Annotation of imach/src/imach.c, revision 1.136
1.136 ! brouard 1: /* $Id: imach.c,v 1.135 2009/10/29 15:33:14 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.136 ! brouard 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:
1.135 brouard 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:
1.134 brouard 10: Revision 1.133 2009/07/06 10:21:25 brouard
11: just nforces
12:
1.133 brouard 13: Revision 1.132 2009/07/06 08:22:05 brouard
14: Many tings
15:
1.132 brouard 16: Revision 1.131 2009/06/20 16:22:47 brouard
17: Some dimensions resccaled
18:
1.131 brouard 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:
1.130 brouard 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:
1.129 lievre 27: Revision 1.128 2006/06/30 13:02:05 brouard
28: (Module): Clarifications on computing e.j
29:
1.128 brouard 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:
1.127 brouard 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:
1.126 brouard 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:
1.133 brouard 183: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 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:
1.133 brouard 316: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
317: Institut national d'études démographiques, Paris.
1.126 brouard 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:
1.136 ! brouard 378: #ifdef GSL
! 379: #include <gsl/gsl_errno.h>
! 380: #include <gsl/gsl_multimin.h>
! 381: #endif
! 382:
1.126 brouard 383: /* #include <libintl.h> */
384: /* #define _(String) gettext (String) */
385:
386: #define MAXLINE 256
387:
388: #define GNUPLOTPROGRAM "gnuplot"
389: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
390: #define FILENAMELENGTH 132
391:
392: #define GLOCK_ERROR_NOPATH -1 /* empty path */
393: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
394:
1.131 brouard 395: #define MAXPARM 128 /* Maximum number of parameters for the optimization */
1.126 brouard 396: #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
397:
398: #define NINTERVMAX 8
399: #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
400: #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
1.130 brouard 401: #define NCOVMAX 20 /* Maximum number of covariates */
1.126 brouard 402: #define MAXN 20000
403: #define YEARM 12. /* Number of months per year */
404: #define AGESUP 130
405: #define AGEBASE 40
406: #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
407: #ifdef UNIX
408: #define DIRSEPARATOR '/'
409: #define CHARSEPARATOR "/"
410: #define ODIRSEPARATOR '\\'
411: #else
412: #define DIRSEPARATOR '\\'
413: #define CHARSEPARATOR "\\"
414: #define ODIRSEPARATOR '/'
415: #endif
416:
1.136 ! brouard 417: /* $Id: imach.c,v 1.135 2009/10/29 15:33:14 brouard Exp $ */
1.126 brouard 418: /* $State: Exp $ */
419:
1.136 ! brouard 420: char version[]="Imach version 0.98m, April 2010, INED-EUROREVES-Institut de longevite ";
! 421: char fullversion[]="$Revision: 1.135 $ $Date: 2009/10/29 15:33:14 $";
1.126 brouard 422: char strstart[80];
423: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 424: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 425: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.130 brouard 426: int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with '*age' */
1.126 brouard 427: int npar=NPARMAX;
428: int nlstate=2; /* Number of live states */
429: int ndeath=1; /* Number of dead states */
1.130 brouard 430: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 431: int popbased=0;
432:
433: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 434: int maxwav=0; /* Maxim number of waves */
435: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
436: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
437: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 438: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 439: int mle=1, weightopt=0;
1.126 brouard 440: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
441: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
442: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
443: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 444: double jmean=1; /* Mean space between 2 waves */
1.126 brouard 445: double **oldm, **newm, **savm; /* Working pointers to matrices */
446: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 ! brouard 447: /*FILE *fic ; */ /* Used in readdata only */
! 448: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 449: FILE *ficlog, *ficrespow;
1.130 brouard 450: int globpr=0; /* Global variable for printing or not */
1.126 brouard 451: double fretone; /* Only one call to likelihood */
1.130 brouard 452: long ipmx=0; /* Number of contributions */
1.126 brouard 453: double sw; /* Sum of weights */
454: char filerespow[FILENAMELENGTH];
455: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
456: FILE *ficresilk;
457: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
458: FILE *ficresprobmorprev;
459: FILE *fichtm, *fichtmcov; /* Html File */
460: FILE *ficreseij;
461: char filerese[FILENAMELENGTH];
462: FILE *ficresstdeij;
463: char fileresstde[FILENAMELENGTH];
464: FILE *ficrescveij;
465: char filerescve[FILENAMELENGTH];
466: FILE *ficresvij;
467: char fileresv[FILENAMELENGTH];
468: FILE *ficresvpl;
469: char fileresvpl[FILENAMELENGTH];
470: char title[MAXLINE];
471: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
472: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
473: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
474: char command[FILENAMELENGTH];
475: int outcmd=0;
476:
477: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
478:
479: char filelog[FILENAMELENGTH]; /* Log file */
480: char filerest[FILENAMELENGTH];
481: char fileregp[FILENAMELENGTH];
482: char popfile[FILENAMELENGTH];
483:
484: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
485:
486: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
487: struct timezone tzp;
488: extern int gettimeofday();
489: struct tm tmg, tm, tmf, *gmtime(), *localtime();
490: long time_value;
491: extern long time();
492: char strcurr[80], strfor[80];
493:
494: char *endptr;
495: long lval;
496: double dval;
497:
498: #define NR_END 1
499: #define FREE_ARG char*
500: #define FTOL 1.0e-10
501:
502: #define NRANSI
503: #define ITMAX 200
504:
505: #define TOL 2.0e-4
506:
507: #define CGOLD 0.3819660
508: #define ZEPS 1.0e-10
509: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
510:
511: #define GOLD 1.618034
512: #define GLIMIT 100.0
513: #define TINY 1.0e-20
514:
515: static double maxarg1,maxarg2;
516: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
517: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
518:
519: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
520: #define rint(a) floor(a+0.5)
521:
522: static double sqrarg;
523: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
524: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
525: int agegomp= AGEGOMP;
526:
527: int imx;
528: int stepm=1;
529: /* Stepm, step in month: minimum step interpolation*/
530:
531: int estepm;
532: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
533:
534: int m,nb;
535: long *num;
536: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
537: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
538: double **pmmij, ***probs;
539: double *ageexmed,*agecens;
540: double dateintmean=0;
541:
542: double *weight;
543: int **s; /* Status */
544: double *agedc, **covar, idx;
1.131 brouard 545: int **nbcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 546: double *lsurv, *lpop, *tpop;
547:
548: double ftol=FTOL; /* Tolerance for computing Max Likelihood */
549: double ftolhess; /* Tolerance for computing hessian */
550:
551: /**************** split *************************/
552: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
553: {
554: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
555: the name of the file (name), its extension only (ext) and its first part of the name (finame)
556: */
557: char *ss; /* pointer */
558: int l1, l2; /* length counters */
559:
560: l1 = strlen(path ); /* length of path */
561: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
562: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
563: if ( ss == NULL ) { /* no directory, so determine current directory */
564: strcpy( name, path ); /* we got the fullname name because no directory */
565: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
566: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
567: /* get current working directory */
568: /* extern char* getcwd ( char *buf , int len);*/
569: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
570: return( GLOCK_ERROR_GETCWD );
571: }
572: /* got dirc from getcwd*/
573: printf(" DIRC = %s \n",dirc);
574: } else { /* strip direcotry from path */
575: ss++; /* after this, the filename */
576: l2 = strlen( ss ); /* length of filename */
577: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
578: strcpy( name, ss ); /* save file name */
579: strncpy( dirc, path, l1 - l2 ); /* now the directory */
580: dirc[l1-l2] = 0; /* add zero */
581: printf(" DIRC2 = %s \n",dirc);
582: }
583: /* We add a separator at the end of dirc if not exists */
584: l1 = strlen( dirc ); /* length of directory */
585: if( dirc[l1-1] != DIRSEPARATOR ){
586: dirc[l1] = DIRSEPARATOR;
587: dirc[l1+1] = 0;
588: printf(" DIRC3 = %s \n",dirc);
589: }
590: ss = strrchr( name, '.' ); /* find last / */
591: if (ss >0){
592: ss++;
593: strcpy(ext,ss); /* save extension */
594: l1= strlen( name);
595: l2= strlen(ss)+1;
596: strncpy( finame, name, l1-l2);
597: finame[l1-l2]= 0;
598: }
599:
600: return( 0 ); /* we're done */
601: }
602:
603:
604: /******************************************/
605:
606: void replace_back_to_slash(char *s, char*t)
607: {
608: int i;
609: int lg=0;
610: i=0;
611: lg=strlen(t);
612: for(i=0; i<= lg; i++) {
613: (s[i] = t[i]);
614: if (t[i]== '\\') s[i]='/';
615: }
616: }
617:
1.132 brouard 618: char *trimbb(char *out, char *in)
619: { /* Trim multiple blanks in line */
620: char *s;
621: s=out;
622: while (*in != '\0'){
623: while( *in == ' ' && *(in+1) == ' ' && *(in+1) != '\0'){
624: in++;
625: }
626: *out++ = *in++;
627: }
628: *out='\0';
629: return s;
630: }
631:
1.126 brouard 632: int nbocc(char *s, char occ)
633: {
634: int i,j=0;
635: int lg=20;
636: i=0;
637: lg=strlen(s);
638: for(i=0; i<= lg; i++) {
639: if (s[i] == occ ) j++;
640: }
641: return j;
642: }
643:
644: void cutv(char *u,char *v, char*t, char occ)
645: {
646: /* cuts string t into u and v where u ends before first occurence of char 'occ'
647: and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
648: gives u="abcedf" and v="ghi2j" */
649: int i,lg,j,p=0;
650: i=0;
651: for(j=0; j<=strlen(t)-1; j++) {
652: if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
653: }
654:
655: lg=strlen(t);
656: for(j=0; j<p; j++) {
657: (u[j] = t[j]);
658: }
659: u[p]='\0';
660:
661: for(j=0; j<= lg; j++) {
662: if (j>=(p+1))(v[j-p-1] = t[j]);
663: }
664: }
665:
666: /********************** nrerror ********************/
667:
668: void nrerror(char error_text[])
669: {
670: fprintf(stderr,"ERREUR ...\n");
671: fprintf(stderr,"%s\n",error_text);
672: exit(EXIT_FAILURE);
673: }
674: /*********************** vector *******************/
675: double *vector(int nl, int nh)
676: {
677: double *v;
678: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
679: if (!v) nrerror("allocation failure in vector");
680: return v-nl+NR_END;
681: }
682:
683: /************************ free vector ******************/
684: void free_vector(double*v, int nl, int nh)
685: {
686: free((FREE_ARG)(v+nl-NR_END));
687: }
688:
689: /************************ivector *******************************/
690: int *ivector(long nl,long nh)
691: {
692: int *v;
693: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
694: if (!v) nrerror("allocation failure in ivector");
695: return v-nl+NR_END;
696: }
697:
698: /******************free ivector **************************/
699: void free_ivector(int *v, long nl, long nh)
700: {
701: free((FREE_ARG)(v+nl-NR_END));
702: }
703:
704: /************************lvector *******************************/
705: long *lvector(long nl,long nh)
706: {
707: long *v;
708: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
709: if (!v) nrerror("allocation failure in ivector");
710: return v-nl+NR_END;
711: }
712:
713: /******************free lvector **************************/
714: void free_lvector(long *v, long nl, long nh)
715: {
716: free((FREE_ARG)(v+nl-NR_END));
717: }
718:
719: /******************* imatrix *******************************/
720: int **imatrix(long nrl, long nrh, long ncl, long nch)
721: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
722: {
723: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
724: int **m;
725:
726: /* allocate pointers to rows */
727: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
728: if (!m) nrerror("allocation failure 1 in matrix()");
729: m += NR_END;
730: m -= nrl;
731:
732:
733: /* allocate rows and set pointers to them */
734: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
735: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
736: m[nrl] += NR_END;
737: m[nrl] -= ncl;
738:
739: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
740:
741: /* return pointer to array of pointers to rows */
742: return m;
743: }
744:
745: /****************** free_imatrix *************************/
746: void free_imatrix(m,nrl,nrh,ncl,nch)
747: int **m;
748: long nch,ncl,nrh,nrl;
749: /* free an int matrix allocated by imatrix() */
750: {
751: free((FREE_ARG) (m[nrl]+ncl-NR_END));
752: free((FREE_ARG) (m+nrl-NR_END));
753: }
754:
755: /******************* matrix *******************************/
756: double **matrix(long nrl, long nrh, long ncl, long nch)
757: {
758: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
759: double **m;
760:
761: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
762: if (!m) nrerror("allocation failure 1 in matrix()");
763: m += NR_END;
764: m -= nrl;
765:
766: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
767: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
768: m[nrl] += NR_END;
769: m[nrl] -= ncl;
770:
771: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
772: return m;
773: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
774: */
775: }
776:
777: /*************************free matrix ************************/
778: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
779: {
780: free((FREE_ARG)(m[nrl]+ncl-NR_END));
781: free((FREE_ARG)(m+nrl-NR_END));
782: }
783:
784: /******************* ma3x *******************************/
785: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
786: {
787: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
788: double ***m;
789:
790: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
791: if (!m) nrerror("allocation failure 1 in matrix()");
792: m += NR_END;
793: m -= nrl;
794:
795: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
796: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
797: m[nrl] += NR_END;
798: m[nrl] -= ncl;
799:
800: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
801:
802: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
803: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
804: m[nrl][ncl] += NR_END;
805: m[nrl][ncl] -= nll;
806: for (j=ncl+1; j<=nch; j++)
807: m[nrl][j]=m[nrl][j-1]+nlay;
808:
809: for (i=nrl+1; i<=nrh; i++) {
810: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
811: for (j=ncl+1; j<=nch; j++)
812: m[i][j]=m[i][j-1]+nlay;
813: }
814: return m;
815: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
816: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
817: */
818: }
819:
820: /*************************free ma3x ************************/
821: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
822: {
823: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
824: free((FREE_ARG)(m[nrl]+ncl-NR_END));
825: free((FREE_ARG)(m+nrl-NR_END));
826: }
827:
828: /*************** function subdirf ***********/
829: char *subdirf(char fileres[])
830: {
831: /* Caution optionfilefiname is hidden */
832: strcpy(tmpout,optionfilefiname);
833: strcat(tmpout,"/"); /* Add to the right */
834: strcat(tmpout,fileres);
835: return tmpout;
836: }
837:
838: /*************** function subdirf2 ***********/
839: char *subdirf2(char fileres[], char *preop)
840: {
841:
842: /* Caution optionfilefiname is hidden */
843: strcpy(tmpout,optionfilefiname);
844: strcat(tmpout,"/");
845: strcat(tmpout,preop);
846: strcat(tmpout,fileres);
847: return tmpout;
848: }
849:
850: /*************** function subdirf3 ***********/
851: char *subdirf3(char fileres[], char *preop, char *preop2)
852: {
853:
854: /* Caution optionfilefiname is hidden */
855: strcpy(tmpout,optionfilefiname);
856: strcat(tmpout,"/");
857: strcat(tmpout,preop);
858: strcat(tmpout,preop2);
859: strcat(tmpout,fileres);
860: return tmpout;
861: }
862:
863: /***************** f1dim *************************/
864: extern int ncom;
865: extern double *pcom,*xicom;
866: extern double (*nrfunc)(double []);
867:
868: double f1dim(double x)
869: {
870: int j;
871: double f;
872: double *xt;
873:
874: xt=vector(1,ncom);
875: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
876: f=(*nrfunc)(xt);
877: free_vector(xt,1,ncom);
878: return f;
879: }
880:
881: /*****************brent *************************/
882: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
883: {
884: int iter;
885: double a,b,d,etemp;
886: double fu,fv,fw,fx;
887: double ftemp;
888: double p,q,r,tol1,tol2,u,v,w,x,xm;
889: double e=0.0;
890:
891: a=(ax < cx ? ax : cx);
892: b=(ax > cx ? ax : cx);
893: x=w=v=bx;
894: fw=fv=fx=(*f)(x);
895: for (iter=1;iter<=ITMAX;iter++) {
896: xm=0.5*(a+b);
897: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
898: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
899: printf(".");fflush(stdout);
900: fprintf(ficlog,".");fflush(ficlog);
901: #ifdef DEBUG
902: 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);
903: 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);
904: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
905: #endif
906: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
907: *xmin=x;
908: return fx;
909: }
910: ftemp=fu;
911: if (fabs(e) > tol1) {
912: r=(x-w)*(fx-fv);
913: q=(x-v)*(fx-fw);
914: p=(x-v)*q-(x-w)*r;
915: q=2.0*(q-r);
916: if (q > 0.0) p = -p;
917: q=fabs(q);
918: etemp=e;
919: e=d;
920: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
921: d=CGOLD*(e=(x >= xm ? a-x : b-x));
922: else {
923: d=p/q;
924: u=x+d;
925: if (u-a < tol2 || b-u < tol2)
926: d=SIGN(tol1,xm-x);
927: }
928: } else {
929: d=CGOLD*(e=(x >= xm ? a-x : b-x));
930: }
931: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
932: fu=(*f)(u);
933: if (fu <= fx) {
934: if (u >= x) a=x; else b=x;
935: SHFT(v,w,x,u)
936: SHFT(fv,fw,fx,fu)
937: } else {
938: if (u < x) a=u; else b=u;
939: if (fu <= fw || w == x) {
940: v=w;
941: w=u;
942: fv=fw;
943: fw=fu;
944: } else if (fu <= fv || v == x || v == w) {
945: v=u;
946: fv=fu;
947: }
948: }
949: }
950: nrerror("Too many iterations in brent");
951: *xmin=x;
952: return fx;
953: }
954:
955: /****************** mnbrak ***********************/
956:
957: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
958: double (*func)(double))
959: {
960: double ulim,u,r,q, dum;
961: double fu;
962:
963: *fa=(*func)(*ax);
964: *fb=(*func)(*bx);
965: if (*fb > *fa) {
966: SHFT(dum,*ax,*bx,dum)
967: SHFT(dum,*fb,*fa,dum)
968: }
969: *cx=(*bx)+GOLD*(*bx-*ax);
970: *fc=(*func)(*cx);
971: while (*fb > *fc) {
972: r=(*bx-*ax)*(*fb-*fc);
973: q=(*bx-*cx)*(*fb-*fa);
974: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
975: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
976: ulim=(*bx)+GLIMIT*(*cx-*bx);
977: if ((*bx-u)*(u-*cx) > 0.0) {
978: fu=(*func)(u);
979: } else if ((*cx-u)*(u-ulim) > 0.0) {
980: fu=(*func)(u);
981: if (fu < *fc) {
982: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
983: SHFT(*fb,*fc,fu,(*func)(u))
984: }
985: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
986: u=ulim;
987: fu=(*func)(u);
988: } else {
989: u=(*cx)+GOLD*(*cx-*bx);
990: fu=(*func)(u);
991: }
992: SHFT(*ax,*bx,*cx,u)
993: SHFT(*fa,*fb,*fc,fu)
994: }
995: }
996:
997: /*************** linmin ************************/
998:
999: int ncom;
1000: double *pcom,*xicom;
1001: double (*nrfunc)(double []);
1002:
1003: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1004: {
1005: double brent(double ax, double bx, double cx,
1006: double (*f)(double), double tol, double *xmin);
1007: double f1dim(double x);
1008: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1009: double *fc, double (*func)(double));
1010: int j;
1011: double xx,xmin,bx,ax;
1012: double fx,fb,fa;
1013:
1014: ncom=n;
1015: pcom=vector(1,n);
1016: xicom=vector(1,n);
1017: nrfunc=func;
1018: for (j=1;j<=n;j++) {
1019: pcom[j]=p[j];
1020: xicom[j]=xi[j];
1021: }
1022: ax=0.0;
1023: xx=1.0;
1024: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1025: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1026: #ifdef DEBUG
1027: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1028: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1029: #endif
1030: for (j=1;j<=n;j++) {
1031: xi[j] *= xmin;
1032: p[j] += xi[j];
1033: }
1034: free_vector(xicom,1,n);
1035: free_vector(pcom,1,n);
1036: }
1037:
1038: char *asc_diff_time(long time_sec, char ascdiff[])
1039: {
1040: long sec_left, days, hours, minutes;
1041: days = (time_sec) / (60*60*24);
1042: sec_left = (time_sec) % (60*60*24);
1043: hours = (sec_left) / (60*60) ;
1044: sec_left = (sec_left) %(60*60);
1045: minutes = (sec_left) /60;
1046: sec_left = (sec_left) % (60);
1047: sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
1048: return ascdiff;
1049: }
1050:
1051: /*************** powell ************************/
1052: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1053: double (*func)(double []))
1054: {
1055: void linmin(double p[], double xi[], int n, double *fret,
1056: double (*func)(double []));
1057: int i,ibig,j;
1058: double del,t,*pt,*ptt,*xit;
1059: double fp,fptt;
1060: double *xits;
1061: int niterf, itmp;
1062:
1063: pt=vector(1,n);
1064: ptt=vector(1,n);
1065: xit=vector(1,n);
1066: xits=vector(1,n);
1067: *fret=(*func)(p);
1068: for (j=1;j<=n;j++) pt[j]=p[j];
1069: for (*iter=1;;++(*iter)) {
1070: fp=(*fret);
1071: ibig=0;
1072: del=0.0;
1073: last_time=curr_time;
1074: (void) gettimeofday(&curr_time,&tzp);
1075: 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);
1076: 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);
1077: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1078: for (i=1;i<=n;i++) {
1079: printf(" %d %.12f",i, p[i]);
1080: fprintf(ficlog," %d %.12lf",i, p[i]);
1081: fprintf(ficrespow," %.12lf", p[i]);
1082: }
1083: printf("\n");
1084: fprintf(ficlog,"\n");
1085: fprintf(ficrespow,"\n");fflush(ficrespow);
1086: if(*iter <=3){
1087: tm = *localtime(&curr_time.tv_sec);
1088: strcpy(strcurr,asctime(&tm));
1089: /* asctime_r(&tm,strcurr); */
1090: forecast_time=curr_time;
1091: itmp = strlen(strcurr);
1092: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1093: strcurr[itmp-1]='\0';
1094: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1095: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1096: for(niterf=10;niterf<=30;niterf+=10){
