintf(ficlog,"%.3e ",hess[i][j]);
1885: }
1886: printf("\n");
1887: fprintf(ficlog,"\n");
1888: }
1889:
1890: /* Recompute Inverse */
1891: for (i=1;i<=npar;i++)
1892: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1893: ludcmp(a,npar,indx,&pd);
1894:
1895: /* printf("\n#Hessian matrix recomputed#\n");
1896:
1897: for (j=1;j<=npar;j++) {
1898: for (i=1;i<=npar;i++) x[i]=0;
1899: x[j]=1;
1900: lubksb(a,npar,indx,x);
1901: for (i=1;i<=npar;i++){
1902: y[i][j]=x[i];
1903: printf("%.3e ",y[i][j]);
1904: fprintf(ficlog,"%.3e ",y[i][j]);
1905: }
1906: printf("\n");
1907: fprintf(ficlog,"\n");
1908: }
1909: */
1910:
1911: free_matrix(a,1,npar,1,npar);
1912: free_matrix(y,1,npar,1,npar);
1913: free_vector(x,1,npar);
1914: free_ivector(indx,1,npar);
1915: free_matrix(hess,1,npar,1,npar);
1916:
1917:
1918: }
1919:
1920: /*************** hessian matrix ****************/
1921: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1922: {
1923: int i;
1924: int l=1, lmax=20;
1925: double k1,k2;
1926: double p2[MAXPARM+1]; /* identical to x */
1927: double res;
1928: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1929: double fx;
1930: int k=0,kmax=10;
1931: double l1;
1932:
1933: fx=func(x);
1934: for (i=1;i<=npar;i++) p2[i]=x[i];
1935: for(l=0 ; l <=lmax; l++){
1936: l1=pow(10,l);
1937: delts=delt;
1938: for(k=1 ; k <kmax; k=k+1){
1939: delt = delta*(l1*k);
1940: p2[theta]=x[theta] +delt;
1941: k1=func(p2)-fx;
1942: p2[theta]=x[theta]-delt;
1943: k2=func(p2)-fx;
1944: /*res= (k1-2.0*fx+k2)/delt/delt; */
1945: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1946:
1947: #ifdef DEBUGHESS
1948: 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);
1949: 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);
1950: #endif
1951: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1952: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1953: k=kmax;
1954: }
1955: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1956: k=kmax; l=lmax*10.;
1957: }
1958: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1959: delts=delt;
1960: }
1961: }
1962: }
1963: delti[theta]=delts;
1964: return res;
1965:
1966: }
1967:
1968: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1969: {
1970: int i;
1971: int l=1, l1, lmax=20;
1972: double k1,k2,k3,k4,res,fx;
1973: double p2[MAXPARM+1];
1974: int k;
1975:
1976: fx=func(x);
1977: for (k=1; k<=2; k++) {
1978: for (i=1;i<=npar;i++) p2[i]=x[i];
1979: p2[thetai]=x[thetai]+delti[thetai]/k;
1980: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1981: k1=func(p2)-fx;
1982:
1983: p2[thetai]=x[thetai]+delti[thetai]/k;
1984: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1985: k2=func(p2)-fx;
1986:
1987: p2[thetai]=x[thetai]-delti[thetai]/k;
1988: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1989: k3=func(p2)-fx;
1990:
1991: p2[thetai]=x[thetai]-delti[thetai]/k;
1992: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1993: k4=func(p2)-fx;
1994: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
1995: #ifdef DEBUG
1996: 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);
1997: 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);
1998: #endif
1999: }
2000: return res;
2001: }
2002:
2003: /************** Inverse of matrix **************/
2004: void ludcmp(double **a, int n, int *indx, double *d)
2005: {
2006: int i,imax,j,k;
2007: double big,dum,sum,temp;
2008: double *vv;
2009:
2010: vv=vector(1,n);
2011: *d=1.0;
2012: for (i=1;i<=n;i++) {
2013: big=0.0;
2014: for (j=1;j<=n;j++)
2015: if ((temp=fabs(a[i][j])) > big) big=temp;
2016: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2017: vv[i]=1.0/big;
2018: }
2019: for (j=1;j<=n;j++) {
2020: for (i=1;i<j;i++) {
2021: sum=a[i][j];
2022: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2023: a[i][j]=sum;
2024: }
2025: big=0.0;
2026: for (i=j;i<=n;i++) {
2027: sum=a[i][j];
2028: for (k=1;k<j;k++)
2029: sum -= a[i][k]*a[k][j];
2030: a[i][j]=sum;
2031: if ( (dum=vv[i]*fabs(sum)) >= big) {
2032: big=dum;
2033: imax=i;
2034: }
2035: }
2036: if (j != imax) {
2037: for (k=1;k<=n;k++) {
2038: dum=a[imax][k];
2039: a[imax][k]=a[j][k];
2040: a[j][k]=dum;
2041: }
2042: *d = -(*d);
2043: vv[imax]=vv[j];
2044: }
2045: indx[j]=imax;
2046: if (a[j][j] == 0.0) a[j][j]=TINY;
2047: if (j != n) {
2048: dum=1.0/(a[j][j]);
2049: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2050: }
2051: }
2052: free_vector(vv,1,n); /* Doesn't work */
2053: ;
2054: }
2055:
2056: void lubksb(double **a, int n, int *indx, double b[])
2057: {
2058: int i,ii=0,ip,j;
2059: double sum;
2060:
2061: for (i=1;i<=n;i++) {
2062: ip=indx[i];
2063: sum=b[ip];
2064: b[ip]=b[i];
2065: if (ii)
2066: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2067: else if (sum) ii=i;
2068: b[i]=sum;
2069: }
2070: for (i=n;i>=1;i--) {
2071: sum=b[i];
2072: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2073: b[i]=sum/a[i][i];
2074: }
2075: }
2076:
2077: void pstamp(FILE *fichier)
2078: {
2079: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2080: }
2081:
2082: /************ Frequencies ********************/
2083: 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[])
2084: { /* Some frequencies */
2085:
2086: int i, m, jk, k1,i1, j1, bool, z1,j;
2087: int first;
2088: double ***freq; /* Frequencies */
2089: double *pp, **prop;
2090: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2091: char fileresp[FILENAMELENGTH];
2092:
2093: pp=vector(1,nlstate);
2094: prop=matrix(1,nlstate,iagemin,iagemax+3);
2095: strcpy(fileresp,"p");
2096: strcat(fileresp,fileres);
2097: if((ficresp=fopen(fileresp,"w"))==NULL) {
2098: printf("Problem with prevalence resultfile: %s\n", fileresp);
2099: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2100: exit(0);
2101: }
2102: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2103: j1=0;
2104:
2105: j=cptcoveff;
2106: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2107:
2108: first=1;
2109:
2110: for(k1=1; k1<=j;k1++){
2111: for(i1=1; i1<=ncodemax[k1];i1++){
2112: j1++;
2113: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2114: scanf("%d", i);*/
2115: for (i=-5; i<=nlstate+ndeath; i++)
2116: for (jk=-5; jk<=nlstate+ndeath; jk++)
2117: for(m=iagemin; m <= iagemax+3; m++)
2118: freq[i][jk][m]=0;
2119:
2120: for (i=1; i<=nlstate; i++)
2121: for(m=iagemin; m <= iagemax+3; m++)
2122: prop[i][m]=0;
2123:
2124: dateintsum=0;
2125: k2cpt=0;
2126: for (i=1; i<=imx; i++) {
2127: bool=1;
2128: if (cptcovn>0) {
2129: for (z1=1; z1<=cptcoveff; z1++)
2130: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2131: bool=0;
2132: }
2133: if (bool==1){
2134: for(m=firstpass; m<=lastpass; m++){
2135: k2=anint[m][i]+(mint[m][i]/12.);
2136: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2137: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2138: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2139: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2140: if (m<lastpass) {
2141: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2142: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2143: }
2144:
2145: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2146: dateintsum=dateintsum+k2;
2147: k2cpt++;
2148: }
2149: /*}*/
2150: }
2151: }
2152: }
2153:
2154: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2155: pstamp(ficresp);
2156: if (cptcovn>0) {
2157: fprintf(ficresp, "\n#********** Variable ");
2158: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2159: fprintf(ficresp, "**********\n#");
2160: }
2161: for(i=1; i<=nlstate;i++)
2162: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2163: fprintf(ficresp, "\n");
2164:
2165: for(i=iagemin; i <= iagemax+3; i++){
2166: if(i==iagemax+3){
2167: fprintf(ficlog,"Total");
2168: }else{
2169: if(first==1){
2170: first=0;
2171: printf("See log file for details...\n");
2172: }
2173: fprintf(ficlog,"Age %d", i);
2174: }
2175: for(jk=1; jk <=nlstate ; jk++){
2176: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2177: pp[jk] += freq[jk][m][i];
2178: }
2179: for(jk=1; jk <=nlstate ; jk++){
2180: for(m=-1, pos=0; m <=0 ; m++)
2181: pos += freq[jk][m][i];
2182: if(pp[jk]>=1.e-10){
2183: if(first==1){
2184: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2185: }
2186: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2187: }else{
2188: if(first==1)
2189: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2190: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2191: }
2192: }
2193:
2194: for(jk=1; jk <=nlstate ; jk++){
2195: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2196: pp[jk] += freq[jk][m][i];
2197: }
2198: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2199: pos += pp[jk];
2200: posprop += prop[jk][i];
2201: }
2202: for(jk=1; jk <=nlstate ; jk++){
2203: if(pos>=1.e-5){
2204: if(first==1)
2205: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2206: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2207: }else{
2208: if(first==1)
2209: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2210: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2211: }
2212: if( i <= iagemax){
2213: if(pos>=1.e-5){
2214: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2215: /*probs[i][jk][j1]= pp[jk]/pos;*/
2216: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2217: }
2218: else
2219: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2220: }
2221: }
2222:
2223: for(jk=-1; jk <=nlstate+ndeath; jk++)
2224: for(m=-1; m <=nlstate+ndeath; m++)
2225: if(freq[jk][m][i] !=0 ) {
2226: if(first==1)
2227: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2228: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2229: }
2230: if(i <= iagemax)
2231: fprintf(ficresp,"\n");
2232: if(first==1)
2233: printf("Others in log...\n");
2234: fprintf(ficlog,"\n");
2235: }
2236: }
2237: }
2238: dateintmean=dateintsum/k2cpt;
2239:
2240: fclose(ficresp);
2241: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2242: free_vector(pp,1,nlstate);
2243: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2244: /* End of Freq */
2245: }
2246:
2247: /************ Prevalence ********************/
2248: 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)
2249: {
2250: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2251: in each health status at the date of interview (if between dateprev1 and dateprev2).
2252: We still use firstpass and lastpass as another selection.
2253: */
2254:
2255: int i, m, jk, k1, i1, j1, bool, z1,j;
2256: double ***freq; /* Frequencies */
2257: double *pp, **prop;
2258: double pos,posprop;
2259: double y2; /* in fractional years */
2260: int iagemin, iagemax;
2261:
2262: iagemin= (int) agemin;
2263: iagemax= (int) agemax;
2264: /*pp=vector(1,nlstate);*/
2265: prop=matrix(1,nlstate,iagemin,iagemax+3);
2266: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2267: j1=0;
2268:
2269: j=cptcoveff;
2270: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2271:
2272: for(k1=1; k1<=j;k1++){
2273: for(i1=1; i1<=ncodemax[k1];i1++){
2274: j1++;
2275:
2276: for (i=1; i<=nlstate; i++)
2277: for(m=iagemin; m <= iagemax+3; m++)
2278: prop[i][m]=0.0;
2279:
2280: for (i=1; i<=imx; i++) { /* Each individual */
2281: bool=1;
2282: if (cptcovn>0) {
2283: for (z1=1; z1<=cptcoveff; z1++)
2284: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2285: bool=0;
2286: }
2287: if (bool==1) {
2288: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2289: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2290: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2291: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2292: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2293: 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);
2294: if (s[m][i]>0 && s[m][i]<=nlstate) {
2295: /*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]]);*/
2296: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2297: prop[s[m][i]][iagemax+3] += weight[i];
2298: }
2299: }
2300: } /* end selection of waves */
2301: }
2302: }
2303: for(i=iagemin; i <= iagemax+3; i++){
2304:
2305: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2306: posprop += prop[jk][i];
2307: }
2308:
2309: for(jk=1; jk <=nlstate ; jk++){
2310: if( i <= iagemax){
2311: if(posprop>=1.e-5){
2312: probs[i][jk][j1]= prop[jk][i]/posprop;
2313: } else
2314: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
2315: }
2316: }/* end jk */
2317: }/* end i */
2318: } /* end i1 */
2319: } /* end k1 */
2320:
2321: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2322: /*free_vector(pp,1,nlstate);*/
2323: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2324: } /* End of prevalence */
2325:
2326: /************* Waves Concatenation ***************/
2327:
2328: 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)
2329: {
2330: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2331: Death is a valid wave (if date is known).
2332: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2333: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2334: and mw[mi+1][i]. dh depends on stepm.
2335: */
2336:
2337: int i, mi, m;
2338: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2339: double sum=0., jmean=0.;*/
2340: int first;
2341: int j, k=0,jk, ju, jl;
2342: double sum=0.;
2343: first=0;
2344: jmin=1e+5;
2345: jmax=-1;
2346: jmean=0.;
2347: for(i=1; i<=imx; i++){
2348: mi=0;
2349: m=firstpass;
2350: while(s[m][i] <= nlstate){
2351: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2352: mw[++mi][i]=m;
2353: if(m >=lastpass)
2354: break;
2355: else
2356: m++;
2357: }/* end while */
2358: if (s[m][i] > nlstate){
2359: mi++; /* Death is another wave */
2360: /* if(mi==0) never been interviewed correctly before death */
2361: /* Only death is a correct wave */
2362: mw[mi][i]=m;
2363: }
2364:
2365: wav[i]=mi;
2366: if(mi==0){
2367: nbwarn++;
2368: if(first==0){
2369: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2370: first=1;
2371: }
2372: if(first==1){
2373: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2374: }
2375: } /* end mi==0 */
2376: } /* End individuals */
2377:
2378: for(i=1; i<=imx; i++){
2379: for(mi=1; mi<wav[i];mi++){
2380: if (stepm <=0)
2381: dh[mi][i]=1;
2382: else{
2383: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2384: if (agedc[i] < 2*AGESUP) {
2385: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2386: if(j==0) j=1; /* Survives at least one month after exam */
2387: else if(j<0){
2388: nberr++;
2389: 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]);
2390: j=1; /* Temporary Dangerous patch */
2391: 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);
2392: 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]);
2393: 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);
2394: }
2395: k=k+1;
2396: if (j >= jmax){
2397: jmax=j;
2398: ijmax=i;
2399: }
2400: if (j <= jmin){
2401: jmin=j;
2402: ijmin=i;
2403: }
2404: sum=sum+j;
2405: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2406: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2407: }
2408: }
2409: else{
2410: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2411: /* 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]); */
2412:
2413: k=k+1;
2414: if (j >= jmax) {
2415: jmax=j;
2416: ijmax=i;
2417: }
2418: else if (j <= jmin){
2419: jmin=j;
2420: ijmin=i;
2421: }
2422: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2423: /*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]);*/
2424: if(j<0){
2425: nberr++;
2426: 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]);
2427: 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]);
2428: }
2429: sum=sum+j;
2430: }
2431: jk= j/stepm;
2432: jl= j -jk*stepm;
2433: ju= j -(jk+1)*stepm;
2434: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2435: if(jl==0){
2436: dh[mi][i]=jk;
2437: bh[mi][i]=0;
2438: }else{ /* We want a negative bias in order to only have interpolation ie
2439: * at the price of an extra matrix product in likelihood */
2440: dh[mi][i]=jk+1;
2441: bh[mi][i]=ju;
2442: }
2443: }else{
2444: if(jl <= -ju){
2445: dh[mi][i]=jk;
2446: bh[mi][i]=jl; /* bias is positive if real duration
2447: * is higher than the multiple of stepm and negative otherwise.
