Annotation of imach/src/imach.c, revision 1.151
1.151 ! brouard 1: /* $Id: imach.c,v 1.150 2014/06/18 16:42:35 brouard Exp $
1.126 brouard 2: $State: Exp $
3: $Log: imach.c,v $
1.151 ! brouard 4: Revision 1.150 2014/06/18 16:42:35 brouard
! 5: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
! 6: Author: brouard
! 7:
1.150 brouard 8: Revision 1.149 2014/06/18 15:51:14 brouard
9: Summary: Some fixes in parameter files errors
10: Author: Nicolas Brouard
11:
1.149 brouard 12: Revision 1.148 2014/06/17 17:38:48 brouard
13: Summary: Nothing new
14: Author: Brouard
15:
16: Just a new packaging for OS/X version 0.98nS
17:
1.148 brouard 18: Revision 1.147 2014/06/16 10:33:11 brouard
19: *** empty log message ***
20:
1.147 brouard 21: Revision 1.146 2014/06/16 10:20:28 brouard
22: Summary: Merge
23: Author: Brouard
24:
25: Merge, before building revised version.
26:
1.146 brouard 27: Revision 1.145 2014/06/10 21:23:15 brouard
28: Summary: Debugging with valgrind
29: Author: Nicolas Brouard
30:
31: Lot of changes in order to output the results with some covariates
32: After the Edimburgh REVES conference 2014, it seems mandatory to
33: improve the code.
34: No more memory valgrind error but a lot has to be done in order to
35: continue the work of splitting the code into subroutines.
36: Also, decodemodel has been improved. Tricode is still not
37: optimal. nbcode should be improved. Documentation has been added in
38: the source code.
39:
1.144 brouard 40: Revision 1.143 2014/01/26 09:45:38 brouard
41: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
42:
43: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
44: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
45:
1.143 brouard 46: Revision 1.142 2014/01/26 03:57:36 brouard
47: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
48:
49: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
50:
1.142 brouard 51: Revision 1.141 2014/01/26 02:42:01 brouard
52: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
53:
1.141 brouard 54: Revision 1.140 2011/09/02 10:37:54 brouard
55: Summary: times.h is ok with mingw32 now.
56:
1.140 brouard 57: Revision 1.139 2010/06/14 07:50:17 brouard
58: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
59: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
60:
1.139 brouard 61: Revision 1.138 2010/04/30 18:19:40 brouard
62: *** empty log message ***
63:
1.138 brouard 64: Revision 1.137 2010/04/29 18:11:38 brouard
65: (Module): Checking covariates for more complex models
66: than V1+V2. A lot of change to be done. Unstable.
67:
1.137 brouard 68: Revision 1.136 2010/04/26 20:30:53 brouard
69: (Module): merging some libgsl code. Fixing computation
70: of likelione (using inter/intrapolation if mle = 0) in order to
71: get same likelihood as if mle=1.
72: Some cleaning of code and comments added.
73:
1.136 brouard 74: Revision 1.135 2009/10/29 15:33:14 brouard
75: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
76:
1.135 brouard 77: Revision 1.134 2009/10/29 13:18:53 brouard
78: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
79:
1.134 brouard 80: Revision 1.133 2009/07/06 10:21:25 brouard
81: just nforces
82:
1.133 brouard 83: Revision 1.132 2009/07/06 08:22:05 brouard
84: Many tings
85:
1.132 brouard 86: Revision 1.131 2009/06/20 16:22:47 brouard
87: Some dimensions resccaled
88:
1.131 brouard 89: Revision 1.130 2009/05/26 06:44:34 brouard
90: (Module): Max Covariate is now set to 20 instead of 8. A
91: lot of cleaning with variables initialized to 0. Trying to make
92: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
93:
1.130 brouard 94: Revision 1.129 2007/08/31 13:49:27 lievre
95: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
96:
1.129 lievre 97: Revision 1.128 2006/06/30 13:02:05 brouard
98: (Module): Clarifications on computing e.j
99:
1.128 brouard 100: Revision 1.127 2006/04/28 18:11:50 brouard
101: (Module): Yes the sum of survivors was wrong since
102: imach-114 because nhstepm was no more computed in the age
103: loop. Now we define nhstepma in the age loop.
104: (Module): In order to speed up (in case of numerous covariates) we
105: compute health expectancies (without variances) in a first step
106: and then all the health expectancies with variances or standard
107: deviation (needs data from the Hessian matrices) which slows the
108: computation.
109: In the future we should be able to stop the program is only health
110: expectancies and graph are needed without standard deviations.
111:
1.127 brouard 112: Revision 1.126 2006/04/28 17:23:28 brouard
113: (Module): Yes the sum of survivors was wrong since
114: imach-114 because nhstepm was no more computed in the age
115: loop. Now we define nhstepma in the age loop.
116: Version 0.98h
117:
1.126 brouard 118: Revision 1.125 2006/04/04 15:20:31 lievre
119: Errors in calculation of health expectancies. Age was not initialized.
120: Forecasting file added.
121:
122: Revision 1.124 2006/03/22 17:13:53 lievre
123: Parameters are printed with %lf instead of %f (more numbers after the comma).
124: The log-likelihood is printed in the log file
125:
126: Revision 1.123 2006/03/20 10:52:43 brouard
127: * imach.c (Module): <title> changed, corresponds to .htm file
128: name. <head> headers where missing.
129:
130: * imach.c (Module): Weights can have a decimal point as for
131: English (a comma might work with a correct LC_NUMERIC environment,
132: otherwise the weight is truncated).
133: Modification of warning when the covariates values are not 0 or
134: 1.
135: Version 0.98g
136:
137: Revision 1.122 2006/03/20 09:45:41 brouard
138: (Module): Weights can have a decimal point as for
139: English (a comma might work with a correct LC_NUMERIC environment,
140: otherwise the weight is truncated).
141: Modification of warning when the covariates values are not 0 or
142: 1.
143: Version 0.98g
144:
145: Revision 1.121 2006/03/16 17:45:01 lievre
146: * imach.c (Module): Comments concerning covariates added
147:
148: * imach.c (Module): refinements in the computation of lli if
149: status=-2 in order to have more reliable computation if stepm is
150: not 1 month. Version 0.98f
151:
152: Revision 1.120 2006/03/16 15:10:38 lievre
153: (Module): refinements in the computation of lli if
154: status=-2 in order to have more reliable computation if stepm is
155: not 1 month. Version 0.98f
156:
157: Revision 1.119 2006/03/15 17:42:26 brouard
158: (Module): Bug if status = -2, the loglikelihood was
159: computed as likelihood omitting the logarithm. Version O.98e
160:
161: Revision 1.118 2006/03/14 18:20:07 brouard
162: (Module): varevsij Comments added explaining the second
163: table of variances if popbased=1 .
164: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
165: (Module): Function pstamp added
166: (Module): Version 0.98d
167:
168: Revision 1.117 2006/03/14 17:16:22 brouard
169: (Module): varevsij Comments added explaining the second
170: table of variances if popbased=1 .
171: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
172: (Module): Function pstamp added
173: (Module): Version 0.98d
174:
175: Revision 1.116 2006/03/06 10:29:27 brouard
176: (Module): Variance-covariance wrong links and
177: varian-covariance of ej. is needed (Saito).
178:
179: Revision 1.115 2006/02/27 12:17:45 brouard
180: (Module): One freematrix added in mlikeli! 0.98c
181:
182: Revision 1.114 2006/02/26 12:57:58 brouard
183: (Module): Some improvements in processing parameter
184: filename with strsep.
185:
186: Revision 1.113 2006/02/24 14:20:24 brouard
187: (Module): Memory leaks checks with valgrind and:
188: datafile was not closed, some imatrix were not freed and on matrix
189: allocation too.
190:
191: Revision 1.112 2006/01/30 09:55:26 brouard
192: (Module): Back to gnuplot.exe instead of wgnuplot.exe
193:
194: Revision 1.111 2006/01/25 20:38:18 brouard
195: (Module): Lots of cleaning and bugs added (Gompertz)
196: (Module): Comments can be added in data file. Missing date values
197: can be a simple dot '.'.
198:
199: Revision 1.110 2006/01/25 00:51:50 brouard
200: (Module): Lots of cleaning and bugs added (Gompertz)
201:
202: Revision 1.109 2006/01/24 19:37:15 brouard
203: (Module): Comments (lines starting with a #) are allowed in data.
204:
205: Revision 1.108 2006/01/19 18:05:42 lievre
206: Gnuplot problem appeared...
207: To be fixed
208:
209: Revision 1.107 2006/01/19 16:20:37 brouard
210: Test existence of gnuplot in imach path
211:
212: Revision 1.106 2006/01/19 13:24:36 brouard
213: Some cleaning and links added in html output
214:
215: Revision 1.105 2006/01/05 20:23:19 lievre
216: *** empty log message ***
217:
218: Revision 1.104 2005/09/30 16:11:43 lievre
219: (Module): sump fixed, loop imx fixed, and simplifications.
220: (Module): If the status is missing at the last wave but we know
221: that the person is alive, then we can code his/her status as -2
222: (instead of missing=-1 in earlier versions) and his/her
223: contributions to the likelihood is 1 - Prob of dying from last
224: health status (= 1-p13= p11+p12 in the easiest case of somebody in
225: the healthy state at last known wave). Version is 0.98
226:
227: Revision 1.103 2005/09/30 15:54:49 lievre
228: (Module): sump fixed, loop imx fixed, and simplifications.
229:
230: Revision 1.102 2004/09/15 17:31:30 brouard
231: Add the possibility to read data file including tab characters.
232:
233: Revision 1.101 2004/09/15 10:38:38 brouard
234: Fix on curr_time
235:
236: Revision 1.100 2004/07/12 18:29:06 brouard
237: Add version for Mac OS X. Just define UNIX in Makefile
238:
239: Revision 1.99 2004/06/05 08:57:40 brouard
240: *** empty log message ***
241:
242: Revision 1.98 2004/05/16 15:05:56 brouard
243: New version 0.97 . First attempt to estimate force of mortality
244: directly from the data i.e. without the need of knowing the health
245: state at each age, but using a Gompertz model: log u =a + b*age .
246: This is the basic analysis of mortality and should be done before any
247: other analysis, in order to test if the mortality estimated from the
248: cross-longitudinal survey is different from the mortality estimated
249: from other sources like vital statistic data.
250:
251: The same imach parameter file can be used but the option for mle should be -3.
252:
1.133 brouard 253: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 254: former routines in order to include the new code within the former code.
255:
256: The output is very simple: only an estimate of the intercept and of
257: the slope with 95% confident intervals.