1097: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1098: tmf = *localtime(&forecast_time.tv_sec);
1099: /* asctime_r(&tmf,strfor); */
1100: strcpy(strfor,asctime(&tmf));
1101: itmp = strlen(strfor);
1102: if(strfor[itmp-1]=='\n')
1103: strfor[itmp-1]='\0';
1104: 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);
1105: 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);
1106: }
1107: }
1108: for (i=1;i<=n;i++) {
1109: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1110: fptt=(*fret);
1111: #ifdef DEBUG
1112: printf("fret=%lf \n",*fret);
1113: fprintf(ficlog,"fret=%lf \n",*fret);
1114: #endif
1115: printf("%d",i);fflush(stdout);
1116: fprintf(ficlog,"%d",i);fflush(ficlog);
1117: linmin(p,xit,n,fret,func);
1118: if (fabs(fptt-(*fret)) > del) {
1119: del=fabs(fptt-(*fret));
1120: ibig=i;
1121: }
1122: #ifdef DEBUG
1123: printf("%d %.12e",i,(*fret));
1124: fprintf(ficlog,"%d %.12e",i,(*fret));
1125: for (j=1;j<=n;j++) {
1126: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1127: printf(" x(%d)=%.12e",j,xit[j]);
1128: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1129: }
1130: for(j=1;j<=n;j++) {
1131: printf(" p=%.12e",p[j]);
1132: fprintf(ficlog," p=%.12e",p[j]);
1133: }
1134: printf("\n");
1135: fprintf(ficlog,"\n");
1136: #endif
1137: }
1138: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1139: #ifdef DEBUG
1140: int k[2],l;
1141: k[0]=1;
1142: k[1]=-1;
1143: printf("Max: %.12e",(*func)(p));
1144: fprintf(ficlog,"Max: %.12e",(*func)(p));
1145: for (j=1;j<=n;j++) {
1146: printf(" %.12e",p[j]);
1147: fprintf(ficlog," %.12e",p[j]);
1148: }
1149: printf("\n");
1150: fprintf(ficlog,"\n");
1151: for(l=0;l<=1;l++) {
1152: for (j=1;j<=n;j++) {
1153: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1154: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1155: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1156: }
1157: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1158: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1159: }
1160: #endif
1161:
1162:
1163: free_vector(xit,1,n);
1164: free_vector(xits,1,n);
1165: free_vector(ptt,1,n);
1166: free_vector(pt,1,n);
1167: return;
1168: }
1169: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1170: for (j=1;j<=n;j++) {
1171: ptt[j]=2.0*p[j]-pt[j];
1172: xit[j]=p[j]-pt[j];
1173: pt[j]=p[j];
1174: }
1175: fptt=(*func)(ptt);
1176: if (fptt < fp) {
1177: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1178: if (t < 0.0) {
1179: linmin(p,xit,n,fret,func);
1180: for (j=1;j<=n;j++) {
1181: xi[j][ibig]=xi[j][n];
1182: xi[j][n]=xit[j];
1183: }
1184: #ifdef DEBUG
1185: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1186: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1187: for(j=1;j<=n;j++){
1188: printf(" %.12e",xit[j]);
1189: fprintf(ficlog," %.12e",xit[j]);
1190: }
1191: printf("\n");
1192: fprintf(ficlog,"\n");
1193: #endif
1194: }
1195: }
1196: }
1197: }
1198:
1199: /**** Prevalence limit (stable or period prevalence) ****************/
1200:
1201: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1202: {
1203: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1204: matrix by transitions matrix until convergence is reached */
1205:
1206: int i, ii,j,k;
1207: double min, max, maxmin, maxmax,sumnew=0.;
1208: double **matprod2();
1.131 brouard 1209: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1210: double **newm;
1211: double agefin, delaymax=50 ; /* Max number of years to converge */
1212:
1213: for (ii=1;ii<=nlstate+ndeath;ii++)
1214: for (j=1;j<=nlstate+ndeath;j++){
1215: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1216: }
1217:
1218: cov[1]=1.;
1219:
1220: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1221: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1222: newm=savm;
1223: /* Covariates have to be included here again */
1224: cov[2]=agefin;
1225:
1226: for (k=1; k<=cptcovn;k++) {
1227: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1228: /* 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]]);*/
1229: }
1230: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1231: for (k=1; k<=cptcovprod;k++)
1.136 ! brouard 1232: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 1233:
1234: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1235: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1236: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1237: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
1238:
1239: savm=oldm;
1240: oldm=newm;
1241: maxmax=0.;
1242: for(j=1;j<=nlstate;j++){
1243: min=1.;
1244: max=0.;
1245: for(i=1; i<=nlstate; i++) {
1246: sumnew=0;
1247: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1248: prlim[i][j]= newm[i][j]/(1-sumnew);
1249: max=FMAX(max,prlim[i][j]);
1250: min=FMIN(min,prlim[i][j]);
1251: }
1252: maxmin=max-min;
1253: maxmax=FMAX(maxmax,maxmin);
1254: }
1255: if(maxmax < ftolpl){
1256: return prlim;
1257: }
1258: }
1259: }
1260:
1261: /*************** transition probabilities ***************/
1262:
1263: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1264: {
1265: double s1, s2;
1266: /*double t34;*/
1267: int i,j,j1, nc, ii, jj;
1268:
1269: for(i=1; i<= nlstate; i++){
1270: for(j=1; j<i;j++){
1271: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1272: /*s2 += param[i][j][nc]*cov[nc];*/
1273: s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1274: /* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
1275: }
1276: ps[i][j]=s2;
1277: /* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
1278: }
1279: for(j=i+1; j<=nlstate+ndeath;j++){
1280: for (nc=1, s2=0.;nc <=ncovmodel; nc++){
1281: s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
1282: /* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
1283: }
1284: ps[i][j]=s2;
1285: }
1286: }
1287: /*ps[3][2]=1;*/
1288:
1289: for(i=1; i<= nlstate; i++){
1290: s1=0;
1.131 brouard 1291: for(j=1; j<i; j++){
1.126 brouard 1292: s1+=exp(ps[i][j]);
1.131 brouard 1293: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1294: }
1295: for(j=i+1; j<=nlstate+ndeath; j++){
1.126 brouard 1296: s1+=exp(ps[i][j]);
1.131 brouard 1297: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1298: }
1.126 brouard 1299: ps[i][i]=1./(s1+1.);
1300: for(j=1; j<i; j++)
1301: ps[i][j]= exp(ps[i][j])*ps[i][i];
1302: for(j=i+1; j<=nlstate+ndeath; j++)
1303: ps[i][j]= exp(ps[i][j])*ps[i][i];
1304: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1305: } /* end i */
1306:
1307: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1308: for(jj=1; jj<= nlstate+ndeath; jj++){
1309: ps[ii][jj]=0;
1310: ps[ii][ii]=1;
1311: }
1312: }
1313:
1314:
1315: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1316: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1317: /* printf("ddd %lf ",ps[ii][jj]); */
1318: /* } */
1319: /* printf("\n "); */
1320: /* } */
1321: /* printf("\n ");printf("%lf ",cov[2]); */
1322: /*
1323: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1324: goto end;*/
1325: return ps;
1326: }
1327:
1328: /**************** Product of 2 matrices ******************/
1329:
1330: double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
1331: {
1332: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1333: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1334: /* in, b, out are matrice of pointers which should have been initialized
1335: before: only the contents of out is modified. The function returns
1336: a pointer to pointers identical to out */
1337: long i, j, k;
1338: for(i=nrl; i<= nrh; i++)
1339: for(k=ncolol; k<=ncoloh; k++)
1340: for(j=ncl,out[i][k]=0.; j<=nch; j++)
1341: out[i][k] +=in[i][j]*b[j][k];
1342:
1343: return out;
1344: }
1345:
1346:
1347: /************* Higher Matrix Product ***************/
1348:
1349: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1350: {
1351: /* Computes the transition matrix starting at age 'age' over
1352: 'nhstepm*hstepm*stepm' months (i.e. until
1353: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1354: nhstepm*hstepm matrices.
1355: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1356: (typically every 2 years instead of every month which is too big
1357: for the memory).
1358: Model is determined by parameters x and covariates have to be
1359: included manually here.
1360:
1361: */
1362:
1363: int i, j, d, h, k;
1.131 brouard 1364: double **out, cov[NCOVMAX+1];
1.126 brouard 1365: double **newm;
1366:
1367: /* Hstepm could be zero and should return the unit matrix */
1368: for (i=1;i<=nlstate+ndeath;i++)
1369: for (j=1;j<=nlstate+ndeath;j++){
1370: oldm[i][j]=(i==j ? 1.0 : 0.0);
1371: po[i][j][0]=(i==j ? 1.0 : 0.0);
1372: }
1373: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1374: for(h=1; h <=nhstepm; h++){
1375: for(d=1; d <=hstepm; d++){
1376: newm=savm;
1377: /* Covariates have to be included here again */
1378: cov[1]=1.;
1379: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1380: for (k=1; k<=cptcovn;k++)
1381: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1382: for (k=1; k<=cptcovage;k++)
1383: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1384: for (k=1; k<=cptcovprod;k++)
1385: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1386:
1387:
1388: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1389: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1390: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1391: pmij(pmmij,cov,ncovmodel,x,nlstate));
1392: savm=oldm;
1393: oldm=newm;
1394: }
1395: for(i=1; i<=nlstate+ndeath; i++)
1396: for(j=1;j<=nlstate+ndeath;j++) {
1397: po[i][j][h]=newm[i][j];
1.128 brouard 1398: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1399: }
1.128 brouard 1400: /*printf("h=%d ",h);*/
1.126 brouard 1401: } /* end h */
1.128 brouard 1402: /* printf("\n H=%d \n",h); */
1.126 brouard 1403: return po;
1404: }
1405:
1406:
1407: /*************** log-likelihood *************/
1408: double func( double *x)
1409: {
1410: int i, ii, j, k, mi, d, kk;
1.131 brouard 1411: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1412: double **out;
1413: double sw; /* Sum of weights */
1414: double lli; /* Individual log likelihood */
1415: int s1, s2;
1416: double bbh, survp;
1417: long ipmx;
1418: /*extern weight */
1419: /* We are differentiating ll according to initial status */
1420: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1421: /*for(i=1;i<imx;i++)
1422: printf(" %d\n",s[4][i]);
1423: */
1424: cov[1]=1.;
1425:
1426: for(k=1; k<=nlstate; k++) ll[k]=0.;
1427:
1428: if(mle==1){
1429: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1430: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1431: for(mi=1; mi<= wav[i]-1; mi++){
1432: for (ii=1;ii<=nlstate+ndeath;ii++)
1433: for (j=1;j<=nlstate+ndeath;j++){
1434: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1435: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1436: }
1437: for(d=0; d<dh[mi][i]; d++){
1438: newm=savm;
1439: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1440: for (kk=1; kk<=cptcovage;kk++) {
1441: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1442: }
1443: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1444: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1445: savm=oldm;
1446: oldm=newm;
1447: } /* end mult */
1448:
1449: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1450: /* But now since version 0.9 we anticipate for bias at large stepm.
1451: * If stepm is larger than one month (smallest stepm) and if the exact delay
1452: * (in months) between two waves is not a multiple of stepm, we rounded to
1453: * the nearest (and in case of equal distance, to the lowest) interval but now
1454: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1455: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1456: * probability in order to take into account the bias as a fraction of the way
1457: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1458: * -stepm/2 to stepm/2 .
1459: * For stepm=1 the results are the same as for previous versions of Imach.
1460: * For stepm > 1 the results are less biased than in previous versions.
1461: */
1462: s1=s[mw[mi][i]][i];
1463: s2=s[mw[mi+1][i]][i];
1464: bbh=(double)bh[mi][i]/(double)stepm;
1465: /* bias bh is positive if real duration
1466: * is higher than the multiple of stepm and negative otherwise.
1467: */
1468: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1469: if( s2 > nlstate){
1470: /* i.e. if s2 is a death state and if the date of death is known
1471: then the contribution to the likelihood is the probability to
1472: die between last step unit time and current step unit time,
1473: which is also equal to probability to die before dh
1474: minus probability to die before dh-stepm .
1475: In version up to 0.92 likelihood was computed
1476: as if date of death was unknown. Death was treated as any other
1477: health state: the date of the interview describes the actual state
1478: and not the date of a change in health state. The former idea was
1479: to consider that at each interview the state was recorded
1480: (healthy, disable or death) and IMaCh was corrected; but when we
1481: introduced the exact date of death then we should have modified
1482: the contribution of an exact death to the likelihood. This new
1483: contribution is smaller and very dependent of the step unit
1484: stepm. It is no more the probability to die between last interview
1485: and month of death but the probability to survive from last
1486: interview up to one month before death multiplied by the
1487: probability to die within a month. Thanks to Chris
1488: Jackson for correcting this bug. Former versions increased
1489: mortality artificially. The bad side is that we add another loop
1490: which slows down the processing. The difference can be up to 10%
1491: lower mortality.
1492: */
1493: lli=log(out[s1][s2] - savm[s1][s2]);
1494:
1495:
1496: } else if (s2==-2) {
1497: for (j=1,survp=0. ; j<=nlstate; j++)
1498: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1499: /*survp += out[s1][j]; */
1500: lli= log(survp);
1501: }
1502:
1503: else if (s2==-4) {
1504: for (j=3,survp=0. ; j<=nlstate; j++)
1505: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1506: lli= log(survp);
1507: }
1508:
1509: else if (s2==-5) {
1510: for (j=1,survp=0. ; j<=2; j++)
1511: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1512: lli= log(survp);
1513: }
1514:
1515: else{
1516: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1517: /* 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 */
1518: }
1519: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1520: /*if(lli ==000.0)*/
1521: /*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); */
1522: ipmx +=1;
1523: sw += weight[i];
1524: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1525: } /* end of wave */
1526: } /* end of individual */
1527: } else if(mle==2){
1528: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1529: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1530: for(mi=1; mi<= wav[i]-1; mi++){
1531: for (ii=1;ii<=nlstate+ndeath;ii++)
1532: for (j=1;j<=nlstate+ndeath;j++){
1533: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1534: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1535: }
1536: for(d=0; d<=dh[mi][i]; d++){
1537: newm=savm;
1538: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1539: for (kk=1; kk<=cptcovage;kk++) {
1540: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1541: }
1542: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1543: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1544: savm=oldm;
1545: oldm=newm;
1546: } /* end mult */
1547:
1548: s1=s[mw[mi][i]][i];
1549: s2=s[mw[mi+1][i]][i];
1550: bbh=(double)bh[mi][i]/(double)stepm;
1551: 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 */
1552: ipmx +=1;
1553: sw += weight[i];
1554: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1555: } /* end of wave */
1556: } /* end of individual */
1557: } else if(mle==3){ /* exponential inter-extrapolation */
1558: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1559: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1560: for(mi=1; mi<= wav[i]-1; mi++){
1561: for (ii=1;ii<=nlstate+ndeath;ii++)
1562: for (j=1;j<=nlstate+ndeath;j++){
1563: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1564: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1565: }
1566: for(d=0; d<dh[mi][i]; d++){
1567: newm=savm;
1568: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1569: for (kk=1; kk<=cptcovage;kk++) {
1570: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1571: }
1572: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1573: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1574: savm=oldm;
1575: oldm=newm;
1576: } /* end mult */
1577:
1578: s1=s[mw[mi][i]][i];
1579: s2=s[mw[mi+1][i]][i];
1580: bbh=(double)bh[mi][i]/(double)stepm;
1581: 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 */
1582: ipmx +=1;
1583: sw += weight[i];
1584: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1585: } /* end of wave */
1586: } /* end of individual */
1587: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1588: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1589: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1590: for(mi=1; mi<= wav[i]-1; mi++){
1591: for (ii=1;ii<=nlstate+ndeath;ii++)
1592: for (j=1;j<=nlstate+ndeath;j++){
1593: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1594: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1595: }
1596: for(d=0; d<dh[mi][i]; d++){
1597: newm=savm;
1598: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1599: for (kk=1; kk<=cptcovage;kk++) {
1600: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1601: }
1602:
1603: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1604: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1605: savm=oldm;
1606: oldm=newm;
1607: } /* end mult */
1608:
1609: s1=s[mw[mi][i]][i];
1610: s2=s[mw[mi+1][i]][i];
1611: if( s2 > nlstate){
1612: lli=log(out[s1][s2] - savm[s1][s2]);
1613: }else{
1614: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1615: }
1616: ipmx +=1;
1617: sw += weight[i];
1618: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1619: /* 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]); */
1620: } /* end of wave */
1621: } /* end of individual */
1622: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1623: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1624: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1625: for(mi=1; mi<= wav[i]-1; mi++){
1626: for (ii=1;ii<=nlstate+ndeath;ii++)
1627: for (j=1;j<=nlstate+ndeath;j++){
1628: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1629: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1630: }
1631: for(d=0; d<dh[mi][i]; d++){
1632: newm=savm;
1633: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1634: for (kk=1; kk<=cptcovage;kk++) {
1635: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1636: }
1637:
1638: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1639: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1640: savm=oldm;
1641: oldm=newm;
1642: } /* end mult */
1643:
1644: s1=s[mw[mi][i]][i];
1645: s2=s[mw[mi+1][i]][i];
1646: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1647: ipmx +=1;
1648: sw += weight[i];
1649: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1650: /*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]);*/
1651: } /* end of wave */
1652: } /* end of individual */
1653: } /* End of if */
1654: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1655: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1656: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1657: return -l;
1658: }
1659:
1660: /*************** log-likelihood *************/
1661: double funcone( double *x)
1662: {
1663: /* Same as likeli but slower because of a lot of printf and if */
1664: int i, ii, j, k, mi, d, kk;
1.131 brouard 1665: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1666: double **out;
1667: double lli; /* Individual log likelihood */
1668: double llt;
1669: int s1, s2;
1670: double bbh, survp;
1671: /*extern weight */
1672: /* We are differentiating ll according to initial status */
1673: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1674: /*for(i=1;i<imx;i++)
1675: printf(" %d\n",s[4][i]);
1676: */
1677: cov[1]=1.;
1678:
1679: for(k=1; k<=nlstate; k++) ll[k]=0.;
1680:
1681: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1682: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1683: for(mi=1; mi<= wav[i]-1; mi++){
1684: for (ii=1;ii<=nlstate+ndeath;ii++)
1685: for (j=1;j<=nlstate+ndeath;j++){
1686: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1687: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1688: }
1689: for(d=0; d<dh[mi][i]; d++){
1690: newm=savm;
1691: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1692: for (kk=1; kk<=cptcovage;kk++) {
1693: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1694: }
1695: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1696: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1697: savm=oldm;
1698: oldm=newm;
1699: } /* end mult */
1700:
1701: s1=s[mw[mi][i]][i];
1702: s2=s[mw[mi+1][i]][i];
1703: bbh=(double)bh[mi][i]/(double)stepm;
1704: /* bias is positive if real duration
1705: * is higher than the multiple of stepm and negative otherwise.
1706: */
1707: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1708: lli=log(out[s1][s2] - savm[s1][s2]);
1709: } else if (s2==-2) {
1710: for (j=1,survp=0. ; j<=nlstate; j++)
1711: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1712: lli= log(survp);
1713: }else if (mle==1){
1714: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1715: } else if(mle==2){
1716: 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 */
1717: } else if(mle==3){ /* exponential inter-extrapolation */
1718: 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 */
1719: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1720: lli=log(out[s1][s2]); /* Original formula */
1.136 ! brouard 1721: } else{ /* mle=0 back to 1 */
! 1722: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
! 1723: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 1724: } /* End of if */
1725: ipmx +=1;
1726: sw += weight[i];
1727: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 1728: /*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]); */
1.126 brouard 1729: if(globpr){
1730: fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1731: %11.6f %11.6f %11.6f ", \
1732: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1733: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1734: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1735: llt +=ll[k]*gipmx/gsw;
1736: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1737: }
1738: fprintf(ficresilk," %10.6f\n", -llt);
1739: }
1740: } /* end of wave */
1741: } /* end of individual */
1742: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1743: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1744: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1745: if(globpr==0){ /* First time we count the contributions and weights */
1746: gipmx=ipmx;
1747: gsw=sw;
1748: }
1749: return -l;
1750: }
1751:
1752:
1753: /*************** function likelione ***********/
1754: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1755: {
1756: /* This routine should help understanding what is done with
1757: the selection of individuals/waves and
1758: to check the exact contribution to the likelihood.
1759: Plotting could be done.