2448: */
2449: }
2450: else{
2451: dh[mi][i]=jk+1;
2452: bh[mi][i]=ju;
2453: }
2454: if(dh[mi][i]==0){
2455: dh[mi][i]=1; /* At least one step */
2456: bh[mi][i]=ju; /* At least one step */
2457: /* 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);*/
2458: }
2459: } /* end if mle */
2460: }
2461: } /* end wave */
2462: }
2463: jmean=sum/k;
2464: 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);
2465: 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);
2466: }
2467:
2468: /*********** Tricode ****************************/
2469: void tricode(int *Tvar, int **nbcode, int imx)
2470: {
2471:
2472: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2473:
2474: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2475: int cptcode=0;
2476: cptcoveff=0;
2477:
2478: for (k=0; k<maxncov; k++) Ndum[k]=0;
2479: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
2480:
2481: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate */
2482: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
2483: modality*/
2484: ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
2485: Ndum[ij]++; /*counts the occurence of this modality */
2486: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2487: if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
2488: Tvar[j]. If V=sex and male is 0 and
2489: female is 1, then cptcode=1.*/
2490: }
2491:
2492: for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
2493: if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j
2494: th covariate. In fact
2495: ncodemax[j]=2
2496: (dichotom. variables only) but
2497: it can be more */
2498: } /* Ndum[-1] number of undefined modalities */
2499:
2500: ij=1;
2501: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
2502: for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
2503: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2504: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2505: k is a modality. If we have model=V1+V1*sex
2506: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
2507: ij++;
2508: }
2509: if (ij > ncodemax[j]) break;
2510: }
2511: }
2512: }
2513:
2514: for (k=0; k< maxncov; k++) Ndum[k]=0;
2515:
2516: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2517: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2518: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2519: Ndum[ij]++;
2520: }
2521:
2522: ij=1;
2523: for (i=1; i<= maxncov; i++) {
2524: if((Ndum[i]!=0) && (i<=ncovcol)){
2525: Tvaraff[ij]=i; /*For printing */
2526: ij++;
2527: }
2528: }
2529: ij--;
2530: cptcoveff=ij; /*Number of simple covariates*/
2531: }
2532:
2533: /*********** Health Expectancies ****************/
2534:
2535: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
2536:
2537: {
2538: /* Health expectancies, no variances */
2539: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2540: int nhstepma, nstepma; /* Decreasing with age */
2541: double age, agelim, hf;
2542: double ***p3mat;
2543: double eip;
2544:
2545: pstamp(ficreseij);
2546: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2547: fprintf(ficreseij,"# Age");
2548: for(i=1; i<=nlstate;i++){
2549: for(j=1; j<=nlstate;j++){
2550: fprintf(ficreseij," e%1d%1d ",i,j);
2551: }
2552: fprintf(ficreseij," e%1d. ",i);
2553: }
2554: fprintf(ficreseij,"\n");
2555:
2556:
2557: if(estepm < stepm){
2558: printf ("Problem %d lower than %d\n",estepm, stepm);
2559: }
2560: else hstepm=estepm;
2561: /* We compute the life expectancy from trapezoids spaced every estepm months
2562: * This is mainly to measure the difference between two models: for example
2563: * if stepm=24 months pijx are given only every 2 years and by summing them
2564: * we are calculating an estimate of the Life Expectancy assuming a linear
2565: * progression in between and thus overestimating or underestimating according
2566: * to the curvature of the survival function. If, for the same date, we
2567: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2568: * to compare the new estimate of Life expectancy with the same linear
2569: * hypothesis. A more precise result, taking into account a more precise
2570: * curvature will be obtained if estepm is as small as stepm. */
2571:
2572: /* For example we decided to compute the life expectancy with the smallest unit */
2573: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2574: nhstepm is the number of hstepm from age to agelim
2575: nstepm is the number of stepm from age to agelin.
2576: Look at hpijx to understand the reason of that which relies in memory size
2577: and note for a fixed period like estepm months */
2578: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2579: survival function given by stepm (the optimization length). Unfortunately it
2580: means that if the survival funtion is printed only each two years of age and if
2581: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2582: results. So we changed our mind and took the option of the best precision.
2583: */
2584: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2585:
2586: agelim=AGESUP;
2587: /* If stepm=6 months */
2588: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2589: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2590:
2591: /* nhstepm age range expressed in number of stepm */
2592: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2593: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2594: /* if (stepm >= YEARM) hstepm=1;*/
2595: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2596: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2597:
2598: for (age=bage; age<=fage; age ++){
2599: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2600: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2601: /* if (stepm >= YEARM) hstepm=1;*/
2602: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2603:
2604: /* If stepm=6 months */
2605: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2606: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2607:
2608: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2609:
2610: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2611:
2612: printf("%d|",(int)age);fflush(stdout);
2613: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2614:
2615: /* Computing expectancies */
2616: for(i=1; i<=nlstate;i++)
2617: for(j=1; j<=nlstate;j++)
2618: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2619: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2620:
2621: /* 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]);*/
2622:
2623: }
2624:
2625: fprintf(ficreseij,"%3.0f",age );
2626: for(i=1; i<=nlstate;i++){
2627: eip=0;
2628: for(j=1; j<=nlstate;j++){
2629: eip +=eij[i][j][(int)age];
2630: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2631: }
2632: fprintf(ficreseij,"%9.4f", eip );
2633: }
2634: fprintf(ficreseij,"\n");
2635:
2636: }
2637: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2638: printf("\n");
2639: fprintf(ficlog,"\n");
2640:
2641: }
2642:
2643: 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[] )
2644:
2645: {
2646: /* Covariances of health expectancies eij and of total life expectancies according
2647: to initial status i, ei. .
2648: */
2649: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2650: int nhstepma, nstepma; /* Decreasing with age */
2651: double age, agelim, hf;
2652: double ***p3matp, ***p3matm, ***varhe;
2653: double **dnewm,**doldm;
2654: double *xp, *xm;
2655: double **gp, **gm;
2656: double ***gradg, ***trgradg;
2657: int theta;
2658:
2659: double eip, vip;
2660:
2661: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2662: xp=vector(1,npar);
2663: xm=vector(1,npar);
2664: dnewm=matrix(1,nlstate*nlstate,1,npar);
2665: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2666:
2667: pstamp(ficresstdeij);
2668: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2669: fprintf(ficresstdeij,"# Age");
2670: for(i=1; i<=nlstate;i++){
2671: for(j=1; j<=nlstate;j++)
2672: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2673: fprintf(ficresstdeij," e%1d. ",i);
2674: }
2675: fprintf(ficresstdeij,"\n");
2676:
2677: pstamp(ficrescveij);
2678: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2679: fprintf(ficrescveij,"# Age");
2680: for(i=1; i<=nlstate;i++)
2681: for(j=1; j<=nlstate;j++){
2682: cptj= (j-1)*nlstate+i;
2683: for(i2=1; i2<=nlstate;i2++)
2684: for(j2=1; j2<=nlstate;j2++){
2685: cptj2= (j2-1)*nlstate+i2;
2686: if(cptj2 <= cptj)
2687: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2688: }
2689: }
2690: fprintf(ficrescveij,"\n");
2691:
2692: if(estepm < stepm){
2693: printf ("Problem %d lower than %d\n",estepm, stepm);
2694: }
2695: else hstepm=estepm;
2696: /* We compute the life expectancy from trapezoids spaced every estepm months
2697: * This is mainly to measure the difference between two models: for example
2698: * if stepm=24 months pijx are given only every 2 years and by summing them
2699: * we are calculating an estimate of the Life Expectancy assuming a linear
2700: * progression in between and thus overestimating or underestimating according
2701: * to the curvature of the survival function. If, for the same date, we
2702: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2703: * to compare the new estimate of Life expectancy with the same linear
2704: * hypothesis. A more precise result, taking into account a more precise
2705: * curvature will be obtained if estepm is as small as stepm. */
2706:
2707: /* For example we decided to compute the life expectancy with the smallest unit */
2708: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2709: nhstepm is the number of hstepm from age to agelim
2710: nstepm is the number of stepm from age to agelin.
2711: Look at hpijx to understand the reason of that which relies in memory size
2712: and note for a fixed period like estepm months */
2713: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2714: survival function given by stepm (the optimization length). Unfortunately it
2715: means that if the survival funtion is printed only each two years of age and if
2716: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2717: results. So we changed our mind and took the option of the best precision.
2718: */
2719: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2720:
2721: /* If stepm=6 months */
2722: /* nhstepm age range expressed in number of stepm */
2723: agelim=AGESUP;
2724: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2725: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2726: /* if (stepm >= YEARM) hstepm=1;*/
2727: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2728:
2729: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2730: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2731: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2732: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2733: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2734: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2735:
2736: for (age=bage; age<=fage; age ++){
2737: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2738: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2739: /* if (stepm >= YEARM) hstepm=1;*/
2740: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2741:
2742: /* If stepm=6 months */
2743: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2744: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2745:
2746: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2747:
2748: /* Computing Variances of health expectancies */
2749: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2750: decrease memory allocation */
2751: for(theta=1; theta <=npar; theta++){
2752: for(i=1; i<=npar; i++){
2753: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2754: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2755: }
2756: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2757: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2758:
2759: for(j=1; j<= nlstate; j++){
2760: for(i=1; i<=nlstate; i++){
2761: for(h=0; h<=nhstepm-1; h++){
2762: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2763: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2764: }
2765: }
2766: }
2767:
2768: for(ij=1; ij<= nlstate*nlstate; ij++)
2769: for(h=0; h<=nhstepm-1; h++){
2770: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2771: }
2772: }/* End theta */
2773:
2774:
2775: for(h=0; h<=nhstepm-1; h++)
2776: for(j=1; j<=nlstate*nlstate;j++)
2777: for(theta=1; theta <=npar; theta++)
2778: trgradg[h][j][theta]=gradg[h][theta][j];
2779:
2780:
2781: for(ij=1;ij<=nlstate*nlstate;ij++)
2782: for(ji=1;ji<=nlstate*nlstate;ji++)
2783: varhe[ij][ji][(int)age] =0.;
2784:
2785: printf("%d|",(int)age);fflush(stdout);
2786: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2787: for(h=0;h<=nhstepm-1;h++){
2788: for(k=0;k<=nhstepm-1;k++){
2789: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2790: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2791: for(ij=1;ij<=nlstate*nlstate;ij++)
2792: for(ji=1;ji<=nlstate*nlstate;ji++)
2793: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2794: }
2795: }
2796:
2797: /* Computing expectancies */
2798: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2799: for(i=1; i<=nlstate;i++)
2800: for(j=1; j<=nlstate;j++)
2801: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2802: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2803:
2804: /* 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]);*/
2805:
2806: }
2807:
2808: fprintf(ficresstdeij,"%3.0f",age );
2809: for(i=1; i<=nlstate;i++){
2810: eip=0.;
2811: vip=0.;
2812: for(j=1; j<=nlstate;j++){
2813: eip += eij[i][j][(int)age];
2814: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2815: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2816: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2817: }
2818: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2819: }
2820: fprintf(ficresstdeij,"\n");
2821:
2822: fprintf(ficrescveij,"%3.0f",age );
2823: for(i=1; i<=nlstate;i++)
2824: for(j=1; j<=nlstate;j++){
2825: cptj= (j-1)*nlstate+i;
2826: for(i2=1; i2<=nlstate;i2++)
2827: for(j2=1; j2<=nlstate;j2++){
2828: cptj2= (j2-1)*nlstate+i2;
2829: if(cptj2 <= cptj)
2830: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2831: }
2832: }
2833: fprintf(ficrescveij,"\n");
2834:
2835: }
2836: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2837: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2838: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2839: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2840: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2841: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2842: printf("\n");
2843: fprintf(ficlog,"\n");
2844:
2845: free_vector(xm,1,npar);
2846: free_vector(xp,1,npar);
2847: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2848: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2849: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2850: }
2851:
2852: /************ Variance ******************/
2853: 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[])
2854: {
2855: /* Variance of health expectancies */
2856: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2857: /* double **newm;*/
2858: double **dnewm,**doldm;
2859: double **dnewmp,**doldmp;
2860: int i, j, nhstepm, hstepm, h, nstepm ;
2861: int k, cptcode;
2862: double *xp;
2863: double **gp, **gm; /* for var eij */
2864: double ***gradg, ***trgradg; /*for var eij */
2865: double **gradgp, **trgradgp; /* for var p point j */
2866: double *gpp, *gmp; /* for var p point j */
2867: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2868: double ***p3mat;
2869: double age,agelim, hf;
2870: double ***mobaverage;
2871: int theta;
2872: char digit[4];
2873: char digitp[25];
2874:
2875: char fileresprobmorprev[FILENAMELENGTH];
2876:
2877: if(popbased==1){
2878: if(mobilav!=0)
2879: strcpy(digitp,"-populbased-mobilav-");
2880: else strcpy(digitp,"-populbased-nomobil-");
2881: }
2882: else
2883: strcpy(digitp,"-stablbased-");
2884:
2885: if (mobilav!=0) {
2886: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2887: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2888: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2889: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2890: }
2891: }
2892:
2893: strcpy(fileresprobmorprev,"prmorprev");
2894: sprintf(digit,"%-d",ij);
2895: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2896: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2897: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2898: strcat(fileresprobmorprev,fileres);
2899: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2900: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2901: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2902: }
2903: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2904:
2905: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2906: pstamp(ficresprobmorprev);
2907: 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);
2908: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2909: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2910: fprintf(ficresprobmorprev," p.%-d SE",j);
2911: for(i=1; i<=nlstate;i++)
2912: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2913: }
2914: fprintf(ficresprobmorprev,"\n");
2915: fprintf(ficgp,"\n# Routine varevsij");
2916: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2917: 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");
2918: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2919: /* } */
2920: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2921: pstamp(ficresvij);
2922: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2923: if(popbased==1)
2924: 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);
2925: else
2926: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2927: fprintf(ficresvij,"# Age");
2928: for(i=1; i<=nlstate;i++)
2929: for(j=1; j<=nlstate;j++)
2930: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2931: fprintf(ficresvij,"\n");
2932:
2933: xp=vector(1,npar);
2934: dnewm=matrix(1,nlstate,1,npar);
2935: doldm=matrix(1,nlstate,1,nlstate);
2936: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2937: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2938:
2939: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2940: gpp=vector(nlstate+1,nlstate+ndeath);
2941: gmp=vector(nlstate+1,nlstate+ndeath);
2942: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2943:
2944: if(estepm < stepm){
2945: printf ("Problem %d lower than %d\n",estepm, stepm);
2946: }
2947: else hstepm=estepm;
2948: /* For example we decided to compute the life expectancy with the smallest unit */
2949: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2950: nhstepm is the number of hstepm from age to agelim
2951: nstepm is the number of stepm from age to agelin.
2952: Look at function hpijx to understand why (it is linked to memory size questions) */
2953: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2954: survival function given by stepm (the optimization length). Unfortunately it
2955: means that if the survival funtion is printed every two years of age and if
2956: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2957: results. So we changed our mind and took the option of the best precision.