258:
259: Current limitations:
260: A) Even if you enter covariates, i.e. with the
261: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
262: B) There is no computation of Life Expectancy nor Life Table.
263:
264: Revision 1.97 2004/02/20 13:25:42 lievre
265: Version 0.96d. Population forecasting command line is (temporarily)
266: suppressed.
267:
268: Revision 1.96 2003/07/15 15:38:55 brouard
269: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
270: rewritten within the same printf. Workaround: many printfs.
271:
272: Revision 1.95 2003/07/08 07:54:34 brouard
273: * imach.c (Repository):
274: (Repository): Using imachwizard code to output a more meaningful covariance
275: matrix (cov(a12,c31) instead of numbers.
276:
277: Revision 1.94 2003/06/27 13:00:02 brouard
278: Just cleaning
279:
280: Revision 1.93 2003/06/25 16:33:55 brouard
281: (Module): On windows (cygwin) function asctime_r doesn't
282: exist so I changed back to asctime which exists.
283: (Module): Version 0.96b
284:
285: Revision 1.92 2003/06/25 16:30:45 brouard
286: (Module): On windows (cygwin) function asctime_r doesn't
287: exist so I changed back to asctime which exists.
288:
289: Revision 1.91 2003/06/25 15:30:29 brouard
290: * imach.c (Repository): Duplicated warning errors corrected.
291: (Repository): Elapsed time after each iteration is now output. It
292: helps to forecast when convergence will be reached. Elapsed time
293: is stamped in powell. We created a new html file for the graphs
294: concerning matrix of covariance. It has extension -cov.htm.
295:
296: Revision 1.90 2003/06/24 12:34:15 brouard
297: (Module): Some bugs corrected for windows. Also, when
298: mle=-1 a template is output in file "or"mypar.txt with the design
299: of the covariance matrix to be input.
300:
301: Revision 1.89 2003/06/24 12:30:52 brouard
302: (Module): Some bugs corrected for windows. Also, when
303: mle=-1 a template is output in file "or"mypar.txt with the design
304: of the covariance matrix to be input.
305:
306: Revision 1.88 2003/06/23 17:54:56 brouard
307: * 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.
308:
309: Revision 1.87 2003/06/18 12:26:01 brouard
310: Version 0.96
311:
312: Revision 1.86 2003/06/17 20:04:08 brouard
313: (Module): Change position of html and gnuplot routines and added
314: routine fileappend.
315:
316: Revision 1.85 2003/06/17 13:12:43 brouard
317: * imach.c (Repository): Check when date of death was earlier that
318: current date of interview. It may happen when the death was just
319: prior to the death. In this case, dh was negative and likelihood
320: was wrong (infinity). We still send an "Error" but patch by
321: assuming that the date of death was just one stepm after the
322: interview.
323: (Repository): Because some people have very long ID (first column)
324: we changed int to long in num[] and we added a new lvector for
325: memory allocation. But we also truncated to 8 characters (left
326: truncation)
327: (Repository): No more line truncation errors.
328:
329: Revision 1.84 2003/06/13 21:44:43 brouard
330: * imach.c (Repository): Replace "freqsummary" at a correct
331: place. It differs from routine "prevalence" which may be called
332: many times. Probs is memory consuming and must be used with
333: parcimony.
334: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
335:
336: Revision 1.83 2003/06/10 13:39:11 lievre
337: *** empty log message ***
338:
339: Revision 1.82 2003/06/05 15:57:20 brouard
340: Add log in imach.c and fullversion number is now printed.
341:
342: */
343: /*
344: Interpolated Markov Chain
345:
346: Short summary of the programme:
347:
348: This program computes Healthy Life Expectancies from
349: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
350: first survey ("cross") where individuals from different ages are
351: interviewed on their health status or degree of disability (in the
352: case of a health survey which is our main interest) -2- at least a
353: second wave of interviews ("longitudinal") which measure each change
354: (if any) in individual health status. Health expectancies are
355: computed from the time spent in each health state according to a
356: model. More health states you consider, more time is necessary to reach the
357: Maximum Likelihood of the parameters involved in the model. The
358: simplest model is the multinomial logistic model where pij is the
359: probability to be observed in state j at the second wave
360: conditional to be observed in state i at the first wave. Therefore
361: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
362: 'age' is age and 'sex' is a covariate. If you want to have a more
363: complex model than "constant and age", you should modify the program
364: where the markup *Covariates have to be included here again* invites
365: you to do it. More covariates you add, slower the
366: convergence.
367:
368: The advantage of this computer programme, compared to a simple
369: multinomial logistic model, is clear when the delay between waves is not
370: identical for each individual. Also, if a individual missed an
371: intermediate interview, the information is lost, but taken into
372: account using an interpolation or extrapolation.
373:
374: hPijx is the probability to be observed in state i at age x+h
375: conditional to the observed state i at age x. The delay 'h' can be
376: split into an exact number (nh*stepm) of unobserved intermediate
377: states. This elementary transition (by month, quarter,
378: semester or year) is modelled as a multinomial logistic. The hPx
379: matrix is simply the matrix product of nh*stepm elementary matrices
380: and the contribution of each individual to the likelihood is simply
381: hPijx.
382:
383: Also this programme outputs the covariance matrix of the parameters but also
384: of the life expectancies. It also computes the period (stable) prevalence.
385:
1.133 brouard 386: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
387: Institut national d'études démographiques, Paris.
1.126 brouard 388: This software have been partly granted by Euro-REVES, a concerted action
389: from the European Union.
390: It is copyrighted identically to a GNU software product, ie programme and
391: software can be distributed freely for non commercial use. Latest version
392: can be accessed at http://euroreves.ined.fr/imach .
393:
394: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
395: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
396:
397: **********************************************************************/
398: /*
399: main
400: read parameterfile
401: read datafile
402: concatwav
403: freqsummary
404: if (mle >= 1)
405: mlikeli
406: print results files
407: if mle==1
408: computes hessian
409: read end of parameter file: agemin, agemax, bage, fage, estepm
410: begin-prev-date,...
411: open gnuplot file
412: open html file
1.145 brouard 413: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
414: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
415: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
416: freexexit2 possible for memory heap.
417:
418: h Pij x | pij_nom ficrestpij
419: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
420: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
421: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
422:
423: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
424: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
425: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
426: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
427: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
428:
1.126 brouard 429: forecasting if prevfcast==1 prevforecast call prevalence()
430: health expectancies
431: Variance-covariance of DFLE
432: prevalence()
433: movingaverage()
434: varevsij()
435: if popbased==1 varevsij(,popbased)
436: total life expectancies
437: Variance of period (stable) prevalence
438: end
439: */
440:
441:
442:
443:
444: #include <math.h>
445: #include <stdio.h>
446: #include <stdlib.h>
447: #include <string.h>
448: #include <unistd.h>
449:
450: #include <limits.h>
451: #include <sys/types.h>
452: #include <sys/stat.h>
453: #include <errno.h>
454: extern int errno;
455:
1.141 brouard 456: #ifdef LINUX
1.126 brouard 457: #include <time.h>
458: #include "timeval.h"
1.141 brouard 459: #else
460: #include <sys/time.h>
461: #endif
1.126 brouard 462:
1.136 brouard 463: #ifdef GSL
464: #include <gsl/gsl_errno.h>
465: #include <gsl/gsl_multimin.h>
466: #endif
467:
1.126 brouard 468: /* #include <libintl.h> */
469: /* #define _(String) gettext (String) */
470:
1.141 brouard 471: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 472:
473: #define GNUPLOTPROGRAM "gnuplot"
474: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
475: #define FILENAMELENGTH 132
476:
477: #define GLOCK_ERROR_NOPATH -1 /* empty path */
478: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
479:
1.144 brouard 480: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
481: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 482:
483: #define NINTERVMAX 8
1.144 brouard 484: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
485: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
486: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 487: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 488: #define MAXN 20000
1.144 brouard 489: #define YEARM 12. /**< Number of months per year */
1.126 brouard 490: #define AGESUP 130
491: #define AGEBASE 40
1.144 brouard 492: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
1.126 brouard 493: #ifdef UNIX
494: #define DIRSEPARATOR '/'
495: #define CHARSEPARATOR "/"
496: #define ODIRSEPARATOR '\\'
497: #else
498: #define DIRSEPARATOR '\\'
499: #define CHARSEPARATOR "\\"
500: #define ODIRSEPARATOR '/'
501: #endif
502:
1.151 ! brouard 503: /* $Id: imach.c,v 1.150 2014/06/18 16:42:35 brouard Exp $ */
1.126 brouard 504: /* $State: Exp $ */
505:
1.149 brouard 506: char version[]="Imach version 0.98nT, January 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
1.151 ! brouard 507: char fullversion[]="$Revision: 1.150 $ $Date: 2014/06/18 16:42:35 $";
1.126 brouard 508: char strstart[80];
509: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 510: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 511: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 512: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
513: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
514: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
515: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
516: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
517: int cptcovprodnoage=0; /**< Number of covariate products without age */
518: int cptcoveff=0; /* Total number of covariates to vary for printing results */
519: int cptcov=0; /* Working variable */
1.126 brouard 520: int npar=NPARMAX;
521: int nlstate=2; /* Number of live states */
522: int ndeath=1; /* Number of dead states */
1.130 brouard 523: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 524: int popbased=0;
525:
526: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 527: int maxwav=0; /* Maxim number of waves */
528: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
529: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
530: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 531: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 532: int mle=1, weightopt=0;
1.126 brouard 533: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
534: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
535: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