1760: */
1761: int k;
1762:
1763: if(*globpri !=0){ /* Just counts and sums, no printings */
1764: strcpy(fileresilk,"ilk");
1765: strcat(fileresilk,fileres);
1766: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1767: printf("Problem with resultfile: %s\n", fileresilk);
1768: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1769: }
1770: 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");
1771: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1772: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1773: for(k=1; k<=nlstate; k++)
1774: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1775: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1776: }
1777:
1778: *fretone=(*funcone)(p);
1779: if(*globpri !=0){
1780: fclose(ficresilk);
1781: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1782: fflush(fichtm);
1783: }
1784: return;
1785: }
1786:
1787:
1788: /*********** Maximum Likelihood Estimation ***************/
1789:
1790: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1791: {
1792: int i,j, iter;
1793: double **xi;
1794: double fret;
1795: double fretone; /* Only one call to likelihood */
1796: /* char filerespow[FILENAMELENGTH];*/
1797: xi=matrix(1,npar,1,npar);
1798: for (i=1;i<=npar;i++)
1799: for (j=1;j<=npar;j++)
1800: xi[i][j]=(i==j ? 1.0 : 0.0);
1801: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1802: strcpy(filerespow,"pow");
1803: strcat(filerespow,fileres);
1804: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1805: printf("Problem with resultfile: %s\n", filerespow);
1806: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1807: }
1808: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1809: for (i=1;i<=nlstate;i++)
1810: for(j=1;j<=nlstate+ndeath;j++)
1811: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
1812: fprintf(ficrespow,"\n");
1813:
1814: powell(p,xi,npar,ftol,&iter,&fret,func);
1815:
1816: free_matrix(xi,1,npar,1,npar);
1817: fclose(ficrespow);
1818: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
1819: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1820: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
1821:
1822: }
1823:
1824: /**** Computes Hessian and covariance matrix ***/
1825: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1826: {
1827: double **a,**y,*x,pd;
1828: double **hess;
1829: int i, j,jk;
1830: int *indx;
1831:
1832: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1833: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
1834: void lubksb(double **a, int npar, int *indx, double b[]) ;
1835: void ludcmp(double **a, int npar, int *indx, double *d) ;
1836: double gompertz(double p[]);
1837: hess=matrix(1,npar,1,npar);
1838:
1839: printf("\nCalculation of the hessian matrix. Wait...\n");
1840: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
1841: for (i=1;i<=npar;i++){
1842: printf("%d",i);fflush(stdout);
1843: fprintf(ficlog,"%d",i);fflush(ficlog);
1844:
1845: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
1846:
1847: /* printf(" %f ",p[i]);
1848: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
1849: }
1850:
1851: for (i=1;i<=npar;i++) {
1852: for (j=1;j<=npar;j++) {
1853: if (j>i) {
1854: printf(".%d%d",i,j);fflush(stdout);
1855: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
1856: hess[i][j]=hessij(p,delti,i,j,func,npar);
1857:
1858: hess[j][i]=hess[i][j];
1859: /*printf(" %lf ",hess[i][j]);*/
1860: }
1861: }
1862: }
1863: printf("\n");
1864: fprintf(ficlog,"\n");
1865:
1866: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
1867: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
1868:
1869: a=matrix(1,npar,1,npar);
1870: y=matrix(1,npar,1,npar);
1871: x=vector(1,npar);
1872: indx=ivector(1,npar);
1873: for (i=1;i<=npar;i++)
1874: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
1875: ludcmp(a,npar,indx,&pd);
1876:
1877: for (j=1;j<=npar;j++) {
1878: for (i=1;i<=npar;i++) x[i]=0;
1879: x[j]=1;
1880: lubksb(a,npar,indx,x);
1881: for (i=1;i<=npar;i++){
1882: matcov[i][j]=x[i];
1883: }
1884: }
1885:
1886: printf("\n#Hessian matrix#\n");
1887: fprintf(ficlog,"\n#Hessian matrix#\n");
1888: for (i=1;i<=npar;i++) {
1889: for (j=1;j<=npar;j++) {
1890: printf("%.3e ",hess[i][j]);
1891: fprintf(ficlog,"%.3e ",hess[i][j]);
1892: }
1893: printf("\n");
1894: fprintf(ficlog,"\n");
1895: }
1896:
1897: /* Recompute Inverse */
1898: for (i=1;i<=npar;i++)
1899: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
1900: ludcmp(a,npar,indx,&pd);
1901:
1902: /* printf("\n#Hessian matrix recomputed#\n");
1903:
1904: for (j=1;j<=npar;j++) {
1905: for (i=1;i<=npar;i++) x[i]=0;
1906: x[j]=1;
1907: lubksb(a,npar,indx,x);
1908: for (i=1;i<=npar;i++){
1909: y[i][j]=x[i];
1910: printf("%.3e ",y[i][j]);
1911: fprintf(ficlog,"%.3e ",y[i][j]);
1912: }
1913: printf("\n");
1914: fprintf(ficlog,"\n");
1915: }
1916: */
1917:
1918: free_matrix(a,1,npar,1,npar);
1919: free_matrix(y,1,npar,1,npar);
1920: free_vector(x,1,npar);
1921: free_ivector(indx,1,npar);
1922: free_matrix(hess,1,npar,1,npar);
1923:
1924:
1925: }
1926:
1927: /*************** hessian matrix ****************/
1928: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1929: {
1930: int i;
1931: int l=1, lmax=20;
1932: double k1,k2;
1.132 brouard 1933: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 1934: double res;
1935: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
1936: double fx;
1937: int k=0,kmax=10;
1938: double l1;
1939:
1940: fx=func(x);
1941: for (i=1;i<=npar;i++) p2[i]=x[i];
1942: for(l=0 ; l <=lmax; l++){
1943: l1=pow(10,l);
1944: delts=delt;
1945: for(k=1 ; k <kmax; k=k+1){
1946: delt = delta*(l1*k);
1947: p2[theta]=x[theta] +delt;
1948: k1=func(p2)-fx;
1949: p2[theta]=x[theta]-delt;
1950: k2=func(p2)-fx;
1951: /*res= (k1-2.0*fx+k2)/delt/delt; */
1952: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
1953:
1.132 brouard 1954: #ifdef DEBUGHESS
1.126 brouard 1955: 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);
1956: 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);
1957: #endif
1958: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
1959: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
1960: k=kmax;
1961: }
1962: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1963: k=kmax; l=lmax*10.;
1964: }
1965: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
1966: delts=delt;
1967: }
1968: }
1969: }
1970: delti[theta]=delts;
1971: return res;
1972:
1973: }
1974:
1975: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1976: {
1977: int i;
1978: int l=1, l1, lmax=20;
1979: double k1,k2,k3,k4,res,fx;
1.132 brouard 1980: double p2[MAXPARM+1];
1.126 brouard 1981: int k;
1982:
1983: fx=func(x);
1984: for (k=1; k<=2; k++) {
1985: for (i=1;i<=npar;i++) p2[i]=x[i];
1986: p2[thetai]=x[thetai]+delti[thetai]/k;
1987: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1988: k1=func(p2)-fx;
1989:
1990: p2[thetai]=x[thetai]+delti[thetai]/k;
1991: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
1992: k2=func(p2)-fx;
1993:
1994: p2[thetai]=x[thetai]-delti[thetai]/k;
1995: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
1996: k3=func(p2)-fx;
1997:
1998: p2[thetai]=x[thetai]-delti[thetai]/k;
1999: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2000: k4=func(p2)-fx;
2001: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2002: #ifdef DEBUG
2003: 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);
2004: 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);
2005: #endif
2006: }
2007: return res;
2008: }
2009:
2010: /************** Inverse of matrix **************/
2011: void ludcmp(double **a, int n, int *indx, double *d)
2012: {
2013: int i,imax,j,k;
2014: double big,dum,sum,temp;
2015: double *vv;
2016:
2017: vv=vector(1,n);
2018: *d=1.0;
2019: for (i=1;i<=n;i++) {
2020: big=0.0;
2021: for (j=1;j<=n;j++)
2022: if ((temp=fabs(a[i][j])) > big) big=temp;
2023: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2024: vv[i]=1.0/big;
2025: }
2026: for (j=1;j<=n;j++) {
2027: for (i=1;i<j;i++) {
2028: sum=a[i][j];
2029: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2030: a[i][j]=sum;
2031: }
2032: big=0.0;
2033: for (i=j;i<=n;i++) {
2034: sum=a[i][j];
2035: for (k=1;k<j;k++)
2036: sum -= a[i][k]*a[k][j];
2037: a[i][j]=sum;
2038: if ( (dum=vv[i]*fabs(sum)) >= big) {
2039: big=dum;
2040: imax=i;
2041: }
2042: }
2043: if (j != imax) {
2044: for (k=1;k<=n;k++) {
2045: dum=a[imax][k];
2046: a[imax][k]=a[j][k];
2047: a[j][k]=dum;
2048: }
2049: *d = -(*d);
2050: vv[imax]=vv[j];
2051: }
2052: indx[j]=imax;
2053: if (a[j][j] == 0.0) a[j][j]=TINY;
2054: if (j != n) {
2055: dum=1.0/(a[j][j]);
2056: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2057: }
2058: }
2059: free_vector(vv,1,n); /* Doesn't work */
2060: ;
2061: }
2062:
2063: void lubksb(double **a, int n, int *indx, double b[])
2064: {
2065: int i,ii=0,ip,j;
2066: double sum;
2067:
2068: for (i=1;i<=n;i++) {
2069: ip=indx[i];
2070: sum=b[ip];
2071: b[ip]=b[i];
2072: if (ii)
2073: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2074: else if (sum) ii=i;
2075: b[i]=sum;
2076: }
2077: for (i=n;i>=1;i--) {
2078: sum=b[i];
2079: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2080: b[i]=sum/a[i][i];
2081: }
2082: }
2083:
2084: void pstamp(FILE *fichier)
2085: {
2086: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2087: }
2088:
2089: /************ Frequencies ********************/
2090: 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[])
2091: { /* Some frequencies */
2092:
1.130 brouard 2093: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2094: int first;
2095: double ***freq; /* Frequencies */
2096: double *pp, **prop;
2097: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2098: char fileresp[FILENAMELENGTH];
2099:
2100: pp=vector(1,nlstate);
2101: prop=matrix(1,nlstate,iagemin,iagemax+3);
2102: strcpy(fileresp,"p");
2103: strcat(fileresp,fileres);
2104: if((ficresp=fopen(fileresp,"w"))==NULL) {
2105: printf("Problem with prevalence resultfile: %s\n", fileresp);
2106: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2107: exit(0);
2108: }
2109: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2110: j1=0;
2111:
2112: j=cptcoveff;
2113: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2114:
2115: first=1;
2116:
2117: for(k1=1; k1<=j;k1++){
2118: for(i1=1; i1<=ncodemax[k1];i1++){
2119: j1++;
2120: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2121: scanf("%d", i);*/
2122: for (i=-5; i<=nlstate+ndeath; i++)
2123: for (jk=-5; jk<=nlstate+ndeath; jk++)
2124: for(m=iagemin; m <= iagemax+3; m++)
2125: freq[i][jk][m]=0;
2126:
2127: for (i=1; i<=nlstate; i++)
2128: for(m=iagemin; m <= iagemax+3; m++)
2129: prop[i][m]=0;
2130:
2131: dateintsum=0;
2132: k2cpt=0;
2133: for (i=1; i<=imx; i++) {
2134: bool=1;
2135: if (cptcovn>0) {
2136: for (z1=1; z1<=cptcoveff; z1++)
2137: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2138: bool=0;
2139: }
2140: if (bool==1){
2141: for(m=firstpass; m<=lastpass; m++){
2142: k2=anint[m][i]+(mint[m][i]/12.);
2143: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2144: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2145: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2146: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2147: if (m<lastpass) {
2148: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2149: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2150: }
2151:
2152: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2153: dateintsum=dateintsum+k2;
2154: k2cpt++;
2155: }
2156: /*}*/
2157: }
2158: }
2159: }
2160:
2161: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2162: pstamp(ficresp);
2163: if (cptcovn>0) {
2164: fprintf(ficresp, "\n#********** Variable ");
2165: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2166: fprintf(ficresp, "**********\n#");
2167: }
2168: for(i=1; i<=nlstate;i++)
2169: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2170: fprintf(ficresp, "\n");
2171:
2172: for(i=iagemin; i <= iagemax+3; i++){
2173: if(i==iagemax+3){
2174: fprintf(ficlog,"Total");
2175: }else{
2176: if(first==1){
2177: first=0;
2178: printf("See log file for details...\n");
2179: }
2180: fprintf(ficlog,"Age %d", i);
2181: }
2182: for(jk=1; jk <=nlstate ; jk++){
2183: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2184: pp[jk] += freq[jk][m][i];
2185: }
2186: for(jk=1; jk <=nlstate ; jk++){
2187: for(m=-1, pos=0; m <=0 ; m++)
2188: pos += freq[jk][m][i];
2189: if(pp[jk]>=1.e-10){
2190: if(first==1){
1.132 brouard 2191: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2192: }
2193: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2194: }else{
2195: if(first==1)
2196: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2197: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2198: }
2199: }
2200:
2201: for(jk=1; jk <=nlstate ; jk++){
2202: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2203: pp[jk] += freq[jk][m][i];
2204: }
2205: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2206: pos += pp[jk];
2207: posprop += prop[jk][i];
2208: }
2209: for(jk=1; jk <=nlstate ; jk++){
2210: if(pos>=1.e-5){
2211: if(first==1)
2212: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2213: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2214: }else{
2215: if(first==1)
2216: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2217: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2218: }
2219: if( i <= iagemax){
2220: if(pos>=1.e-5){
2221: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2222: /*probs[i][jk][j1]= pp[jk]/pos;*/
2223: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2224: }
2225: else
2226: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2227: }
2228: }
2229:
2230: for(jk=-1; jk <=nlstate+ndeath; jk++)
2231: for(m=-1; m <=nlstate+ndeath; m++)
2232: if(freq[jk][m][i] !=0 ) {
2233: if(first==1)
2234: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2235: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2236: }
2237: if(i <= iagemax)
2238: fprintf(ficresp,"\n");
2239: if(first==1)
2240: printf("Others in log...\n");
2241: fprintf(ficlog,"\n");
2242: }
2243: }
2244: }
2245: dateintmean=dateintsum/k2cpt;
2246:
2247: fclose(ficresp);
2248: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2249: free_vector(pp,1,nlstate);
2250: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2251: /* End of Freq */
2252: }
2253:
2254: /************ Prevalence ********************/
2255: 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)
2256: {
2257: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2258: in each health status at the date of interview (if between dateprev1 and dateprev2).
2259: We still use firstpass and lastpass as another selection.
2260: */
2261:
1.130 brouard 2262: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2263: double ***freq; /* Frequencies */
2264: double *pp, **prop;
2265: double pos,posprop;
2266: double y2; /* in fractional years */
2267: int iagemin, iagemax;
2268:
2269: iagemin= (int) agemin;
2270: iagemax= (int) agemax;
2271: /*pp=vector(1,nlstate);*/
2272: prop=matrix(1,nlstate,iagemin,iagemax+3);
2273: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2274: j1=0;
2275:
2276: j=cptcoveff;
2277: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2278:
2279: for(k1=1; k1<=j;k1++){
2280: for(i1=1; i1<=ncodemax[k1];i1++){
2281: j1++;
2282:
2283: for (i=1; i<=nlstate; i++)
2284: for(m=iagemin; m <= iagemax+3; m++)
2285: prop[i][m]=0.0;
2286:
2287: for (i=1; i<=imx; i++) { /* Each individual */
2288: bool=1;
2289: if (cptcovn>0) {
2290: for (z1=1; z1<=cptcoveff; z1++)
2291: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2292: bool=0;
2293: }
2294: if (bool==1) {
2295: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2296: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2297: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2298: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2299: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2300: 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);
2301: if (s[m][i]>0 && s[m][i]<=nlstate) {
2302: /*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]]);*/
2303: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2304: prop[s[m][i]][iagemax+3] += weight[i];
2305: }
2306: }
2307: } /* end selection of waves */
2308: }
2309: }
2310: for(i=iagemin; i <= iagemax+3; i++){
2311:
2312: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2313: posprop += prop[jk][i];
2314: }
2315:
2316: for(jk=1; jk <=nlstate ; jk++){
2317: if( i <= iagemax){
2318: if(posprop>=1.e-5){
2319: probs[i][jk][j1]= prop[jk][i]/posprop;
1.128 brouard 2320: } else
2321: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
1.126 brouard 2322: }
2323: }/* end jk */
2324: }/* end i */
2325: } /* end i1 */
2326: } /* end k1 */
2327:
2328: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2329: /*free_vector(pp,1,nlstate);*/
2330: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2331: } /* End of prevalence */
2332:
2333: /************* Waves Concatenation ***************/
2334:
2335: 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)
2336: {
2337: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2338: Death is a valid wave (if date is known).
2339: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2340: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2341: and mw[mi+1][i]. dh depends on stepm.
2342: */
2343:
2344: int i, mi, m;
2345: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2346: double sum=0., jmean=0.;*/
2347: int first;
2348: int j, k=0,jk, ju, jl;
2349: double sum=0.;
2350: first=0;
2351: jmin=1e+5;
2352: jmax=-1;
2353: jmean=0.;
2354: for(i=1; i<=imx; i++){
2355: mi=0;
2356: m=firstpass;
2357: while(s[m][i] <= nlstate){
2358: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2359: mw[++mi][i]=m;
2360: if(m >=lastpass)
2361: break;
2362: else
2363: m++;
2364: }/* end while */
2365: if (s[m][i] > nlstate){
2366: mi++; /* Death is another wave */
2367: /* if(mi==0) never been interviewed correctly before death */
2368: /* Only death is a correct wave */
2369: mw[mi][i]=m;
2370: }
2371:
2372: wav[i]=mi;
2373: if(mi==0){
2374: nbwarn++;
2375: if(first==0){
2376: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2377: first=1;
2378: }
2379: if(first==1){
2380: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2381: }
2382: } /* end mi==0 */
2383: } /* End individuals */
2384:
2385: for(i=1; i<=imx; i++){
2386: for(mi=1; mi<wav[i];mi++){
2387: if (stepm <=0)
2388: dh[mi][i]=1;
2389: else{
2390: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2391: if (agedc[i] < 2*AGESUP) {
2392: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2393: if(j==0) j=1; /* Survives at least one month after exam */
2394: else if(j<0){
2395: nberr++;
2396: 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]);
2397: j=1; /* Temporary Dangerous patch */
2398: 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);
2399: 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]);
2400: 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);
2401: }
2402: k=k+1;
2403: if (j >= jmax){
2404: jmax=j;
2405: ijmax=i;
2406: }
2407: if (j <= jmin){
2408: jmin=j;
2409: ijmin=i;
2410: }
2411: sum=sum+j;
2412: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2413: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2414: }
2415: }
2416: else{
2417: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2418: /* 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]); */
2419:
2420: k=k+1;
2421: if (j >= jmax) {
2422: jmax=j;
2423: ijmax=i;
2424: }
2425: else if (j <= jmin){
2426: jmin=j;
2427: ijmin=i;
2428: }
2429: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2430: /*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]);*/
2431: if(j<0){
2432: nberr++;
2433: 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]);
2434: 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]);
2435: }
2436: sum=sum+j;
2437: }
2438: jk= j/stepm;
2439: jl= j -jk*stepm;
2440: ju= j -(jk+1)*stepm;
2441: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2442: if(jl==0){
2443: dh[mi][i]=jk;
2444: bh[mi][i]=0;
2445: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 ! brouard 2446: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2447: dh[mi][i]=jk+1;
2448: bh[mi][i]=ju;
2449: }
2450: }else{
2451: if(jl <= -ju){
2452: dh[mi][i]=jk;
2453: bh[mi][i]=jl; /* bias is positive if real duration
2454: * is higher than the multiple of stepm and negative otherwise.
2455: */
2456: }
2457: else{
2458: dh[mi][i]=jk+1;
2459: bh[mi][i]=ju;
2460: }
2461: if(dh[mi][i]==0){
2462: dh[mi][i]=1; /* At least one step */
2463: bh[mi][i]=ju; /* At least one step */
2464: /* 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);*/
2465: }
2466: } /* end if mle */
2467: }
2468: } /* end wave */
2469: }
2470: jmean=sum/k;
2471: 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);
2472: 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);
2473: }
2474:
2475: /*********** Tricode ****************************/
2476: void tricode(int *Tvar, int **nbcode, int imx)
2477: {
1.136 ! brouard 2478: /* Uses cptcovn+2*cptcovprod as the number of covariates */
1.130 brouard 2479: /* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */
2480:
1.131 brouard 2481: int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 ! brouard 2482: int modmaxcovj=0; /* Modality max of covariates j */
1.126 brouard 2483: cptcoveff=0;
2484:
2485: for (k=0; k<maxncov; k++) Ndum[k]=0;
1.131 brouard 2486: for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */
1.126 brouard 2487:
1.136 ! brouard 2488: for (j=1; j<=(cptcovn+2*cptcovprod); j++) { /* For each covariate j */
! 2489: for (i=1; i<=imx; i++) { /*reads the data file to get the maximum value of the
! 2490: modality of this covariate Vj*/
! 2491: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Finds for covariate j, n=Tvar[j] of Vn . ij is the
! 2492: modality of the nth covariate of individual i. */
! 2493: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.126 brouard 2494: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 ! brouard 2495: if (ij > modmaxcovj) modmaxcovj=ij;
! 2496: /* getting the maximum value of the modality of the covariate
! 2497: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
! 2498: female is 1, then modmaxcovj=1.*/
1.126 brouard 2499: }
2500:
1.136 ! brouard 2501: for (i=0; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*/
! 2502: if( Ndum[i] != 0 )
! 2503: ncodemax[j]++;
! 2504: /* Number of modalities of the j th covariate. In fact
! 2505: ncodemax[j]=2 (dichotom. variables only) but it could be more for
! 2506: historical reasons */
1.131 brouard 2507: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2508:
1.136 ! brouard 2509: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.126 brouard 2510: ij=1;
1.136 ! brouard 2511: for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 for dichotomous */
! 2512: for (k=0; k<= maxncov; k++) { /* k=-1 ? NCOVMAX*/
1.131 brouard 2513: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2514: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2515: k is a modality. If we have model=V1+V1*sex
2516: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2517: ij++;
2518: }
2519: if (ij > ncodemax[j]) break;
2520: }
2521: }
2522: }
2523:
2524: for (k=0; k< maxncov; k++) Ndum[k]=0;
2525:
1.131 brouard 2526: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
1.126 brouard 2527: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
1.131 brouard 2528: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.126 brouard 2529: Ndum[ij]++;
2530: }
2531:
2532: ij=1;
2533: for (i=1; i<= maxncov; i++) {
2534: if((Ndum[i]!=0) && (i<=ncovcol)){
2535: Tvaraff[ij]=i; /*For printing */
2536: ij++;
2537: }
2538: }
1.131 brouard 2539: ij--;
2540: cptcoveff=ij; /*Number of simple covariates*/
1.126 brouard 2541: }
2542:
2543: /*********** Health Expectancies ****************/
2544:
1.127 brouard 2545: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 2546:
2547: {
2548: /* Health expectancies, no variances */
2549: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2550: int nhstepma, nstepma; /* Decreasing with age */
2551: double age, agelim, hf;
2552: double ***p3mat;
2553: double eip;
2554:
2555: pstamp(ficreseij);
2556: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2557: fprintf(ficreseij,"# Age");
2558: for(i=1; i<=nlstate;i++){
2559: for(j=1; j<=nlstate;j++){
2560: fprintf(ficreseij," e%1d%1d ",i,j);
2561: }
2562: fprintf(ficreseij," e%1d. ",i);
2563: }
2564: fprintf(ficreseij,"\n");
2565:
2566:
2567: if(estepm < stepm){
2568: printf ("Problem %d lower than %d\n",estepm, stepm);
2569: }
2570: else hstepm=estepm;
2571: /* We compute the life expectancy from trapezoids spaced every estepm months
2572: * This is mainly to measure the difference between two models: for example
2573: * if stepm=24 months pijx are given only every 2 years and by summing them
2574: * we are calculating an estimate of the Life Expectancy assuming a linear
2575: * progression in between and thus overestimating or underestimating according
2576: * to the curvature of the survival function. If, for the same date, we
2577: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2578: * to compare the new estimate of Life expectancy with the same linear
2579: * hypothesis. A more precise result, taking into account a more precise
2580: * curvature will be obtained if estepm is as small as stepm. */
2581:
2582: /* For example we decided to compute the life expectancy with the smallest unit */
2583: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2584: nhstepm is the number of hstepm from age to agelim
2585: nstepm is the number of stepm from age to agelin.
2586: Look at hpijx to understand the reason of that which relies in memory size
2587: and note for a fixed period like estepm months */
2588: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2589: survival function given by stepm (the optimization length). Unfortunately it
2590: means that if the survival funtion is printed only each two years of age and if
2591: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2592: results. So we changed our mind and took the option of the best precision.
2593: */
2594: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2595:
2596: agelim=AGESUP;
2597: /* If stepm=6 months */
2598: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2599: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2600:
2601: /* nhstepm age range expressed in number of stepm */
2602: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2603: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2604: /* if (stepm >= YEARM) hstepm=1;*/
2605: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2606: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2607:
2608: for (age=bage; age<=fage; age ++){
2609: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2610: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2611: /* if (stepm >= YEARM) hstepm=1;*/
2612: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2613:
2614: /* If stepm=6 months */
2615: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2616: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2617:
2618: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2619:
2620: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2621:
2622: printf("%d|",(int)age);fflush(stdout);
2623: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2624:
2625: /* Computing expectancies */
2626: for(i=1; i<=nlstate;i++)
2627: for(j=1; j<=nlstate;j++)
2628: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2629: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2630:
2631: /* 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]);*/
2632:
2633: }
2634:
2635: fprintf(ficreseij,"%3.0f",age );
2636: for(i=1; i<=nlstate;i++){
2637: eip=0;
2638: for(j=1; j<=nlstate;j++){
2639: eip +=eij[i][j][(int)age];
2640: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2641: }
2642: fprintf(ficreseij,"%9.4f", eip );
2643: }
2644: fprintf(ficreseij,"\n");
2645:
2646: }
2647: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2648: printf("\n");
2649: fprintf(ficlog,"\n");
2650:
2651: }
2652:
1.127 brouard 2653: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 2654:
2655: {
2656: /* Covariances of health expectancies eij and of total life expectancies according
2657: to initial status i, ei. .