2958: */
2959: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2960: agelim = AGESUP;
2961: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2962: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2963: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2964: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2965: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2966: gp=matrix(0,nhstepm,1,nlstate);
2967: gm=matrix(0,nhstepm,1,nlstate);
2968:
2969:
2970: for(theta=1; theta <=npar; theta++){
2971: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2972: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2973: }
2974: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2975: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2976:
2977: if (popbased==1) {
2978: if(mobilav ==0){
2979: for(i=1; i<=nlstate;i++)
2980: prlim[i][i]=probs[(int)age][i][ij];
2981: }else{ /* mobilav */
2982: for(i=1; i<=nlstate;i++)
2983: prlim[i][i]=mobaverage[(int)age][i][ij];
2984: }
2985: }
2986:
2987: for(j=1; j<= nlstate; j++){
2988: for(h=0; h<=nhstepm; h++){
2989: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
2990: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
2991: }
2992: }
2993: /* This for computing probability of death (h=1 means
2994: computed over hstepm matrices product = hstepm*stepm months)
2995: as a weighted average of prlim.
2996: */
2997: for(j=nlstate+1;j<=nlstate+ndeath;j++){
2998: for(i=1,gpp[j]=0.; i<= nlstate; i++)
2999: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3000: }
3001: /* end probability of death */
3002:
3003: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3004: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3005: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3006: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3007:
3008: if (popbased==1) {
3009: if(mobilav ==0){
3010: for(i=1; i<=nlstate;i++)
3011: prlim[i][i]=probs[(int)age][i][ij];
3012: }else{ /* mobilav */
3013: for(i=1; i<=nlstate;i++)
3014: prlim[i][i]=mobaverage[(int)age][i][ij];
3015: }
3016: }
3017:
3018: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3019: for(h=0; h<=nhstepm; h++){
3020: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3021: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3022: }
3023: }
3024: /* This for computing probability of death (h=1 means
3025: computed over hstepm matrices product = hstepm*stepm months)
3026: as a weighted average of prlim.
3027: */
3028: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3029: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3030: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3031: }
3032: /* end probability of death */
3033:
3034: for(j=1; j<= nlstate; j++) /* vareij */
3035: for(h=0; h<=nhstepm; h++){
3036: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3037: }
3038:
3039: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3040: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3041: }
3042:
3043: } /* End theta */
3044:
3045: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3046:
3047: for(h=0; h<=nhstepm; h++) /* veij */
3048: for(j=1; j<=nlstate;j++)
3049: for(theta=1; theta <=npar; theta++)
3050: trgradg[h][j][theta]=gradg[h][theta][j];
3051:
3052: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3053: for(theta=1; theta <=npar; theta++)
3054: trgradgp[j][theta]=gradgp[theta][j];
3055:
3056:
3057: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3058: for(i=1;i<=nlstate;i++)
3059: for(j=1;j<=nlstate;j++)
3060: vareij[i][j][(int)age] =0.;
3061:
3062: for(h=0;h<=nhstepm;h++){
3063: for(k=0;k<=nhstepm;k++){
3064: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3065: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3066: for(i=1;i<=nlstate;i++)
3067: for(j=1;j<=nlstate;j++)
3068: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3069: }
3070: }
3071:
3072: /* pptj */
3073: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3074: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3075: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3076: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3077: varppt[j][i]=doldmp[j][i];
3078: /* end ppptj */
3079: /* x centered again */
3080: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3081: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3082:
3083: if (popbased==1) {
3084: if(mobilav ==0){
3085: for(i=1; i<=nlstate;i++)
3086: prlim[i][i]=probs[(int)age][i][ij];
3087: }else{ /* mobilav */
3088: for(i=1; i<=nlstate;i++)
3089: prlim[i][i]=mobaverage[(int)age][i][ij];
3090: }
3091: }
3092:
3093: /* This for computing probability of death (h=1 means
3094: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3095: as a weighted average of prlim.
3096: */
3097: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3098: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3099: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3100: }
3101: /* end probability of death */
3102:
3103: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3104: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3105: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3106: for(i=1; i<=nlstate;i++){
3107: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3108: }
3109: }
3110: fprintf(ficresprobmorprev,"\n");
3111:
3112: fprintf(ficresvij,"%.0f ",age );
3113: for(i=1; i<=nlstate;i++)
3114: for(j=1; j<=nlstate;j++){
3115: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3116: }
3117: fprintf(ficresvij,"\n");
3118: free_matrix(gp,0,nhstepm,1,nlstate);
3119: free_matrix(gm,0,nhstepm,1,nlstate);
3120: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3121: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3122: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3123: } /* End age */
3124: free_vector(gpp,nlstate+1,nlstate+ndeath);
3125: free_vector(gmp,nlstate+1,nlstate+ndeath);
3126: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3127: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3128: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
3129: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3130: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3131: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3132: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3133: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3134: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3135: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3136: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3137: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3138: 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);
3139: /* 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);
3140: */
3141: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3142: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3143:
3144: free_vector(xp,1,npar);
3145: free_matrix(doldm,1,nlstate,1,nlstate);
3146: free_matrix(dnewm,1,nlstate,1,npar);
3147: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3148: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3149: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3150: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3151: fclose(ficresprobmorprev);
3152: fflush(ficgp);
3153: fflush(fichtm);
3154: } /* end varevsij */
3155:
3156: /************ Variance of prevlim ******************/
3157: 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[])
3158: {
3159: /* Variance of prevalence limit */
3160: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3161: double **newm;
3162: double **dnewm,**doldm;
3163: int i, j, nhstepm, hstepm;
3164: int k, cptcode;
3165: double *xp;
3166: double *gp, *gm;
3167: double **gradg, **trgradg;
3168: double age,agelim;
3169: int theta;
3170:
3171: pstamp(ficresvpl);
3172: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3173: fprintf(ficresvpl,"# Age");
3174: for(i=1; i<=nlstate;i++)
3175: fprintf(ficresvpl," %1d-%1d",i,i);
3176: fprintf(ficresvpl,"\n");
3177:
3178: xp=vector(1,npar);
3179: dnewm=matrix(1,nlstate,1,npar);
3180: doldm=matrix(1,nlstate,1,nlstate);
3181:
3182: hstepm=1*YEARM; /* Every year of age */
3183: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3184: agelim = AGESUP;
3185: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3186: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3187: if (stepm >= YEARM) hstepm=1;
3188: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3189: gradg=matrix(1,npar,1,nlstate);
3190: gp=vector(1,nlstate);
3191: gm=vector(1,nlstate);
3192:
3193: for(theta=1; theta <=npar; theta++){
3194: for(i=1; i<=npar; i++){ /* Computes gradient */
3195: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3196: }
3197: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3198: for(i=1;i<=nlstate;i++)
3199: gp[i] = prlim[i][i];
3200:
3201: for(i=1; i<=npar; i++) /* Computes gradient */
3202: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3203: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3204: for(i=1;i<=nlstate;i++)
3205: gm[i] = prlim[i][i];
3206:
3207: for(i=1;i<=nlstate;i++)
3208: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3209: } /* End theta */
3210:
3211: trgradg =matrix(1,nlstate,1,npar);
3212:
3213: for(j=1; j<=nlstate;j++)
3214: for(theta=1; theta <=npar; theta++)
3215: trgradg[j][theta]=gradg[theta][j];
3216:
3217: for(i=1;i<=nlstate;i++)
3218: varpl[i][(int)age] =0.;
3219: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3220: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3221: for(i=1;i<=nlstate;i++)
3222: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3223:
3224: fprintf(ficresvpl,"%.0f ",age );
3225: for(i=1; i<=nlstate;i++)
3226: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3227: fprintf(ficresvpl,"\n");
3228: free_vector(gp,1,nlstate);
3229: free_vector(gm,1,nlstate);
3230: free_matrix(gradg,1,npar,1,nlstate);
3231: free_matrix(trgradg,1,nlstate,1,npar);
3232: } /* End age */
3233:
3234: free_vector(xp,1,npar);
3235: free_matrix(doldm,1,nlstate,1,npar);
3236: free_matrix(dnewm,1,nlstate,1,nlstate);
3237:
3238: }
3239:
3240: /************ Variance of one-step probabilities ******************/
3241: 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[])
3242: {
3243: int i, j=0, i1, k1, l1, t, tj;
3244: int k2, l2, j1, z1;
3245: int k=0,l, cptcode;
3246: int first=1, first1;
3247: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3248: double **dnewm,**doldm;
3249: double *xp;
3250: double *gp, *gm;
3251: double **gradg, **trgradg;
3252: double **mu;
3253: double age,agelim, cov[NCOVMAX];
3254: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3255: int theta;
3256: char fileresprob[FILENAMELENGTH];
3257: char fileresprobcov[FILENAMELENGTH];
3258: char fileresprobcor[FILENAMELENGTH];
3259:
3260: double ***varpij;
3261:
3262: strcpy(fileresprob,"prob");
3263: strcat(fileresprob,fileres);
3264: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3265: printf("Problem with resultfile: %s\n", fileresprob);
3266: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3267: }
3268: strcpy(fileresprobcov,"probcov");
3269: strcat(fileresprobcov,fileres);
3270: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3271: printf("Problem with resultfile: %s\n", fileresprobcov);
3272: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3273: }
3274: strcpy(fileresprobcor,"probcor");
3275: strcat(fileresprobcor,fileres);
3276: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3277: printf("Problem with resultfile: %s\n", fileresprobcor);
3278: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3279: }
3280: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3281: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3282: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3283: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3284: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3285: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3286: pstamp(ficresprob);
3287: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3288: fprintf(ficresprob,"# Age");
3289: pstamp(ficresprobcov);
3290: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3291: fprintf(ficresprobcov,"# Age");
3292: pstamp(ficresprobcor);
3293: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3294: fprintf(ficresprobcor,"# Age");
3295:
3296:
3297: for(i=1; i<=nlstate;i++)
3298: for(j=1; j<=(nlstate+ndeath);j++){
3299: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3300: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3301: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3302: }
3303: /* fprintf(ficresprob,"\n");
3304: fprintf(ficresprobcov,"\n");
3305: fprintf(ficresprobcor,"\n");
3306: */
3307: xp=vector(1,npar);
3308: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3309: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3310: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3311: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3312: first=1;
3313: fprintf(ficgp,"\n# Routine varprob");
3314: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3315: fprintf(fichtm,"\n");
3316:
3317: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3318: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3319: file %s<br>\n",optionfilehtmcov);
3320: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3321: and drawn. It helps understanding how is the covariance between two incidences.\
3322: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3323: 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. \
3324: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3325: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3326: standard deviations wide on each axis. <br>\
3327: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3328: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3329: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3330:
3331: cov[1]=1;
3332: tj=cptcoveff;
3333: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3334: j1=0;
3335: for(t=1; t<=tj;t++){
3336: for(i1=1; i1<=ncodemax[t];i1++){
3337: j1++;
3338: if (cptcovn>0) {
3339: fprintf(ficresprob, "\n#********** Variable ");
3340: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3341: fprintf(ficresprob, "**********\n#\n");
3342: fprintf(ficresprobcov, "\n#********** Variable ");
3343: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3344: fprintf(ficresprobcov, "**********\n#\n");
3345:
3346: fprintf(ficgp, "\n#********** Variable ");
3347: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3348: fprintf(ficgp, "**********\n#\n");
3349:
3350:
3351: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3352: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3353: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3354:
3355: fprintf(ficresprobcor, "\n#********** Variable ");
3356: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3357: fprintf(ficresprobcor, "**********\n#");
3358: }
3359:
3360: for (age=bage; age<=fage; age ++){
3361: cov[2]=age;
3362: for (k=1; k<=cptcovn;k++) {
3363: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3364: }
3365: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3366: for (k=1; k<=cptcovprod;k++)
3367: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3368:
3369: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3370: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3371: gp=vector(1,(nlstate)*(nlstate+ndeath));
3372: gm=vector(1,(nlstate)*(nlstate+ndeath));
3373:
3374: for(theta=1; theta <=npar; theta++){
3375: for(i=1; i<=npar; i++)
3376: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3377:
3378: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3379:
3380: k=0;
3381: for(i=1; i<= (nlstate); i++){
3382: for(j=1; j<=(nlstate+ndeath);j++){
3383: k=k+1;
3384: gp[k]=pmmij[i][j];
3385: }
3386: }
3387:
3388: for(i=1; i<=npar; i++)
3389: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3390:
3391: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3392: k=0;
3393: for(i=1; i<=(nlstate); i++){
3394: for(j=1; j<=(nlstate+ndeath);j++){
3395: k=k+1;
3396: gm[k]=pmmij[i][j];
3397: }
3398: }
3399:
3400: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3401: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3402: }
3403:
3404: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3405: for(theta=1; theta <=npar; theta++)
3406: trgradg[j][theta]=gradg[theta][j];
3407:
3408: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3409: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3410: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3411: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3412: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3413: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3414:
3415: pmij(pmmij,cov,ncovmodel,x,nlstate);
3416:
3417: k=0;
3418: for(i=1; i<=(nlstate); i++){
3419: for(j=1; j<=(nlstate+ndeath);j++){
3420: k=k+1;
3421: mu[k][(int) age]=pmmij[i][j];
3422: }
3423: }
3424: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3425: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3426: varpij[i][j][(int)age] = doldm[i][j];
3427:
3428: /*printf("\n%d ",(int)age);
3429: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3430: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3431: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3432: }*/
3433:
3434: fprintf(ficresprob,"\n%d ",(int)age);
3435: fprintf(ficresprobcov,"\n%d ",(int)age);
3436: fprintf(ficresprobcor,"\n%d ",(int)age);
3437:
3438: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3439: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3440: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3441: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3442: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3443: }
3444: i=0;
3445: for (k=1; k<=(nlstate);k++){
3446: for (l=1; l<=(nlstate+ndeath);l++){
3447: i=i++;
3448: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3449: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3450: for (j=1; j<=i;j++){
3451: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3452: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3453: }
3454: }
3455: }/* end of loop for state */
3456: } /* end of loop for age */
3457:
3458: /* Confidence intervalle of pij */