536: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.130 brouard 537: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 538: double **matprod2(); /* test */
1.126 brouard 539: double **oldm, **newm, **savm; /* Working pointers to matrices */
540: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 541: /*FILE *fic ; */ /* Used in readdata only */
542: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 543: FILE *ficlog, *ficrespow;
1.130 brouard 544: int globpr=0; /* Global variable for printing or not */
1.126 brouard 545: double fretone; /* Only one call to likelihood */
1.130 brouard 546: long ipmx=0; /* Number of contributions */
1.126 brouard 547: double sw; /* Sum of weights */
548: char filerespow[FILENAMELENGTH];
549: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
550: FILE *ficresilk;
551: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
552: FILE *ficresprobmorprev;
553: FILE *fichtm, *fichtmcov; /* Html File */
554: FILE *ficreseij;
555: char filerese[FILENAMELENGTH];
556: FILE *ficresstdeij;
557: char fileresstde[FILENAMELENGTH];
558: FILE *ficrescveij;
559: char filerescve[FILENAMELENGTH];
560: FILE *ficresvij;
561: char fileresv[FILENAMELENGTH];
562: FILE *ficresvpl;
563: char fileresvpl[FILENAMELENGTH];
564: char title[MAXLINE];
565: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
566: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
567: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
568: char command[FILENAMELENGTH];
569: int outcmd=0;
570:
571: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
572:
573: char filelog[FILENAMELENGTH]; /* Log file */
574: char filerest[FILENAMELENGTH];
575: char fileregp[FILENAMELENGTH];
576: char popfile[FILENAMELENGTH];
577:
578: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
579:
580: struct timeval start_time, end_time, curr_time, last_time, forecast_time;
581: struct timezone tzp;
582: extern int gettimeofday();
583: struct tm tmg, tm, tmf, *gmtime(), *localtime();
584: long time_value;
585: extern long time();
586: char strcurr[80], strfor[80];
587:
588: char *endptr;
589: long lval;
590: double dval;
591:
592: #define NR_END 1
593: #define FREE_ARG char*
594: #define FTOL 1.0e-10
595:
596: #define NRANSI
597: #define ITMAX 200
598:
599: #define TOL 2.0e-4
600:
601: #define CGOLD 0.3819660
602: #define ZEPS 1.0e-10
603: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
604:
605: #define GOLD 1.618034
606: #define GLIMIT 100.0
607: #define TINY 1.0e-20
608:
609: static double maxarg1,maxarg2;
610: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
611: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
612:
613: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
614: #define rint(a) floor(a+0.5)
615:
616: static double sqrarg;
617: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
618: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
619: int agegomp= AGEGOMP;
620:
621: int imx;
622: int stepm=1;
623: /* Stepm, step in month: minimum step interpolation*/
624:
625: int estepm;
626: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
627:
628: int m,nb;
629: long *num;
630: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
631: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
632: double **pmmij, ***probs;
633: double *ageexmed,*agecens;
634: double dateintmean=0;
635:
636: double *weight;
637: int **s; /* Status */
1.141 brouard 638: double *agedc;
1.145 brouard 639: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 640: * covar=matrix(0,NCOVMAX,1,n);
641: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
642: double idx;
643: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 644: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 645: int **codtab; /**< codtab=imatrix(1,100,1,10); */
646: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 647: double *lsurv, *lpop, *tpop;
648:
1.143 brouard 649: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
650: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 651:
652: /**************** split *************************/
653: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
654: {
655: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
656: the name of the file (name), its extension only (ext) and its first part of the name (finame)
657: */
658: char *ss; /* pointer */
659: int l1, l2; /* length counters */
660:
661: l1 = strlen(path ); /* length of path */
662: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
663: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
664: if ( ss == NULL ) { /* no directory, so determine current directory */
665: strcpy( name, path ); /* we got the fullname name because no directory */
666: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
667: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
668: /* get current working directory */
669: /* extern char* getcwd ( char *buf , int len);*/
670: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
671: return( GLOCK_ERROR_GETCWD );
672: }
673: /* got dirc from getcwd*/
674: printf(" DIRC = %s \n",dirc);
675: } else { /* strip direcotry from path */
676: ss++; /* after this, the filename */
677: l2 = strlen( ss ); /* length of filename */
678: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
679: strcpy( name, ss ); /* save file name */
680: strncpy( dirc, path, l1 - l2 ); /* now the directory */
681: dirc[l1-l2] = 0; /* add zero */
682: printf(" DIRC2 = %s \n",dirc);
683: }
684: /* We add a separator at the end of dirc if not exists */
685: l1 = strlen( dirc ); /* length of directory */
686: if( dirc[l1-1] != DIRSEPARATOR ){
687: dirc[l1] = DIRSEPARATOR;
688: dirc[l1+1] = 0;
689: printf(" DIRC3 = %s \n",dirc);
690: }
691: ss = strrchr( name, '.' ); /* find last / */
692: if (ss >0){
693: ss++;
694: strcpy(ext,ss); /* save extension */
695: l1= strlen( name);
696: l2= strlen(ss)+1;
697: strncpy( finame, name, l1-l2);
698: finame[l1-l2]= 0;
699: }
700:
701: return( 0 ); /* we're done */
702: }
703:
704:
705: /******************************************/
706:
707: void replace_back_to_slash(char *s, char*t)
708: {
709: int i;
710: int lg=0;
711: i=0;
712: lg=strlen(t);
713: for(i=0; i<= lg; i++) {
714: (s[i] = t[i]);
715: if (t[i]== '\\') s[i]='/';
716: }
717: }
718:
1.132 brouard 719: char *trimbb(char *out, char *in)
1.137 brouard 720: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 721: char *s;
722: s=out;
723: while (*in != '\0'){
1.137 brouard 724: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 725: in++;
726: }
727: *out++ = *in++;
728: }
729: *out='\0';
730: return s;
731: }
732:
1.145 brouard 733: char *cutl(char *blocc, char *alocc, char *in, char occ)
734: {
735: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
736: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
737: gives blocc="abcdef2ghi" and alocc="j".
738: If occ is not found blocc is null and alocc is equal to in. Returns blocc
739: */
740: char *s, *t, *bl;
741: t=in;s=in;
742: while ((*in != occ) && (*in != '\0')){
743: *alocc++ = *in++;
744: }
745: if( *in == occ){
746: *(alocc)='\0';
747: s=++in;
748: }
749:
750: if (s == t) {/* occ not found */
751: *(alocc-(in-s))='\0';
752: in=s;
753: }
754: while ( *in != '\0'){
755: *blocc++ = *in++;
756: }
757:
758: *blocc='\0';
759: return t;
760: }
1.137 brouard 761: char *cutv(char *blocc, char *alocc, char *in, char occ)
762: {
763: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
764: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
765: gives blocc="abcdef2ghi" and alocc="j".
766: If occ is not found blocc is null and alocc is equal to in. Returns alocc
767: */
768: char *s, *t;
769: t=in;s=in;
770: while (*in != '\0'){
771: while( *in == occ){
772: *blocc++ = *in++;
773: s=in;
774: }
775: *blocc++ = *in++;
776: }
777: if (s == t) /* occ not found */
778: *(blocc-(in-s))='\0';
779: else
780: *(blocc-(in-s)-1)='\0';
781: in=s;
782: while ( *in != '\0'){
783: *alocc++ = *in++;
784: }
785:
786: *alocc='\0';
787: return s;
788: }
789:
1.126 brouard 790: int nbocc(char *s, char occ)
791: {
792: int i,j=0;
793: int lg=20;
794: i=0;
795: lg=strlen(s);
796: for(i=0; i<= lg; i++) {
797: if (s[i] == occ ) j++;
798: }
799: return j;
800: }
801:
1.137 brouard 802: /* void cutv(char *u,char *v, char*t, char occ) */
803: /* { */
804: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
805: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
806: /* gives u="abcdef2ghi" and v="j" *\/ */
807: /* int i,lg,j,p=0; */
808: /* i=0; */
809: /* lg=strlen(t); */
810: /* for(j=0; j<=lg-1; j++) { */
811: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
812: /* } */
1.126 brouard 813:
1.137 brouard 814: /* for(j=0; j<p; j++) { */
815: /* (u[j] = t[j]); */
816: /* } */
817: /* u[p]='\0'; */
1.126 brouard 818:
1.137 brouard 819: /* for(j=0; j<= lg; j++) { */
820: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
821: /* } */
822: /* } */
1.126 brouard 823:
824: /********************** nrerror ********************/
825:
826: void nrerror(char error_text[])
827: {
828: fprintf(stderr,"ERREUR ...\n");
829: fprintf(stderr,"%s\n",error_text);
830: exit(EXIT_FAILURE);
831: }
832: /*********************** vector *******************/
833: double *vector(int nl, int nh)
834: {
835: double *v;
836: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
837: if (!v) nrerror("allocation failure in vector");
838: return v-nl+NR_END;
839: }
840:
841: /************************ free vector ******************/
842: void free_vector(double*v, int nl, int nh)
843: {
844: free((FREE_ARG)(v+nl-NR_END));
845: }
846:
847: /************************ivector *******************************/
848: int *ivector(long nl,long nh)
849: {
850: int *v;
851: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
852: if (!v) nrerror("allocation failure in ivector");
853: return v-nl+NR_END;
854: }
855:
856: /******************free ivector **************************/
857: void free_ivector(int *v, long nl, long nh)
858: {
859: free((FREE_ARG)(v+nl-NR_END));
860: }
861:
862: /************************lvector *******************************/
863: long *lvector(long nl,long nh)
864: {
865: long *v;
866: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
867: if (!v) nrerror("allocation failure in ivector");
868: return v-nl+NR_END;
869: }
870:
871: /******************free lvector **************************/
872: void free_lvector(long *v, long nl, long nh)
873: {
874: free((FREE_ARG)(v+nl-NR_END));
875: }
876:
877: /******************* imatrix *******************************/
878: int **imatrix(long nrl, long nrh, long ncl, long nch)
879: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
880: {
881: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
882: int **m;
883:
884: /* allocate pointers to rows */
885: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
886: if (!m) nrerror("allocation failure 1 in matrix()");
887: m += NR_END;
888: m -= nrl;
889:
890:
891: /* allocate rows and set pointers to them */
892: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
893: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
894: m[nrl] += NR_END;
895: m[nrl] -= ncl;
896:
897: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
898:
899: /* return pointer to array of pointers to rows */
900: return m;
901: }
902:
903: /****************** free_imatrix *************************/
904: void free_imatrix(m,nrl,nrh,ncl,nch)
905: int **m;
906: long nch,ncl,nrh,nrl;
907: /* free an int matrix allocated by imatrix() */
908: {
909: free((FREE_ARG) (m[nrl]+ncl-NR_END));
910: free((FREE_ARG) (m+nrl-NR_END));
911: }
912:
913: /******************* matrix *******************************/
914: double **matrix(long nrl, long nrh, long ncl, long nch)