2658: */
2659: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2660: int nhstepma, nstepma; /* Decreasing with age */
2661: double age, agelim, hf;
2662: double ***p3matp, ***p3matm, ***varhe;
2663: double **dnewm,**doldm;
2664: double *xp, *xm;
2665: double **gp, **gm;
2666: double ***gradg, ***trgradg;
2667: int theta;
2668:
2669: double eip, vip;
2670:
2671: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2672: xp=vector(1,npar);
2673: xm=vector(1,npar);
2674: dnewm=matrix(1,nlstate*nlstate,1,npar);
2675: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2676:
2677: pstamp(ficresstdeij);
2678: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2679: fprintf(ficresstdeij,"# Age");
2680: for(i=1; i<=nlstate;i++){
2681: for(j=1; j<=nlstate;j++)
2682: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2683: fprintf(ficresstdeij," e%1d. ",i);
2684: }
2685: fprintf(ficresstdeij,"\n");
2686:
2687: pstamp(ficrescveij);
2688: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2689: fprintf(ficrescveij,"# Age");
2690: for(i=1; i<=nlstate;i++)
2691: for(j=1; j<=nlstate;j++){
2692: cptj= (j-1)*nlstate+i;
2693: for(i2=1; i2<=nlstate;i2++)
2694: for(j2=1; j2<=nlstate;j2++){
2695: cptj2= (j2-1)*nlstate+i2;
2696: if(cptj2 <= cptj)
2697: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2698: }
2699: }
2700: fprintf(ficrescveij,"\n");
2701:
2702: if(estepm < stepm){
2703: printf ("Problem %d lower than %d\n",estepm, stepm);
2704: }
2705: else hstepm=estepm;
2706: /* We compute the life expectancy from trapezoids spaced every estepm months
2707: * This is mainly to measure the difference between two models: for example
2708: * if stepm=24 months pijx are given only every 2 years and by summing them
2709: * we are calculating an estimate of the Life Expectancy assuming a linear
2710: * progression in between and thus overestimating or underestimating according
2711: * to the curvature of the survival function. If, for the same date, we
2712: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2713: * to compare the new estimate of Life expectancy with the same linear
2714: * hypothesis. A more precise result, taking into account a more precise
2715: * curvature will be obtained if estepm is as small as stepm. */
2716:
2717: /* For example we decided to compute the life expectancy with the smallest unit */
2718: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2719: nhstepm is the number of hstepm from age to agelim
2720: nstepm is the number of stepm from age to agelin.
2721: Look at hpijx to understand the reason of that which relies in memory size
2722: and note for a fixed period like estepm months */
2723: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2724: survival function given by stepm (the optimization length). Unfortunately it
2725: means that if the survival funtion is printed only each two years of age and if
2726: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2727: results. So we changed our mind and took the option of the best precision.
2728: */
2729: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2730:
2731: /* If stepm=6 months */
2732: /* nhstepm age range expressed in number of stepm */
2733: agelim=AGESUP;
2734: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2735: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2736: /* if (stepm >= YEARM) hstepm=1;*/
2737: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2738:
2739: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2740: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2741: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2742: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2743: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2744: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2745:
2746: for (age=bage; age<=fage; age ++){
2747: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2748: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2749: /* if (stepm >= YEARM) hstepm=1;*/
2750: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2751:
2752: /* If stepm=6 months */
2753: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2754: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2755:
2756: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2757:
2758: /* Computing Variances of health expectancies */
2759: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
2760: decrease memory allocation */
2761: for(theta=1; theta <=npar; theta++){
2762: for(i=1; i<=npar; i++){
2763: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2764: xm[i] = x[i] - (i==theta ?delti[theta]:0);
2765: }
2766: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
2767: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
2768:
2769: for(j=1; j<= nlstate; j++){
2770: for(i=1; i<=nlstate; i++){
2771: for(h=0; h<=nhstepm-1; h++){
2772: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
2773: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
2774: }
2775: }
2776: }
2777:
2778: for(ij=1; ij<= nlstate*nlstate; ij++)
2779: for(h=0; h<=nhstepm-1; h++){
2780: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
2781: }
2782: }/* End theta */
2783:
2784:
2785: for(h=0; h<=nhstepm-1; h++)
2786: for(j=1; j<=nlstate*nlstate;j++)
2787: for(theta=1; theta <=npar; theta++)
2788: trgradg[h][j][theta]=gradg[h][theta][j];
2789:
2790:
2791: for(ij=1;ij<=nlstate*nlstate;ij++)
2792: for(ji=1;ji<=nlstate*nlstate;ji++)
2793: varhe[ij][ji][(int)age] =0.;
2794:
2795: printf("%d|",(int)age);fflush(stdout);
2796: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2797: for(h=0;h<=nhstepm-1;h++){
2798: for(k=0;k<=nhstepm-1;k++){
2799: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
2800: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
2801: for(ij=1;ij<=nlstate*nlstate;ij++)
2802: for(ji=1;ji<=nlstate*nlstate;ji++)
2803: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
2804: }
2805: }
2806:
2807: /* Computing expectancies */
2808: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2809: for(i=1; i<=nlstate;i++)
2810: for(j=1; j<=nlstate;j++)
2811: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2812: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
2813:
2814: /* 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]);*/
2815:
2816: }
2817:
2818: fprintf(ficresstdeij,"%3.0f",age );
2819: for(i=1; i<=nlstate;i++){
2820: eip=0.;
2821: vip=0.;
2822: for(j=1; j<=nlstate;j++){
2823: eip += eij[i][j][(int)age];
2824: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
2825: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
2826: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
2827: }
2828: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
2829: }
2830: fprintf(ficresstdeij,"\n");
2831:
2832: fprintf(ficrescveij,"%3.0f",age );
2833: for(i=1; i<=nlstate;i++)
2834: for(j=1; j<=nlstate;j++){
2835: cptj= (j-1)*nlstate+i;
2836: for(i2=1; i2<=nlstate;i2++)
2837: for(j2=1; j2<=nlstate;j2++){
2838: cptj2= (j2-1)*nlstate+i2;
2839: if(cptj2 <= cptj)
2840: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
2841: }
2842: }
2843: fprintf(ficrescveij,"\n");
2844:
2845: }
2846: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
2847: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
2848: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
2849: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
2850: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2851: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2852: printf("\n");
2853: fprintf(ficlog,"\n");
2854:
2855: free_vector(xm,1,npar);
2856: free_vector(xp,1,npar);
2857: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
2858: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
2859: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
2860: }
2861:
2862: /************ Variance ******************/
2863: 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[])
2864: {
2865: /* Variance of health expectancies */
2866: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
2867: /* double **newm;*/
2868: double **dnewm,**doldm;
2869: double **dnewmp,**doldmp;
2870: int i, j, nhstepm, hstepm, h, nstepm ;
2871: int k, cptcode;
2872: double *xp;
2873: double **gp, **gm; /* for var eij */
2874: double ***gradg, ***trgradg; /*for var eij */
2875: double **gradgp, **trgradgp; /* for var p point j */
2876: double *gpp, *gmp; /* for var p point j */
2877: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
2878: double ***p3mat;
2879: double age,agelim, hf;
2880: double ***mobaverage;
2881: int theta;
2882: char digit[4];
2883: char digitp[25];
2884:
2885: char fileresprobmorprev[FILENAMELENGTH];
2886:
2887: if(popbased==1){
2888: if(mobilav!=0)
2889: strcpy(digitp,"-populbased-mobilav-");
2890: else strcpy(digitp,"-populbased-nomobil-");
2891: }
2892: else
2893: strcpy(digitp,"-stablbased-");
2894:
2895: if (mobilav!=0) {
2896: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
2897: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
2898: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
2899: printf(" Error in movingaverage mobilav=%d\n",mobilav);
2900: }
2901: }
2902:
2903: strcpy(fileresprobmorprev,"prmorprev");
2904: sprintf(digit,"%-d",ij);
2905: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
2906: strcat(fileresprobmorprev,digit); /* Tvar to be done */
2907: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
2908: strcat(fileresprobmorprev,fileres);
2909: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
2910: printf("Problem with resultfile: %s\n", fileresprobmorprev);
2911: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
2912: }
2913: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2914:
2915: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
2916: pstamp(ficresprobmorprev);
2917: 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);
2918: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
2919: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
2920: fprintf(ficresprobmorprev," p.%-d SE",j);
2921: for(i=1; i<=nlstate;i++)
2922: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
2923: }
2924: fprintf(ficresprobmorprev,"\n");
2925: fprintf(ficgp,"\n# Routine varevsij");
2926: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
2927: 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");
2928: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
2929: /* } */
2930: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2931: pstamp(ficresvij);
2932: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
2933: if(popbased==1)
1.128 brouard 2934: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 2935: else
2936: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
2937: fprintf(ficresvij,"# Age");
2938: for(i=1; i<=nlstate;i++)
2939: for(j=1; j<=nlstate;j++)
2940: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
2941: fprintf(ficresvij,"\n");
2942:
2943: xp=vector(1,npar);
2944: dnewm=matrix(1,nlstate,1,npar);
2945: doldm=matrix(1,nlstate,1,nlstate);
2946: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
2947: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
2948:
2949: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
2950: gpp=vector(nlstate+1,nlstate+ndeath);
2951: gmp=vector(nlstate+1,nlstate+ndeath);
2952: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
2953:
2954: if(estepm < stepm){
2955: printf ("Problem %d lower than %d\n",estepm, stepm);
2956: }
2957: else hstepm=estepm;
2958: /* For example we decided to compute the life expectancy with the smallest unit */
2959: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2960: nhstepm is the number of hstepm from age to agelim
2961: nstepm is the number of stepm from age to agelin.
1.128 brouard 2962: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 2963: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2964: survival function given by stepm (the optimization length). Unfortunately it
2965: means that if the survival funtion is printed every two years of age and if
2966: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2967: results. So we changed our mind and took the option of the best precision.
2968: */
2969: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2970: agelim = AGESUP;
2971: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
2972: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
2973: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2974: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2975: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
2976: gp=matrix(0,nhstepm,1,nlstate);
2977: gm=matrix(0,nhstepm,1,nlstate);
2978:
2979:
2980: for(theta=1; theta <=npar; theta++){
2981: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
2982: xp[i] = x[i] + (i==theta ?delti[theta]:0);
2983: }
2984: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
2985: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
2986:
2987: if (popbased==1) {
2988: if(mobilav ==0){
2989: for(i=1; i<=nlstate;i++)
2990: prlim[i][i]=probs[(int)age][i][ij];
2991: }else{ /* mobilav */
2992: for(i=1; i<=nlstate;i++)
2993: prlim[i][i]=mobaverage[(int)age][i][ij];
2994: }
2995: }
2996:
2997: for(j=1; j<= nlstate; j++){
2998: for(h=0; h<=nhstepm; h++){
2999: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3000: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3001: }
3002: }
3003: /* This for computing probability of death (h=1 means
3004: computed over hstepm matrices product = hstepm*stepm months)
3005: as a weighted average of prlim.
3006: */
3007: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3008: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3009: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3010: }
3011: /* end probability of death */
3012:
3013: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3014: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3015: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3016: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3017:
3018: if (popbased==1) {
3019: if(mobilav ==0){
3020: for(i=1; i<=nlstate;i++)
3021: prlim[i][i]=probs[(int)age][i][ij];
3022: }else{ /* mobilav */
3023: for(i=1; i<=nlstate;i++)
3024: prlim[i][i]=mobaverage[(int)age][i][ij];
3025: }
3026: }
3027:
1.128 brouard 3028: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3029: for(h=0; h<=nhstepm; h++){
3030: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3031: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3032: }
3033: }
3034: /* This for computing probability of death (h=1 means
3035: computed over hstepm matrices product = hstepm*stepm months)
3036: as a weighted average of prlim.
3037: */
3038: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3039: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3040: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3041: }
3042: /* end probability of death */
3043:
3044: for(j=1; j<= nlstate; j++) /* vareij */
3045: for(h=0; h<=nhstepm; h++){
3046: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3047: }
3048:
3049: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3050: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3051: }
3052:
3053: } /* End theta */
3054:
3055: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3056:
3057: for(h=0; h<=nhstepm; h++) /* veij */
3058: for(j=1; j<=nlstate;j++)
3059: for(theta=1; theta <=npar; theta++)
3060: trgradg[h][j][theta]=gradg[h][theta][j];
3061:
3062: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3063: for(theta=1; theta <=npar; theta++)
3064: trgradgp[j][theta]=gradgp[theta][j];
3065:
3066:
3067: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3068: for(i=1;i<=nlstate;i++)
3069: for(j=1;j<=nlstate;j++)
3070: vareij[i][j][(int)age] =0.;
3071:
3072: for(h=0;h<=nhstepm;h++){
3073: for(k=0;k<=nhstepm;k++){
3074: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3075: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3076: for(i=1;i<=nlstate;i++)
3077: for(j=1;j<=nlstate;j++)
3078: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3079: }
3080: }
3081:
3082: /* pptj */
3083: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3084: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3085: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3086: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3087: varppt[j][i]=doldmp[j][i];
3088: /* end ppptj */
3089: /* x centered again */
3090: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3091: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3092:
3093: if (popbased==1) {
3094: if(mobilav ==0){
3095: for(i=1; i<=nlstate;i++)
3096: prlim[i][i]=probs[(int)age][i][ij];
3097: }else{ /* mobilav */
3098: for(i=1; i<=nlstate;i++)
3099: prlim[i][i]=mobaverage[(int)age][i][ij];
3100: }
3101: }
3102:
3103: /* This for computing probability of death (h=1 means
3104: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3105: as a weighted average of prlim.
3106: */
3107: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3108: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3109: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3110: }
3111: /* end probability of death */
3112:
3113: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3114: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3115: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3116: for(i=1; i<=nlstate;i++){
3117: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3118: }
3119: }
3120: fprintf(ficresprobmorprev,"\n");
3121:
3122: fprintf(ficresvij,"%.0f ",age );
3123: for(i=1; i<=nlstate;i++)
3124: for(j=1; j<=nlstate;j++){
3125: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3126: }
3127: fprintf(ficresvij,"\n");
3128: free_matrix(gp,0,nhstepm,1,nlstate);
3129: free_matrix(gm,0,nhstepm,1,nlstate);
3130: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3131: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3132: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3133: } /* End age */
3134: free_vector(gpp,nlstate+1,nlstate+ndeath);
3135: free_vector(gmp,nlstate+1,nlstate+ndeath);
3136: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3137: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.131 brouard 3138: fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
1.126 brouard 3139: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3140: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3141: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3142: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3143: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3144: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
3145: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
3146: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
3147: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3148: 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);
3149: /* 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);
3150: */
3151: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3152: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3153:
3154: free_vector(xp,1,npar);
3155: free_matrix(doldm,1,nlstate,1,nlstate);
3156: free_matrix(dnewm,1,nlstate,1,npar);
3157: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3158: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3159: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3160: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3161: fclose(ficresprobmorprev);
3162: fflush(ficgp);
3163: fflush(fichtm);
3164: } /* end varevsij */
3165:
3166: /************ Variance of prevlim ******************/
3167: 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[])
3168: {
3169: /* Variance of prevalence limit */
3170: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3171: double **newm;
3172: double **dnewm,**doldm;
3173: int i, j, nhstepm, hstepm;
3174: int k, cptcode;
3175: double *xp;
3176: double *gp, *gm;
3177: double **gradg, **trgradg;
3178: double age,agelim;
3179: int theta;
3180:
3181: pstamp(ficresvpl);
3182: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3183: fprintf(ficresvpl,"# Age");
3184: for(i=1; i<=nlstate;i++)
3185: fprintf(ficresvpl," %1d-%1d",i,i);
3186: fprintf(ficresvpl,"\n");
3187:
3188: xp=vector(1,npar);
3189: dnewm=matrix(1,nlstate,1,npar);
3190: doldm=matrix(1,nlstate,1,nlstate);
3191:
3192: hstepm=1*YEARM; /* Every year of age */
3193: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3194: agelim = AGESUP;
3195: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3196: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3197: if (stepm >= YEARM) hstepm=1;
3198: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3199: gradg=matrix(1,npar,1,nlstate);
3200: gp=vector(1,nlstate);
3201: gm=vector(1,nlstate);
3202:
3203: for(theta=1; theta <=npar; theta++){
3204: for(i=1; i<=npar; i++){ /* Computes gradient */
3205: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3206: }
3207: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3208: for(i=1;i<=nlstate;i++)
3209: gp[i] = prlim[i][i];
3210:
3211: for(i=1; i<=npar; i++) /* Computes gradient */
3212: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3213: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3214: for(i=1;i<=nlstate;i++)
3215: gm[i] = prlim[i][i];
3216:
3217: for(i=1;i<=nlstate;i++)
3218: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3219: } /* End theta */
3220:
3221: trgradg =matrix(1,nlstate,1,npar);
3222:
3223: for(j=1; j<=nlstate;j++)
3224: for(theta=1; theta <=npar; theta++)
3225: trgradg[j][theta]=gradg[theta][j];
3226:
3227: for(i=1;i<=nlstate;i++)
3228: varpl[i][(int)age] =0.;
3229: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3230: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3231: for(i=1;i<=nlstate;i++)
3232: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3233:
3234: fprintf(ficresvpl,"%.0f ",age );
3235: for(i=1; i<=nlstate;i++)
3236: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3237: fprintf(ficresvpl,"\n");
3238: free_vector(gp,1,nlstate);
3239: free_vector(gm,1,nlstate);
3240: free_matrix(gradg,1,npar,1,nlstate);
3241: free_matrix(trgradg,1,nlstate,1,npar);
3242: } /* End age */
3243:
3244: free_vector(xp,1,npar);
3245: free_matrix(doldm,1,nlstate,1,npar);
3246: free_matrix(dnewm,1,nlstate,1,nlstate);
3247:
3248: }
3249:
3250: /************ Variance of one-step probabilities ******************/
3251: 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[])
3252: {
3253: int i, j=0, i1, k1, l1, t, tj;
3254: int k2, l2, j1, z1;
3255: int k=0,l, cptcode;
3256: int first=1, first1;
3257: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3258: double **dnewm,**doldm;
3259: double *xp;
3260: double *gp, *gm;
3261: double **gradg, **trgradg;
3262: double **mu;
3263: double age,agelim, cov[NCOVMAX];
3264: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3265: int theta;
3266: char fileresprob[FILENAMELENGTH];
3267: char fileresprobcov[FILENAMELENGTH];
3268: char fileresprobcor[FILENAMELENGTH];
3269:
3270: double ***varpij;
3271:
3272: strcpy(fileresprob,"prob");
3273: strcat(fileresprob,fileres);
3274: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3275: printf("Problem with resultfile: %s\n", fileresprob);
3276: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3277: }
3278: strcpy(fileresprobcov,"probcov");
3279: strcat(fileresprobcov,fileres);
3280: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3281: printf("Problem with resultfile: %s\n", fileresprobcov);
3282: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3283: }
3284: strcpy(fileresprobcor,"probcor");
3285: strcat(fileresprobcor,fileres);
3286: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3287: printf("Problem with resultfile: %s\n", fileresprobcor);
3288: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3289: }
3290: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3291: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3292: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3293: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3294: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3295: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3296: pstamp(ficresprob);
3297: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3298: fprintf(ficresprob,"# Age");
3299: pstamp(ficresprobcov);
3300: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3301: fprintf(ficresprobcov,"# Age");
3302: pstamp(ficresprobcor);
3303: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3304: fprintf(ficresprobcor,"# Age");
3305:
3306:
3307: for(i=1; i<=nlstate;i++)
3308: for(j=1; j<=(nlstate+ndeath);j++){
3309: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3310: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3311: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3312: }
3313: /* fprintf(ficresprob,"\n");
3314: fprintf(ficresprobcov,"\n");
3315: fprintf(ficresprobcor,"\n");
3316: */
1.131 brouard 3317: xp=vector(1,npar);
1.126 brouard 3318: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3319: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3320: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3321: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3322: first=1;
3323: fprintf(ficgp,"\n# Routine varprob");
3324: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3325: fprintf(fichtm,"\n");
3326:
3327: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3328: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3329: file %s<br>\n",optionfilehtmcov);
3330: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3331: and drawn. It helps understanding how is the covariance between two incidences.\
3332: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3333: 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. \
3334: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3335: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3336: standard deviations wide on each axis. <br>\
3337: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3338: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3339: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3340:
3341: cov[1]=1;
3342: tj=cptcoveff;
3343: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3344: j1=0;
3345: for(t=1; t<=tj;t++){
3346: for(i1=1; i1<=ncodemax[t];i1++){
3347: j1++;
3348: if (cptcovn>0) {
3349: fprintf(ficresprob, "\n#********** Variable ");
3350: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3351: fprintf(ficresprob, "**********\n#\n");
3352: fprintf(ficresprobcov, "\n#********** Variable ");
3353: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3354: fprintf(ficresprobcov, "**********\n#\n");
3355:
3356: fprintf(ficgp, "\n#********** Variable ");
3357: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3358: fprintf(ficgp, "**********\n#\n");
3359:
3360:
3361: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3362: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3363: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3364:
3365: fprintf(ficresprobcor, "\n#********** Variable ");
3366: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3367: fprintf(ficresprobcor, "**********\n#");
3368: }
3369:
3370: for (age=bage; age<=fage; age ++){
3371: cov[2]=age;
3372: for (k=1; k<=cptcovn;k++) {
3373: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
3374: }
3375: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3376: for (k=1; k<=cptcovprod;k++)
3377: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3378:
3379: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3380: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3381: gp=vector(1,(nlstate)*(nlstate+ndeath));
3382: gm=vector(1,(nlstate)*(nlstate+ndeath));
3383:
3384: for(theta=1; theta <=npar; theta++){
3385: for(i=1; i<=npar; i++)
3386: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3387:
3388: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3389:
3390: k=0;
3391: for(i=1; i<= (nlstate); i++){
3392: for(j=1; j<=(nlstate+ndeath);j++){
3393: k=k+1;
3394: gp[k]=pmmij[i][j];
3395: }
3396: }
3397:
3398: for(i=1; i<=npar; i++)
3399: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3400:
3401: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3402: k=0;
3403: for(i=1; i<=(nlstate); i++){
3404: for(j=1; j<=(nlstate+ndeath);j++){
3405: k=k+1;
3406: gm[k]=pmmij[i][j];
3407: }
3408: }
3409:
3410: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3411: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3412: }
3413:
3414: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3415: for(theta=1; theta <=npar; theta++)
3416: trgradg[j][theta]=gradg[theta][j];
3417:
3418: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3419: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3420: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3421: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3422: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3423: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3424:
3425: pmij(pmmij,cov,ncovmodel,x,nlstate);
3426:
3427: k=0;
3428: for(i=1; i<=(nlstate); i++){
3429: for(j=1; j<=(nlstate+ndeath);j++){
3430: k=k+1;
3431: mu[k][(int) age]=pmmij[i][j];
3432: }
3433: }
3434: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3435: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3436: varpij[i][j][(int)age] = doldm[i][j];
3437:
3438: /*printf("\n%d ",(int)age);
3439: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3440: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3441: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3442: }*/
3443:
3444: fprintf(ficresprob,"\n%d ",(int)age);
3445: fprintf(ficresprobcov,"\n%d ",(int)age);
3446: fprintf(ficresprobcor,"\n%d ",(int)age);
3447:
3448: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3449: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3450: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3451: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3452: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3453: }
3454: i=0;
3455: for (k=1; k<=(nlstate);k++){
3456: for (l=1; l<=(nlstate+ndeath);l++){
3457: i=i++;
3458: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3459: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3460: for (j=1; j<=i;j++){
3461: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3462: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3463: }
3464: }
3465: }/* end of loop for state */
3466: } /* end of loop for age */
3467:
3468: /* Confidence intervalle of pij */
3469: /*
1.131 brouard 3470: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3471: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3472: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3473: 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);
3474: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3475: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3476: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3477: */
3478:
3479: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3480: first1=1;
3481: for (k2=1; k2<=(nlstate);k2++){
3482: for (l2=1; l2<=(nlstate+ndeath);l2++){
3483: if(l2==k2) continue;
3484: j=(k2-1)*(nlstate+ndeath)+l2;
3485: for (k1=1; k1<=(nlstate);k1++){
3486: for (l1=1; l1<=(nlstate+ndeath);l1++){
3487: if(l1==k1) continue;
3488: i=(k1-1)*(nlstate+ndeath)+l1;
3489: if(i<=j) continue;
3490: for (age=bage; age<=fage; age ++){
3491: if ((int)age %5==0){
3492: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3493: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3494: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3495: mu1=mu[i][(int) age]/stepm*YEARM ;
3496: mu2=mu[j][(int) age]/stepm*YEARM;
3497: c12=cv12/sqrt(v1*v2);
3498: /* Computing eigen value of matrix of covariance */
3499: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3500: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3501: if ((lc2 <0) || (lc1 <0) ){
3502: 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);
3503: 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);
3504: lc1=fabs(lc1);
3505: lc2=fabs(lc2);
3506: }
3507:
1.126 brouard 3508: /* Eigen vectors */
3509: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3510: /*v21=sqrt(1.-v11*v11); *//* error */
3511: v21=(lc1-v1)/cv12*v11;
3512: v12=-v21;
3513: v22=v11;
3514: tnalp=v21/v11;
3515: if(first1==1){
3516: first1=0;
3517: 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);
3518: }
3519: 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);
3520: /*printf(fignu*/
3521: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3522: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3523: if(first==1){
3524: first=0;
3525: fprintf(ficgp,"\nset parametric;unset label");
3526: 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);
3527: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3528: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3529: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3530: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3531: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3532: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3533: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3534: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3535: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3536: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3537: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3538: 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",\
3539: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3540: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3541: }else{
3542: first=0;
3543: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3544: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3545: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3546: 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",\
3547: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3548: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3549: }/* if first */
3550: } /* age mod 5 */
3551: } /* end loop age */
3552: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3553: first=1;
3554: } /*l12 */
3555: } /* k12 */
3556: } /*l1 */
3557: }/* k1 */
3558: } /* loop covariates */
3559: }
3560: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3561: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3562: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3563: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3564: free_vector(xp,1,npar);
3565: fclose(ficresprob);
3566: fclose(ficresprobcov);
3567: fclose(ficresprobcor);
3568: fflush(ficgp);
3569: fflush(fichtmcov);
3570: }
3571:
3572:
3573: /******************* Printing html file ***********/
3574: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3575: int lastpass, int stepm, int weightopt, char model[],\
3576: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3577: int popforecast, int estepm ,\
3578: double jprev1, double mprev1,double anprev1, \
3579: double jprev2, double mprev2,double anprev2){
3580: int jj1, k1, i1, cpt;
3581:
3582: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3583: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3584: </ul>");
3585: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3586: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3587: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3588: fprintf(fichtm,"\
3589: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3590: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3591: fprintf(fichtm,"\
3592: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3593: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3594: fprintf(fichtm,"\
1.128 brouard 3595: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 3596: <a href=\"%s\">%s</a> <br>\n",
3597: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3598: fprintf(fichtm,"\
3599: - Population projections by age and states: \
3600: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3601:
3602: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3603:
3604: m=cptcoveff;
3605: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3606:
3607: jj1=0;
3608: for(k1=1; k1<=m;k1++){
3609: for(i1=1; i1<=ncodemax[k1];i1++){
3610: jj1++;
3611: if (cptcovn > 0) {
3612: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3613: for (cpt=1; cpt<=cptcoveff;cpt++)
3614: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3615: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3616: }
3617: /* Pij */
3618: 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> \
3619: <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3620: /* Quasi-incidences */
3621: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
3622: 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> \
3623: <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
3624: /* Period (stable) prevalence in each health state */
3625: for(cpt=1; cpt<nlstate;cpt++){
3626: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
3627: <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
3628: }
3629: for(cpt=1; cpt<=nlstate;cpt++) {
3630: 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> \
3631: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3632: }
3633: } /* end i1 */
3634: }/* End k1 */
3635: fprintf(fichtm,"</ul>");
3636:
3637:
3638: fprintf(fichtm,"\
3639: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3640: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3641:
3642: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3643: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3644: fprintf(fichtm,"\
3645: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3646: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3647:
3648: fprintf(fichtm,"\
3649: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3650: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3651: fprintf(fichtm,"\
3652: - 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): \
3653: <a href=\"%s\">%s</a> <br>\n</li>",
3654: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3655: fprintf(fichtm,"\
3656: - (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): \
3657: <a href=\"%s\">%s</a> <br>\n</li>",
3658: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3659: fprintf(fichtm,"\
1.128 brouard 3660: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.126 brouard 3661: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3662: fprintf(fichtm,"\
1.128 brouard 3663: - 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",
3664: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3665: fprintf(fichtm,"\
3666: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3667: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3668:
3669: /* if(popforecast==1) fprintf(fichtm,"\n */
3670: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3671: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3672: /* <br>",fileres,fileres,fileres,fileres); */
3673: /* else */
3674: /* 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); */
3675: fflush(fichtm);
3676: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3677:
3678: m=cptcoveff;
3679: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3680:
3681: jj1=0;
3682: for(k1=1; k1<=m;k1++){
3683: for(i1=1; i1<=ncodemax[k1];i1++){
3684: jj1++;
3685: if (cptcovn > 0) {
3686: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3687: for (cpt=1; cpt<=cptcoveff;cpt++)
3688: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3689: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3690: }
3691: for(cpt=1; cpt<=nlstate;cpt++) {
3692: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
3693: prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
3694: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
3695: }
3696: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3697: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3698: true period expectancies (those weighted with period prevalences are also\
3699: drawn in addition to the population based expectancies computed using\
3700: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3701: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3702: } /* end i1 */
3703: }/* End k1 */
3704: fprintf(fichtm,"</ul>");
3705: fflush(fichtm);
3706: }
3707:
3708: /******************* Gnuplot file **************/
3709: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3710:
3711: char dirfileres[132],optfileres[132];
1.130 brouard 3712: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3713: int ng=0;
1.126 brouard 3714: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3715: /* printf("Problem with file %s",optionfilegnuplot); */
3716: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3717: /* } */
3718:
3719: /*#ifdef windows */
3720: fprintf(ficgp,"cd \"%s\" \n",pathc);
3721: /*#endif */
3722: m=pow(2,cptcoveff);
3723:
3724: strcpy(dirfileres,optionfilefiname);
3725: strcpy(optfileres,"vpl");
3726: /* 1eme*/
3727: for (cpt=1; cpt<= nlstate ; cpt ++) {
3728: for (k1=1; k1<= m ; k1 ++) {
3729: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3730: fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
3731: fprintf(ficgp,"set xlabel \"Age\" \n\
3732: set ylabel \"Probability\" \n\
3733: set ter png small\n\
3734: set size 0.65,0.65\n\
3735: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3736:
3737: for (i=1; i<= nlstate ; i ++) {
3738: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 3739: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3740: }
3741: 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);
3742: for (i=1; i<= nlstate ; i ++) {
3743: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3744: else fprintf(ficgp," \%%*lf (\%%*lf)");
3745: }
3746: fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
3747: for (i=1; i<= nlstate ; i ++) {
3748: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
3749: else fprintf(ficgp," \%%*lf (\%%*lf)");
3750: }
3751: fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
3752: }
3753: }
3754: /*2 eme*/
3755:
3756: for (k1=1; k1<= m ; k1 ++) {
3757: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
3758: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
3759:
3760: for (i=1; i<= nlstate+1 ; i ++) {
3761: k=2*i;
3762: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3763: for (j=1; j<= nlstate+1 ; j ++) {
3764: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3765: else fprintf(ficgp," \%%*lf (\%%*lf)");
3766: }
3767: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
3768: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
3769: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3770: for (j=1; j<= nlstate+1 ; j ++) {
3771: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3772: else fprintf(ficgp," \%%*lf (\%%*lf)");
3773: }
3774: fprintf(ficgp,"\" t\"\" w l 0,");
3775: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
3776: for (j=1; j<= nlstate+1 ; j ++) {
3777: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
3778: else fprintf(ficgp," \%%*lf (\%%*lf)");
3779: }
3780: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
3781: else fprintf(ficgp,"\" t\"\" w l 0,");
3782: }
3783: }
3784:
3785: /*3eme*/
3786:
3787: for (k1=1; k1<= m ; k1 ++) {
3788: for (cpt=1; cpt<= nlstate ; cpt ++) {
3789: /* k=2+nlstate*(2*cpt-2); */
3790: k=2+(nlstate+1)*(cpt-1);
3791: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
3792: fprintf(ficgp,"set ter png small\n\
3793: set size 0.65,0.65\n\
3794: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
3795: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3796: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3797: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3798: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
3799: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
3800: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
3801:
3802: */
3803: for (i=1; i< nlstate ; i ++) {
3804: 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);
3805: /* 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);*/
3806:
3807: }
3808: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
3809: }
3810: }
3811:
3812: /* CV preval stable (period) */
3813: for (k1=1; k1<= m ; k1 ++) {
3814: for (cpt=1; cpt<=nlstate ; cpt ++) {
3815: k=3;
3816: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
3817: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
3818: set ter png small\nset size 0.65,0.65\n\
3819: unset log y\n\
3820: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
3821:
3822: for (i=1; i< nlstate ; i ++)
3823: fprintf(ficgp,"+$%d",k+i+1);
3824: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
3825:
3826: l=3+(nlstate+ndeath)*cpt;
3827: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
3828: for (i=1; i< nlstate ; i ++) {
3829: l=3+(nlstate+ndeath)*cpt;
3830: fprintf(ficgp,"+$%d",l+i+1);
3831: }
3832: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
3833: }
3834: }
3835:
3836: /* proba elementaires */
3837: for(i=1,jk=1; i <=nlstate; i++){
3838: for(k=1; k <=(nlstate+ndeath); k++){
3839: if (k != i) {
3840: for(j=1; j <=ncovmodel; j++){
3841: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
3842: jk++;
3843: fprintf(ficgp,"\n");
3844: }
3845: }
3846: }
3847: }
3848:
3849: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
3850: for(jk=1; jk <=m; jk++) {
3851: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
3852: if (ng==2)
3853: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
3854: else
3855: fprintf(ficgp,"\nset title \"Probability\"\n");
3856: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
3857: i=1;
3858: for(k2=1; k2<=nlstate; k2++) {
3859: k3=i;
3860: for(k=1; k<=(nlstate+ndeath); k++) {
3861: if (k != k2){
3862: if(ng==2)
3863: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
3864: else
3865: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
3866: ij=1;
3867: for(j=3; j <=ncovmodel; j++) {
3868: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3869: fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3870: ij++;
3871: }
3872: else
3873: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3874: }
3875: fprintf(ficgp,")/(1");
3876:
3877: for(k1=1; k1 <=nlstate; k1++){
3878: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
3879: ij=1;
3880: for(j=3; j <=ncovmodel; j++){
3881: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
3882: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
3883: ij++;
3884: }
3885: else
3886: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
3887: }
3888: fprintf(ficgp,")");
3889: }
3890: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
3891: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
3892: i=i+ncovmodel;
3893: }
3894: } /* end k */
3895: } /* end k2 */
3896: } /* end jk */
3897: } /* end ng */
3898: fflush(ficgp);
3899: } /* end gnuplot */
3900:
3901:
3902: /*************** Moving average **************/
3903: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
3904:
3905: int i, cpt, cptcod;
3906: int modcovmax =1;
3907: int mobilavrange, mob;
3908: double age;
3909:
3910: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
3911: a covariate has 2 modalities */
3912: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
3913:
3914: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
3915: if(mobilav==1) mobilavrange=5; /* default */
3916: else mobilavrange=mobilav;
3917: for (age=bage; age<=fage; age++)
3918: for (i=1; i<=nlstate;i++)
3919: for (cptcod=1;cptcod<=modcovmax;cptcod++)
3920: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
3921: /* We keep the original values on the extreme ages bage, fage and for
3922: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
3923: we use a 5 terms etc. until the borders are no more concerned.
3924: */
3925: for (mob=3;mob <=mobilavrange;mob=mob+2){
3926: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
3927: for (i=1; i<=nlstate;i++){
3928: for (cptcod=1;cptcod<=modcovmax;cptcod++){
3929: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
3930: for (cpt=1;cpt<=(mob-1)/2;cpt++){
3931: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
3932: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
3933: }
3934: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
3935: }
3936: }
3937: }/* end age */
3938: }/* end mob */
3939: }else return -1;
3940: return 0;
3941: }/* End movingaverage */
3942:
3943:
3944: /************** Forecasting ******************/
3945: 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){
3946: /* proj1, year, month, day of starting projection
3947: agemin, agemax range of age
3948: dateprev1 dateprev2 range of dates during which prevalence is computed
3949: anproj2 year of en of projection (same day and month as proj1).
3950: */
3951: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
3952: int *popage;
3953: double agec; /* generic age */
3954: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
3955: double *popeffectif,*popcount;
3956: double ***p3mat;
3957: double ***mobaverage;
3958: char fileresf[FILENAMELENGTH];
3959:
3960: agelim=AGESUP;
3961: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
3962:
3963: strcpy(fileresf,"f");
3964: strcat(fileresf,fileres);
3965: if((ficresf=fopen(fileresf,"w"))==NULL) {
3966: printf("Problem with forecast resultfile: %s\n", fileresf);
3967: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
3968: }
3969: printf("Computing forecasting: result on file '%s' \n", fileresf);
3970: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
3971:
3972: if (cptcoveff==0) ncodemax[cptcoveff]=1;
3973:
3974: if (mobilav!=0) {
3975: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3976: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
3977: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3978: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3979: }
3980: }
3981:
3982: stepsize=(int) (stepm+YEARM-1)/YEARM;
3983: if (stepm<=12) stepsize=1;
3984: if(estepm < stepm){
3985: printf ("Problem %d lower than %d\n",estepm, stepm);
3986: }
3987: else hstepm=estepm;
3988:
3989: hstepm=hstepm/stepm;
3990: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
3991: fractional in yp1 */
3992: anprojmean=yp;
3993: yp2=modf((yp1*12),&yp);
3994: mprojmean=yp;
3995: yp1=modf((yp2*30.5),&yp);
3996: jprojmean=yp;
3997: if(jprojmean==0) jprojmean=1;
3998: if(mprojmean==0) jprojmean=1;
3999:
4000: i1=cptcoveff;
4001: if (cptcovn < 1){i1=1;}
4002:
4003: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4004:
4005: fprintf(ficresf,"#****** Routine prevforecast **\n");
4006:
4007: /* if (h==(int)(YEARM*yearp)){ */
4008: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4009: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4010: k=k+1;
4011: fprintf(ficresf,"\n#******");
4012: for(j=1;j<=cptcoveff;j++) {
4013: 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]]);
4014: }
4015: fprintf(ficresf,"******\n");
4016: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4017: for(j=1; j<=nlstate+ndeath;j++){
4018: for(i=1; i<=nlstate;i++)
4019: fprintf(ficresf," p%d%d",i,j);
4020: fprintf(ficresf," p.%d",j);
4021: }
4022: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4023: fprintf(ficresf,"\n");
4024: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4025:
4026: for (agec=fage; agec>=(ageminpar-1); agec--){
4027: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4028: nhstepm = nhstepm/hstepm;
4029: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4030: oldm=oldms;savm=savms;
4031: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4032:
4033: for (h=0; h<=nhstepm; h++){
4034: if (h*hstepm/YEARM*stepm ==yearp) {
4035: fprintf(ficresf,"\n");
4036: for(j=1;j<=cptcoveff;j++)
4037: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4038: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4039: }
4040: for(j=1; j<=nlstate+ndeath;j++) {
4041: ppij=0.;
4042: for(i=1; i<=nlstate;i++) {
4043: if (mobilav==1)
4044: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4045: else {
4046: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4047: }
4048: if (h*hstepm/YEARM*stepm== yearp) {