3459: /*
3460: fprintf(ficgp,"\nunset parametric;unset label");
3461: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3462: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3463: 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);
3464: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3465: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3466: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3467: */
3468:
3469: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3470: first1=1;
3471: for (k2=1; k2<=(nlstate);k2++){
3472: for (l2=1; l2<=(nlstate+ndeath);l2++){
3473: if(l2==k2) continue;
3474: j=(k2-1)*(nlstate+ndeath)+l2;
3475: for (k1=1; k1<=(nlstate);k1++){
3476: for (l1=1; l1<=(nlstate+ndeath);l1++){
3477: if(l1==k1) continue;
3478: i=(k1-1)*(nlstate+ndeath)+l1;
3479: if(i<=j) continue;
3480: for (age=bage; age<=fage; age ++){
3481: if ((int)age %5==0){
3482: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3483: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3484: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3485: mu1=mu[i][(int) age]/stepm*YEARM ;
3486: mu2=mu[j][(int) age]/stepm*YEARM;
3487: c12=cv12/sqrt(v1*v2);
3488: /* Computing eigen value of matrix of covariance */
3489: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3490: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3491: if ((lc2 <0) || (lc1 <0) ){
3492: printf("Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e.\n It means that the matrix was not well estimated (varpij), for i=%2d, j=%2d, age=%4d .\n See files %s and %s. Continuing by making them positive: WRONG RESULTS.\n", lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3493: fprintf(ficlog,"Error: One eigen value of 2x2 matrix of covariance is negative, lc1=%11.3e, lc2=%11.3e, v1=%11.3e, v2=%11.3e, cv12=%11.3e\n", lc1, lc2, v1, v2, cv12);fflush(ficlog);
3494: lc1=fabs(lc1);
3495: lc2=fabs(lc2);
3496: }
3497:
3498: /* Eigen vectors */
3499: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3500: /*v21=sqrt(1.-v11*v11); *//* error */
3501: v21=(lc1-v1)/cv12*v11;
3502: v12=-v21;
3503: v22=v11;
3504: tnalp=v21/v11;
3505: if(first1==1){
3506: first1=0;
3507: 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);
3508: }
3509: 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);
3510: /*printf(fignu*/
3511: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3512: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3513: if(first==1){
3514: first=0;
3515: fprintf(ficgp,"\nset parametric;unset label");
3516: 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);
3517: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3518: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3519: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3520: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3521: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3522: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3523: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3524: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3525: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3526: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3527: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3528: 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",\
3529: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3530: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3531: }else{
3532: first=0;
3533: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3534: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3535: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3536: 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",\
3537: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3538: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3539: }/* if first */
3540: } /* age mod 5 */
3541: } /* end loop age */
3542: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3543: first=1;
3544: } /*l12 */
3545: } /* k12 */
3546: } /*l1 */
3547: }/* k1 */
3548: } /* loop covariates */
3549: }
3550: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3551: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3552: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3553: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3554: free_vector(xp,1,npar);
3555: fclose(ficresprob);
3556: fclose(ficresprobcov);
3557: fclose(ficresprobcor);
3558: fflush(ficgp);
3559: fflush(fichtmcov);
3560: }
3561:
3562:
3563: /******************* Printing html file ***********/
3564: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3565: int lastpass, int stepm, int weightopt, char model[],\
3566: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3567: int popforecast, int estepm ,\
3568: double jprev1, double mprev1,double anprev1, \
3569: double jprev2, double mprev2,double anprev2){
3570: int jj1, k1, i1, cpt;
3571:
3572: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3573: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3574: </ul>");
3575: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3576: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3577: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3578: fprintf(fichtm,"\
3579: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3580: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3581: fprintf(fichtm,"\
3582: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3583: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3584: fprintf(fichtm,"\
3585: - (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): \
3586: <a href=\"%s\">%s</a> <br>\n",
3587: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3588: fprintf(fichtm,"\
3589: - Population projections by age and states: \
3590: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3591:
3592: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3593:
3594: m=cptcoveff;
3595: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3596:
3597: jj1=0;
3598: for(k1=1; k1<=m;k1++){
3599: for(i1=1; i1<=ncodemax[k1];i1++){
3600: jj1++;
3601: if (cptcovn > 0) {
3602: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3603: for (cpt=1; cpt<=cptcoveff;cpt++)
3604: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3605: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3606: }
3607: /* Pij */
3608: 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> \
3609: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3610: /* Quasi-incidences */
3611: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3612: 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> \
3613: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3614: /* Period (stable) prevalence in each health state */
3615: for(cpt=1; cpt<nlstate;cpt++){
3616: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3617: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3618: }
3619: for(cpt=1; cpt<=nlstate;cpt++) {
3620: 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> \
3621: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3622: }
3623: } /* end i1 */
3624: }/* End k1 */
3625: fprintf(fichtm,"</ul>");
3626:
3627:
3628: fprintf(fichtm,"\
3629: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3630: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3631:
3632: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3633: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3634: fprintf(fichtm,"\
3635: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3636: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3637:
3638: fprintf(fichtm,"\
3639: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3640: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3641: fprintf(fichtm,"\
3642: - 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): \
3643: <a href=\"%s\">%s</a> <br>\n</li>",
3644: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3645: fprintf(fichtm,"\
3646: - (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): \
3647: <a href=\"%s\">%s</a> <br>\n</li>",
3648: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3649: fprintf(fichtm,"\
3650: - 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",
3651: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3652: fprintf(fichtm,"\
3653: - 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",
3654: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
3655: fprintf(fichtm,"\
3656: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3657: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3658:
3659: /* if(popforecast==1) fprintf(fichtm,"\n */
3660: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3661: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3662: /* <br>",fileres,fileres,fileres,fileres); */
3663: /* else */
3664: /* 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); */
3665: fflush(fichtm);
3666: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3667:
3668: m=cptcoveff;
3669: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3670:
3671: jj1=0;
3672: for(k1=1; k1<=m;k1++){
3673: for(i1=1; i1<=ncodemax[k1];i1++){
3674: jj1++;
3675: if (cptcovn > 0) {
3676: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3677: for (cpt=1; cpt<=cptcoveff;cpt++)
3678: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3679: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3680: }
3681: for(cpt=1; cpt<=nlstate;cpt++) {
3682: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3683: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3684: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3685: }
3686: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
3687: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3688: true period expectancies (those weighted with period prevalences are also\
3689: drawn in addition to the population based expectancies computed using\
3690: observed and cahotic prevalences: %s%d.png<br>\
3691: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3692: } /* end i1 */
3693: }/* End k1 */
3694: fprintf(fichtm,"</ul>");
3695: fflush(fichtm);
3696: }
3697:
3698: /******************* Gnuplot file **************/
3699: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3700:
3701: char dirfileres[132],optfileres[132];
3702: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3703: int ng=0;
3704: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3705: /* printf("Problem with file %s",optionfilegnuplot); */
3706: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3707: /* } */
3708:
3709: /*#ifdef windows */
3710: fprintf(ficgp,"cd \"%s\" \n",pathc);
3711: /*#endif */
3712: m=pow(2,cptcoveff);
3713:
3714: strcpy(dirfileres,optionfilefiname);
3715: strcpy(optfileres,"vpl");
3716: /* 1eme*/
3717: for (cpt=1; cpt<= nlstate ; cpt ++) {
3718: for (k1=1; k1<= m ; k1 ++) {
3719: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3720: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3721: fprintf(ficgp,"set xlabel \"Age\" \n\
3722: set ylabel \"Probability\" \n\
3723: set ter png small\n\
3724: set size 0.65,0.65\n\
3725: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3726:
3727: for (i=1; i<= nlstate ; i ++) {
3728: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3729: else fprintf(ficgp," \%%*lf (\%%*lf)");
3730: }
3731: 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);
3732: for (i=1; i<= nlstate ; i ++) {
3733: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3734: else fprintf(ficgp," \%%*lf (\%%*lf)");
3735: }
3736: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3737: for (i=1; i<= nlstate ; i ++) {
3738: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3739: else fprintf(ficgp," \%%*lf (\%%*lf)");
3740: }
3741: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3742: }
3743: }
3744: /*2 eme*/
3745:
3746: for (k1=1; k1<= m ; k1 ++) {
3747: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3748: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3749:
3750: for (i=1; i<= nlstate+1 ; i ++) {
3751: k=2*i;
3752: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%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== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3758: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3759: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3760: for (j=1; j<= nlstate+1 ; j ++) {
3761: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3762: else fprintf(ficgp," \%%*lf (\%%*lf)");
3763: }
3764: fprintf(ficgp,"\" t\"\" w l 0,");
3765: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3766: for (j=1; j<= nlstate+1 ; j ++) {
3767: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3768: else fprintf(ficgp," \%%*lf (\%%*lf)");
3769: }
3770: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3771: else fprintf(ficgp,"\" t\"\" w l 0,");
3772: }
3773: }
3774:
3775: /*3eme*/
3776:
3777: for (k1=1; k1<= m ; k1 ++) {
3778: for (cpt=1; cpt<= nlstate ; cpt ++) {
3779: /* k=2+nlstate*(2*cpt-2); */
3780: k=2+(nlstate+1)*(cpt-1);
3781: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3782: fprintf(ficgp,"set ter png small\n\
3783: set size 0.65,0.65\n\
3784: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3785: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3786: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3787: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3788: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3789: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3790: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3791:
3792: */
3793: for (i=1; i< nlstate ; i ++) {
3794: 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);
3795: /* 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);*/
3796:
3797: }
3798: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3799: }
3800: }
3801:
3802: /* CV preval stable (period) */
3803: for (k1=1; k1<= m ; k1 ++) {
3804: for (cpt=1; cpt<=nlstate ; cpt ++) {
3805: k=3;
3806: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3807: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3808: set ter png small\nset size 0.65,0.65\n\
3809: unset log y\n\
3810: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3811:
3812: for (i=1; i< nlstate ; i ++)
3813: fprintf(ficgp,"+$%d",k+i+1);
3814: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3815:
3816: l=3+(nlstate+ndeath)*cpt;
3817: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3818: for (i=1; i< nlstate ; i ++) {
3819: l=3+(nlstate+ndeath)*cpt;
3820: fprintf(ficgp,"+$%d",l+i+1);
3821: }
3822: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3823: }
3824: }
3825:
3826: /* proba elementaires */
3827: for(i=1,jk=1; i <=nlstate; i++){
3828: for(k=1; k <=(nlstate+ndeath); k++){
3829: if (k != i) {
3830: for(j=1; j <=ncovmodel; j++){
3831: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3832: jk++;
3833: fprintf(ficgp,"\n");
3834: }
3835: }
3836: }
3837: }
3838:
3839: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3840: for(jk=1; jk <=m; jk++) {
3841: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3842: if (ng==2)
3843: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3844: else
3845: fprintf(ficgp,"\nset title \"Probability\"\n");
3846: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3847: i=1;
3848: for(k2=1; k2<=nlstate; k2++) {
3849: k3=i;
3850: for(k=1; k<=(nlstate+ndeath); k++) {
3851: if (k != k2){
3852: if(ng==2)
3853: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3854: else
3855: fprintf(ficgp," exp(p%d+p%d*x",i,i+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",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3860: ij++;
3861: }
3862: else
3863: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3864: }
3865: fprintf(ficgp,")/(1");
3866:
3867: for(k1=1; k1 <=nlstate; k1++){
3868: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3869: ij=1;
3870: for(j=3; j <=ncovmodel; j++){
3871: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3872: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3873: ij++;
3874: }
3875: else
3876: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3877: }
3878: fprintf(ficgp,")");
3879: }
3880: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3881: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3882: i=i+ncovmodel;
3883: }
3884: } /* end k */
3885: } /* end k2 */
3886: } /* end jk */
3887: } /* end ng */
3888: fflush(ficgp);
3889: } /* end gnuplot */
3890:
3891:
3892: /*************** Moving average **************/
3893: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3894:
3895: int i, cpt, cptcod;
3896: int modcovmax =1;
3897: int mobilavrange, mob;
3898: double age;
3899:
3900: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3901: a covariate has 2 modalities */
3902: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3903:
3904: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3905: if(mobilav==1) mobilavrange=5; /* default */
3906: else mobilavrange=mobilav;
3907: for (age=bage; age<=fage; age++)
3908: for (i=1; i<=nlstate;i++)
3909: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3910: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3911: /* We keep the original values on the extreme ages bage, fage and for
3912: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3913: we use a 5 terms etc. until the borders are no more concerned.
3914: */
3915: for (mob=3;mob <=mobilavrange;mob=mob+2){
3916: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3917: for (i=1; i<=nlstate;i++){
3918: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3919: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3920: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3921: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3922: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3923: }
3924: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3925: }
3926: }
3927: }/* end age */
3928: }/* end mob */
3929: }else return -1;
3930: return 0;
3931: }/* End movingaverage */
3932:
3933:
3934: /************** Forecasting ******************/
3935: 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){
3936: /* proj1, year, month, day of starting projection
3937: agemin, agemax range of age
3938: dateprev1 dateprev2 range of dates during which prevalence is computed
3939: anproj2 year of en of projection (same day and month as proj1).