915: {
916: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
917: double **m;
918:
919: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
920: if (!m) nrerror("allocation failure 1 in matrix()");
921: m += NR_END;
922: m -= nrl;
923:
924: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
925: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
926: m[nrl] += NR_END;
927: m[nrl] -= ncl;
928:
929: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
930: return m;
1.145 brouard 931: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
932: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
933: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 934: */
935: }
936:
937: /*************************free matrix ************************/
938: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
939: {
940: free((FREE_ARG)(m[nrl]+ncl-NR_END));
941: free((FREE_ARG)(m+nrl-NR_END));
942: }
943:
944: /******************* ma3x *******************************/
945: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
946: {
947: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
948: double ***m;
949:
950: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
951: if (!m) nrerror("allocation failure 1 in matrix()");
952: m += NR_END;
953: m -= nrl;
954:
955: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
956: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
957: m[nrl] += NR_END;
958: m[nrl] -= ncl;
959:
960: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
961:
962: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
963: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
964: m[nrl][ncl] += NR_END;
965: m[nrl][ncl] -= nll;
966: for (j=ncl+1; j<=nch; j++)
967: m[nrl][j]=m[nrl][j-1]+nlay;
968:
969: for (i=nrl+1; i<=nrh; i++) {
970: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
971: for (j=ncl+1; j<=nch; j++)
972: m[i][j]=m[i][j-1]+nlay;
973: }
974: return m;
975: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
976: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
977: */
978: }
979:
980: /*************************free ma3x ************************/
981: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
982: {
983: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
984: free((FREE_ARG)(m[nrl]+ncl-NR_END));
985: free((FREE_ARG)(m+nrl-NR_END));
986: }
987:
988: /*************** function subdirf ***********/
989: char *subdirf(char fileres[])
990: {
991: /* Caution optionfilefiname is hidden */
992: strcpy(tmpout,optionfilefiname);
993: strcat(tmpout,"/"); /* Add to the right */
994: strcat(tmpout,fileres);
995: return tmpout;
996: }
997:
998: /*************** function subdirf2 ***********/
999: char *subdirf2(char fileres[], char *preop)
1000: {
1001:
1002: /* Caution optionfilefiname is hidden */
1003: strcpy(tmpout,optionfilefiname);
1004: strcat(tmpout,"/");
1005: strcat(tmpout,preop);
1006: strcat(tmpout,fileres);
1007: return tmpout;
1008: }
1009:
1010: /*************** function subdirf3 ***********/
1011: char *subdirf3(char fileres[], char *preop, char *preop2)
1012: {
1013:
1014: /* Caution optionfilefiname is hidden */
1015: strcpy(tmpout,optionfilefiname);
1016: strcat(tmpout,"/");
1017: strcat(tmpout,preop);
1018: strcat(tmpout,preop2);
1019: strcat(tmpout,fileres);
1020: return tmpout;
1021: }
1022:
1023: /***************** f1dim *************************/
1024: extern int ncom;
1025: extern double *pcom,*xicom;
1026: extern double (*nrfunc)(double []);
1027:
1028: double f1dim(double x)
1029: {
1030: int j;
1031: double f;
1032: double *xt;
1033:
1034: xt=vector(1,ncom);
1035: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1036: f=(*nrfunc)(xt);
1037: free_vector(xt,1,ncom);
1038: return f;
1039: }
1040:
1041: /*****************brent *************************/
1042: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1043: {
1044: int iter;
1045: double a,b,d,etemp;
1046: double fu,fv,fw,fx;
1047: double ftemp;
1048: double p,q,r,tol1,tol2,u,v,w,x,xm;
1049: double e=0.0;
1050:
1051: a=(ax < cx ? ax : cx);
1052: b=(ax > cx ? ax : cx);
1053: x=w=v=bx;
1054: fw=fv=fx=(*f)(x);
1055: for (iter=1;iter<=ITMAX;iter++) {
1056: xm=0.5*(a+b);
1057: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1058: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1059: printf(".");fflush(stdout);
1060: fprintf(ficlog,".");fflush(ficlog);
1061: #ifdef DEBUG
1062: 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);
1063: 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);
1064: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1065: #endif
1066: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1067: *xmin=x;
1068: return fx;
1069: }
1070: ftemp=fu;
1071: if (fabs(e) > tol1) {
1072: r=(x-w)*(fx-fv);
1073: q=(x-v)*(fx-fw);
1074: p=(x-v)*q-(x-w)*r;
1075: q=2.0*(q-r);
1076: if (q > 0.0) p = -p;
1077: q=fabs(q);
1078: etemp=e;
1079: e=d;
1080: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1081: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1082: else {
1083: d=p/q;
1084: u=x+d;
1085: if (u-a < tol2 || b-u < tol2)
1086: d=SIGN(tol1,xm-x);
1087: }
1088: } else {
1089: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1090: }
1091: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1092: fu=(*f)(u);
1093: if (fu <= fx) {
1094: if (u >= x) a=x; else b=x;
1095: SHFT(v,w,x,u)
1096: SHFT(fv,fw,fx,fu)
1097: } else {
1098: if (u < x) a=u; else b=u;
1099: if (fu <= fw || w == x) {
1100: v=w;
1101: w=u;
1102: fv=fw;
1103: fw=fu;
1104: } else if (fu <= fv || v == x || v == w) {
1105: v=u;
1106: fv=fu;
1107: }
1108: }
1109: }
1110: nrerror("Too many iterations in brent");
1111: *xmin=x;
1112: return fx;
1113: }
1114:
1115: /****************** mnbrak ***********************/
1116:
1117: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1118: double (*func)(double))
1119: {
1120: double ulim,u,r,q, dum;
1121: double fu;
1122:
1123: *fa=(*func)(*ax);
1124: *fb=(*func)(*bx);
1125: if (*fb > *fa) {
1126: SHFT(dum,*ax,*bx,dum)
1127: SHFT(dum,*fb,*fa,dum)
1128: }
1129: *cx=(*bx)+GOLD*(*bx-*ax);
1130: *fc=(*func)(*cx);
1131: while (*fb > *fc) {
1132: r=(*bx-*ax)*(*fb-*fc);
1133: q=(*bx-*cx)*(*fb-*fa);
1134: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1135: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
1136: ulim=(*bx)+GLIMIT*(*cx-*bx);
1137: if ((*bx-u)*(u-*cx) > 0.0) {
1138: fu=(*func)(u);
1139: } else if ((*cx-u)*(u-ulim) > 0.0) {
1140: fu=(*func)(u);
1141: if (fu < *fc) {
1142: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1143: SHFT(*fb,*fc,fu,(*func)(u))
1144: }
1145: } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
1146: u=ulim;
1147: fu=(*func)(u);
1148: } else {
1149: u=(*cx)+GOLD*(*cx-*bx);
1150: fu=(*func)(u);
1151: }
1152: SHFT(*ax,*bx,*cx,u)
1153: SHFT(*fa,*fb,*fc,fu)
1154: }
1155: }
1156:
1157: /*************** linmin ************************/
1158:
1159: int ncom;
1160: double *pcom,*xicom;
1161: double (*nrfunc)(double []);
1162:
1163: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1164: {
1165: double brent(double ax, double bx, double cx,
1166: double (*f)(double), double tol, double *xmin);
1167: double f1dim(double x);
1168: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1169: double *fc, double (*func)(double));
1170: int j;
1171: double xx,xmin,bx,ax;
1172: double fx,fb,fa;
1173:
1174: ncom=n;
1175: pcom=vector(1,n);
1176: xicom=vector(1,n);
1177: nrfunc=func;
1178: for (j=1;j<=n;j++) {
1179: pcom[j]=p[j];
1180: xicom[j]=xi[j];
1181: }
1182: ax=0.0;
1183: xx=1.0;
1184: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
1185: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
1186: #ifdef DEBUG
1187: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1188: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1189: #endif
1190: for (j=1;j<=n;j++) {
1191: xi[j] *= xmin;
1192: p[j] += xi[j];
1193: }
1194: free_vector(xicom,1,n);
1195: free_vector(pcom,1,n);
1196: }
1197:
1198: char *asc_diff_time(long time_sec, char ascdiff[])
1199: {
1200: long sec_left, days, hours, minutes;
1201: days = (time_sec) / (60*60*24);
1202: sec_left = (time_sec) % (60*60*24);
1203: hours = (sec_left) / (60*60) ;
1204: sec_left = (sec_left) %(60*60);
1205: minutes = (sec_left) /60;
1206: sec_left = (sec_left) % (60);
1.141 brouard 1207: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1.126 brouard 1208: return ascdiff;
1209: }
1210:
1211: /*************** powell ************************/
1212: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1213: double (*func)(double []))
1214: {
1215: void linmin(double p[], double xi[], int n, double *fret,
1216: double (*func)(double []));
1217: int i,ibig,j;
1218: double del,t,*pt,*ptt,*xit;
1219: double fp,fptt;
1220: double *xits;
1221: int niterf, itmp;
1222:
1223: pt=vector(1,n);
1224: ptt=vector(1,n);
1225: xit=vector(1,n);
1226: xits=vector(1,n);
1227: *fret=(*func)(p);
1228: for (j=1;j<=n;j++) pt[j]=p[j];
1229: for (*iter=1;;++(*iter)) {
1230: fp=(*fret);
1231: ibig=0;
1232: del=0.0;
1233: last_time=curr_time;
1234: (void) gettimeofday(&curr_time,&tzp);
1235: 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);
1236: 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);
1237: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
1238: for (i=1;i<=n;i++) {
1239: printf(" %d %.12f",i, p[i]);
1240: fprintf(ficlog," %d %.12lf",i, p[i]);
1241: fprintf(ficrespow," %.12lf", p[i]);
1242: }
1243: printf("\n");
1244: fprintf(ficlog,"\n");
1245: fprintf(ficrespow,"\n");fflush(ficrespow);
1246: if(*iter <=3){
1247: tm = *localtime(&curr_time.tv_sec);
1248: strcpy(strcurr,asctime(&tm));
1249: /* asctime_r(&tm,strcurr); */
1250: forecast_time=curr_time;
1251: itmp = strlen(strcurr);
1252: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1253: strcurr[itmp-1]='\0';
1254: printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1255: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
1256: for(niterf=10;niterf<=30;niterf+=10){
1257: forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
1258: tmf = *localtime(&forecast_time.tv_sec);
1259: /* asctime_r(&tmf,strfor); */
1260: strcpy(strfor,asctime(&tmf));
1261: itmp = strlen(strfor);
1262: if(strfor[itmp-1]=='\n')
1263: strfor[itmp-1]='\0';
1264: 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);
1265: 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);
1266: }
1267: }
1268: for (i=1;i<=n;i++) {
1269: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1270: fptt=(*fret);
1271: #ifdef DEBUG
1272: printf("fret=%lf \n",*fret);
1273: fprintf(ficlog,"fret=%lf \n",*fret);
1274: #endif
1275: printf("%d",i);fflush(stdout);
1276: fprintf(ficlog,"%d",i);fflush(ficlog);
1277: linmin(p,xit,n,fret,func);
1278: if (fabs(fptt-(*fret)) > del) {
1279: del=fabs(fptt-(*fret));
1280: ibig=i;
1281: }
1282: #ifdef DEBUG
1283: printf("%d %.12e",i,(*fret));
1284: fprintf(ficlog,"%d %.12e",i,(*fret));
1285: for (j=1;j<=n;j++) {
1286: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1287: printf(" x(%d)=%.12e",j,xit[j]);
1288: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1289: }
1290: for(j=1;j<=n;j++) {
1291: printf(" p=%.12e",p[j]);
1292: fprintf(ficlog," p=%.12e",p[j]);
1293: }
1294: printf("\n");
1295: fprintf(ficlog,"\n");
1296: #endif
1297: }
1298: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1299: #ifdef DEBUG
1300: int k[2],l;
1301: k[0]=1;
1302: k[1]=-1;
1303: printf("Max: %.12e",(*func)(p));
1304: fprintf(ficlog,"Max: %.12e",(*func)(p));
1305: for (j=1;j<=n;j++) {
1306: printf(" %.12e",p[j]);
1307: fprintf(ficlog," %.12e",p[j]);
1308: }
1309: printf("\n");
1310: fprintf(ficlog,"\n");
1311: for(l=0;l<=1;l++) {
1312: for (j=1;j<=n;j++) {