4049: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4050: }
4051: } /* end i */
4052: if (h*hstepm/YEARM*stepm==yearp) {
4053: fprintf(ficresf," %.3f", ppij);
4054: }
4055: }/* end j */
4056: } /* end h */
4057: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4058: } /* end agec */
4059: } /* end yearp */
4060: } /* end cptcod */
4061: } /* end cptcov */
4062:
4063: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4064:
4065: fclose(ficresf);
4066: }
4067:
4068: /************** Forecasting *****not tested NB*************/
4069: 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){
4070:
4071: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4072: int *popage;
4073: double calagedatem, agelim, kk1, kk2;
4074: double *popeffectif,*popcount;
4075: double ***p3mat,***tabpop,***tabpopprev;
4076: double ***mobaverage;
4077: char filerespop[FILENAMELENGTH];
4078:
4079: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4080: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4081: agelim=AGESUP;
4082: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4083:
4084: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4085:
4086:
4087: strcpy(filerespop,"pop");
4088: strcat(filerespop,fileres);
4089: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4090: printf("Problem with forecast resultfile: %s\n", filerespop);
4091: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4092: }
4093: printf("Computing forecasting: result on file '%s' \n", filerespop);
4094: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4095:
4096: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4097:
4098: if (mobilav!=0) {
4099: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4100: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4101: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4102: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4103: }
4104: }
4105:
4106: stepsize=(int) (stepm+YEARM-1)/YEARM;
4107: if (stepm<=12) stepsize=1;
4108:
4109: agelim=AGESUP;
4110:
4111: hstepm=1;
4112: hstepm=hstepm/stepm;
4113:
4114: if (popforecast==1) {
4115: if((ficpop=fopen(popfile,"r"))==NULL) {
4116: printf("Problem with population file : %s\n",popfile);exit(0);
4117: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4118: }
4119: popage=ivector(0,AGESUP);
4120: popeffectif=vector(0,AGESUP);
4121: popcount=vector(0,AGESUP);
4122:
4123: i=1;
4124: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4125:
4126: imx=i;
4127: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4128: }
4129:
4130: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4131: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4132: k=k+1;
4133: fprintf(ficrespop,"\n#******");
4134: for(j=1;j<=cptcoveff;j++) {
4135: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4136: }
4137: fprintf(ficrespop,"******\n");
4138: fprintf(ficrespop,"# Age");
4139: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4140: if (popforecast==1) fprintf(ficrespop," [Population]");
4141:
4142: for (cpt=0; cpt<=0;cpt++) {
4143: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4144:
4145: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4146: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4147: nhstepm = nhstepm/hstepm;
4148:
4149: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4150: oldm=oldms;savm=savms;
4151: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4152:
4153: for (h=0; h<=nhstepm; h++){
4154: if (h==(int) (calagedatem+YEARM*cpt)) {
4155: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4156: }
4157: for(j=1; j<=nlstate+ndeath;j++) {
4158: kk1=0.;kk2=0;
4159: for(i=1; i<=nlstate;i++) {
4160: if (mobilav==1)
4161: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4162: else {
4163: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4164: }
4165: }
4166: if (h==(int)(calagedatem+12*cpt)){
4167: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4168: /*fprintf(ficrespop," %.3f", kk1);
4169: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4170: }
4171: }
4172: for(i=1; i<=nlstate;i++){
4173: kk1=0.;
4174: for(j=1; j<=nlstate;j++){
4175: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4176: }
4177: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4178: }
4179:
4180: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4181: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4182: }
4183: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4184: }
4185: }
4186:
4187: /******/
4188:
4189: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4190: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4191: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4192: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4193: nhstepm = nhstepm/hstepm;
4194:
4195: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4196: oldm=oldms;savm=savms;
4197: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4198: for (h=0; h<=nhstepm; h++){
4199: if (h==(int) (calagedatem+YEARM*cpt)) {
4200: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4201: }
4202: for(j=1; j<=nlstate+ndeath;j++) {
4203: kk1=0.;kk2=0;
4204: for(i=1; i<=nlstate;i++) {
4205: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4206: }
4207: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4208: }
4209: }
4210: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4211: }
4212: }
4213: }
4214: }
4215:
4216: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4217:
4218: if (popforecast==1) {
4219: free_ivector(popage,0,AGESUP);
4220: free_vector(popeffectif,0,AGESUP);
4221: free_vector(popcount,0,AGESUP);
4222: }
4223: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4224: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4225: fclose(ficrespop);
4226: } /* End of popforecast */
4227:
4228: int fileappend(FILE *fichier, char *optionfich)
4229: {
4230: if((fichier=fopen(optionfich,"a"))==NULL) {
4231: printf("Problem with file: %s\n", optionfich);
4232: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4233: return (0);
4234: }
4235: fflush(fichier);
4236: return (1);
4237: }
4238:
4239:
4240: /**************** function prwizard **********************/
4241: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4242: {
4243:
4244: /* Wizard to print covariance matrix template */
4245:
4246: char ca[32], cb[32], cc[32];
4247: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4248: int numlinepar;
4249:
4250: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4251: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4252: for(i=1; i <=nlstate; i++){
4253: jj=0;
4254: for(j=1; j <=nlstate+ndeath; j++){
4255: if(j==i) continue;
4256: jj++;
4257: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4258: printf("%1d%1d",i,j);
4259: fprintf(ficparo,"%1d%1d",i,j);
4260: for(k=1; k<=ncovmodel;k++){
4261: /* printf(" %lf",param[i][j][k]); */
4262: /* fprintf(ficparo," %lf",param[i][j][k]); */
4263: printf(" 0.");
4264: fprintf(ficparo," 0.");
4265: }
4266: printf("\n");
4267: fprintf(ficparo,"\n");
4268: }
4269: }
4270: printf("# Scales (for hessian or gradient estimation)\n");
4271: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4272: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4273: for(i=1; i <=nlstate; i++){
4274: jj=0;
4275: for(j=1; j <=nlstate+ndeath; j++){
4276: if(j==i) continue;
4277: jj++;
4278: fprintf(ficparo,"%1d%1d",i,j);
4279: printf("%1d%1d",i,j);
4280: fflush(stdout);
4281: for(k=1; k<=ncovmodel;k++){
4282: /* printf(" %le",delti3[i][j][k]); */
4283: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4284: printf(" 0.");
4285: fprintf(ficparo," 0.");
4286: }
4287: numlinepar++;
4288: printf("\n");
4289: fprintf(ficparo,"\n");
4290: }
4291: }
4292: printf("# Covariance matrix\n");
4293: /* # 121 Var(a12)\n\ */
4294: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4295: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4296: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4297: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4298: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4299: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4300: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4301: fflush(stdout);
4302: fprintf(ficparo,"# Covariance matrix\n");
4303: /* # 121 Var(a12)\n\ */
4304: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4305: /* # ...\n\ */
4306: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4307:
4308: for(itimes=1;itimes<=2;itimes++){
4309: jj=0;
4310: for(i=1; i <=nlstate; i++){
4311: for(j=1; j <=nlstate+ndeath; j++){
4312: if(j==i) continue;
4313: for(k=1; k<=ncovmodel;k++){
4314: jj++;
4315: ca[0]= k+'a'-1;ca[1]='\0';
4316: if(itimes==1){
4317: printf("#%1d%1d%d",i,j,k);
4318: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4319: }else{
4320: printf("%1d%1d%d",i,j,k);
4321: fprintf(ficparo,"%1d%1d%d",i,j,k);
4322: /* printf(" %.5le",matcov[i][j]); */
4323: }
4324: ll=0;
4325: for(li=1;li <=nlstate; li++){
4326: for(lj=1;lj <=nlstate+ndeath; lj++){
4327: if(lj==li) continue;
4328: for(lk=1;lk<=ncovmodel;lk++){
4329: ll++;
4330: if(ll<=jj){
4331: cb[0]= lk +'a'-1;cb[1]='\0';
4332: if(ll<jj){
4333: if(itimes==1){
4334: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4335: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4336: }else{
4337: printf(" 0.");
4338: fprintf(ficparo," 0.");
4339: }
4340: }else{
4341: if(itimes==1){
4342: printf(" Var(%s%1d%1d)",ca,i,j);
4343: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4344: }else{
4345: printf(" 0.");
4346: fprintf(ficparo," 0.");
4347: }
4348: }
4349: }
4350: } /* end lk */
4351: } /* end lj */
4352: } /* end li */
4353: printf("\n");
4354: fprintf(ficparo,"\n");
4355: numlinepar++;
4356: } /* end k*/
4357: } /*end j */
4358: } /* end i */
4359: } /* end itimes */
4360:
4361: } /* end of prwizard */
4362: /******************* Gompertz Likelihood ******************************/
4363: double gompertz(double x[])
4364: {
4365: double A,B,L=0.0,sump=0.,num=0.;
4366: int i,n=0; /* n is the size of the sample */
4367:
4368: for (i=0;i<=imx-1 ; i++) {
4369: sump=sump+weight[i];
4370: /* sump=sump+1;*/
4371: num=num+1;
4372: }
4373:
4374:
4375: /* for (i=0; i<=imx; i++)
4376: 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]);*/
4377:
4378: for (i=1;i<=imx ; i++)
4379: {
4380: if (cens[i] == 1 && wav[i]>1)
4381: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4382:
4383: if (cens[i] == 0 && wav[i]>1)
4384: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4385: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4386:
4387: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4388: if (wav[i] > 1 ) { /* ??? */
4389: L=L+A*weight[i];
4390: /* 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]);*/
4391: }
4392: }
4393:
4394: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4395:
4396: return -2*L*num/sump;
4397: }
4398:
1.136 ! brouard 4399: #ifdef GSL
! 4400: /******************* Gompertz_f Likelihood ******************************/
! 4401: double gompertz_f(const gsl_vector *v, void *params)
! 4402: {
! 4403: double A,B,LL=0.0,sump=0.,num=0.;
! 4404: double *x= (double *) v->data;
! 4405: int i,n=0; /* n is the size of the sample */
! 4406:
! 4407: for (i=0;i<=imx-1 ; i++) {
! 4408: sump=sump+weight[i];
! 4409: /* sump=sump+1;*/
! 4410: num=num+1;
! 4411: }
! 4412:
! 4413:
! 4414: /* for (i=0; i<=imx; i++)
! 4415: 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]);*/
! 4416: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
! 4417: for (i=1;i<=imx ; i++)
! 4418: {
! 4419: if (cens[i] == 1 && wav[i]>1)
! 4420: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
! 4421:
! 4422: if (cens[i] == 0 && wav[i]>1)
! 4423: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
! 4424: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
! 4425:
! 4426: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
! 4427: if (wav[i] > 1 ) { /* ??? */
! 4428: LL=LL+A*weight[i];
! 4429: /* 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]);*/
! 4430: }
! 4431: }
! 4432:
! 4433: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
! 4434: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
! 4435:
! 4436: return -2*LL*num/sump;
! 4437: }
! 4438: #endif
! 4439:
1.126 brouard 4440: /******************* Printing html file ***********/
4441: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4442: int lastpass, int stepm, int weightopt, char model[],\
4443: int imx, double p[],double **matcov,double agemortsup){
4444: int i,k;
4445:
4446: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4447: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4448: for (i=1;i<=2;i++)
4449: 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]));
4450: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4451: fprintf(fichtm,"</ul>");
4452:
4453: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4454:
4455: 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>");
4456:
4457: for (k=agegomp;k<(agemortsup-2);k++)
4458: 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]);
4459:
4460:
4461: fflush(fichtm);
4462: }
4463:
4464: /******************* Gnuplot file **************/
4465: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4466:
4467: char dirfileres[132],optfileres[132];
4468: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4469: int ng;
4470:
4471:
4472: /*#ifdef windows */
4473: fprintf(ficgp,"cd \"%s\" \n",pathc);
4474: /*#endif */
4475:
4476:
4477: strcpy(dirfileres,optionfilefiname);
4478: strcpy(optfileres,"vpl");
4479: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4480: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4481: fprintf(ficgp, "set ter png small\n set log y\n");
4482: fprintf(ficgp, "set size 0.65,0.65\n");
4483: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4484:
4485: }
4486:
1.136 ! brouard 4487: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
! 4488: {
1.126 brouard 4489:
1.136 ! brouard 4490: /*-------- data file ----------*/
! 4491: FILE *fic;
! 4492: char dummy[]=" ";
! 4493: int i, j, n;
! 4494: int linei, month, year,iout;
! 4495: char line[MAXLINE], linetmp[MAXLINE];
! 4496: char stra[80], strb[80];
! 4497: char *stratrunc;
! 4498: int lstra;
1.126 brouard 4499:
4500:
1.136 ! brouard 4501: if((fic=fopen(datafile,"r"))==NULL) {
! 4502: printf("Problem while opening datafile: %s\n", datafile);return 1;
! 4503: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
! 4504: }
1.126 brouard 4505:
1.136 ! brouard 4506: i=1;
! 4507: linei=0;
! 4508: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
! 4509: linei=linei+1;
! 4510: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
! 4511: if(line[j] == '\t')
! 4512: line[j] = ' ';
! 4513: }
! 4514: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
! 4515: ;
! 4516: };
! 4517: line[j+1]=0; /* Trims blanks at end of line */
! 4518: if(line[0]=='#'){
! 4519: fprintf(ficlog,"Comment line\n%s\n",line);
! 4520: printf("Comment line\n%s\n",line);
! 4521: continue;
! 4522: }
! 4523: trimbb(linetmp,line); /* Trims multiple blanks in line */
! 4524: for (j=0; line[j]!='\0';j++){
! 4525: line[j]=linetmp[j];
! 4526: }
! 4527:
1.126 brouard 4528:
1.136 ! brouard 4529: for (j=maxwav;j>=1;j--){
! 4530: cutv(stra, strb,line,' ');
! 4531: if(strb[0]=='.') { /* Missing status */
! 4532: lval=-1;
! 4533: }else{
! 4534: errno=0;
! 4535: lval=strtol(strb,&endptr,10);
! 4536: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
! 4537: if( strb[0]=='\0' || (*endptr != '\0')){
! 4538: 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);
! 4539: 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);
! 4540: return 1;
! 4541: }
! 4542: }
! 4543: s[j][i]=lval;
! 4544:
! 4545: strcpy(line,stra);
! 4546: cutv(stra, strb,line,' ');
! 4547: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4548: }
! 4549: else if(iout=sscanf(strb,"%s.") != 0){
! 4550: month=99;
! 4551: year=9999;
! 4552: }else{
! 4553: 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);
! 4554: 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);
! 4555: return 1;
! 4556: }
! 4557: anint[j][i]= (double) year;
! 4558: mint[j][i]= (double)month;
! 4559: strcpy(line,stra);
! 4560: } /* ENd Waves */
! 4561:
! 4562: cutv(stra, strb,line,' ');
! 4563: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4564: }
! 4565: else if(iout=sscanf(strb,"%s.",dummy) != 0){
! 4566: month=99;
! 4567: year=9999;
! 4568: }else{
! 4569: 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);
! 4570: 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);
! 4571: return 1;
! 4572: }
! 4573: andc[i]=(double) year;
! 4574: moisdc[i]=(double) month;
! 4575: strcpy(line,stra);
! 4576:
! 4577: cutv(stra, strb,line,' ');
! 4578: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
! 4579: }
! 4580: else if(iout=sscanf(strb,"%s.") != 0){
! 4581: month=99;
! 4582: year=9999;
! 4583: }else{
! 4584: 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);
! 4585: 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);
! 4586: return 1;
! 4587: }
! 4588: if (year==9999) {
! 4589: 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);
! 4590: 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);
! 4591: return 1;
1.126 brouard 4592:
1.136 ! brouard 4593: }
! 4594: annais[i]=(double)(year);
! 4595: moisnais[i]=(double)(month);
! 4596: strcpy(line,stra);
! 4597:
! 4598: cutv(stra, strb,line,' ');
! 4599: errno=0;
! 4600: dval=strtod(strb,&endptr);
! 4601: if( strb[0]=='\0' || (*endptr != '\0')){
! 4602: printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
! 4603: 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);
! 4604: fflush(ficlog);
! 4605: return 1;
! 4606: }
! 4607: weight[i]=dval;
! 4608: strcpy(line,stra);
! 4609:
! 4610: for (j=ncovcol;j>=1;j--){
! 4611: cutv(stra, strb,line,' ');
! 4612: if(strb[0]=='.') { /* Missing status */
! 4613: lval=-1;
! 4614: }else{
! 4615: errno=0;
! 4616: lval=strtol(strb,&endptr,10);
! 4617: if( strb[0]=='\0' || (*endptr != '\0')){
! 4618: 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);
! 4619: 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);
! 4620: return 1;
! 4621: }
! 4622: }
! 4623: if(lval <-1 || lval >1){
! 4624: printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
! 4625: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 4626: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 4627: For example, for multinomial values like 1, 2 and 3,\n \
! 4628: build V1=0 V2=0 for the reference value (1),\n \
! 4629: V1=1 V2=0 for (2) \n \
! 4630: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 4631: output of IMaCh is often meaningless.\n \
! 4632: Exiting.\n",lval,linei, i,line,j);
! 4633: fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
! 4634: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
! 4635: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
! 4636: For example, for multinomial values like 1, 2 and 3,\n \
! 4637: build V1=0 V2=0 for the reference value (1),\n \
! 4638: V1=1 V2=0 for (2) \n \
! 4639: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
! 4640: output of IMaCh is often meaningless.\n \
! 4641: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
! 4642: return 1;
! 4643: }
! 4644: covar[j][i]=(double)(lval);
! 4645: strcpy(line,stra);
! 4646: }
! 4647: lstra=strlen(stra);
! 4648:
! 4649: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
! 4650: stratrunc = &(stra[lstra-9]);
! 4651: num[i]=atol(stratrunc);
! 4652: }
! 4653: else
! 4654: num[i]=atol(stra);
! 4655: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
! 4656: 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;}*/
! 4657:
! 4658: i=i+1;
! 4659: } /* End loop reading data */
1.126 brouard 4660:
1.136 ! brouard 4661: *imax=i-1; /* Number of individuals */
! 4662: fclose(fic);
! 4663:
! 4664: return (0);
! 4665: endread:
! 4666: printf("Exiting readdata: ");
! 4667: fclose(fic);
! 4668: return (1);
1.126 brouard 4669:
4670:
4671:
1.136 ! brouard 4672: }
1.126 brouard 4673:
1.136 ! brouard 4674: int decodemodel ( char model[], int lastobs)
! 4675: {
! 4676: int i, j, k;
! 4677: int i1, j1, k1, k2;
! 4678: char modelsav[80];
! 4679: char stra[80], strb[80], strc[80], strd[80],stre[80];
! 4680:
! 4681: if (strlen(model) >1){ /* If there is at least 1 covariate */
! 4682: j=0, j1=0, k1=1, k2=1;
! 4683: j=nbocc(model,'+'); /* j=Number of '+' */
! 4684: j1=nbocc(model,'*'); /* j1=Number of '*' */
! 4685: cptcovn=j+1; /* Number of covariates V1+V2*age+V3 =>(2 plus signs) + 1=3
! 4686: but the covariates which are product must be computed and stored. */
! 4687: cptcovprod=j1; /*Number of products V1*V2 +v3*age = 2 */
! 4688:
! 4689: strcpy(modelsav,model);
! 4690: if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
! 4691: printf("Error. Non available option model=%s ",model);
! 4692: fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
! 4693: return 1;
! 4694: }
! 4695:
! 4696: /* This loop fills the array Tvar from the string 'model'.*/
! 4697: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
! 4698: /* modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
! 4699: i=1 Tvar[1]=3 Tage[1]=1
! 4700: i=2 Tvar[2]=2
! 4701: i=3 Tvar[3]=1
! 4702: i=4 Tvar[4]= 4
! 4703: i=5 Tvar[5]
! 4704: for (k=1; k<=cptcovn;k++) {
! 4705: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
! 4706: */
! 4707: for(k=1; k<=(j+1);k++){
! 4708: cutv(strb,stra,modelsav,'+'); /* keeps in strb after the first '+'
! 4709: modelsav=V3*age+V2+V1+V4 strb=V3*age stra=V2+V1+V4
! 4710: */
! 4711: /* if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);*/ /* and analyzes it */
! 4712: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
! 4713: /*scanf("%d",i);*/
! 4714: if (strchr(strb,'*')) { /* Model includes a product V3*age+V2+V1+V4 strb=V3*age */
! 4715: cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn: strb=V3*age strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
! 4716: if (strcmp(strc,"age")==0) { /* Vn*age */
! 4717: cptcovprod--;
! 4718: cutv(strb,stre,strd,'V'); /* stre="V3" */
! 4719: Tvar[k]=atoi(stre); /* V1+V3*age+V2 Tvar[2]=3, and Tvar[3]=2 */
! 4720: cptcovage++; /* Sums the number of covariates which include age as a product */
! 4721: Tage[cptcovage]=k; /* Tage[1] =2 */
! 4722: /*printf("stre=%s ", stre);*/
! 4723: }
! 4724: else if (strcmp(strd,"age")==0) { /* or age*Vn */
! 4725: cptcovprod--;
! 4726: cutv(strb,stre,strc,'V');
! 4727: Tvar[k]=atoi(stre);
! 4728: cptcovage++;
! 4729: Tage[cptcovage]=k;
! 4730: }
! 4731: else { /* Age is not in the model V1+V3*V2+V2 strb=V3*V2*/
! 4732: cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
! 4733: Tvar[k]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
! 4734: If already ncovcol=2 and model=V2*V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc */
! 4735: cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
! 4736: Tprod[k1]=k; /* Tprod[1] */
! 4737: Tvard[k1][1]=atoi(strc); /* m*/
! 4738: Tvard[k1][2]=atoi(stre); /* n */
! 4739: Tvar[cptcovn+k2]=Tvard[k1][1];
! 4740: Tvar[cptcovn+k2+1]=Tvard[k1][2];
! 4741: for (i=1; i<=lastobs;i++) /* Computes the new covariate which is a product of covar[n][i]* covar[m][i]
! 4742: and is stored at ncovol+k1 */
! 4743: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
! 4744: k1++;
! 4745: k2=k2+2;
! 4746: }
! 4747: }
! 4748: else { /* no more sum */
! 4749: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
! 4750: /* scanf("%d",i);*/
! 4751: cutv(strd,strc,strb,'V');
! 4752: Tvar[i]=atoi(strc);
! 4753: }
! 4754: strcpy(modelsav,stra); /* modelsav=V2+V3*age+V1+V4 strb=V3*age+V1+V4 */
! 4755: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
! 4756: scanf("%d",i);*/
! 4757: } /* end of loop + */
! 4758: } /* end model */
! 4759:
! 4760: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
! 4761: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
! 4762:
! 4763: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
! 4764: printf("cptcovprod=%d ", cptcovprod);
! 4765: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
! 4766:
! 4767: scanf("%d ",i);*/
! 4768:
! 4769:
! 4770: return (0);
! 4771: endread:
! 4772: printf("Exiting decodemodel: ");
! 4773: return (1);
! 4774: }
! 4775:
! 4776: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
! 4777: {
! 4778: int i, m;
! 4779:
! 4780: for (i=1; i<=imx; i++) {
! 4781: for(m=2; (m<= maxwav); m++) {
! 4782: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
! 4783: anint[m][i]=9999;
! 4784: s[m][i]=-1;
! 4785: }
! 4786: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
! 4787: *nberr++;
! 4788: 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);
! 4789: 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);
! 4790: s[m][i]=-1;
! 4791: }
! 4792: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
! 4793: *nberr++;
! 4794: 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]);
! 4795: 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]);
! 4796: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
! 4797: }
! 4798: }
! 4799: }
! 4800:
! 4801: for (i=1; i<=imx; i++) {
! 4802: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
! 4803: for(m=firstpass; (m<= lastpass); m++){
! 4804: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
! 4805: if (s[m][i] >= nlstate+1) {
! 4806: if(agedc[i]>0)
! 4807: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
! 4808: agev[m][i]=agedc[i];
! 4809: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
! 4810: else {
! 4811: if ((int)andc[i]!=9999){
! 4812: nbwarn++;
! 4813: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
! 4814: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
! 4815: agev[m][i]=-1;
! 4816: }
! 4817: }
! 4818: }
! 4819: else if(s[m][i] !=9){ /* Standard case, age in fractional
! 4820: years but with the precision of a month */
! 4821: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
! 4822: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
! 4823: agev[m][i]=1;
! 4824: else if(agev[m][i] < *agemin){
! 4825: *agemin=agev[m][i];
! 4826: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