3940: */
3941: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3942: int *popage;
3943: double agec; /* generic age */
3944: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3945: double *popeffectif,*popcount;
3946: double ***p3mat;
3947: double ***mobaverage;
3948: char fileresf[FILENAMELENGTH];
3949:
3950: agelim=AGESUP;
3951: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3952:
3953: strcpy(fileresf,"f");
3954: strcat(fileresf,fileres);
3955: if((ficresf=fopen(fileresf,"w"))==NULL) {
3956: printf("Problem with forecast resultfile: %s\n", fileresf);
3957: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3958: }
3959: printf("Computing forecasting: result on file '%s' \n", fileresf);
3960: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3961:
3962: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3963:
3964: if (mobilav!=0) {
3965: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3966: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3967: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3968: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3969: }
3970: }
3971:
3972: stepsize=(int) (stepm+YEARM-1)/YEARM;
3973: if (stepm<=12) stepsize=1;
3974: if(estepm < stepm){
3975: printf ("Problem %d lower than %d\n",estepm, stepm);
3976: }
3977: else hstepm=estepm;
3978:
3979: hstepm=hstepm/stepm;
3980: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3981: fractional in yp1 */
3982: anprojmean=yp;
3983: yp2=modf((yp1*12),&yp);
3984: mprojmean=yp;
3985: yp1=modf((yp2*30.5),&yp);
3986: jprojmean=yp;
3987: if(jprojmean==0) jprojmean=1;
3988: if(mprojmean==0) jprojmean=1;
3989:
3990: i1=cptcoveff;
3991: if (cptcovn < 1){i1=1;}
3992:
3993: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
3994:
3995: fprintf(ficresf,"#****** Routine prevforecast **\n");
3996:
3997: /* if (h==(int)(YEARM*yearp)){ */
3998: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
3999: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4000: k=k+1;
4001: fprintf(ficresf,"\n#******");
4002: for(j=1;j<=cptcoveff;j++) {
4003: 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]]);
4004: }
4005: fprintf(ficresf,"******\n");
4006: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4007: for(j=1; j<=nlstate+ndeath;j++){
4008: for(i=1; i<=nlstate;i++)
4009: fprintf(ficresf," p%d%d",i,j);
4010: fprintf(ficresf," p.%d",j);
4011: }
4012: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4013: fprintf(ficresf,"\n");
4014: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4015:
4016: for (agec=fage; agec>=(ageminpar-1); agec--){
4017: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4018: nhstepm = nhstepm/hstepm;
4019: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4020: oldm=oldms;savm=savms;
4021: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4022:
4023: for (h=0; h<=nhstepm; h++){
4024: if (h*hstepm/YEARM*stepm ==yearp) {
4025: fprintf(ficresf,"\n");
4026: for(j=1;j<=cptcoveff;j++)
4027: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4028: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4029: }
4030: for(j=1; j<=nlstate+ndeath;j++) {
4031: ppij=0.;
4032: for(i=1; i<=nlstate;i++) {
4033: if (mobilav==1)
4034: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4035: else {
4036: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4037: }
4038: if (h*hstepm/YEARM*stepm== yearp) {
4039: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4040: }
4041: } /* end i */
4042: if (h*hstepm/YEARM*stepm==yearp) {
4043: fprintf(ficresf," %.3f", ppij);
4044: }
4045: }/* end j */
4046: } /* end h */
4047: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4048: } /* end agec */
4049: } /* end yearp */
4050: } /* end cptcod */
4051: } /* end cptcov */
4052:
4053: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4054:
4055: fclose(ficresf);
4056: }
4057:
4058: /************** Forecasting *****not tested NB*************/
4059: 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){
4060:
4061: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4062: int *popage;
4063: double calagedatem, agelim, kk1, kk2;
4064: double *popeffectif,*popcount;
4065: double ***p3mat,***tabpop,***tabpopprev;
4066: double ***mobaverage;
4067: char filerespop[FILENAMELENGTH];
4068:
4069: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4070: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4071: agelim=AGESUP;
4072: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4073:
4074: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4075:
4076:
4077: strcpy(filerespop,"pop");
4078: strcat(filerespop,fileres);
4079: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4080: printf("Problem with forecast resultfile: %s\n", filerespop);
4081: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4082: }
4083: printf("Computing forecasting: result on file '%s' \n", filerespop);
4084: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4085:
4086: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4087:
4088: if (mobilav!=0) {
4089: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4090: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4091: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4092: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4093: }
4094: }
4095:
4096: stepsize=(int) (stepm+YEARM-1)/YEARM;
4097: if (stepm<=12) stepsize=1;
4098:
4099: agelim=AGESUP;
4100:
4101: hstepm=1;
4102: hstepm=hstepm/stepm;
4103:
4104: if (popforecast==1) {
4105: if((ficpop=fopen(popfile,"r"))==NULL) {
4106: printf("Problem with population file : %s\n",popfile);exit(0);
4107: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4108: }
4109: popage=ivector(0,AGESUP);
4110: popeffectif=vector(0,AGESUP);
4111: popcount=vector(0,AGESUP);
4112:
4113: i=1;
4114: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4115:
4116: imx=i;
4117: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4118: }
4119:
4120: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4121: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4122: k=k+1;
4123: fprintf(ficrespop,"\n#******");
4124: for(j=1;j<=cptcoveff;j++) {
4125: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4126: }
4127: fprintf(ficrespop,"******\n");
4128: fprintf(ficrespop,"# Age");
4129: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4130: if (popforecast==1) fprintf(ficrespop," [Population]");
4131:
4132: for (cpt=0; cpt<=0;cpt++) {
4133: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4134:
4135: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4136: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4137: nhstepm = nhstepm/hstepm;
4138:
4139: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4140: oldm=oldms;savm=savms;
4141: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4142:
4143: for (h=0; h<=nhstepm; h++){
4144: if (h==(int) (calagedatem+YEARM*cpt)) {
4145: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4146: }
4147: for(j=1; j<=nlstate+ndeath;j++) {
4148: kk1=0.;kk2=0;
4149: for(i=1; i<=nlstate;i++) {
4150: if (mobilav==1)
4151: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4152: else {
4153: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4154: }
4155: }
4156: if (h==(int)(calagedatem+12*cpt)){
4157: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4158: /*fprintf(ficrespop," %.3f", kk1);
4159: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4160: }
4161: }
4162: for(i=1; i<=nlstate;i++){
4163: kk1=0.;
4164: for(j=1; j<=nlstate;j++){
4165: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4166: }
4167: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4168: }
4169:
4170: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4171: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4172: }
4173: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4174: }
4175: }
4176:
4177: /******/
4178:
4179: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4180: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4181: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4182: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4183: nhstepm = nhstepm/hstepm;
4184:
4185: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4186: oldm=oldms;savm=savms;
4187: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4188: for (h=0; h<=nhstepm; h++){
4189: if (h==(int) (calagedatem+YEARM*cpt)) {
4190: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4191: }
4192: for(j=1; j<=nlstate+ndeath;j++) {
4193: kk1=0.;kk2=0;
4194: for(i=1; i<=nlstate;i++) {
4195: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4196: }
4197: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4198: }
4199: }
4200: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4201: }
4202: }
4203: }
4204: }
4205:
4206: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4207:
4208: if (popforecast==1) {
4209: free_ivector(popage,0,AGESUP);
4210: free_vector(popeffectif,0,AGESUP);
4211: free_vector(popcount,0,AGESUP);
4212: }
4213: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4214: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4215: fclose(ficrespop);
4216: } /* End of popforecast */
4217:
4218: int fileappend(FILE *fichier, char *optionfich)
4219: {
4220: if((fichier=fopen(optionfich,"a"))==NULL) {
4221: printf("Problem with file: %s\n", optionfich);
4222: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4223: return (0);
4224: }
4225: fflush(fichier);
4226: return (1);
4227: }
4228:
4229:
4230: /**************** function prwizard **********************/
4231: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4232: {
4233:
4234: /* Wizard to print covariance matrix template */
4235:
4236: char ca[32], cb[32], cc[32];
4237: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4238: int numlinepar;
4239:
4240: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4241: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4242: for(i=1; i <=nlstate; i++){
4243: jj=0;
4244: for(j=1; j <=nlstate+ndeath; j++){
4245: if(j==i) continue;
4246: jj++;
4247: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4248: printf("%1d%1d",i,j);
4249: fprintf(ficparo,"%1d%1d",i,j);
4250: for(k=1; k<=ncovmodel;k++){
4251: /* printf(" %lf",param[i][j][k]); */
4252: /* fprintf(ficparo," %lf",param[i][j][k]); */
4253: printf(" 0.");
4254: fprintf(ficparo," 0.");
4255: }
4256: printf("\n");
4257: fprintf(ficparo,"\n");
4258: }
4259: }
4260: printf("# Scales (for hessian or gradient estimation)\n");
4261: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4262: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4263: for(i=1; i <=nlstate; i++){
4264: jj=0;
4265: for(j=1; j <=nlstate+ndeath; j++){
4266: if(j==i) continue;
4267: jj++;
4268: fprintf(ficparo,"%1d%1d",i,j);
4269: printf("%1d%1d",i,j);
4270: fflush(stdout);
4271: for(k=1; k<=ncovmodel;k++){
4272: /* printf(" %le",delti3[i][j][k]); */
4273: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4274: printf(" 0.");
4275: fprintf(ficparo," 0.");
4276: }
4277: numlinepar++;
4278: printf("\n");
4279: fprintf(ficparo,"\n");
4280: }
4281: }
4282: printf("# Covariance matrix\n");
4283: /* # 121 Var(a12)\n\ */
4284: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4285: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4286: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4287: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4288: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4289: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4290: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4291: fflush(stdout);
4292: fprintf(ficparo,"# Covariance matrix\n");
4293: /* # 121 Var(a12)\n\ */
4294: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4295: /* # ...\n\ */
4296: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4297:
4298: for(itimes=1;itimes<=2;itimes++){
4299: jj=0;
4300: for(i=1; i <=nlstate; i++){
4301: for(j=1; j <=nlstate+ndeath; j++){
4302: if(j==i) continue;
4303: for(k=1; k<=ncovmodel;k++){
4304: jj++;
4305: ca[0]= k+'a'-1;ca[1]='\0';
4306: if(itimes==1){
4307: printf("#%1d%1d%d",i,j,k);
4308: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4309: }else{
4310: printf("%1d%1d%d",i,j,k);
4311: fprintf(ficparo,"%1d%1d%d",i,j,k);
4312: /* printf(" %.5le",matcov[i][j]); */
4313: }
4314: ll=0;
4315: for(li=1;li <=nlstate; li++){
4316: for(lj=1;lj <=nlstate+ndeath; lj++){
4317: if(lj==li) continue;
4318: for(lk=1;lk<=ncovmodel;lk++){
4319: ll++;
4320: if(ll<=jj){
4321: cb[0]= lk +'a'-1;cb[1]='\0';
4322: if(ll<jj){
4323: if(itimes==1){
4324: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4325: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4326: }else{
4327: printf(" 0.");
4328: fprintf(ficparo," 0.");
4329: }
4330: }else{
4331: if(itimes==1){
4332: printf(" Var(%s%1d%1d)",ca,i,j);
4333: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4334: }else{
4335: printf(" 0.");
4336: fprintf(ficparo," 0.");
4337: }
4338: }
4339: }
4340: } /* end lk */
4341: } /* end lj */
4342: } /* end li */
4343: printf("\n");
4344: fprintf(ficparo,"\n");
4345: numlinepar++;
4346: } /* end k*/
4347: } /*end j */
4348: } /* end i */
4349: } /* end itimes */
4350:
4351: } /* end of prwizard */
4352: /******************* Gompertz Likelihood ******************************/
4353: double gompertz(double x[])
4354: {
4355: double A,B,L=0.0,sump=0.,num=0.;
4356: int i,n=0; /* n is the size of the sample */
4357:
4358: for (i=0;i<=imx-1 ; i++) {
4359: sump=sump+weight[i];
4360: /* sump=sump+1;*/
4361: num=num+1;
4362: }
4363:
4364:
4365: /* for (i=0; i<=imx; i++)
4366: 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]);*/
4367:
4368: for (i=1;i<=imx ; i++)
4369: {
4370: if (cens[i] == 1 && wav[i]>1)
4371: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4372:
4373: if (cens[i] == 0 && wav[i]>1)
4374: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4375: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4376:
4377: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4378: if (wav[i] > 1 ) { /* ??? */
4379: L=L+A*weight[i];
4380: /* 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]);*/
4381: }
4382: }
4383:
4384: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4385:
4386: return -2*L*num/sump;
4387: }
4388:
4389: /******************* Printing html file ***********/
4390: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4391: int lastpass, int stepm, int weightopt, char model[],\
4392: int imx, double p[],double **matcov,double agemortsup){
4393: int i,k;
4394:
4395: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4396: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4397: for (i=1;i<=2;i++)
4398: 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]));
4399: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4400: fprintf(fichtm,"</ul>");
4401:
4402: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4403:
4404: 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>");
4405:
4406: for (k=agegomp;k<(agemortsup-2);k++)
4407: 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]);
4408:
4409:
4410: fflush(fichtm);
4411: }
4412:
4413: /******************* Gnuplot file **************/
4414: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4415:
4416: char dirfileres[132],optfileres[132];
4417: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4418: int ng;
4419:
4420:
4421: /*#ifdef windows */
4422: fprintf(ficgp,"cd \"%s\" \n",pathc);
4423: /*#endif */
4424:
4425:
4426: strcpy(dirfileres,optionfilefiname);
4427: strcpy(optfileres,"vpl");
4428: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4429: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4430: fprintf(ficgp, "set ter png small\n set log y\n");
4431: fprintf(ficgp, "set size 0.65,0.65\n");
4432: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4433:
4434: }
4435:
4436:
4437:
4438:
4439:
4440: /***********************************************/
4441: /**************** Main Program *****************/
4442: /***********************************************/
4443:
4444: int main(int argc, char *argv[])
4445: {
4446: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
4447: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
4448: int linei, month, year,iout;
4449: int jj, ll, li, lj, lk, imk;
4450: int numlinepar=0; /* Current linenumber of parameter file */
4451: int itimes;
4452: int NDIM=2;
4453: int vpopbased=0;
4454:
4455: char ca[32], cb[32], cc[32];
4456: char dummy[]=" ";
4457: /* FILE *fichtm; *//* Html File */
4458: /* FILE *ficgp;*/ /*Gnuplot File */
4459: struct stat info;
4460: double agedeb, agefin,hf;
4461: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
4462:
4463: double fret;
4464: double **xi,tmp,delta;
4465:
4466: double dum; /* Dummy variable */
4467: double ***p3mat;
4468: double ***mobaverage;
4469: int *indx;
4470: char line[MAXLINE], linepar[MAXLINE];
4471: char linetmp[MAXLINE];
4472: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
4473: char pathr[MAXLINE], pathimach[MAXLINE];
4474: char **bp, *tok, *val; /* pathtot */
4475: int firstobs=1, lastobs=10;
4476: int sdeb, sfin; /* Status at beginning and end */
4477: int c, h , cpt,l;
4478: int ju,jl, mi;
4479: int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
4480: int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
4481: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
4482: int mobilav=0,popforecast=0;
4483: int hstepm, nhstepm;
4484: int agemortsup;
4485: float sumlpop=0.;
4486: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
4487: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
4488:
4489: double bage, fage, age, agelim, agebase;
4490: double ftolpl=FTOL;
4491: double **prlim;
4492: double *severity;
4493: double ***param; /* Matrix of parameters */
4494: double *p;
4495: double **matcov; /* Matrix of covariance */
4496: double ***delti3; /* Scale */
4497: double *delti; /* Scale */
4498: double ***eij, ***vareij;
4499: double **varpl; /* Variances of prevalence limits by age */
4500: double *epj, vepp;
4501: double kk1, kk2;
4502: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
4503: double **ximort;
4504: char *alph[]={"a","a","b","c","d","e"}, str[4];
4505: int *dcwave;
4506:
4507: char z[1]="c", occ;
4508:
4509: char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
4510: char *strt, strtend[80];
4511: char *stratrunc;
4512: int lstra;
4513:
4514: long total_usecs;
4515:
4516: /* setlocale (LC_ALL, ""); */
4517: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4518: /* textdomain (PACKAGE); */