1313: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1314: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1315: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1316: }
1317: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1318: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1319: }
1320: #endif
1321:
1322:
1323: free_vector(xit,1,n);
1324: free_vector(xits,1,n);
1325: free_vector(ptt,1,n);
1326: free_vector(pt,1,n);
1327: return;
1328: }
1329: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1330: for (j=1;j<=n;j++) {
1331: ptt[j]=2.0*p[j]-pt[j];
1332: xit[j]=p[j]-pt[j];
1333: pt[j]=p[j];
1334: }
1335: fptt=(*func)(ptt);
1336: if (fptt < fp) {
1337: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
1338: if (t < 0.0) {
1339: linmin(p,xit,n,fret,func);
1340: for (j=1;j<=n;j++) {
1341: xi[j][ibig]=xi[j][n];
1342: xi[j][n]=xit[j];
1343: }
1344: #ifdef DEBUG
1345: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1346: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1347: for(j=1;j<=n;j++){
1348: printf(" %.12e",xit[j]);
1349: fprintf(ficlog," %.12e",xit[j]);
1350: }
1351: printf("\n");
1352: fprintf(ficlog,"\n");
1353: #endif
1354: }
1355: }
1356: }
1357: }
1358:
1359: /**** Prevalence limit (stable or period prevalence) ****************/
1360:
1361: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1362: {
1363: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1364: matrix by transitions matrix until convergence is reached */
1365:
1366: int i, ii,j,k;
1367: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1368: /* double **matprod2(); */ /* test */
1.131 brouard 1369: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1370: double **newm;
1371: double agefin, delaymax=50 ; /* Max number of years to converge */
1372:
1373: for (ii=1;ii<=nlstate+ndeath;ii++)
1374: for (j=1;j<=nlstate+ndeath;j++){
1375: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1376: }
1377:
1378: cov[1]=1.;
1379:
1380: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1381: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1382: newm=savm;
1383: /* Covariates have to be included here again */
1.138 brouard 1384: cov[2]=agefin;
1385:
1386: for (k=1; k<=cptcovn;k++) {
1387: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1388: /*printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1389: }
1.145 brouard 1390: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1391: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1392: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1.138 brouard 1393:
1394: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1395: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1396: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1397: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1398: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1399: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1400:
1.126 brouard 1401: savm=oldm;
1402: oldm=newm;
1403: maxmax=0.;
1404: for(j=1;j<=nlstate;j++){
1405: min=1.;
1406: max=0.;
1407: for(i=1; i<=nlstate; i++) {
1408: sumnew=0;
1409: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1410: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1411: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1412: max=FMAX(max,prlim[i][j]);
1413: min=FMIN(min,prlim[i][j]);
1414: }
1415: maxmin=max-min;
1416: maxmax=FMAX(maxmax,maxmin);
1417: }
1418: if(maxmax < ftolpl){
1419: return prlim;
1420: }
1421: }
1422: }
1423:
1424: /*************** transition probabilities ***************/
1425:
1426: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1427: {
1.138 brouard 1428: /* According to parameters values stored in x and the covariate's values stored in cov,
1429: computes the probability to be observed in state j being in state i by appying the
1430: model to the ncovmodel covariates (including constant and age).
1431: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1432: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1433: ncth covariate in the global vector x is given by the formula:
1434: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1435: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1436: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1437: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1438: Outputs ps[i][j] the probability to be observed in j being in j according to
1439: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1440: */
1441: double s1, lnpijopii;
1.126 brouard 1442: /*double t34;*/
1443: int i,j,j1, nc, ii, jj;
1444:
1445: for(i=1; i<= nlstate; i++){
1446: for(j=1; j<i;j++){
1.138 brouard 1447: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1448: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1449: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1450: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1451: }
1.138 brouard 1452: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1453: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1454: }
1455: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1456: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1457: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1458: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1459: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1460: }
1.138 brouard 1461: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1462: }
1463: }
1464:
1465: for(i=1; i<= nlstate; i++){
1466: s1=0;
1.131 brouard 1467: for(j=1; j<i; j++){
1.138 brouard 1468: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1469: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1470: }
1471: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1472: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1473: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1474: }
1.138 brouard 1475: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1476: ps[i][i]=1./(s1+1.);
1.138 brouard 1477: /* Computing other pijs */
1.126 brouard 1478: for(j=1; j<i; j++)
1479: ps[i][j]= exp(ps[i][j])*ps[i][i];
1480: for(j=i+1; j<=nlstate+ndeath; j++)
1481: ps[i][j]= exp(ps[i][j])*ps[i][i];
1482: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1483: } /* end i */
1484:
1485: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1486: for(jj=1; jj<= nlstate+ndeath; jj++){
1487: ps[ii][jj]=0;
1488: ps[ii][ii]=1;
1489: }
1490: }
1491:
1.145 brouard 1492:
1493: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1494: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1495: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1496: /* } */
1497: /* printf("\n "); */
1498: /* } */
1499: /* printf("\n ");printf("%lf ",cov[2]);*/
1500: /*
1.126 brouard 1501: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1502: goto end;*/
1503: return ps;
1504: }
1505:
1506: /**************** Product of 2 matrices ******************/
1507:
1.145 brouard 1508: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1509: {
1510: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1511: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1512: /* in, b, out are matrice of pointers which should have been initialized
1513: before: only the contents of out is modified. The function returns
1514: a pointer to pointers identical to out */
1.145 brouard 1515: int i, j, k;
1.126 brouard 1516: for(i=nrl; i<= nrh; i++)
1.145 brouard 1517: for(k=ncolol; k<=ncoloh; k++){
1518: out[i][k]=0.;
1519: for(j=ncl; j<=nch; j++)
1520: out[i][k] +=in[i][j]*b[j][k];
1521: }
1.126 brouard 1522: return out;
1523: }
1524:
1525:
1526: /************* Higher Matrix Product ***************/
1527:
1528: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1529: {
1530: /* Computes the transition matrix starting at age 'age' over
1531: 'nhstepm*hstepm*stepm' months (i.e. until
1532: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1533: nhstepm*hstepm matrices.
1534: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1535: (typically every 2 years instead of every month which is too big
1536: for the memory).
1537: Model is determined by parameters x and covariates have to be
1538: included manually here.
1539:
1540: */
1541:
1542: int i, j, d, h, k;
1.131 brouard 1543: double **out, cov[NCOVMAX+1];
1.126 brouard 1544: double **newm;
1545:
1546: /* Hstepm could be zero and should return the unit matrix */
1547: for (i=1;i<=nlstate+ndeath;i++)
1548: for (j=1;j<=nlstate+ndeath;j++){
1549: oldm[i][j]=(i==j ? 1.0 : 0.0);
1550: po[i][j][0]=(i==j ? 1.0 : 0.0);
1551: }
1552: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1553: for(h=1; h <=nhstepm; h++){
1554: for(d=1; d <=hstepm; d++){
1555: newm=savm;
1556: /* Covariates have to be included here again */
1557: cov[1]=1.;
1558: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1559: for (k=1; k<=cptcovn;k++)
1560: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1561: for (k=1; k<=cptcovage;k++)
1562: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1563: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1564: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1565:
1566:
1567: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1568: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1569: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1570: pmij(pmmij,cov,ncovmodel,x,nlstate));
1571: savm=oldm;
1572: oldm=newm;
1573: }
1574: for(i=1; i<=nlstate+ndeath; i++)
1575: for(j=1;j<=nlstate+ndeath;j++) {
1576: po[i][j][h]=newm[i][j];
1.128 brouard 1577: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1578: }
1.128 brouard 1579: /*printf("h=%d ",h);*/
1.126 brouard 1580: } /* end h */
1.128 brouard 1581: /* printf("\n H=%d \n",h); */
1.126 brouard 1582: return po;
1583: }
1584:
1585:
1586: /*************** log-likelihood *************/
1587: double func( double *x)
1588: {
1589: int i, ii, j, k, mi, d, kk;
1.131 brouard 1590: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1591: double **out;
1592: double sw; /* Sum of weights */
1593: double lli; /* Individual log likelihood */
1594: int s1, s2;
1595: double bbh, survp;
1596: long ipmx;
1597: /*extern weight */
1598: /* We are differentiating ll according to initial status */
1599: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1600: /*for(i=1;i<imx;i++)
1601: printf(" %d\n",s[4][i]);
1602: */
1603: cov[1]=1.;
1604:
1605: for(k=1; k<=nlstate; k++) ll[k]=0.;
1606:
1607: if(mle==1){
1608: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1609: /* Computes the values of the ncovmodel covariates of the model
1610: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1611: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1612: to be observed in j being in i according to the model.
1613: */
1.145 brouard 1614: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1615: cov[2+k]=covar[Tvar[k]][i];
1616: }
1.137 brouard 1617: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1618: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1619: has been calculated etc */
1.126 brouard 1620: for(mi=1; mi<= wav[i]-1; mi++){
1621: for (ii=1;ii<=nlstate+ndeath;ii++)
1622: for (j=1;j<=nlstate+ndeath;j++){
1623: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1624: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1625: }
1626: for(d=0; d<dh[mi][i]; d++){
1627: newm=savm;
1628: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1629: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1630: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1631: }
1632: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1633: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1634: savm=oldm;
1635: oldm=newm;
1636: } /* end mult */
1637:
1638: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1639: /* But now since version 0.9 we anticipate for bias at large stepm.