! 4827: }
! 4828: else if(agev[m][i] >*agemax){
! 4829: *agemax=agev[m][i];
! 4830: /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
! 4831: }
! 4832: /*agev[m][i]=anint[m][i]-annais[i];*/
! 4833: /* agev[m][i] = age[i]+2*m;*/
! 4834: }
! 4835: else { /* =9 */
! 4836: agev[m][i]=1;
! 4837: s[m][i]=-1;
! 4838: }
! 4839: }
! 4840: else /*= 0 Unknown */
! 4841: agev[m][i]=1;
! 4842: }
! 4843:
! 4844: }
! 4845: for (i=1; i<=imx; i++) {
! 4846: for(m=firstpass; (m<=lastpass); m++){
! 4847: if (s[m][i] > (nlstate+ndeath)) {
! 4848: *nberr++;
! 4849: 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);
! 4850: 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);
! 4851: return 1;
! 4852: }
! 4853: }
! 4854: }
! 4855:
! 4856: /*for (i=1; i<=imx; i++){
! 4857: for (m=firstpass; (m<lastpass); m++){
! 4858: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
! 4859: }
! 4860:
! 4861: }*/
! 4862:
! 4863:
! 4864: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 4865: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
! 4866:
! 4867: return (0);
! 4868: endread:
! 4869: printf("Exiting calandcheckages: ");
! 4870: return (1);
! 4871: }
! 4872:
! 4873:
! 4874: /***********************************************/
! 4875: /**************** Main Program *****************/
! 4876: /***********************************************/
! 4877:
! 4878: int main(int argc, char *argv[])
! 4879: {
! 4880: #ifdef GSL
! 4881: const gsl_multimin_fminimizer_type *T;
! 4882: size_t iteri = 0, it;
! 4883: int rval = GSL_CONTINUE;
! 4884: int status = GSL_SUCCESS;
! 4885: double ssval;
! 4886: #endif
! 4887: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
! 4888: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
! 4889: int linei, month, year,iout;
! 4890: int jj, ll, li, lj, lk, imk;
! 4891: int numlinepar=0; /* Current linenumber of parameter file */
! 4892: int itimes;
! 4893: int NDIM=2;
! 4894: int vpopbased=0;
! 4895:
! 4896: char ca[32], cb[32], cc[32];
! 4897: /* FILE *fichtm; *//* Html File */
! 4898: /* FILE *ficgp;*/ /*Gnuplot File */
! 4899: struct stat info;
! 4900: double agedeb, agefin,hf;
! 4901: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
! 4902:
! 4903: double fret;
! 4904: double **xi,tmp,delta;
! 4905:
! 4906: double dum; /* Dummy variable */
! 4907: double ***p3mat;
! 4908: double ***mobaverage;
! 4909: int *indx;
! 4910: char line[MAXLINE], linepar[MAXLINE];
! 4911: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
! 4912: char pathr[MAXLINE], pathimach[MAXLINE];
! 4913: char **bp, *tok, *val; /* pathtot */
! 4914: int firstobs=1, lastobs=10;
! 4915: int sdeb, sfin; /* Status at beginning and end */
! 4916: int c, h , cpt,l;
! 4917: int ju,jl, mi;
! 4918: int i1,j1, jk,aa,bb, stepsize, ij;
! 4919: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
! 4920: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
! 4921: int mobilav=0,popforecast=0;
! 4922: int hstepm, nhstepm;
! 4923: int agemortsup;
! 4924: float sumlpop=0.;
! 4925: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
! 4926: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
! 4927:
! 4928: double bage, fage, age, agelim, agebase;
! 4929: double ftolpl=FTOL;
! 4930: double **prlim;
! 4931: double ***param; /* Matrix of parameters */
! 4932: double *p;
! 4933: double **matcov; /* Matrix of covariance */
! 4934: double ***delti3; /* Scale */
! 4935: double *delti; /* Scale */
! 4936: double ***eij, ***vareij;
! 4937: double **varpl; /* Variances of prevalence limits by age */
! 4938: double *epj, vepp;
! 4939: double kk1, kk2;
! 4940: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
! 4941: double **ximort;
! 4942: char *alph[]={"a","a","b","c","d","e"}, str[4];
! 4943: int *dcwave;
! 4944:
! 4945: char z[1]="c", occ;
! 4946:
! 4947: /*char *strt;*/
! 4948: char strtend[80];
1.126 brouard 4949:
4950: long total_usecs;
4951:
4952: /* setlocale (LC_ALL, ""); */
4953: /* bindtextdomain (PACKAGE, LOCALEDIR); */
4954: /* textdomain (PACKAGE); */
4955: /* setlocale (LC_CTYPE, ""); */
4956: /* setlocale (LC_MESSAGES, ""); */
4957:
4958: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
4959: (void) gettimeofday(&start_time,&tzp);
4960: curr_time=start_time;
4961: tm = *localtime(&start_time.tv_sec);
4962: tmg = *gmtime(&start_time.tv_sec);
4963: strcpy(strstart,asctime(&tm));
4964:
4965: /* printf("Localtime (at start)=%s",strstart); */
4966: /* tp.tv_sec = tp.tv_sec +86400; */
4967: /* tm = *localtime(&start_time.tv_sec); */
4968: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
4969: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
4970: /* tmg.tm_hour=tmg.tm_hour + 1; */
4971: /* tp.tv_sec = mktime(&tmg); */
4972: /* strt=asctime(&tmg); */
4973: /* printf("Time(after) =%s",strstart); */
4974: /* (void) time (&time_value);
4975: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
4976: * tm = *localtime(&time_value);
4977: * strstart=asctime(&tm);
4978: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
4979: */
4980:
4981: nberr=0; /* Number of errors and warnings */
4982: nbwarn=0;
4983: getcwd(pathcd, size);
4984:
4985: printf("\n%s\n%s",version,fullversion);
4986: if(argc <=1){
4987: printf("\nEnter the parameter file name: ");
4988: fgets(pathr,FILENAMELENGTH,stdin);
4989: i=strlen(pathr);
4990: if(pathr[i-1]=='\n')
4991: pathr[i-1]='\0';
4992: for (tok = pathr; tok != NULL; ){
4993: printf("Pathr |%s|\n",pathr);
4994: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
4995: printf("val= |%s| pathr=%s\n",val,pathr);
4996: strcpy (pathtot, val);
4997: if(pathr[0] == '\0') break; /* Dirty */
4998: }
4999: }
5000: else{
5001: strcpy(pathtot,argv[1]);
5002: }
5003: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5004: /*cygwin_split_path(pathtot,path,optionfile);
5005: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5006: /* cutv(path,optionfile,pathtot,'\\');*/
5007:
5008: /* Split argv[0], imach program to get pathimach */
5009: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5010: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5011: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5012: /* strcpy(pathimach,argv[0]); */
5013: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5014: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5015: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5016: chdir(path); /* Can be a relative path */
5017: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5018: printf("Current directory %s!\n",pathcd);
5019: strcpy(command,"mkdir ");
5020: strcat(command,optionfilefiname);
5021: if((outcmd=system(command)) != 0){
5022: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5023: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5024: /* fclose(ficlog); */
5025: /* exit(1); */
5026: }
5027: /* if((imk=mkdir(optionfilefiname))<0){ */
5028: /* perror("mkdir"); */
5029: /* } */
5030:
5031: /*-------- arguments in the command line --------*/
5032:
5033: /* Log file */
5034: strcat(filelog, optionfilefiname);
5035: strcat(filelog,".log"); /* */
5036: if((ficlog=fopen(filelog,"w"))==NULL) {
5037: printf("Problem with logfile %s\n",filelog);
5038: goto end;
5039: }
5040: fprintf(ficlog,"Log filename:%s\n",filelog);
5041: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5042: fprintf(ficlog,"\nEnter the parameter file name: \n");
5043: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5044: path=%s \n\
5045: optionfile=%s\n\
5046: optionfilext=%s\n\
5047: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5048:
5049: printf("Local time (at start):%s",strstart);
5050: fprintf(ficlog,"Local time (at start): %s",strstart);
5051: fflush(ficlog);
5052: /* (void) gettimeofday(&curr_time,&tzp); */
5053: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5054:
5055: /* */
5056: strcpy(fileres,"r");
5057: strcat(fileres, optionfilefiname);
5058: strcat(fileres,".txt"); /* Other files have txt extension */
5059:
5060: /*---------arguments file --------*/
5061:
5062: if((ficpar=fopen(optionfile,"r"))==NULL) {
5063: printf("Problem with optionfile %s\n",optionfile);
5064: fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
5065: fflush(ficlog);
5066: goto end;
5067: }
5068:
5069:
5070:
5071: strcpy(filereso,"o");
5072: strcat(filereso,fileres);
5073: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5074: printf("Problem with Output resultfile: %s\n", filereso);
5075: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5076: fflush(ficlog);
5077: goto end;
5078: }
5079:
5080: /* Reads comments: lines beginning with '#' */
5081: numlinepar=0;
5082: while((c=getc(ficpar))=='#' && c!= EOF){
5083: ungetc(c,ficpar);
5084: fgets(line, MAXLINE, ficpar);
5085: numlinepar++;
5086: puts(line);
5087: fputs(line,ficparo);
5088: fputs(line,ficlog);
5089: }
5090: ungetc(c,ficpar);
5091:
5092: 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);
5093: numlinepar++;
5094: 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);
5095: 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);
5096: 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);
5097: fflush(ficlog);
5098: while((c=getc(ficpar))=='#' && c!= EOF){
5099: ungetc(c,ficpar);
5100: fgets(line, MAXLINE, ficpar);
5101: numlinepar++;
5102: puts(line);
5103: fputs(line,ficparo);
5104: fputs(line,ficlog);
5105: }
5106: ungetc(c,ficpar);
5107:
5108:
5109: covar=matrix(0,NCOVMAX,1,n);
1.136 ! brouard 5110: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
! 5111: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
! 5112: v1+v2*age+v2*v3 makes cptcovn = 3
! 5113: */
! 5114: if (strlen(model)>1)
! 5115: cptcovn=nbocc(model,'+')+1;
! 5116: /* ncovprod */
! 5117: ncovmodel=2+cptcovn; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
1.126 brouard 5118: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5119: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5120: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5121: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5122: 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);
5123: 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);
5124: fflush(stdout);
5125: fclose (ficlog);
5126: goto end;
5127: }
1.126 brouard 5128: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5129: delti=delti3[1][1];
5130: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5131: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5132: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5133: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5134: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5135: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5136: fclose (ficparo);
5137: fclose (ficlog);
5138: goto end;
5139: exit(0);
5140: }
5141: else if(mle==-3) {
5142: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5143: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5144: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5145: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5146: matcov=matrix(1,npar,1,npar);
5147: }
5148: else{
5149: /* Read guess parameters */
5150: /* Reads comments: lines beginning with '#' */
5151: while((c=getc(ficpar))=='#' && c!= EOF){
5152: ungetc(c,ficpar);
5153: fgets(line, MAXLINE, ficpar);
5154: numlinepar++;
5155: puts(line);
5156: fputs(line,ficparo);
5157: fputs(line,ficlog);
5158: }
5159: ungetc(c,ficpar);
5160:
5161: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5162: for(i=1; i <=nlstate; i++){
5163: j=0;
5164: for(jj=1; jj <=nlstate+ndeath; jj++){
5165: if(jj==i) continue;
5166: j++;
5167: fscanf(ficpar,"%1d%1d",&i1,&j1);
5168: if ((i1 != i) && (j1 != j)){
5169: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5170: It might be a problem of design; if ncovcol and the model are correct\n \
5171: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5172: exit(1);
5173: }
5174: fprintf(ficparo,"%1d%1d",i1,j1);
5175: if(mle==1)
5176: printf("%1d%1d",i,j);
5177: fprintf(ficlog,"%1d%1d",i,j);
5178: for(k=1; k<=ncovmodel;k++){
5179: fscanf(ficpar," %lf",¶m[i][j][k]);
5180: if(mle==1){
5181: printf(" %lf",param[i][j][k]);
5182: fprintf(ficlog," %lf",param[i][j][k]);
5183: }
5184: else
5185: fprintf(ficlog," %lf",param[i][j][k]);
5186: fprintf(ficparo," %lf",param[i][j][k]);
5187: }
5188: fscanf(ficpar,"\n");
5189: numlinepar++;
5190: if(mle==1)
5191: printf("\n");
5192: fprintf(ficlog,"\n");
5193: fprintf(ficparo,"\n");
5194: }
5195: }
5196: fflush(ficlog);
5197:
5198: p=param[1][1];
5199:
5200: /* Reads comments: lines beginning with '#' */
5201: while((c=getc(ficpar))=='#' && c!= EOF){
5202: ungetc(c,ficpar);
5203: fgets(line, MAXLINE, ficpar);
5204: numlinepar++;
5205: puts(line);
5206: fputs(line,ficparo);
5207: fputs(line,ficlog);
5208: }
5209: ungetc(c,ficpar);
5210:
5211: for(i=1; i <=nlstate; i++){
5212: for(j=1; j <=nlstate+ndeath-1; j++){
5213: fscanf(ficpar,"%1d%1d",&i1,&j1);
5214: if ((i1-i)*(j1-j)!=0){
5215: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5216: exit(1);
5217: }
5218: printf("%1d%1d",i,j);
5219: fprintf(ficparo,"%1d%1d",i1,j1);
5220: fprintf(ficlog,"%1d%1d",i1,j1);
5221: for(k=1; k<=ncovmodel;k++){
5222: fscanf(ficpar,"%le",&delti3[i][j][k]);
5223: printf(" %le",delti3[i][j][k]);
5224: fprintf(ficparo," %le",delti3[i][j][k]);
5225: fprintf(ficlog," %le",delti3[i][j][k]);
5226: }
5227: fscanf(ficpar,"\n");
5228: numlinepar++;
5229: printf("\n");
5230: fprintf(ficparo,"\n");
5231: fprintf(ficlog,"\n");
5232: }
5233: }
5234: fflush(ficlog);
5235:
5236: delti=delti3[1][1];
5237:
5238:
5239: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5240:
5241: /* Reads comments: lines beginning with '#' */
5242: while((c=getc(ficpar))=='#' && c!= EOF){
5243: ungetc(c,ficpar);
5244: fgets(line, MAXLINE, ficpar);
5245: numlinepar++;
5246: puts(line);
5247: fputs(line,ficparo);
5248: fputs(line,ficlog);
5249: }
5250: ungetc(c,ficpar);
5251:
5252: matcov=matrix(1,npar,1,npar);
1.131 brouard 5253: for(i=1; i <=npar; i++)
5254: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5255:
1.126 brouard 5256: for(i=1; i <=npar; i++){
5257: fscanf(ficpar,"%s",&str);
5258: if(mle==1)
5259: printf("%s",str);
5260: fprintf(ficlog,"%s",str);
5261: fprintf(ficparo,"%s",str);
5262: for(j=1; j <=i; j++){
5263: fscanf(ficpar," %le",&matcov[i][j]);
5264: if(mle==1){
5265: printf(" %.5le",matcov[i][j]);
5266: }
5267: fprintf(ficlog," %.5le",matcov[i][j]);
5268: fprintf(ficparo," %.5le",matcov[i][j]);
5269: }
5270: fscanf(ficpar,"\n");
5271: numlinepar++;
5272: if(mle==1)
5273: printf("\n");
5274: fprintf(ficlog,"\n");
5275: fprintf(ficparo,"\n");
5276: }
5277: for(i=1; i <=npar; i++)
5278: for(j=i+1;j<=npar;j++)
5279: matcov[i][j]=matcov[j][i];
5280:
5281: if(mle==1)
5282: printf("\n");
5283: fprintf(ficlog,"\n");
5284:
5285: fflush(ficlog);
5286:
5287: /*-------- Rewriting parameter file ----------*/
5288: strcpy(rfileres,"r"); /* "Rparameterfile */
5289: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5290: strcat(rfileres,"."); /* */
5291: strcat(rfileres,optionfilext); /* Other files have txt extension */
5292: if((ficres =fopen(rfileres,"w"))==NULL) {
5293: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5294: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5295: }
5296: fprintf(ficres,"#%s\n",version);
5297: } /* End of mle != -3 */
5298:
5299:
5300: n= lastobs;
5301: num=lvector(1,n);
5302: moisnais=vector(1,n);
5303: annais=vector(1,n);
5304: moisdc=vector(1,n);
5305: andc=vector(1,n);
5306: agedc=vector(1,n);
5307: cod=ivector(1,n);
5308: weight=vector(1,n);
5309: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5310: mint=matrix(1,maxwav,1,n);
5311: anint=matrix(1,maxwav,1,n);
1.131 brouard 5312: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5313: tab=ivector(1,NCOVMAX);
5314: ncodemax=ivector(1,8);
5315:
1.136 ! brouard 5316: /* Reads data from file datafile */
! 5317: if (readdata(datafile, firstobs, lastobs, &imx)==1)
! 5318: goto end;
! 5319:
! 5320: /* Calculation of the number of parameters from char model */
! 5321: 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 */
! 5322: Tprod=ivector(1,15);
! 5323: Tvaraff=ivector(1,15);
! 5324: Tvard=imatrix(1,15,1,2);
! 5325: Tage=ivector(1,15);
! 5326:
! 5327: if(decodemodel(model, lastobs) == 1)
! 5328: goto end;
! 5329:
! 5330: /* if(mle==1){*/
! 5331: if (weightopt != 1) { /* Maximisation without weights*/
! 5332: for(i=1;i<=n;i++) weight[i]=1.0;
! 5333: }
! 5334:
! 5335: /*-calculation of age at interview from date of interview and age at death -*/
! 5336: agev=matrix(1,maxwav,1,imx);
! 5337:
! 5338: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
! 5339: goto end;
! 5340:
1.126 brouard 5341:
1.136 ! brouard 5342: agegomp=(int)agemin;
! 5343: free_vector(moisnais,1,n);
! 5344: free_vector(annais,1,n);
1.126 brouard 5345: /* free_matrix(mint,1,maxwav,1,n);
5346: free_matrix(anint,1,maxwav,1,n);*/
5347: free_vector(moisdc,1,n);
5348: free_vector(andc,1,n);
5349:
5350:
5351: wav=ivector(1,imx);
5352: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5353: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5354: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5355:
5356: /* Concatenates waves */
5357: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
5358:
5359: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5360:
5361: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5362: ncodemax[1]=1;
5363: if (cptcovn > 0) tricode(Tvar,nbcode,imx);
5364:
5365: codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
5366: the estimations*/
5367: h=0;
5368: m=pow(2,cptcoveff);
5369:
1.131 brouard 5370: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
5371: 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 */
5372: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
5373: 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 */
1.126 brouard 5374: h++;
1.136 ! brouard 5375: if (h>m) {
! 5376: h=1;
! 5377: codtab[h][k]=j;
! 5378: codtab[h][Tvar[k]]=j;
! 5379: }
1.130 brouard 5380: 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]]);
1.126 brouard 5381: }
5382: }
5383: }
5384: }
5385: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5386: codtab[1][2]=1;codtab[2][2]=2; */
5387: /* for(i=1; i <=m ;i++){
5388: for(k=1; k <=cptcovn; k++){
1.131 brouard 5389: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5390: }
5391: printf("\n");
5392: }
5393: scanf("%d",i);*/
5394:
5395: /*------------ gnuplot -------------*/
5396: strcpy(optionfilegnuplot,optionfilefiname);
5397: if(mle==-3)
5398: strcat(optionfilegnuplot,"-mort");
5399: strcat(optionfilegnuplot,".gp");
5400:
5401: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5402: printf("Problem with file %s",optionfilegnuplot);
5403: }
5404: else{
5405: fprintf(ficgp,"\n# %s\n", version);
5406: fprintf(ficgp,"# %s\n", optionfilegnuplot);
5407: fprintf(ficgp,"set missing 'NaNq'\n");
5408: }
5409: /* fclose(ficgp);*/
5410: /*--------- index.htm --------*/
5411:
5412: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5413: if(mle==-3)
5414: strcat(optionfilehtm,"-mort");
5415: strcat(optionfilehtm,".htm");
5416: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 5417: printf("Problem with %s \n",optionfilehtm);
5418: exit(0);
1.126 brouard 5419: }
5420:
5421: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5422: strcat(optionfilehtmcov,"-cov.htm");
5423: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5424: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5425: }
5426: else{
5427: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5428: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5429: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5430: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5431: }
5432:
5433: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5434: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5435: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5436: \n\
5437: <hr size=\"2\" color=\"#EC5E5E\">\
5438: <ul><li><h4>Parameter files</h4>\n\
5439: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5440: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5441: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5442: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5443: - Date and time at start: %s</ul>\n",\
5444: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5445: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5446: fileres,fileres,\
5447: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5448: fflush(fichtm);
5449:
5450: strcpy(pathr,path);
5451: strcat(pathr,optionfilefiname);
5452: chdir(optionfilefiname); /* Move to directory named optionfile */
5453:
5454: /* Calculates basic frequencies. Computes observed prevalence at single age
5455: and prints on file fileres'p'. */
5456: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5457:
5458: fprintf(fichtm,"\n");
5459: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5460: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5461: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5462: imx,agemin,agemax,jmin,jmax,jmean);
5463: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5464: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5465: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5466: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5467: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5468:
5469:
5470: /* For Powell, parameters are in a vector p[] starting at p[1]
5471: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5472: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5473:
5474: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5475:
5476: if (mle==-3){
1.136 ! brouard 5477: ximort=matrix(1,NDIM,1,NDIM);
! 5478: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 5479: cens=ivector(1,n);
5480: ageexmed=vector(1,n);
5481: agecens=vector(1,n);
5482: dcwave=ivector(1,n);
5483:
5484: for (i=1; i<=imx; i++){
5485: dcwave[i]=-1;
5486: for (m=firstpass; m<=lastpass; m++)
5487: if (s[m][i]>nlstate) {
5488: dcwave[i]=m;
5489: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5490: break;
5491: }
5492: }
5493:
5494: for (i=1; i<=imx; i++) {
5495: if (wav[i]>0){
5496: ageexmed[i]=agev[mw[1][i]][i];
5497: j=wav[i];
5498: agecens[i]=1.;
5499:
5500: if (ageexmed[i]> 1 && wav[i] > 0){
5501: agecens[i]=agev[mw[j][i]][i];
5502: cens[i]= 1;
5503: }else if (ageexmed[i]< 1)
5504: cens[i]= -1;
5505: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5506: cens[i]=0 ;
5507: }
5508: else cens[i]=-1;
5509: }
5510:
5511: for (i=1;i<=NDIM;i++) {
5512: for (j=1;j<=NDIM;j++)
5513: ximort[i][j]=(i == j ? 1.0 : 0.0);
5514: }
5515:
5516: p[1]=0.0268; p[NDIM]=0.083;
5517: /*printf("%lf %lf", p[1], p[2]);*/
5518:
5519:
1.136 ! brouard 5520: #ifdef GSL
! 5521: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
! 5522: #elsedef
1.126 brouard 5523: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 ! brouard 5524: #endif
1.126 brouard 5525: strcpy(filerespow,"pow-mort");
5526: strcat(filerespow,fileres);
5527: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5528: printf("Problem with resultfile: %s\n", filerespow);
5529: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5530: }
1.136 ! brouard 5531: #ifdef GSL
! 5532: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
! 5533: #elsedef
1.126 brouard 5534: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 ! brouard 5535: #endif
1.126 brouard 5536: /* for (i=1;i<=nlstate;i++)
5537: for(j=1;j<=nlstate+ndeath;j++)
5538: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5539: */
5540: fprintf(ficrespow,"\n");
1.136 ! brouard 5541: #ifdef GSL
! 5542: /* gsl starts here */
! 5543: T = gsl_multimin_fminimizer_nmsimplex;
! 5544: gsl_multimin_fminimizer *sfm = NULL;
! 5545: gsl_vector *ss, *x;
! 5546: gsl_multimin_function minex_func;
! 5547:
! 5548: /* Initial vertex size vector */
! 5549: ss = gsl_vector_alloc (NDIM);
! 5550:
! 5551: if (ss == NULL){
! 5552: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
! 5553: }
! 5554: /* Set all step sizes to 1 */
! 5555: gsl_vector_set_all (ss, 0.001);
! 5556:
! 5557: /* Starting point */
1.126 brouard 5558:
1.136 ! brouard 5559: x = gsl_vector_alloc (NDIM);
! 5560:
! 5561: if (x == NULL){
! 5562: gsl_vector_free(ss);
! 5563: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
! 5564: }
! 5565:
! 5566: /* Initialize method and iterate */
! 5567: /* p[1]=0.0268; p[NDIM]=0.083; */
! 5568: /* gsl_vector_set(x, 0, 0.0268); */
! 5569: /* gsl_vector_set(x, 1, 0.083); */
! 5570: gsl_vector_set(x, 0, p[1]);
! 5571: gsl_vector_set(x, 1, p[2]);
! 5572:
! 5573: minex_func.f = &gompertz_f;
! 5574: minex_func.n = NDIM;
! 5575: minex_func.params = (void *)&p; /* ??? */
! 5576:
! 5577: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
! 5578: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
! 5579:
! 5580: printf("Iterations beginning .....\n\n");
! 5581: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
! 5582:
! 5583: iteri=0;
! 5584: while (rval == GSL_CONTINUE){
! 5585: iteri++;
! 5586: status = gsl_multimin_fminimizer_iterate(sfm);
! 5587:
! 5588: if (status) printf("error: %s\n", gsl_strerror (status));
! 5589: fflush(0);
! 5590:
! 5591: if (status)
! 5592: break;
! 5593:
! 5594: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
! 5595: ssval = gsl_multimin_fminimizer_size (sfm);
! 5596:
! 5597: if (rval == GSL_SUCCESS)
! 5598: printf ("converged to a local maximum at\n");
! 5599:
! 5600: printf("%5d ", iteri);
! 5601: for (it = 0; it < NDIM; it++){
! 5602: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
! 5603: }
! 5604: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
! 5605: }
! 5606:
! 5607: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
! 5608:
! 5609: gsl_vector_free(x); /* initial values */
! 5610: gsl_vector_free(ss); /* inital step size */
! 5611: for (it=0; it<NDIM; it++){
! 5612: p[it+1]=gsl_vector_get(sfm->x,it);
! 5613: fprintf(ficrespow," %.12lf", p[it]);
! 5614: }
! 5615: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
! 5616: #endif
! 5617: #ifdef POWELL