4519: /* setlocale (LC_CTYPE, ""); */
4520: /* setlocale (LC_MESSAGES, ""); */
4521:
4522: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4523: (void) gettimeofday(&start_time,&tzp);
4524: curr_time=start_time;
4525: tm = *localtime(&start_time.tv_sec);
4526: tmg = *gmtime(&start_time.tv_sec);
4527: strcpy(strstart,asctime(&tm));
4528:
4529: /* printf("Localtime (at start)=%s",strstart); */
4530: /* tp.tv_sec = tp.tv_sec +86400; */
4531: /* tm = *localtime(&start_time.tv_sec); */
4532: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4533: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4534: /* tmg.tm_hour=tmg.tm_hour + 1; */
4535: /* tp.tv_sec = mktime(&tmg); */
4536: /* strt=asctime(&tmg); */
4537: /* printf("Time(after) =%s",strstart); */
4538: /* (void) time (&time_value);
4539: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4540: * tm = *localtime(&time_value);
4541: * strstart=asctime(&tm);
4542: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4543: */
4544:
4545: nberr=0; /* Number of errors and warnings */
4546: nbwarn=0;
4547: getcwd(pathcd, size);
4548:
4549: printf("\n%s\n%s",version,fullversion);
4550: if(argc <=1){
4551: printf("\nEnter the parameter file name: ");
4552: fgets(pathr,FILENAMELENGTH,stdin);
4553: i=strlen(pathr);
4554: if(pathr[i-1]=='\n')
4555: pathr[i-1]='\0';
4556: for (tok = pathr; tok != NULL; ){
4557: printf("Pathr |%s|\n",pathr);
4558: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4559: printf("val= |%s| pathr=%s\n",val,pathr);
4560: strcpy (pathtot, val);
4561: if(pathr[0] == '\0') break; /* Dirty */
4562: }
4563: }
4564: else{
4565: strcpy(pathtot,argv[1]);
4566: }
4567: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
4568: /*cygwin_split_path(pathtot,path,optionfile);
4569: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
4570: /* cutv(path,optionfile,pathtot,'\\');*/
4571:
4572: /* Split argv[0], imach program to get pathimach */
4573: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
4574: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4575: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
4576: /* strcpy(pathimach,argv[0]); */
4577: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
4578: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
4579: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
4580: chdir(path); /* Can be a relative path */
4581: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
4582: printf("Current directory %s!\n",pathcd);
4583: strcpy(command,"mkdir ");
4584: strcat(command,optionfilefiname);
4585: if((outcmd=system(command)) != 0){
4586: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
4587: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
4588: /* fclose(ficlog); */
4589: /* exit(1); */
4590: }
4591: /* if((imk=mkdir(optionfilefiname))<0){ */
4592: /* perror("mkdir"); */
4593: /* } */
4594:
4595: /*-------- arguments in the command line --------*/
4596:
4597: /* Log file */
4598: strcat(filelog, optionfilefiname);
4599: strcat(filelog,".log"); /* */
4600: if((ficlog=fopen(filelog,"w"))==NULL) {
4601: printf("Problem with logfile %s\n",filelog);
4602: goto end;
4603: }
4604: fprintf(ficlog,"Log filename:%s\n",filelog);
4605: fprintf(ficlog,"\n%s\n%s",version,fullversion);
4606: fprintf(ficlog,"\nEnter the parameter file name: \n");
4607: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
4608: path=%s \n\
4609: optionfile=%s\n\
4610: optionfilext=%s\n\
4611: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
4612:
4613: printf("Local time (at start):%s",strstart);
4614: fprintf(ficlog,"Local time (at start): %s",strstart);
4615: fflush(ficlog);
4616: /* (void) gettimeofday(&curr_time,&tzp); */
4617: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
4618:
4619: /* */
4620: strcpy(fileres,"r");
4621: strcat(fileres, optionfilefiname);
4622: strcat(fileres,".txt"); /* Other files have txt extension */
4623:
4624: /*---------arguments file --------*/
4625:
4626: if((ficpar=fopen(optionfile,"r"))==NULL) {
4627: printf("Problem with optionfile %s\n",optionfile);
4628: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
4629: fflush(ficlog);
4630: goto end;
4631: }
4632:
4633:
4634:
4635: strcpy(filereso,"o");
4636: strcat(filereso,fileres);
4637: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
4638: printf("Problem with Output resultfile: %s\n", filereso);
4639: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
4640: fflush(ficlog);
4641: goto end;
4642: }
4643:
4644: /* Reads comments: lines beginning with '#' */
4645: numlinepar=0;
4646: while((c=getc(ficpar))=='#' && c!= EOF){
4647: ungetc(c,ficpar);
4648: fgets(line, MAXLINE, ficpar);
4649: numlinepar++;
4650: puts(line);
4651: fputs(line,ficparo);
4652: fputs(line,ficlog);
4653: }
4654: ungetc(c,ficpar);
4655:
4656: 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);
4657: numlinepar++;
4658: 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);
4659: 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);
4660: 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);
4661: fflush(ficlog);
4662: while((c=getc(ficpar))=='#' && c!= EOF){
4663: ungetc(c,ficpar);
4664: fgets(line, MAXLINE, ficpar);
4665: numlinepar++;
4666: puts(line);
4667: fputs(line,ficparo);
4668: fputs(line,ficlog);
4669: }
4670: ungetc(c,ficpar);
4671:
4672:
4673: covar=matrix(0,NCOVMAX,1,n);
4674: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
4675: if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
4676: /* where is ncovprod ?*/
4677: ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
4678: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
4679: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
4680: npar= nforce*ncovmodel; /* Number of parameters like aij*/
4681: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
4682: 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);
4683: 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);
4684: fflush(stdout);
4685: fclose (ficlog);
4686: goto end;
4687: }
4688: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4689: delti=delti3[1][1];
4690: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
4691: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
4692: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4693: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4694: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
4695: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
4696: fclose (ficparo);
4697: fclose (ficlog);
4698: goto end;
4699: exit(0);
4700: }
4701: else if(mle==-3) {
4702: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
4703: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4704: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
4705: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4706: matcov=matrix(1,npar,1,npar);
4707: }
4708: else{
4709: /* Read guess parameters */
4710: /* Reads comments: lines beginning with '#' */
4711: while((c=getc(ficpar))=='#' && c!= EOF){
4712: ungetc(c,ficpar);
4713: fgets(line, MAXLINE, ficpar);
4714: numlinepar++;
4715: puts(line);
4716: fputs(line,ficparo);
4717: fputs(line,ficlog);
4718: }
4719: ungetc(c,ficpar);
4720:
4721: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
4722: for(i=1; i <=nlstate; i++){
4723: j=0;
4724: for(jj=1; jj <=nlstate+ndeath; jj++){
4725: if(jj==i) continue;
4726: j++;
4727: fscanf(ficpar,"%1d%1d",&i1,&j1);
4728: if ((i1 != i) && (j1 != j)){
4729: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
4730: It might be a problem of design; if ncovcol and the model are correct\n \
4731: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
4732: exit(1);
4733: }
4734: fprintf(ficparo,"%1d%1d",i1,j1);
4735: if(mle==1)
4736: printf("%1d%1d",i,j);
4737: fprintf(ficlog,"%1d%1d",i,j);
4738: for(k=1; k<=ncovmodel;k++){
4739: fscanf(ficpar," %lf",¶m[i][j][k]);
4740: if(mle==1){
4741: printf(" %lf",param[i][j][k]);
4742: fprintf(ficlog," %lf",param[i][j][k]);
4743: }
4744: else
4745: fprintf(ficlog," %lf",param[i][j][k]);
4746: fprintf(ficparo," %lf",param[i][j][k]);
4747: }
4748: fscanf(ficpar,"\n");
4749: numlinepar++;
4750: if(mle==1)
4751: printf("\n");
4752: fprintf(ficlog,"\n");
4753: fprintf(ficparo,"\n");
4754: }
4755: }
4756: fflush(ficlog);
4757:
4758: p=param[1][1];
4759:
4760: /* Reads comments: lines beginning with '#' */
4761: while((c=getc(ficpar))=='#' && c!= EOF){
4762: ungetc(c,ficpar);
4763: fgets(line, MAXLINE, ficpar);
4764: numlinepar++;
4765: puts(line);
4766: fputs(line,ficparo);
4767: fputs(line,ficlog);
4768: }
4769: ungetc(c,ficpar);
4770:
4771: for(i=1; i <=nlstate; i++){
4772: for(j=1; j <=nlstate+ndeath-1; j++){
4773: fscanf(ficpar,"%1d%1d",&i1,&j1);
4774: if ((i1-i)*(j1-j)!=0){
4775: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
4776: exit(1);
4777: }
4778: printf("%1d%1d",i,j);
4779: fprintf(ficparo,"%1d%1d",i1,j1);
4780: fprintf(ficlog,"%1d%1d",i1,j1);
4781: for(k=1; k<=ncovmodel;k++){
4782: fscanf(ficpar,"%le",&delti3[i][j][k]);
4783: printf(" %le",delti3[i][j][k]);
4784: fprintf(ficparo," %le",delti3[i][j][k]);
4785: fprintf(ficlog," %le",delti3[i][j][k]);
4786: }
4787: fscanf(ficpar,"\n");
4788: numlinepar++;
4789: printf("\n");
4790: fprintf(ficparo,"\n");
4791: fprintf(ficlog,"\n");
4792: }
4793: }
4794: fflush(ficlog);
4795:
4796: delti=delti3[1][1];
4797:
4798:
4799: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
4800:
4801: /* Reads comments: lines beginning with '#' */
4802: while((c=getc(ficpar))=='#' && c!= EOF){
4803: ungetc(c,ficpar);
4804: fgets(line, MAXLINE, ficpar);
4805: numlinepar++;
4806: puts(line);
4807: fputs(line,ficparo);
4808: fputs(line,ficlog);
4809: }
4810: ungetc(c,ficpar);
4811:
4812: matcov=matrix(1,npar,1,npar);
4813: for(i=1; i <=npar; i++)
4814: for(j=1; j <=npar; j++) matcov[i][j]=0.;
4815:
4816: for(i=1; i <=npar; i++){
4817: fscanf(ficpar,"%s",&str);
4818: if(mle==1)
4819: printf("%s",str);
4820: fprintf(ficlog,"%s",str);
4821: fprintf(ficparo,"%s",str);
4822: for(j=1; j <=i; j++){
4823: fscanf(ficpar," %le",&matcov[i][j]);
4824: if(mle==1){
4825: printf(" %.5le",matcov[i][j]);
4826: }
4827: fprintf(ficlog," %.5le",matcov[i][j]);
4828: fprintf(ficparo," %.5le",matcov[i][j]);
4829: }
4830: fscanf(ficpar,"\n");
4831: numlinepar++;
4832: if(mle==1)
4833: printf("\n");
4834: fprintf(ficlog,"\n");
4835: fprintf(ficparo,"\n");
4836: }
4837: for(i=1; i <=npar; i++)
4838: for(j=i+1;j<=npar;j++)
4839: matcov[i][j]=matcov[j][i];
4840:
4841: if(mle==1)
4842: printf("\n");
4843: fprintf(ficlog,"\n");
4844:
4845: fflush(ficlog);
4846:
4847: /*-------- Rewriting parameter file ----------*/
4848: strcpy(rfileres,"r"); /* "Rparameterfile */
4849: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
4850: strcat(rfileres,"."); /* */
4851: strcat(rfileres,optionfilext); /* Other files have txt extension */
4852: if((ficres =fopen(rfileres,"w"))==NULL) {
4853: printf("Problem writing new parameter file: %s\n", fileres);goto end;
4854: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
4855: }
4856: fprintf(ficres,"#%s\n",version);
4857: } /* End of mle != -3 */
4858:
4859: /*-------- data file ----------*/
4860: if((fic=fopen(datafile,"r"))==NULL) {
4861: printf("Problem while opening datafile: %s\n", datafile);goto end;
4862: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
4863: }
4864:
4865: n= lastobs;
4866: severity = vector(1,maxwav);
4867: outcome=imatrix(1,maxwav+1,1,n);
4868: num=lvector(1,n);
4869: moisnais=vector(1,n);
4870: annais=vector(1,n);
4871: moisdc=vector(1,n);
4872: andc=vector(1,n);
4873: agedc=vector(1,n);
4874: cod=ivector(1,n);
4875: weight=vector(1,n);
4876: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
4877: mint=matrix(1,maxwav,1,n);
4878: anint=matrix(1,maxwav,1,n);
4879: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
4880: tab=ivector(1,NCOVMAX);
4881: ncodemax=ivector(1,8);
4882:
4883: i=1;
4884: linei=0;
4885: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4886: linei=linei+1;
4887: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4888: if(line[j] == '\t')
4889: line[j] = ' ';
4890: }
4891: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4892: ;
4893: };
4894: line[j+1]=0; /* Trims blanks at end of line */
4895: if(line[0]=='#'){
4896: fprintf(ficlog,"Comment line\n%s\n",line);
4897: printf("Comment line\n%s\n",line);
4898: continue;
4899: }
4900: trimbb(linetmp,line); /* Trims multiple blanks in line */
4901: for (j=0; line[j]!='\0';j++){
4902: line[j]=linetmp[j];
4903: }
4904:
4905:
4906: for (j=maxwav;j>=1;j--){
4907: cutv(stra, strb,line,' ');
4908: if(strb[0]=='.') { /* Missing status */
4909: lval=-1;
4910: }else{
4911: errno=0;
4912: lval=strtol(strb,&endptr,10);
4913: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4914: if( strb[0]=='\0' || (*endptr != '\0')){
4915: 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);
4916: 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);
4917: goto end;
4918: }
4919: }
4920: s[j][i]=lval;
4921:
4922: strcpy(line,stra);
4923: cutv(stra, strb,line,' ');
4924: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4925: }
4926: else if(iout=sscanf(strb,"%s.") != 0){
4927: month=99;
4928: year=9999;
4929: }else{
4930: 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);
4931: 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);
4932: goto end;
4933: }
4934: anint[j][i]= (double) year;
4935: mint[j][i]= (double)month;
4936: strcpy(line,stra);
4937: } /* ENd Waves */
4938:
4939: cutv(stra, strb,line,' ');
4940: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4941: }
4942: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4943: month=99;
4944: year=9999;
4945: }else{
4946: 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);
4947: 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);
4948: goto end;
4949: }
4950: andc[i]=(double) year;
4951: moisdc[i]=(double) month;
4952: strcpy(line,stra);
4953:
4954: cutv(stra, strb,line,' ');
4955: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4956: }
4957: else if(iout=sscanf(strb,"%s.") != 0){
4958: month=99;
4959: year=9999;
4960: }else{
4961: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4962: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
4963: goto end;
4964: }
4965: if (year==9999) {
4966: printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);
4967: fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
4968: goto end;
4969:
4970: }
4971: annais[i]=(double)(year);
4972: moisnais[i]=(double)(month);
4973: strcpy(line,stra);
4974:
4975: cutv(stra, strb,line,' ');
4976: errno=0;
4977: dval=strtod(strb,&endptr);
4978: if( strb[0]=='\0' || (*endptr != '\0')){
4979: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4980: 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);
4981: fflush(ficlog);
4982: goto end;
4983: }
4984: weight[i]=dval;
4985: strcpy(line,stra);
4986:
4987: for (j=ncovcol;j>=1;j--){
4988: cutv(stra, strb,line,' ');
4989: if(strb[0]=='.') { /* Missing status */
4990: lval=-1;
4991: }else{
4992: errno=0;
4993: lval=strtol(strb,&endptr,10);
4994: if( strb[0]=='\0' || (*endptr != '\0')){
4995: 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);
4996: 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);
4997: goto end;
4998: }
4999: }
5000: if(lval <-1 || lval >1){
5001: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
5002: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5003: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5004: For example, for multinomial values like 1, 2 and 3,\n \
5005: build V1=0 V2=0 for the reference value (1),\n \
5006: V1=1 V2=0 for (2) \n \
5007: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5008: output of IMaCh is often meaningless.\n \
5009: Exiting.\n",lval,linei, i,line,j);
5010: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
5011: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5012: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5013: For example, for multinomial values like 1, 2 and 3,\n \
5014: build V1=0 V2=0 for the reference value (1),\n \
5015: V1=1 V2=0 for (2) \n \
5016: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5017: output of IMaCh is often meaningless.\n \
5018: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5019: goto end;
5020: }
5021: covar[j][i]=(double)(lval);
5022: strcpy(line,stra);
5023: }
5024: lstra=strlen(stra);
5025:
5026: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5027: stratrunc = &(stra[lstra-9]);
5028: num[i]=atol(stratrunc);
5029: }
5030: else
5031: num[i]=atol(stra);
5032: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5033: 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;}*/
5034:
5035: i=i+1;
5036: } /* End loop reading data */
5037: fclose(fic);
5038: /* printf("ii=%d", ij);
5039: scanf("%d",i);*/
5040: imx=i-1; /* Number of individuals */
5041:
5042: /* for (i=1; i<=imx; i++){
5043: if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
5044: if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
5045: if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
5046: }*/
5047: /* for (i=1; i<=imx; i++){
5048: if (s[4][i]==9) s[4][i]=-1;
5049: 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]));}*/
5050:
5051: /* for (i=1; i<=imx; i++) */
5052:
5053: /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
5054: else weight[i]=1;*/
5055:
5056: /* Calculation of the number of parameters from char model */
5057: 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 */
5058: Tprod=ivector(1,15);
5059: Tvaraff=ivector(1,15);
5060: Tvard=imatrix(1,15,1,2);
5061: Tage=ivector(1,15);
5062:
5063: if (strlen(model) >1){ /* If there is at least 1 covariate */
5064: j=0, j1=0, k1=1, k2=1;
5065: j=nbocc(model,'+'); /* j=Number of '+' */
5066: j1=nbocc(model,'*'); /* j1=Number of '*' */
5067: cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
5068: cptcovprod=j1; /*Number of products V1*V2 =1 */
5069:
5070: strcpy(modelsav,model);
5071: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
5072: printf("Error. Non available option model=%s ",model);
5073: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
5074: goto end;
5075: }
5076:
5077: /* This loop fills the array Tvar from the string 'model'.*/
5078: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5079: for(i=(j+1); i>=1;i--){
5080: cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5081: modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4
5082: stra=V2
5083: */