1640: * If stepm is larger than one month (smallest stepm) and if the exact delay
1641: * (in months) between two waves is not a multiple of stepm, we rounded to
1642: * the nearest (and in case of equal distance, to the lowest) interval but now
1643: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1644: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1645: * probability in order to take into account the bias as a fraction of the way
1646: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1647: * -stepm/2 to stepm/2 .
1648: * For stepm=1 the results are the same as for previous versions of Imach.
1649: * For stepm > 1 the results are less biased than in previous versions.
1650: */
1651: s1=s[mw[mi][i]][i];
1652: s2=s[mw[mi+1][i]][i];
1653: bbh=(double)bh[mi][i]/(double)stepm;
1654: /* bias bh is positive if real duration
1655: * is higher than the multiple of stepm and negative otherwise.
1656: */
1657: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1658: if( s2 > nlstate){
1659: /* i.e. if s2 is a death state and if the date of death is known
1660: then the contribution to the likelihood is the probability to
1661: die between last step unit time and current step unit time,
1662: which is also equal to probability to die before dh
1663: minus probability to die before dh-stepm .
1664: In version up to 0.92 likelihood was computed
1665: as if date of death was unknown. Death was treated as any other
1666: health state: the date of the interview describes the actual state
1667: and not the date of a change in health state. The former idea was
1668: to consider that at each interview the state was recorded
1669: (healthy, disable or death) and IMaCh was corrected; but when we
1670: introduced the exact date of death then we should have modified
1671: the contribution of an exact death to the likelihood. This new
1672: contribution is smaller and very dependent of the step unit
1673: stepm. It is no more the probability to die between last interview
1674: and month of death but the probability to survive from last
1675: interview up to one month before death multiplied by the
1676: probability to die within a month. Thanks to Chris
1677: Jackson for correcting this bug. Former versions increased
1678: mortality artificially. The bad side is that we add another loop
1679: which slows down the processing. The difference can be up to 10%
1680: lower mortality.
1681: */
1682: lli=log(out[s1][s2] - savm[s1][s2]);
1683:
1684:
1685: } else if (s2==-2) {
1686: for (j=1,survp=0. ; j<=nlstate; j++)
1687: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1688: /*survp += out[s1][j]; */
1689: lli= log(survp);
1690: }
1691:
1692: else if (s2==-4) {
1693: for (j=3,survp=0. ; j<=nlstate; j++)
1694: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1695: lli= log(survp);
1696: }
1697:
1698: else if (s2==-5) {
1699: for (j=1,survp=0. ; j<=2; j++)
1700: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1701: lli= log(survp);
1702: }
1703:
1704: else{
1705: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1706: /* 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 */
1707: }
1708: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1709: /*if(lli ==000.0)*/
1710: /*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); */
1711: ipmx +=1;
1712: sw += weight[i];
1713: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1714: } /* end of wave */
1715: } /* end of individual */
1716: } else if(mle==2){
1717: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1718: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1719: for(mi=1; mi<= wav[i]-1; mi++){
1720: for (ii=1;ii<=nlstate+ndeath;ii++)
1721: for (j=1;j<=nlstate+ndeath;j++){
1722: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1723: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1724: }
1725: for(d=0; d<=dh[mi][i]; d++){
1726: newm=savm;
1727: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1728: for (kk=1; kk<=cptcovage;kk++) {
1729: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1730: }
1731: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1732: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1733: savm=oldm;
1734: oldm=newm;
1735: } /* end mult */
1736:
1737: s1=s[mw[mi][i]][i];
1738: s2=s[mw[mi+1][i]][i];
1739: bbh=(double)bh[mi][i]/(double)stepm;
1740: 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 */
1741: ipmx +=1;
1742: sw += weight[i];
1743: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1744: } /* end of wave */
1745: } /* end of individual */
1746: } else if(mle==3){ /* exponential inter-extrapolation */
1747: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1748: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1749: for(mi=1; mi<= wav[i]-1; mi++){
1750: for (ii=1;ii<=nlstate+ndeath;ii++)
1751: for (j=1;j<=nlstate+ndeath;j++){
1752: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1753: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1754: }
1755: for(d=0; d<dh[mi][i]; d++){
1756: newm=savm;
1757: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1758: for (kk=1; kk<=cptcovage;kk++) {
1759: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1760: }
1761: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1762: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1763: savm=oldm;
1764: oldm=newm;
1765: } /* end mult */
1766:
1767: s1=s[mw[mi][i]][i];
1768: s2=s[mw[mi+1][i]][i];
1769: bbh=(double)bh[mi][i]/(double)stepm;
1770: 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 */
1771: ipmx +=1;
1772: sw += weight[i];
1773: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1774: } /* end of wave */
1775: } /* end of individual */
1776: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1777: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1778: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1779: for(mi=1; mi<= wav[i]-1; mi++){
1780: for (ii=1;ii<=nlstate+ndeath;ii++)
1781: for (j=1;j<=nlstate+ndeath;j++){
1782: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1783: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1784: }
1785: for(d=0; d<dh[mi][i]; d++){
1786: newm=savm;
1787: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1788: for (kk=1; kk<=cptcovage;kk++) {
1789: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1790: }
1791:
1792: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1793: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1794: savm=oldm;
1795: oldm=newm;
1796: } /* end mult */
1797:
1798: s1=s[mw[mi][i]][i];
1799: s2=s[mw[mi+1][i]][i];
1800: if( s2 > nlstate){
1801: lli=log(out[s1][s2] - savm[s1][s2]);
1802: }else{
1803: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1804: }
1805: ipmx +=1;
1806: sw += weight[i];
1807: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1808: /* 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]); */
1809: } /* end of wave */
1810: } /* end of individual */
1811: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1812: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1813: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1814: for(mi=1; mi<= wav[i]-1; mi++){
1815: for (ii=1;ii<=nlstate+ndeath;ii++)
1816: for (j=1;j<=nlstate+ndeath;j++){
1817: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1818: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1819: }
1820: for(d=0; d<dh[mi][i]; d++){
1821: newm=savm;
1822: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1823: for (kk=1; kk<=cptcovage;kk++) {
1824: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1825: }
1826:
1827: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1828: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1829: savm=oldm;
1830: oldm=newm;
1831: } /* end mult */
1832:
1833: s1=s[mw[mi][i]][i];
1834: s2=s[mw[mi+1][i]][i];
1835: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1836: ipmx +=1;
1837: sw += weight[i];
1838: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1839: /*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]);*/
1840: } /* end of wave */
1841: } /* end of individual */
1842: } /* End of if */
1843: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1844: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1845: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1846: return -l;
1847: }
1848:
1849: /*************** log-likelihood *************/
1850: double funcone( double *x)
1851: {
1852: /* Same as likeli but slower because of a lot of printf and if */
1853: int i, ii, j, k, mi, d, kk;
1.131 brouard 1854: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1855: double **out;
1856: double lli; /* Individual log likelihood */
1857: double llt;
1858: int s1, s2;
1859: double bbh, survp;
1860: /*extern weight */
1861: /* We are differentiating ll according to initial status */
1862: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1863: /*for(i=1;i<imx;i++)
1864: printf(" %d\n",s[4][i]);
1865: */
1866: cov[1]=1.;
1867:
1868: for(k=1; k<=nlstate; k++) ll[k]=0.;
1869:
1870: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1871: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1872: for(mi=1; mi<= wav[i]-1; mi++){
1873: for (ii=1;ii<=nlstate+ndeath;ii++)
1874: for (j=1;j<=nlstate+ndeath;j++){
1875: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1876: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1877: }
1878: for(d=0; d<dh[mi][i]; d++){
1879: newm=savm;
1880: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1881: for (kk=1; kk<=cptcovage;kk++) {
1882: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1883: }
1.145 brouard 1884: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 1885: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1886: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 1887: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
1888: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 1889: savm=oldm;
1890: oldm=newm;
1891: } /* end mult */
1892:
1893: s1=s[mw[mi][i]][i];
1894: s2=s[mw[mi+1][i]][i];
1895: bbh=(double)bh[mi][i]/(double)stepm;
1896: /* bias is positive if real duration
1897: * is higher than the multiple of stepm and negative otherwise.
1898: */
1899: if( s2 > nlstate && (mle <5) ){ /* Jackson */
1900: lli=log(out[s1][s2] - savm[s1][s2]);
1901: } else if (s2==-2) {
1902: for (j=1,survp=0. ; j<=nlstate; j++)
1903: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1904: lli= log(survp);
1905: }else if (mle==1){
1906: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1907: } else if(mle==2){
1908: 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 */
1909: } else if(mle==3){ /* exponential inter-extrapolation */
1910: 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 */
1911: } else if (mle==4){ /* mle=4 no inter-extrapolation */
1912: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 1913: } else{ /* mle=0 back to 1 */
1914: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1915: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 1916: } /* End of if */
1917: ipmx +=1;
1918: sw += weight[i];
1919: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 1920: /*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 1921: if(globpr){
1.141 brouard 1922: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 1923: %11.6f %11.6f %11.6f ", \
1924: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
1925: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
1926: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
1927: llt +=ll[k]*gipmx/gsw;
1928: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
1929: }
1930: fprintf(ficresilk," %10.6f\n", -llt);
1931: }
1932: } /* end of wave */
1933: } /* end of individual */
1934: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
1935: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
1936: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
1937: if(globpr==0){ /* First time we count the contributions and weights */
1938: gipmx=ipmx;
1939: gsw=sw;
1940: }
1941: return -l;
1942: }
1943:
1944:
1945: /*************** function likelione ***********/
1946: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
1947: {
1948: /* This routine should help understanding what is done with
1949: the selection of individuals/waves and
1950: to check the exact contribution to the likelihood.
1951: Plotting could be done.