! 5618: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
! 5619: #endif
1.126 brouard 5620: fclose(ficrespow);
5621:
5622: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
5623:
5624: for(i=1; i <=NDIM; i++)
5625: for(j=i+1;j<=NDIM;j++)
5626: matcov[i][j]=matcov[j][i];
5627:
5628: printf("\nCovariance matrix\n ");
5629: for(i=1; i <=NDIM; i++) {
5630: for(j=1;j<=NDIM;j++){
5631: printf("%f ",matcov[i][j]);
5632: }
5633: printf("\n ");
5634: }
5635:
5636: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
5637: for (i=1;i<=NDIM;i++)
5638: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
5639:
5640: lsurv=vector(1,AGESUP);
5641: lpop=vector(1,AGESUP);
5642: tpop=vector(1,AGESUP);
5643: lsurv[agegomp]=100000;
5644:
5645: for (k=agegomp;k<=AGESUP;k++) {
5646: agemortsup=k;
5647: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
5648: }
5649:
5650: for (k=agegomp;k<agemortsup;k++)
5651: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
5652:
5653: for (k=agegomp;k<agemortsup;k++){
5654: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
5655: sumlpop=sumlpop+lpop[k];
5656: }
5657:
5658: tpop[agegomp]=sumlpop;
5659: for (k=agegomp;k<(agemortsup-3);k++){
5660: /* tpop[k+1]=2;*/
5661: tpop[k+1]=tpop[k]-lpop[k];
5662: }
5663:
5664:
5665: printf("\nAge lx qx dx Lx Tx e(x)\n");
5666: for (k=agegomp;k<(agemortsup-2);k++)
5667: 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]);
5668:
5669:
5670: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5671: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5672:
5673: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
5674: stepm, weightopt,\
5675: model,imx,p,matcov,agemortsup);
5676:
5677: free_vector(lsurv,1,AGESUP);
5678: free_vector(lpop,1,AGESUP);
5679: free_vector(tpop,1,AGESUP);
1.136 ! brouard 5680: #ifdef GSL
! 5681: free_ivector(cens,1,n);
! 5682: free_vector(agecens,1,n);
! 5683: free_ivector(dcwave,1,n);
! 5684: free_matrix(ximort,1,NDIM,1,NDIM);
! 5685: #endif
1.126 brouard 5686: } /* Endof if mle==-3 */
5687:
5688: else{ /* For mle >=1 */
1.132 brouard 5689: globpr=0;/* debug */
5690: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 5691: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5692: for (k=1; k<=npar;k++)
5693: printf(" %d %8.5f",k,p[k]);
5694: printf("\n");
5695: globpr=1; /* to print the contributions */
5696: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
5697: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
5698: for (k=1; k<=npar;k++)
5699: printf(" %d %8.5f",k,p[k]);
5700: printf("\n");
5701: if(mle>=1){ /* Could be 1 or 2 */
5702: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
5703: }
5704:
5705: /*--------- results files --------------*/
5706: 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);
5707:
5708:
5709: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5710: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5711: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5712: for(i=1,jk=1; i <=nlstate; i++){
5713: for(k=1; k <=(nlstate+ndeath); k++){
5714: if (k != i) {
5715: printf("%d%d ",i,k);
5716: fprintf(ficlog,"%d%d ",i,k);
5717: fprintf(ficres,"%1d%1d ",i,k);
5718: for(j=1; j <=ncovmodel; j++){
5719: printf("%lf ",p[jk]);
5720: fprintf(ficlog,"%lf ",p[jk]);
5721: fprintf(ficres,"%lf ",p[jk]);
5722: jk++;
5723: }
5724: printf("\n");
5725: fprintf(ficlog,"\n");
5726: fprintf(ficres,"\n");
5727: }
5728: }
5729: }
5730: if(mle!=0){
5731: /* Computing hessian and covariance matrix */
5732: ftolhess=ftol; /* Usually correct */
5733: hesscov(matcov, p, npar, delti, ftolhess, func);
5734: }
5735: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
5736: printf("# Scales (for hessian or gradient estimation)\n");
5737: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
5738: for(i=1,jk=1; i <=nlstate; i++){
5739: for(j=1; j <=nlstate+ndeath; j++){
5740: if (j!=i) {
5741: fprintf(ficres,"%1d%1d",i,j);
5742: printf("%1d%1d",i,j);
5743: fprintf(ficlog,"%1d%1d",i,j);
5744: for(k=1; k<=ncovmodel;k++){
5745: printf(" %.5e",delti[jk]);
5746: fprintf(ficlog," %.5e",delti[jk]);
5747: fprintf(ficres," %.5e",delti[jk]);
5748: jk++;
5749: }
5750: printf("\n");
5751: fprintf(ficlog,"\n");
5752: fprintf(ficres,"\n");
5753: }
5754: }
5755: }
5756:
5757: 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");
5758: if(mle>=1)
5759: 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");
5760: 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");
5761: /* # 121 Var(a12)\n\ */
5762: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5763: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5764: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5765: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5766: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5767: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5768: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5769:
5770:
5771: /* Just to have a covariance matrix which will be more understandable
5772: even is we still don't want to manage dictionary of variables
5773: */
5774: for(itimes=1;itimes<=2;itimes++){
5775: jj=0;
5776: for(i=1; i <=nlstate; i++){
5777: for(j=1; j <=nlstate+ndeath; j++){
5778: if(j==i) continue;
5779: for(k=1; k<=ncovmodel;k++){
5780: jj++;
5781: ca[0]= k+'a'-1;ca[1]='\0';
5782: if(itimes==1){
5783: if(mle>=1)
5784: printf("#%1d%1d%d",i,j,k);
5785: fprintf(ficlog,"#%1d%1d%d",i,j,k);
5786: fprintf(ficres,"#%1d%1d%d",i,j,k);
5787: }else{
5788: if(mle>=1)
5789: printf("%1d%1d%d",i,j,k);
5790: fprintf(ficlog,"%1d%1d%d",i,j,k);
5791: fprintf(ficres,"%1d%1d%d",i,j,k);
5792: }
5793: ll=0;
5794: for(li=1;li <=nlstate; li++){
5795: for(lj=1;lj <=nlstate+ndeath; lj++){
5796: if(lj==li) continue;
5797: for(lk=1;lk<=ncovmodel;lk++){
5798: ll++;
5799: if(ll<=jj){
5800: cb[0]= lk +'a'-1;cb[1]='\0';
5801: if(ll<jj){
5802: if(itimes==1){
5803: if(mle>=1)
5804: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5805: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5806: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5807: }else{
5808: if(mle>=1)
5809: printf(" %.5e",matcov[jj][ll]);
5810: fprintf(ficlog," %.5e",matcov[jj][ll]);
5811: fprintf(ficres," %.5e",matcov[jj][ll]);
5812: }
5813: }else{
5814: if(itimes==1){
5815: if(mle>=1)
5816: printf(" Var(%s%1d%1d)",ca,i,j);
5817: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
5818: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
5819: }else{
5820: if(mle>=1)
5821: printf(" %.5e",matcov[jj][ll]);
5822: fprintf(ficlog," %.5e",matcov[jj][ll]);
5823: fprintf(ficres," %.5e",matcov[jj][ll]);
5824: }
5825: }
5826: }
5827: } /* end lk */
5828: } /* end lj */
5829: } /* end li */
5830: if(mle>=1)
5831: printf("\n");
5832: fprintf(ficlog,"\n");
5833: fprintf(ficres,"\n");
5834: numlinepar++;
5835: } /* end k*/
5836: } /*end j */
5837: } /* end i */
5838: } /* end itimes */
5839:
5840: fflush(ficlog);
5841: fflush(ficres);
5842:
5843: while((c=getc(ficpar))=='#' && c!= EOF){
5844: ungetc(c,ficpar);
5845: fgets(line, MAXLINE, ficpar);
5846: puts(line);
5847: fputs(line,ficparo);
5848: }
5849: ungetc(c,ficpar);
5850:
5851: estepm=0;
5852: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
5853: if (estepm==0 || estepm < stepm) estepm=stepm;
5854: if (fage <= 2) {
5855: bage = ageminpar;
5856: fage = agemaxpar;
5857: }
5858:
5859: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
5860: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5861: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
5862:
5863: while((c=getc(ficpar))=='#' && c!= EOF){
5864: ungetc(c,ficpar);
5865: fgets(line, MAXLINE, ficpar);
5866: puts(line);
5867: fputs(line,ficparo);
5868: }
5869: ungetc(c,ficpar);
5870:
5871: 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);
5872: 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);
5873: 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);
5874: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
5875: 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);
5876:
5877: while((c=getc(ficpar))=='#' && c!= EOF){
5878: ungetc(c,ficpar);
5879: fgets(line, MAXLINE, ficpar);
5880: puts(line);
5881: fputs(line,ficparo);
5882: }
5883: ungetc(c,ficpar);
5884:
5885:
5886: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
5887: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
5888:
5889: fscanf(ficpar,"pop_based=%d\n",&popbased);
5890: fprintf(ficparo,"pop_based=%d\n",popbased);
5891: fprintf(ficres,"pop_based=%d\n",popbased);
5892:
5893: while((c=getc(ficpar))=='#' && c!= EOF){
5894: ungetc(c,ficpar);
5895: fgets(line, MAXLINE, ficpar);
5896: puts(line);
5897: fputs(line,ficparo);
5898: }
5899: ungetc(c,ficpar);
5900:
5901: 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);
5902: 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);
5903: 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);
5904: 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);
5905: 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);
5906: /* day and month of proj2 are not used but only year anproj2.*/
5907:
5908:
5909:
5910: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
5911: /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
5912:
5913: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
5914: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
5915:
5916: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
5917: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
5918: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
5919:
5920: /*------------ free_vector -------------*/
5921: /* chdir(path); */
5922:
5923: free_ivector(wav,1,imx);
5924: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
5925: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
5926: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
5927: free_lvector(num,1,n);
5928: free_vector(agedc,1,n);
5929: /*free_matrix(covar,0,NCOVMAX,1,n);*/
5930: /*free_matrix(covar,1,NCOVMAX,1,n);*/
5931: fclose(ficparo);
5932: fclose(ficres);
5933:
5934:
5935: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
5936:
5937: strcpy(filerespl,"pl");
5938: strcat(filerespl,fileres);
5939: if((ficrespl=fopen(filerespl,"w"))==NULL) {
5940: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5941: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
5942: }
5943: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5944: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
5945: pstamp(ficrespl);
5946: fprintf(ficrespl,"# Period (stable) prevalence \n");
5947: fprintf(ficrespl,"#Age ");
5948: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
5949: fprintf(ficrespl,"\n");
5950:
5951: prlim=matrix(1,nlstate,1,nlstate);
5952:
5953: agebase=ageminpar;
5954: agelim=agemaxpar;
5955: ftolpl=1.e-10;
5956: i1=cptcoveff;
5957: if (cptcovn < 1){i1=1;}
5958:
5959: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
5960: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
5961: k=k+1;
1.131 brouard 5962: /* to clean */
5963: printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
1.126 brouard 5964: fprintf(ficrespl,"\n#******");
5965: printf("\n#******");
5966: fprintf(ficlog,"\n#******");
5967: for(j=1;j<=cptcoveff;j++) {
5968: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5969: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5970: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5971: }
5972: fprintf(ficrespl,"******\n");
5973: printf("******\n");
5974: fprintf(ficlog,"******\n");
5975:
5976: for (age=agebase; age<=agelim; age++){
5977: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
5978: fprintf(ficrespl,"%.0f ",age );
5979: for(j=1;j<=cptcoveff;j++)
5980: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5981: for(i=1; i<=nlstate;i++)
5982: fprintf(ficrespl," %.5f", prlim[i][i]);
5983: fprintf(ficrespl,"\n");
5984: }
5985: }
5986: }
5987: fclose(ficrespl);
5988:
5989: /*------------- h Pij x at various ages ------------*/
5990:
5991: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
5992: if((ficrespij=fopen(filerespij,"w"))==NULL) {
5993: printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
5994: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
5995: }
5996: printf("Computing pij: result on file '%s' \n", filerespij);
5997: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
5998:
5999: stepsize=(int) (stepm+YEARM-1)/YEARM;
6000: /*if (stepm<=24) stepsize=2;*/
6001:
6002: agelim=AGESUP;
6003: hstepm=stepsize*YEARM; /* Every year of age */
6004: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6005:
6006: /* hstepm=1; aff par mois*/
6007: pstamp(ficrespij);
6008: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6009: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6010: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6011: k=k+1;
6012: fprintf(ficrespij,"\n#****** ");
6013: for(j=1;j<=cptcoveff;j++)
6014: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6015: fprintf(ficrespij,"******\n");
6016:
6017: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6018: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6019: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6020:
6021: /* nhstepm=nhstepm*YEARM; aff par mois*/
6022:
6023: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6024: oldm=oldms;savm=savms;
6025: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6026: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6027: for(i=1; i<=nlstate;i++)
6028: for(j=1; j<=nlstate+ndeath;j++)
6029: fprintf(ficrespij," %1d-%1d",i,j);
6030: fprintf(ficrespij,"\n");
6031: for (h=0; h<=nhstepm; h++){
6032: fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
6033: for(i=1; i<=nlstate;i++)
6034: for(j=1; j<=nlstate+ndeath;j++)
6035: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6036: fprintf(ficrespij,"\n");
6037: }
6038: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6039: fprintf(ficrespij,"\n");
6040: }
6041: }
6042: }
6043:
6044: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6045:
6046: fclose(ficrespij);
6047:
6048: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6049: for(i=1;i<=AGESUP;i++)
6050: for(j=1;j<=NCOVMAX;j++)
6051: for(k=1;k<=NCOVMAX;k++)
6052: probs[i][j][k]=0.;
6053:
6054: /*---------- Forecasting ------------------*/
6055: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6056: if(prevfcast==1){
6057: /* if(stepm ==1){*/
6058: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6059: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6060: /* } */
6061: /* else{ */
6062: /* erreur=108; */
6063: /* 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); */
6064: /* 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); */
6065: /* } */
6066: }
6067:
6068:
1.127 brouard 6069: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6070:
6071: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6072: /* 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",\
6073: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6074: */
1.126 brouard 6075:
1.127 brouard 6076: if (mobilav!=0) {
6077: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6078: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6079: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6080: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6081: }
1.126 brouard 6082: }
6083:
6084:
1.127 brouard 6085: /*---------- Health expectancies, no variances ------------*/
6086:
1.126 brouard 6087: strcpy(filerese,"e");
6088: strcat(filerese,fileres);
6089: if((ficreseij=fopen(filerese,"w"))==NULL) {
6090: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6091: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6092: }
6093: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6094: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.127 brouard 6095: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6096: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6097: k=k+1;
6098: fprintf(ficreseij,"\n#****** ");
6099: for(j=1;j<=cptcoveff;j++) {
6100: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6101: }
6102: fprintf(ficreseij,"******\n");
6103:
6104: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6105: oldm=oldms;savm=savms;
6106: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6107:
6108: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6109: }
6110: }
6111: fclose(ficreseij);
6112:
6113:
6114: /*---------- Health expectancies and variances ------------*/
6115:
6116:
6117: strcpy(filerest,"t");
6118: strcat(filerest,fileres);
6119: if((ficrest=fopen(filerest,"w"))==NULL) {
6120: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6121: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6122: }
6123: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6124: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6125:
1.126 brouard 6126:
6127: strcpy(fileresstde,"stde");
6128: strcat(fileresstde,fileres);
6129: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6130: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6131: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6132: }
6133: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6134: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6135:
6136: strcpy(filerescve,"cve");
6137: strcat(filerescve,fileres);
6138: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6139: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6140: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6141: }
6142: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6143: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6144:
6145: strcpy(fileresv,"v");
6146: strcat(fileresv,fileres);
6147: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6148: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6149: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6150: }
6151: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6152: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6153:
6154: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6155: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6156: k=k+1;
6157: fprintf(ficrest,"\n#****** ");
6158: for(j=1;j<=cptcoveff;j++)
6159: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6160: fprintf(ficrest,"******\n");
6161:
6162: fprintf(ficresstdeij,"\n#****** ");
6163: fprintf(ficrescveij,"\n#****** ");
6164: for(j=1;j<=cptcoveff;j++) {
6165: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6166: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6167: }
6168: fprintf(ficresstdeij,"******\n");
6169: fprintf(ficrescveij,"******\n");
6170:
6171: fprintf(ficresvij,"\n#****** ");
6172: for(j=1;j<=cptcoveff;j++)
6173: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6174: fprintf(ficresvij,"******\n");
6175:
6176: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6177: oldm=oldms;savm=savms;
1.127 brouard 6178: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.126 brouard 6179:
6180: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6181: pstamp(ficrest);
1.128 brouard 6182: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6183: oldm=oldms;savm=savms;
6184: 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 ");
6185: if(vpopbased==1)
6186: 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);
6187: else
6188: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6189: fprintf(ficrest,"# Age e.. (std) ");
6190: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6191: fprintf(ficrest,"\n");
1.126 brouard 6192:
1.128 brouard 6193: epj=vector(1,nlstate+1);
6194: for(age=bage; age <=fage ;age++){
6195: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6196: if (vpopbased==1) {
6197: if(mobilav ==0){
6198: for(i=1; i<=nlstate;i++)
6199: prlim[i][i]=probs[(int)age][i][k];
6200: }else{ /* mobilav */
6201: for(i=1; i<=nlstate;i++)
6202: prlim[i][i]=mobaverage[(int)age][i][k];
6203: }
1.126 brouard 6204: }
6205:
1.128 brouard 6206: fprintf(ficrest," %4.0f",age);
6207: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6208: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6209: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6210: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6211: }
6212: epj[nlstate+1] +=epj[j];
1.126 brouard 6213: }
6214:
1.128 brouard 6215: for(i=1, vepp=0.;i <=nlstate;i++)
6216: for(j=1;j <=nlstate;j++)
6217: vepp += vareij[i][j][(int)age];
6218: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6219: for(j=1;j <=nlstate;j++){
6220: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6221: }
6222: fprintf(ficrest,"\n");
1.126 brouard 6223: }
6224: }
6225: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6226: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6227: free_vector(epj,1,nlstate+1);
6228: }
6229: }
6230: free_vector(weight,1,n);
6231: free_imatrix(Tvard,1,15,1,2);
6232: free_imatrix(s,1,maxwav+1,1,n);
6233: free_matrix(anint,1,maxwav,1,n);
6234: free_matrix(mint,1,maxwav,1,n);
6235: free_ivector(cod,1,n);
6236: free_ivector(tab,1,NCOVMAX);
6237: fclose(ficresstdeij);
6238: fclose(ficrescveij);
6239: fclose(ficresvij);
6240: fclose(ficrest);
6241: fclose(ficpar);
6242:
6243: /*------- Variance of period (stable) prevalence------*/
6244:
6245: strcpy(fileresvpl,"vpl");
6246: strcat(fileresvpl,fileres);
6247: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6248: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6249: exit(0);
6250: }
6251: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6252:
6253: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6254: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6255: k=k+1;
6256: fprintf(ficresvpl,"\n#****** ");
6257: for(j=1;j<=cptcoveff;j++)
6258: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6259: fprintf(ficresvpl,"******\n");
6260:
6261: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6262: oldm=oldms;savm=savms;
6263: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6264: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6265: }
6266: }
6267:
6268: fclose(ficresvpl);
6269:
6270: /*---------- End : free ----------------*/
6271: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6272: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6273:
6274: } /* mle==-3 arrives here for freeing */
1.131 brouard 6275: endfree:
1.126 brouard 6276: free_matrix(prlim,1,nlstate,1,nlstate);
6277: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6278: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6279: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6280: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6281: free_matrix(covar,0,NCOVMAX,1,n);
6282: free_matrix(matcov,1,npar,1,npar);
6283: /*free_vector(delti,1,npar);*/
6284: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6285: free_matrix(agev,1,maxwav,1,imx);
6286: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6287:
6288: free_ivector(ncodemax,1,8);
6289: free_ivector(Tvar,1,15);
6290: free_ivector(Tprod,1,15);
6291: free_ivector(Tvaraff,1,15);
6292: free_ivector(Tage,1,15);
6293:
6294: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6295: free_imatrix(codtab,1,100,1,10);
6296: fflush(fichtm);
6297: fflush(ficgp);
6298:
6299:
6300: if((nberr >0) || (nbwarn>0)){
6301: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6302: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6303: }else{
6304: printf("End of Imach\n");
6305: fprintf(ficlog,"End of Imach\n");
6306: }
6307: printf("See log file on %s\n",filelog);
6308: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6309: (void) gettimeofday(&end_time,&tzp);
6310: tm = *localtime(&end_time.tv_sec);
6311: tmg = *gmtime(&end_time.tv_sec);
6312: strcpy(strtend,asctime(&tm));
6313: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6314: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6315: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6316:
6317: printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6318: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6319: fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
6320: /* printf("Total time was %d uSec.\n", total_usecs);*/
6321: /* if(fileappend(fichtm,optionfilehtm)){ */
6322: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6323: fclose(fichtm);
6324: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6325: fclose(fichtmcov);
6326: fclose(ficgp);
6327: fclose(ficlog);
6328: /*------ End -----------*/
6329:
6330:
6331: printf("Before Current directory %s!\n",pathcd);
6332: if(chdir(pathcd) != 0)
6333: printf("Can't move to directory %s!\n",path);
6334: if(getcwd(pathcd,MAXLINE) > 0)
6335: printf("Current directory %s!\n",pathcd);
6336: /*strcat(plotcmd,CHARSEPARATOR);*/
6337: sprintf(plotcmd,"gnuplot");
6338: #ifndef UNIX
6339: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6340: #endif
6341: if(!stat(plotcmd,&info)){
6342: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6343: if(!stat(getenv("GNUPLOTBIN"),&info)){
6344: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6345: }else
6346: strcpy(pplotcmd,plotcmd);
6347: #ifdef UNIX
6348: strcpy(plotcmd,GNUPLOTPROGRAM);
6349: if(!stat(plotcmd,&info)){
6350: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6351: }else
6352: strcpy(pplotcmd,plotcmd);
6353: #endif
6354: }else
6355: strcpy(pplotcmd,plotcmd);
6356:
6357: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6358: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6359:
6360: if((outcmd=system(plotcmd)) != 0){
6361: printf("\n Problem with gnuplot\n");
6362: }
6363: printf(" Wait...");
6364: while (z[0] != 'q') {
6365: /* chdir(path); */
6366: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6367: scanf("%s",z);
6368: /* if (z[0] == 'c') system("./imach"); */
6369: if (z[0] == 'e') {
6370: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6371: system(optionfilehtm);
6372: }
6373: else if (z[0] == 'g') system(plotcmd);
6374: else if (z[0] == 'q') exit(0);
6375: }
6376: end:
6377: while (z[0] != 'q') {
6378: printf("\nType q for exiting: ");
6379: scanf("%s",z);
6380: }
6381: }
6382:
6383:
6384:
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