5084: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5085: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5086: /*scanf("%d",i);*/
5087: if (strchr(strb,'*')) { /* Model includes a product V1+V3*age+V2 strb=V3*age*/
5088: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5089: if (strcmp(strc,"age")==0) { /* Vn*age */
5090: cptcovprod--;
5091: cutv(strb,stre,strd,'V');
5092: Tvar[i]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3 */
5093: cptcovage++; /* Sums the number of covariates including age as a product */
5094: Tage[cptcovage]=i; /* Tage[1] =2 */
5095: /*printf("stre=%s ", stre);*/
5096: }
5097: else if (strcmp(strd,"age")==0) { /* or age*Vn */
5098: cptcovprod--;
5099: cutv(strb,stre,strc,'V');
5100: Tvar[i]=atoi(stre);
5101: cptcovage++;
5102: Tage[cptcovage]=i;
5103: }
5104: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
5105: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5106: Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
5107: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
5108: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
5109: Tprod[k1]=i; /* Tprod[1] */
5110: Tvard[k1][1]=atoi(strc); /* m*/
5111: Tvard[k1][2]=atoi(stre); /* n */
5112: Tvar[cptcovn+k2]=Tvard[k1][1];
5113: Tvar[cptcovn+k2+1]=Tvard[k1][2];
5114: for (k=1; k<=lastobs;k++)
5115: covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
5116: k1++;
5117: k2=k2+2;
5118: }
5119: }
5120: else { /* no more sum */
5121: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5122: /* scanf("%d",i);*/
5123: cutv(strd,strc,strb,'V');
5124: Tvar[i]=atoi(strc);
5125: }
5126: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
5127: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5128: scanf("%d",i);*/
5129: } /* end of loop + */
5130: } /* end model */
5131:
5132: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5133: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5134:
5135: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5136: printf("cptcovprod=%d ", cptcovprod);
5137: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5138:
5139: scanf("%d ",i);*/
5140:
5141: /* if(mle==1){*/
5142: if (weightopt != 1) { /* Maximisation without weights*/
5143: for(i=1;i<=n;i++) weight[i]=1.0;
5144: }
5145: /*-calculation of age at interview from date of interview and age at death -*/
5146: agev=matrix(1,maxwav,1,imx);
5147:
5148: for (i=1; i<=imx; i++) {
5149: for(m=2; (m<= maxwav); m++) {
5150: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5151: anint[m][i]=9999;
5152: s[m][i]=-1;
5153: }
5154: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5155: nberr++;
5156: 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);
5157: 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);
5158: s[m][i]=-1;
5159: }
5160: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5161: nberr++;
5162: 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]);
5163: 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]);
5164: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5165: }
5166: }
5167: }
5168:
5169: for (i=1; i<=imx; i++) {
5170: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5171: for(m=firstpass; (m<= lastpass); m++){
5172: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5173: if (s[m][i] >= nlstate+1) {
5174: if(agedc[i]>0)
5175: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5176: agev[m][i]=agedc[i];
5177: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5178: else {
5179: if ((int)andc[i]!=9999){
5180: nbwarn++;
5181: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5182: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5183: agev[m][i]=-1;
5184: }
5185: }
5186: }
5187: else if(s[m][i] !=9){ /* Standard case, age in fractional
5188: years but with the precision of a month */
5189: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5190: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5191: agev[m][i]=1;
5192: else if(agev[m][i] <agemin){
5193: agemin=agev[m][i];
5194: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);
5195: }
5196: else if(agev[m][i] >agemax){
5197: agemax=agev[m][i];
5198: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
5199: }
5200: /*agev[m][i]=anint[m][i]-annais[i];*/
5201: /* agev[m][i] = age[i]+2*m;*/
5202: }
5203: else { /* =9 */
5204: agev[m][i]=1;
5205: s[m][i]=-1;
5206: }
5207: }
5208: else /*= 0 Unknown */
5209: agev[m][i]=1;
5210: }
5211:
5212: }
5213: for (i=1; i<=imx; i++) {
5214: for(m=firstpass; (m<=lastpass); m++){
5215: if (s[m][i] > (nlstate+ndeath)) {
5216: nberr++;
5217: 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);
5218: 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);
5219: goto end;
5220: }
5221: }
5222: }
5223:
5224: /*for (i=1; i<=imx; i++){
5225: for (m=firstpass; (m<lastpass); m++){
5226: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5227: }
5228:
5229: }*/
5230:
5231:
5232: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5233: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
5234:
5235: agegomp=(int)agemin;
5236: free_vector(severity,1,maxwav);
5237: free_imatrix(outcome,1,maxwav+1,1,n);
5238: free_vector(moisnais,1,n);
5239: free_vector(annais,1,n);
5240: /* free_matrix(mint,1,maxwav,1,n);
5241: free_matrix(anint,1,maxwav,1,n);*/
5242: free_vector(moisdc,1,n);
5243: free_vector(andc,1,n);
5244:
5245:
5246: wav=ivector(1,imx);
5247: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5248: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5249: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5250:
5251: /* Concatenates waves */
5252: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5253:
5254: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5255:
5256: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5257: ncodemax[1]=1;
5258: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5259:
5260: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5261: the estimations*/
5262: h=0;
5263: m=pow(2,cptcoveff);
5264:
5265: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5266: 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 */
5267: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5268: 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 */
5269: h++;
5270: if (h>m)
5271: h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
5272: 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]]);
5273: }
5274: }
5275: }
5276: }
5277: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5278: codtab[1][2]=1;codtab[2][2]=2; */
5279: /* for(i=1; i <=m ;i++){
5280: for(k=1; k <=cptcovn; k++){
5281: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
5282: }
5283: printf("\n");
5284: }
5285: scanf("%d",i);*/
5286:
5287: /*------------ gnuplot -------------*/
5288: strcpy(optionfilegnuplot,optionfilefiname);
5289: if(mle==-3)
5290: strcat(optionfilegnuplot,"-mort");
5291: strcat(optionfilegnuplot,".gp");
5292:
5293: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5294: printf("Problem with file %s",optionfilegnuplot);
5295: }
5296: else{
5297: fprintf(ficgp,"\n# %s\n", version);
5298: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5299: fprintf(ficgp,"set missing 'NaNq'\n");
5300: }
5301: /* fclose(ficgp);*/
5302: /*--------- index.htm --------*/
5303:
5304: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5305: if(mle==-3)
5306: strcat(optionfilehtm,"-mort");
5307: strcat(optionfilehtm,".htm");
5308: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
5309: printf("Problem with %s \n",optionfilehtm);
5310: exit(0);
5311: }
5312:
5313: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5314: strcat(optionfilehtmcov,"-cov.htm");
5315: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5316: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5317: }
5318: else{
5319: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5320: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5321: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5322: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5323: }
5324:
5325: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5326: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5327: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5328: \n\
5329: <hr size=\"2\" color=\"#EC5E5E\">\
5330: <ul><li><h4>Parameter files</h4>\n\
5331: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5332: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5333: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5334: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5335: - Date and time at start: %s</ul>\n",\
5336: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5337: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5338: fileres,fileres,\
5339: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5340: fflush(fichtm);
5341:
5342: strcpy(pathr,path);
5343: strcat(pathr,optionfilefiname);
5344: chdir(optionfilefiname); /* Move to directory named optionfile */
5345:
5346: /* Calculates basic frequencies. Computes observed prevalence at single age
5347: and prints on file fileres'p'. */
5348: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5349:
5350: fprintf(fichtm,"\n");
5351: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5352: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5353: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5354: imx,agemin,agemax,jmin,jmax,jmean);
5355: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5356: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5357: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5358: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5359: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5360:
5361:
5362: /* For Powell, parameters are in a vector p[] starting at p[1]
5363: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5364: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5365:
5366: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5367:
5368: if (mle==-3){
5369: ximort=matrix(1,NDIM,1,NDIM);
5370: cens=ivector(1,n);
5371: ageexmed=vector(1,n);
5372: agecens=vector(1,n);
5373: dcwave=ivector(1,n);
5374:
5375: for (i=1; i<=imx; i++){
5376: dcwave[i]=-1;
5377: for (m=firstpass; m<=lastpass; m++)
5378: if (s[m][i]>nlstate) {
5379: dcwave[i]=m;
5380: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5381: break;
5382: }
5383: }
5384:
5385: for (i=1; i<=imx; i++) {
5386: if (wav[i]>0){
5387: ageexmed[i]=agev[mw[1][i]][i];
5388: j=wav[i];
5389: agecens[i]=1.;
5390:
5391: if (ageexmed[i]> 1 && wav[i] > 0){
5392: agecens[i]=agev[mw[j][i]][i];
5393: cens[i]= 1;
5394: }else if (ageexmed[i]< 1)
5395: cens[i]= -1;
5396: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5397: cens[i]=0 ;
5398: }
5399: else cens[i]=-1;
5400: }
5401:
5402: for (i=1;i<=NDIM;i++) {
5403: for (j=1;j<=NDIM;j++)
5404: ximort[i][j]=(i == j ? 1.0 : 0.0);
5405: }
5406:
5407: p[1]=0.0268; p[NDIM]=0.083;
5408: /*printf("%lf %lf", p[1], p[2]);*/
5409:
5410:
5411: printf("Powell\n"); fprintf(ficlog,"Powell\n");
5412: strcpy(filerespow,"pow-mort");
5413: strcat(filerespow,fileres);
5414: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5415: printf("Problem with resultfile: %s\n", filerespow);
5416: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5417: }
5418: fprintf(ficrespow,"# Powell\n# iter -2*LL");
5419: /* for (i=1;i<=nlstate;i++)
5420: for(j=1;j<=nlstate+ndeath;j++)
5421: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5422: */
5423: fprintf(ficrespow,"\n");
5424:
5425: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
5426: fclose(ficrespow);
5427:
5428: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5429:
5430: for(i=1; i <=NDIM; i++)
5431: for(j=i+1;j<=NDIM;j++)
5432: matcov[i][j]=matcov[j][i];
5433:
5434: printf("\nCovariance matrix\n ");
5435: for(i=1; i <=NDIM; i++) {
5436: for(j=1;j<=NDIM;j++){
5437: printf("%f ",matcov[i][j]);
5438: }
5439: printf("\n ");
5440: }
5441:
5442: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5443: for (i=1;i<=NDIM;i++)
5444: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5445:
5446: lsurv=vector(1,AGESUP);
5447: lpop=vector(1,AGESUP);
5448: tpop=vector(1,AGESUP);
5449: lsurv[agegomp]=100000;
5450:
5451: for (k=agegomp;k<=AGESUP;k++) {
5452: agemortsup=k;
5453: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5454: }
5455:
5456: for (k=agegomp;k<agemortsup;k++)
5457: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5458:
5459: for (k=agegomp;k<agemortsup;k++){
5460: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5461: sumlpop=sumlpop+lpop[k];
5462: }
5463:
5464: tpop[agegomp]=sumlpop;
5465: for (k=agegomp;k<(agemortsup-3);k++){
5466: /* tpop[k+1]=2;*/
5467: tpop[k+1]=tpop[k]-lpop[k];
5468: }
5469:
5470:
5471: printf("\nAge lx qx dx Lx Tx e(x)\n");
5472: for (k=agegomp;k<(agemortsup-2);k++)
5473: 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]);
5474:
5475:
5476: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5477: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5478:
5479: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5480: stepm, weightopt,\
5481: model,imx,p,matcov,agemortsup);
5482:
5483: free_vector(lsurv,1,AGESUP);
5484: free_vector(lpop,1,AGESUP);
5485: free_vector(tpop,1,AGESUP);
5486: } /* Endof if mle==-3 */
5487:
5488: else{ /* For mle >=1 */
5489: globpr=0;/* debug */
5490: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5491: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5492: for (k=1; k<=npar;k++)
5493: printf(" %d %8.5f",k,p[k]);
5494: printf("\n");
5495: globpr=1; /* to print the contributions */
5496: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5497: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5498: for (k=1; k<=npar;k++)
5499: printf(" %d %8.5f",k,p[k]);
5500: printf("\n");
5501: if(mle>=1){ /* Could be 1 or 2 */
5502: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5503: }
5504:
5505: /*--------- results files --------------*/
5506: 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);
5507:
5508:
5509: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5510: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5511: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5512: for(i=1,jk=1; i <=nlstate; i++){
5513: for(k=1; k <=(nlstate+ndeath); k++){
5514: if (k != i) {
5515: printf("%d%d ",i,k);
5516: fprintf(ficlog,"%d%d ",i,k);
5517: fprintf(ficres,"%1d%1d ",i,k);
5518: for(j=1; j <=ncovmodel; j++){
5519: printf("%lf ",p[jk]);
5520: fprintf(ficlog,"%lf ",p[jk]);
5521: fprintf(ficres,"%lf ",p[jk]);
5522: jk++;
5523: }
5524: printf("\n");
5525: fprintf(ficlog,"\n");
5526: fprintf(ficres,"\n");
5527: }
5528: }
5529: }
5530: if(mle!=0){
5531: /* Computing hessian and covariance matrix */
5532: ftolhess=ftol; /* Usually correct */
5533: hesscov(matcov, p, npar, delti, ftolhess, func);
5534: }
5535: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5536: printf("# Scales (for hessian or gradient estimation)\n");
5537: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5538: for(i=1,jk=1; i <=nlstate; i++){
5539: for(j=1; j <=nlstate+ndeath; j++){
5540: if (j!=i) {
5541: fprintf(ficres,"%1d%1d",i,j);
5542: printf("%1d%1d",i,j);
5543: fprintf(ficlog,"%1d%1d",i,j);
5544: for(k=1; k<=ncovmodel;k++){
5545: printf(" %.5e",delti[jk]);
5546: fprintf(ficlog," %.5e",delti[jk]);
5547: fprintf(ficres," %.5e",delti[jk]);
5548: jk++;
5549: }
5550: printf("\n");
5551: fprintf(ficlog,"\n");
5552: fprintf(ficres,"\n");
5553: }
5554: }
5555: }
5556:
5557: 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");
5558: if(mle>=1)
5559: 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");
5560: 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");
5561: /* # 121 Var(a12)\n\ */
5562: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5563: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5564: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5565: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5566: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5567: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5568: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5569:
5570:
5571: /* Just to have a covariance matrix which will be more understandable
5572: even is we still don't want to manage dictionary of variables
5573: */
5574: for(itimes=1;itimes<=2;itimes++){
5575: jj=0;
5576: for(i=1; i <=nlstate; i++){
5577: for(j=1; j <=nlstate+ndeath; j++){
5578: if(j==i) continue;
5579: for(k=1; k<=ncovmodel;k++){
5580: jj++;
5581: ca[0]= k+'a'-1;ca[1]='\0';
5582: if(itimes==1){
5583: if(mle>=1)
5584: printf("#%1d%1d%d",i,j,k);
5585: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5586: fprintf(ficres,"#%1d%1d%d",i,j,k);
5587: }else{
5588: if(mle>=1)
5589: printf("%1d%1d%d",i,j,k);
5590: fprintf(ficlog,"%1d%1d%d",i,j,k);
5591: fprintf(ficres,"%1d%1d%d",i,j,k);
5592: }
5593: ll=0;
5594: for(li=1;li <=nlstate; li++){
5595: for(lj=1;lj <=nlstate+ndeath; lj++){
5596: if(lj==li) continue;
5597: for(lk=1;lk<=ncovmodel;lk++){
5598: ll++;
5599: if(ll<=jj){
5600: cb[0]= lk +'a'-1;cb[1]='\0';
5601: if(ll<jj){
5602: if(itimes==1){
5603: if(mle>=1)
5604: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5605: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5606: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5607: }else{
5608: if(mle>=1)
5609: printf(" %.5e",matcov[jj][ll]);
5610: fprintf(ficlog," %.5e",matcov[jj][ll]);
5611: fprintf(ficres," %.5e",matcov[jj][ll]);
5612: }
5613: }else{
5614: if(itimes==1){
5615: if(mle>=1)
5616: printf(" Var(%s%1d%1d)",ca,i,j);
5617: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5618: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5619: }else{
5620: if(mle>=1)
5621: printf(" %.5e",matcov[jj][ll]);
5622: fprintf(ficlog," %.5e",matcov[jj][ll]);
5623: fprintf(ficres," %.5e",matcov[jj][ll]);
5624: }
5625: }
5626: }
5627: } /* end lk */
5628: } /* end lj */
5629: } /* end li */
5630: if(mle>=1)
5631: printf("\n");
5632: fprintf(ficlog,"\n");
5633: fprintf(ficres,"\n");
5634: numlinepar++;
5635: } /* end k*/
5636: } /*end j */
5637: } /* end i */
5638: } /* end itimes */
5639:
5640: fflush(ficlog);
5641: fflush(ficres);
5642:
5643: while((c=getc(ficpar))=='#' && c!= EOF){
5644: ungetc(c,ficpar);
5645: fgets(line, MAXLINE, ficpar);
5646: puts(line);
5647: fputs(line,ficparo);
5648: }
5649: ungetc(c,ficpar);
5650:
5651: estepm=0;
5652: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5653: if (estepm==0 || estepm < stepm) estepm=stepm;
5654: if (fage <= 2) {