1952: */
1953: int k;
1954:
1955: if(*globpri !=0){ /* Just counts and sums, no printings */
1956: strcpy(fileresilk,"ilk");
1957: strcat(fileresilk,fileres);
1958: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
1959: printf("Problem with resultfile: %s\n", fileresilk);
1960: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
1961: }
1962: 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");
1963: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
1964: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
1965: for(k=1; k<=nlstate; k++)
1966: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
1967: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
1968: }
1969:
1970: *fretone=(*funcone)(p);
1971: if(*globpri !=0){
1972: fclose(ficresilk);
1973: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1974: fflush(fichtm);
1975: }
1976: return;
1977: }
1978:
1979:
1980: /*********** Maximum Likelihood Estimation ***************/
1981:
1982: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
1983: {
1984: int i,j, iter;
1985: double **xi;
1986: double fret;
1987: double fretone; /* Only one call to likelihood */
1988: /* char filerespow[FILENAMELENGTH];*/
1989: xi=matrix(1,npar,1,npar);
1990: for (i=1;i<=npar;i++)
1991: for (j=1;j<=npar;j++)
1992: xi[i][j]=(i==j ? 1.0 : 0.0);
1993: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1994: strcpy(filerespow,"pow");
1995: strcat(filerespow,fileres);
1996: if((ficrespow=fopen(filerespow,"w"))==NULL) {
1997: printf("Problem with resultfile: %s\n", filerespow);
1998: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
1999: }
2000: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2001: for (i=1;i<=nlstate;i++)
2002: for(j=1;j<=nlstate+ndeath;j++)
2003: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2004: fprintf(ficrespow,"\n");
2005:
2006: powell(p,xi,npar,ftol,&iter,&fret,func);
2007:
2008: free_matrix(xi,1,npar,1,npar);
2009: fclose(ficrespow);
2010: printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
2011: fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2012: fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
2013:
2014: }
2015:
2016: /**** Computes Hessian and covariance matrix ***/
2017: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2018: {
2019: double **a,**y,*x,pd;
2020: double **hess;
2021: int i, j,jk;
2022: int *indx;
2023:
2024: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2025: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2026: void lubksb(double **a, int npar, int *indx, double b[]) ;
2027: void ludcmp(double **a, int npar, int *indx, double *d) ;
2028: double gompertz(double p[]);
2029: hess=matrix(1,npar,1,npar);
2030:
2031: printf("\nCalculation of the hessian matrix. Wait...\n");
2032: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2033: for (i=1;i<=npar;i++){
2034: printf("%d",i);fflush(stdout);
2035: fprintf(ficlog,"%d",i);fflush(ficlog);
2036:
2037: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2038:
2039: /* printf(" %f ",p[i]);
2040: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2041: }
2042:
2043: for (i=1;i<=npar;i++) {
2044: for (j=1;j<=npar;j++) {
2045: if (j>i) {
2046: printf(".%d%d",i,j);fflush(stdout);
2047: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2048: hess[i][j]=hessij(p,delti,i,j,func,npar);
2049:
2050: hess[j][i]=hess[i][j];
2051: /*printf(" %lf ",hess[i][j]);*/
2052: }
2053: }
2054: }
2055: printf("\n");
2056: fprintf(ficlog,"\n");
2057:
2058: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2059: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2060:
2061: a=matrix(1,npar,1,npar);
2062: y=matrix(1,npar,1,npar);
2063: x=vector(1,npar);
2064: indx=ivector(1,npar);
2065: for (i=1;i<=npar;i++)
2066: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2067: ludcmp(a,npar,indx,&pd);
2068:
2069: for (j=1;j<=npar;j++) {
2070: for (i=1;i<=npar;i++) x[i]=0;
2071: x[j]=1;
2072: lubksb(a,npar,indx,x);
2073: for (i=1;i<=npar;i++){
2074: matcov[i][j]=x[i];
2075: }
2076: }
2077:
2078: printf("\n#Hessian matrix#\n");
2079: fprintf(ficlog,"\n#Hessian matrix#\n");
2080: for (i=1;i<=npar;i++) {
2081: for (j=1;j<=npar;j++) {
2082: printf("%.3e ",hess[i][j]);
2083: fprintf(ficlog,"%.3e ",hess[i][j]);
2084: }
2085: printf("\n");
2086: fprintf(ficlog,"\n");
2087: }
2088:
2089: /* Recompute Inverse */
2090: for (i=1;i<=npar;i++)
2091: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2092: ludcmp(a,npar,indx,&pd);
2093:
2094: /* printf("\n#Hessian matrix recomputed#\n");
2095:
2096: for (j=1;j<=npar;j++) {
2097: for (i=1;i<=npar;i++) x[i]=0;
2098: x[j]=1;
2099: lubksb(a,npar,indx,x);
2100: for (i=1;i<=npar;i++){
2101: y[i][j]=x[i];
2102: printf("%.3e ",y[i][j]);
2103: fprintf(ficlog,"%.3e ",y[i][j]);
2104: }
2105: printf("\n");
2106: fprintf(ficlog,"\n");
2107: }
2108: */
2109:
2110: free_matrix(a,1,npar,1,npar);
2111: free_matrix(y,1,npar,1,npar);
2112: free_vector(x,1,npar);
2113: free_ivector(indx,1,npar);
2114: free_matrix(hess,1,npar,1,npar);
2115:
2116:
2117: }
2118:
2119: /*************** hessian matrix ****************/
2120: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2121: {
2122: int i;
2123: int l=1, lmax=20;
2124: double k1,k2;
1.132 brouard 2125: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2126: double res;
2127: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2128: double fx;
2129: int k=0,kmax=10;
2130: double l1;
2131:
2132: fx=func(x);
2133: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2134: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2135: l1=pow(10,l);
2136: delts=delt;
2137: for(k=1 ; k <kmax; k=k+1){
2138: delt = delta*(l1*k);
2139: p2[theta]=x[theta] +delt;
1.145 brouard 2140: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2141: p2[theta]=x[theta]-delt;
2142: k2=func(p2)-fx;
2143: /*res= (k1-2.0*fx+k2)/delt/delt; */
2144: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2145:
1.132 brouard 2146: #ifdef DEBUGHESS
1.126 brouard 2147: 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);
2148: 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);
2149: #endif
2150: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2151: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2152: k=kmax;
2153: }
2154: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2155: k=kmax; l=lmax*10.;
2156: }
2157: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2158: delts=delt;
2159: }
2160: }
2161: }
2162: delti[theta]=delts;
2163: return res;
2164:
2165: }
2166:
2167: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2168: {
2169: int i;
2170: int l=1, l1, lmax=20;
2171: double k1,k2,k3,k4,res,fx;
1.132 brouard 2172: double p2[MAXPARM+1];
1.126 brouard 2173: int k;
2174:
2175: fx=func(x);
2176: for (k=1; k<=2; k++) {
2177: for (i=1;i<=npar;i++) p2[i]=x[i];
2178: p2[thetai]=x[thetai]+delti[thetai]/k;
2179: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2180: k1=func(p2)-fx;
2181:
2182: p2[thetai]=x[thetai]+delti[thetai]/k;
2183: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2184: k2=func(p2)-fx;
2185:
2186: p2[thetai]=x[thetai]-delti[thetai]/k;
2187: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2188: k3=func(p2)-fx;
2189:
2190: p2[thetai]=x[thetai]-delti[thetai]/k;
2191: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2192: k4=func(p2)-fx;
2193: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2194: #ifdef DEBUG
2195: 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);
2196: 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);
2197: #endif
2198: }
2199: return res;
2200: }
2201:
2202: /************** Inverse of matrix **************/
2203: void ludcmp(double **a, int n, int *indx, double *d)
2204: {
2205: int i,imax,j,k;
2206: double big,dum,sum,temp;
2207: double *vv;
2208:
2209: vv=vector(1,n);
2210: *d=1.0;
2211: for (i=1;i<=n;i++) {
2212: big=0.0;
2213: for (j=1;j<=n;j++)
2214: if ((temp=fabs(a[i][j])) > big) big=temp;
2215: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2216: vv[i]=1.0/big;
2217: }
2218: for (j=1;j<=n;j++) {
2219: for (i=1;i<j;i++) {
2220: sum=a[i][j];
2221: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2222: a[i][j]=sum;
2223: }
2224: big=0.0;
2225: for (i=j;i<=n;i++) {
2226: sum=a[i][j];
2227: for (k=1;k<j;k++)
2228: sum -= a[i][k]*a[k][j];
2229: a[i][j]=sum;
2230: if ( (dum=vv[i]*fabs(sum)) >= big) {
2231: big=dum;
2232: imax=i;
2233: }
2234: }
2235: if (j != imax) {
2236: for (k=1;k<=n;k++) {
2237: dum=a[imax][k];
2238: a[imax][k]=a[j][k];
2239: a[j][k]=dum;
2240: }
2241: *d = -(*d);
2242: vv[imax]=vv[j];
2243: }
2244: indx[j]=imax;
2245: if (a[j][j] == 0.0) a[j][j]=TINY;
2246: if (j != n) {
2247: dum=1.0/(a[j][j]);
2248: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2249: }
2250: }
2251: free_vector(vv,1,n); /* Doesn't work */
2252: ;
2253: }
2254:
2255: void lubksb(double **a, int n, int *indx, double b[])
2256: {
2257: int i,ii=0,ip,j;
2258: double sum;
2259:
2260: for (i=1;i<=n;i++) {
2261: ip=indx[i];
2262: sum=b[ip];
2263: b[ip]=b[i];
2264: if (ii)
2265: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2266: else if (sum) ii=i;
2267: b[i]=sum;
2268: }
2269: for (i=n;i>=1;i--) {
2270: sum=b[i];
2271: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2272: b[i]=sum/a[i][i];
2273: }
2274: }
2275:
2276: void pstamp(FILE *fichier)
2277: {
2278: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2279: }
2280:
2281: /************ Frequencies ********************/
2282: 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[])
2283: { /* Some frequencies */
2284:
1.130 brouard 2285: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2286: int first;
2287: double ***freq; /* Frequencies */
2288: double *pp, **prop;
2289: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2290: char fileresp[FILENAMELENGTH];
2291:
2292: pp=vector(1,nlstate);
2293: prop=matrix(1,nlstate,iagemin,iagemax+3);
2294: strcpy(fileresp,"p");
2295: strcat(fileresp,fileres);
2296: if((ficresp=fopen(fileresp,"w"))==NULL) {
2297: printf("Problem with prevalence resultfile: %s\n", fileresp);
2298: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2299: exit(0);
2300: }
2301: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2302: j1=0;
2303:
2304: j=cptcoveff;
2305: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2306:
2307: first=1;
2308:
1.145 brouard 2309: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2310: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2311: /* j1++;
2312: */
2313: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2314: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2315: scanf("%d", i);*/
2316: for (i=-5; i<=nlstate+ndeath; i++)
2317: for (jk=-5; jk<=nlstate+ndeath; jk++)
2318: for(m=iagemin; m <= iagemax+3; m++)
2319: freq[i][jk][m]=0;
1.143 brouard 2320:
2321: for (i=1; i<=nlstate; i++)
2322: for(m=iagemin; m <= iagemax+3; m++)
2323: prop[i][m]=0;
1.126 brouard 2324:
2325: dateintsum=0;
2326: k2cpt=0;
2327: for (i=1; i<=imx; i++) {
2328: bool=1;
1.144 brouard 2329: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2330: for (z1=1; z1<=cptcoveff; z1++)
2331: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2332: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2333: bool=0;
1.145 brouard 2334: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtab[%d][%d]=%d, nbcode[Tvaraff][codtab[%d][%d]=%d, j1=%d\n",
2335: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2336: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2337: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2338: }
1.126 brouard 2339: }
1.144 brouard 2340:
1.126 brouard 2341: if (bool==1){
2342: for(m=firstpass; m<=lastpass; m++){