5655: bage = ageminpar;
5656: fage = agemaxpar;
5657: }
5658:
5659: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5660: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5661: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5662:
5663: while((c=getc(ficpar))=='#' && c!= EOF){
5664: ungetc(c,ficpar);
5665: fgets(line, MAXLINE, ficpar);
5666: puts(line);
5667: fputs(line,ficparo);
5668: }
5669: ungetc(c,ficpar);
5670:
5671: 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);
5672: 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);
5673: 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);
5674: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5675: 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);
5676:
5677: while((c=getc(ficpar))=='#' && c!= EOF){
5678: ungetc(c,ficpar);
5679: fgets(line, MAXLINE, ficpar);
5680: puts(line);
5681: fputs(line,ficparo);
5682: }
5683: ungetc(c,ficpar);
5684:
5685:
5686: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5687: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5688:
5689: fscanf(ficpar,"pop_based=%d\n",&popbased);
5690: fprintf(ficparo,"pop_based=%d\n",popbased);
5691: fprintf(ficres,"pop_based=%d\n",popbased);
5692:
5693: while((c=getc(ficpar))=='#' && c!= EOF){
5694: ungetc(c,ficpar);
5695: fgets(line, MAXLINE, ficpar);
5696: puts(line);
5697: fputs(line,ficparo);
5698: }
5699: ungetc(c,ficpar);
5700:
5701: 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);
5702: 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);
5703: 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);
5704: 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);
5705: 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);
5706: /* day and month of proj2 are not used but only year anproj2.*/
5707:
5708:
5709:
5710: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5711: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5712:
5713: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5714: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5715:
5716: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5717: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5718: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5719:
5720: /*------------ free_vector -------------*/
5721: /* chdir(path); */
5722:
5723: free_ivector(wav,1,imx);
5724: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5725: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5726: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5727: free_lvector(num,1,n);
5728: free_vector(agedc,1,n);
5729: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5730: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5731: fclose(ficparo);
5732: fclose(ficres);
5733:
5734:
5735: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5736:
5737: strcpy(filerespl,"pl");
5738: strcat(filerespl,fileres);
5739: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5740: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5741: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5742: }
5743: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5744: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5745: pstamp(ficrespl);
5746: fprintf(ficrespl,"# Period (stable) prevalence \n");
5747: fprintf(ficrespl,"#Age ");
5748: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5749: fprintf(ficrespl,"\n");
5750:
5751: prlim=matrix(1,nlstate,1,nlstate);
5752:
5753: agebase=ageminpar;
5754: agelim=agemaxpar;
5755: ftolpl=1.e-10;
5756: i1=cptcoveff;
5757: if (cptcovn < 1){i1=1;}
5758:
5759: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5760: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5761: k=k+1;
5762: /* to clean */
5763: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
5764: fprintf(ficrespl,"\n#******");
5765: printf("\n#******");
5766: fprintf(ficlog,"\n#******");
5767: for(j=1;j<=cptcoveff;j++) {
5768: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5769: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5770: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5771: }
5772: fprintf(ficrespl,"******\n");
5773: printf("******\n");
5774: fprintf(ficlog,"******\n");
5775:
5776: for (age=agebase; age<=agelim; age++){
5777: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5778: fprintf(ficrespl,"%.0f ",age );
5779: for(j=1;j<=cptcoveff;j++)
5780: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5781: for(i=1; i<=nlstate;i++)
5782: fprintf(ficrespl," %.5f", prlim[i][i]);
5783: fprintf(ficrespl,"\n");
5784: }
5785: }
5786: }
5787: fclose(ficrespl);
5788:
5789: /*------------- h Pij x at various ages ------------*/
5790:
5791: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5792: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5793: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5794: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5795: }
5796: printf("Computing pij: result on file '%s' \n", filerespij);
5797: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5798:
5799: stepsize=(int) (stepm+YEARM-1)/YEARM;
5800: /*if (stepm<=24) stepsize=2;*/
5801:
5802: agelim=AGESUP;
5803: hstepm=stepsize*YEARM; /* Every year of age */
5804: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
5805:
5806: /* hstepm=1; aff par mois*/
5807: pstamp(ficrespij);
5808: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
5809: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5810: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5811: k=k+1;
5812: fprintf(ficrespij,"\n#****** ");
5813: for(j=1;j<=cptcoveff;j++)
5814: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5815: fprintf(ficrespij,"******\n");
5816:
5817: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
5818: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
5819: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
5820:
5821: /* nhstepm=nhstepm*YEARM; aff par mois*/
5822:
5823: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5824: oldm=oldms;savm=savms;
5825: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5826: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
5827: for(i=1; i<=nlstate;i++)
5828: for(j=1; j<=nlstate+ndeath;j++)
5829: fprintf(ficrespij," %1d-%1d",i,j);
5830: fprintf(ficrespij,"\n");
5831: for (h=0; h<=nhstepm; h++){
5832: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
5833: for(i=1; i<=nlstate;i++)
5834: for(j=1; j<=nlstate+ndeath;j++)
5835: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
5836: fprintf(ficrespij,"\n");
5837: }
5838: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5839: fprintf(ficrespij,"\n");
5840: }
5841: }
5842: }
5843:
5844: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
5845:
5846: fclose(ficrespij);
5847:
5848: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
5849: for(i=1;i<=AGESUP;i++)
5850: for(j=1;j<=NCOVMAX;j++)
5851: for(k=1;k<=NCOVMAX;k++)
5852: probs[i][j][k]=0.;
5853:
5854: /*---------- Forecasting ------------------*/
5855: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
5856: if(prevfcast==1){
5857: /* if(stepm ==1){*/
5858: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
5859: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
5860: /* } */
5861: /* else{ */
5862: /* erreur=108; */
5863: /* 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); */
5864: /* 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); */
5865: /* } */
5866: }
5867:
5868:
5869: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
5870:
5871: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5872: /* 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",\
5873: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
5874: */
5875:
5876: if (mobilav!=0) {
5877: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5878: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
5879: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5880: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5881: }
5882: }
5883:
5884:
5885: /*---------- Health expectancies, no variances ------------*/
5886:
5887: strcpy(filerese,"e");
5888: strcat(filerese,fileres);
5889: if((ficreseij=fopen(filerese,"w"))==NULL) {
5890: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5891: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
5892: }
5893: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
5894: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
5895: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5896: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5897: k=k+1;
5898: fprintf(ficreseij,"\n#****** ");
5899: for(j=1;j<=cptcoveff;j++) {
5900: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5901: }
5902: fprintf(ficreseij,"******\n");
5903:
5904: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5905: oldm=oldms;savm=savms;
5906: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
5907:
5908: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
5909: }
5910: }
5911: fclose(ficreseij);
5912:
5913:
5914: /*---------- Health expectancies and variances ------------*/
5915:
5916:
5917: strcpy(filerest,"t");
5918: strcat(filerest,fileres);
5919: if((ficrest=fopen(filerest,"w"))==NULL) {
5920: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
5921: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
5922: }
5923: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5924: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
5925:
5926:
5927: strcpy(fileresstde,"stde");
5928: strcat(fileresstde,fileres);
5929: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
5930: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5931: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
5932: }
5933: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5934: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
5935:
5936: strcpy(filerescve,"cve");
5937: strcat(filerescve,fileres);
5938: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
5939: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5940: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
5941: }
5942: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5943: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
5944:
5945: strcpy(fileresv,"v");
5946: strcat(fileresv,fileres);
5947: if((ficresvij=fopen(fileresv,"w"))==NULL) {
5948: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
5949: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
5950: }
5951: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5952: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
5953:
5954: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5955: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5956: k=k+1;
5957: fprintf(ficrest,"\n#****** ");
5958: for(j=1;j<=cptcoveff;j++)
5959: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5960: fprintf(ficrest,"******\n");
5961:
5962: fprintf(ficresstdeij,"\n#****** ");
5963: fprintf(ficrescveij,"\n#****** ");
5964: for(j=1;j<=cptcoveff;j++) {
5965: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5966: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5967: }
5968: fprintf(ficresstdeij,"******\n");
5969: fprintf(ficrescveij,"******\n");
5970:
5971: fprintf(ficresvij,"\n#****** ");
5972: for(j=1;j<=cptcoveff;j++)
5973: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5974: fprintf(ficresvij,"******\n");
5975:
5976: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5977: oldm=oldms;savm=savms;
5978: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
5979:
5980: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
5981: pstamp(ficrest);
5982: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5983: oldm=oldms;savm=savms;
5984: 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 ");
5985: if(vpopbased==1)
5986: 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);
5987: else
5988: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
5989: fprintf(ficrest,"# Age e.. (std) ");
5990: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
5991: fprintf(ficrest,"\n");
5992:
5993: epj=vector(1,nlstate+1);
5994: for(age=bage; age <=fage ;age++){
5995: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5996: if (vpopbased==1) {
5997: if(mobilav ==0){
5998: for(i=1; i<=nlstate;i++)
5999: prlim[i][i]=probs[(int)age][i][k];
6000: }else{ /* mobilav */
6001: for(i=1; i<=nlstate;i++)
6002: prlim[i][i]=mobaverage[(int)age][i][k];
6003: }
6004: }
6005:
6006: fprintf(ficrest," %4.0f",age);
6007: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6008: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6009: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6010: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6011: }
6012: epj[nlstate+1] +=epj[j];
6013: }
6014:
6015: for(i=1, vepp=0.;i <=nlstate;i++)
6016: for(j=1;j <=nlstate;j++)
6017: vepp += vareij[i][j][(int)age];
6018: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6019: for(j=1;j <=nlstate;j++){
6020: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6021: }
6022: fprintf(ficrest,"\n");
6023: }
6024: }
6025: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6026: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6027: free_vector(epj,1,nlstate+1);
6028: }
6029: }
6030: free_vector(weight,1,n);
6031: free_imatrix(Tvard,1,15,1,2);
6032: free_imatrix(s,1,maxwav+1,1,n);
6033: free_matrix(anint,1,maxwav,1,n);
6034: free_matrix(mint,1,maxwav,1,n);
6035: free_ivector(cod,1,n);
6036: free_ivector(tab,1,NCOVMAX);
6037: fclose(ficresstdeij);
6038: fclose(ficrescveij);
6039: fclose(ficresvij);
6040: fclose(ficrest);
6041: fclose(ficpar);
6042:
6043: /*------- Variance of period (stable) prevalence------*/
6044:
6045: strcpy(fileresvpl,"vpl");
6046: strcat(fileresvpl,fileres);
6047: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6048: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6049: exit(0);
6050: }
6051: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6052:
6053: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6054: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6055: k=k+1;
6056: fprintf(ficresvpl,"\n#****** ");
6057: for(j=1;j<=cptcoveff;j++)
6058: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6059: fprintf(ficresvpl,"******\n");
6060:
6061: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6062: oldm=oldms;savm=savms;
6063: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6064: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6065: }
6066: }
6067:
6068: fclose(ficresvpl);
6069:
6070: /*---------- End : free ----------------*/
6071: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6072: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6073:
6074: } /* mle==-3 arrives here for freeing */
6075: endfree:
6076: free_matrix(prlim,1,nlstate,1,nlstate);
6077: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6078: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6079: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6080: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6081: free_matrix(covar,0,NCOVMAX,1,n);
6082: free_matrix(matcov,1,npar,1,npar);
6083: /*free_vector(delti,1,npar);*/
6084: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6085: free_matrix(agev,1,maxwav,1,imx);
6086: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6087:
6088: free_ivector(ncodemax,1,8);
6089: free_ivector(Tvar,1,15);
6090: free_ivector(Tprod,1,15);
6091: free_ivector(Tvaraff,1,15);
6092: free_ivector(Tage,1,15);
6093:
6094: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6095: free_imatrix(codtab,1,100,1,10);
6096: fflush(fichtm);
6097: fflush(ficgp);
6098:
6099:
6100: if((nberr >0) || (nbwarn>0)){
6101: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6102: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6103: }else{
6104: printf("End of Imach\n");
6105: fprintf(ficlog,"End of Imach\n");
6106: }
6107: printf("See log file on %s\n",filelog);
6108: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6109: (void) gettimeofday(&end_time,&tzp);
6110: tm = *localtime(&end_time.tv_sec);
6111: tmg = *gmtime(&end_time.tv_sec);
6112: strcpy(strtend,asctime(&tm));
6113: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6114: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6115: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6116:
6117: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6118: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6119: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6120: /* printf("Total time was %d uSec.\n", total_usecs);*/
6121: /* if(fileappend(fichtm,optionfilehtm)){ */
6122: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6123: fclose(fichtm);
6124: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6125: fclose(fichtmcov);
6126: fclose(ficgp);
6127: fclose(ficlog);
6128: /*------ End -----------*/
6129:
6130:
6131: printf("Before Current directory %s!\n",pathcd);
6132: if(chdir(pathcd) != 0)
6133: printf("Can't move to directory %s!\n",path);
6134: if(getcwd(pathcd,MAXLINE) > 0)
6135: printf("Current directory %s!\n",pathcd);
6136: /*strcat(plotcmd,CHARSEPARATOR);*/
6137: sprintf(plotcmd,"gnuplot");
6138: #ifndef UNIX
6139: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6140: #endif
6141: if(!stat(plotcmd,&info)){
6142: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6143: if(!stat(getenv("GNUPLOTBIN"),&info)){
6144: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6145: }else
6146: strcpy(pplotcmd,plotcmd);
6147: #ifdef UNIX
6148: strcpy(plotcmd,GNUPLOTPROGRAM);
6149: if(!stat(plotcmd,&info)){
6150: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6151: }else
6152: strcpy(pplotcmd,plotcmd);
6153: #endif
6154: }else
6155: strcpy(pplotcmd,plotcmd);
6156:
6157: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6158: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6159:
6160: if((outcmd=system(plotcmd)) != 0){
6161: printf("\n Problem with gnuplot\n");
6162: }
6163: printf(" Wait...");
6164: while (z[0] != 'q') {
6165: /* chdir(path); */
6166: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6167: scanf("%s",z);
6168: /* if (z[0] == 'c') system("./imach"); */
6169: if (z[0] == 'e') {
6170: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6171: system(optionfilehtm);
6172: }
6173: else if (z[0] == 'g') system(plotcmd);
6174: else if (z[0] == 'q') exit(0);
6175: }
6176: end:
6177: while (z[0] != 'q') {
6178: printf("\nType q for exiting: ");
6179: scanf("%s",z);
6180: }
6181: }
6182:
6183:
6184:
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src