2343: k2=anint[m][i]+(mint[m][i]/12.);
2344: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2345: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2346: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2347: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2348: if (m<lastpass) {
2349: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2350: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2351: }
2352:
2353: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2354: dateintsum=dateintsum+k2;
2355: k2cpt++;
2356: }
2357: /*}*/
2358: }
2359: }
1.145 brouard 2360: } /* end i */
1.126 brouard 2361:
2362: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2363: pstamp(ficresp);
2364: if (cptcovn>0) {
2365: fprintf(ficresp, "\n#********** Variable ");
2366: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2367: fprintf(ficresp, "**********\n#");
1.143 brouard 2368: fprintf(ficlog, "\n#********** Variable ");
2369: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2370: fprintf(ficlog, "**********\n#");
1.126 brouard 2371: }
2372: for(i=1; i<=nlstate;i++)
2373: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2374: fprintf(ficresp, "\n");
2375:
2376: for(i=iagemin; i <= iagemax+3; i++){
2377: if(i==iagemax+3){
2378: fprintf(ficlog,"Total");
2379: }else{
2380: if(first==1){
2381: first=0;
2382: printf("See log file for details...\n");
2383: }
2384: fprintf(ficlog,"Age %d", i);
2385: }
2386: for(jk=1; jk <=nlstate ; jk++){
2387: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2388: pp[jk] += freq[jk][m][i];
2389: }
2390: for(jk=1; jk <=nlstate ; jk++){
2391: for(m=-1, pos=0; m <=0 ; m++)
2392: pos += freq[jk][m][i];
2393: if(pp[jk]>=1.e-10){
2394: if(first==1){
1.132 brouard 2395: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2396: }
2397: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2398: }else{
2399: if(first==1)
2400: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2401: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2402: }
2403: }
2404:
2405: for(jk=1; jk <=nlstate ; jk++){
2406: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2407: pp[jk] += freq[jk][m][i];
2408: }
2409: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2410: pos += pp[jk];
2411: posprop += prop[jk][i];
2412: }
2413: for(jk=1; jk <=nlstate ; jk++){
2414: if(pos>=1.e-5){
2415: if(first==1)
2416: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2417: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2418: }else{
2419: if(first==1)
2420: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2421: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2422: }
2423: if( i <= iagemax){
2424: if(pos>=1.e-5){
2425: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2426: /*probs[i][jk][j1]= pp[jk]/pos;*/
2427: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2428: }
2429: else
2430: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2431: }
2432: }
2433:
2434: for(jk=-1; jk <=nlstate+ndeath; jk++)
2435: for(m=-1; m <=nlstate+ndeath; m++)
2436: if(freq[jk][m][i] !=0 ) {
2437: if(first==1)
2438: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2439: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2440: }
2441: if(i <= iagemax)
2442: fprintf(ficresp,"\n");
2443: if(first==1)
2444: printf("Others in log...\n");
2445: fprintf(ficlog,"\n");
2446: }
1.145 brouard 2447: /*}*/
1.126 brouard 2448: }
2449: dateintmean=dateintsum/k2cpt;
2450:
2451: fclose(ficresp);
2452: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2453: free_vector(pp,1,nlstate);
2454: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2455: /* End of Freq */
2456: }
2457:
2458: /************ Prevalence ********************/
2459: 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)
2460: {
2461: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2462: in each health status at the date of interview (if between dateprev1 and dateprev2).
2463: We still use firstpass and lastpass as another selection.
2464: */
2465:
1.130 brouard 2466: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2467: double ***freq; /* Frequencies */
2468: double *pp, **prop;
2469: double pos,posprop;
2470: double y2; /* in fractional years */
2471: int iagemin, iagemax;
1.145 brouard 2472: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2473:
2474: iagemin= (int) agemin;
2475: iagemax= (int) agemax;
2476: /*pp=vector(1,nlstate);*/
2477: prop=matrix(1,nlstate,iagemin,iagemax+3);
2478: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2479: j1=0;
2480:
1.145 brouard 2481: /*j=cptcoveff;*/
1.126 brouard 2482: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2483:
1.145 brouard 2484: first=1;
2485: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2486: /*for(i1=1; i1<=ncodemax[k1];i1++){
2487: j1++;*/
1.126 brouard 2488:
2489: for (i=1; i<=nlstate; i++)
2490: for(m=iagemin; m <= iagemax+3; m++)
2491: prop[i][m]=0.0;
2492:
2493: for (i=1; i<=imx; i++) { /* Each individual */
2494: bool=1;
2495: if (cptcovn>0) {
2496: for (z1=1; z1<=cptcoveff; z1++)
2497: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2498: bool=0;
2499: }
2500: if (bool==1) {
2501: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2502: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2503: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2504: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2505: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2506: 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);
2507: if (s[m][i]>0 && s[m][i]<=nlstate) {
2508: /*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]]);*/
2509: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2510: prop[s[m][i]][iagemax+3] += weight[i];
2511: }
2512: }
2513: } /* end selection of waves */
2514: }
2515: }
2516: for(i=iagemin; i <= iagemax+3; i++){
2517: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2518: posprop += prop[jk][i];
2519: }
1.145 brouard 2520:
1.126 brouard 2521: for(jk=1; jk <=nlstate ; jk++){
2522: if( i <= iagemax){
2523: if(posprop>=1.e-5){
2524: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2525: } else{
2526: if(first==1){
2527: first=0;
2528: printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others on log file...\n",jk,i,j1,probs[i][jk][j1]);
2529: }
2530: }
1.126 brouard 2531: }
2532: }/* end jk */
2533: }/* end i */
1.145 brouard 2534: /*} *//* end i1 */
2535: } /* end j1 */
1.126 brouard 2536:
2537: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2538: /*free_vector(pp,1,nlstate);*/
2539: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2540: } /* End of prevalence */
2541:
2542: /************* Waves Concatenation ***************/
2543:
2544: 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)
2545: {
2546: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2547: Death is a valid wave (if date is known).
2548: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2549: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2550: and mw[mi+1][i]. dh depends on stepm.
2551: */
2552:
2553: int i, mi, m;
2554: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2555: double sum=0., jmean=0.;*/
2556: int first;
2557: int j, k=0,jk, ju, jl;
2558: double sum=0.;
2559: first=0;
2560: jmin=1e+5;
2561: jmax=-1;
2562: jmean=0.;
2563: for(i=1; i<=imx; i++){
2564: mi=0;
2565: m=firstpass;
2566: while(s[m][i] <= nlstate){
2567: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2568: mw[++mi][i]=m;
2569: if(m >=lastpass)
2570: break;
2571: else
2572: m++;
2573: }/* end while */
2574: if (s[m][i] > nlstate){
2575: mi++; /* Death is another wave */
2576: /* if(mi==0) never been interviewed correctly before death */
2577: /* Only death is a correct wave */
2578: mw[mi][i]=m;
2579: }
2580:
2581: wav[i]=mi;
2582: if(mi==0){
2583: nbwarn++;
2584: if(first==0){
2585: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2586: first=1;
2587: }
2588: if(first==1){
2589: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2590: }
2591: } /* end mi==0 */
2592: } /* End individuals */
2593:
2594: for(i=1; i<=imx; i++){
2595: for(mi=1; mi<wav[i];mi++){
2596: if (stepm <=0)
2597: dh[mi][i]=1;
2598: else{
2599: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2600: if (agedc[i] < 2*AGESUP) {
2601: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2602: if(j==0) j=1; /* Survives at least one month after exam */
2603: else if(j<0){
2604: nberr++;
2605: 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]);
2606: j=1; /* Temporary Dangerous patch */
2607: 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);
2608: 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]);
2609: 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);
2610: }
2611: k=k+1;
2612: if (j >= jmax){
2613: jmax=j;
2614: ijmax=i;
2615: }
2616: if (j <= jmin){
2617: jmin=j;
2618: ijmin=i;
2619: }
2620: sum=sum+j;
2621: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2622: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2623: }
2624: }
2625: else{
2626: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2627: /* 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]); */
2628:
2629: k=k+1;
2630: if (j >= jmax) {
2631: jmax=j;
2632: ijmax=i;
2633: }
2634: else if (j <= jmin){
2635: jmin=j;
2636: ijmin=i;
2637: }
2638: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2639: /*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]);*/
2640: if(j<0){
2641: nberr++;
2642: 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]);
2643: 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]);
2644: }
2645: sum=sum+j;
2646: }
2647: jk= j/stepm;
2648: jl= j -jk*stepm;
2649: ju= j -(jk+1)*stepm;
2650: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2651: if(jl==0){
2652: dh[mi][i]=jk;
2653: bh[mi][i]=0;
2654: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2655: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2656: dh[mi][i]=jk+1;
2657: bh[mi][i]=ju;
2658: }
2659: }else{
2660: if(jl <= -ju){
2661: dh[mi][i]=jk;
2662: bh[mi][i]=jl; /* bias is positive if real duration
2663: * is higher than the multiple of stepm and negative otherwise.
2664: */
2665: }
2666: else{
2667: dh[mi][i]=jk+1;
2668: bh[mi][i]=ju;
2669: }
2670: if(dh[mi][i]==0){
2671: dh[mi][i]=1; /* At least one step */
2672: bh[mi][i]=ju; /* At least one step */
2673: /* 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);*/
2674: }
2675: } /* end if mle */
2676: }
2677: } /* end wave */
2678: }
2679: jmean=sum/k;
2680: 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);
1.141 brouard 2681: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 2682: }
2683:
2684: /*********** Tricode ****************************/
1.145 brouard 2685: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2686: {
1.144 brouard 2687: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2688: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2689: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 2690: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2691: /* nbcode[Tvar[j]][1]=
1.144 brouard 2692: */
1.130 brouard 2693:
1.145 brouard 2694: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2695: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 2696: int cptcode=0; /* Modality max of covariates j */
2697: int modmincovj=0; /* Modality min of covariates j */
2698:
2699:
1.126 brouard 2700: cptcoveff=0;
2701:
1.145 brouard 2702: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2703: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2704:
1.145 brouard 2705: /* Loop on covariates without age and products */
2706: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2707: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2708: modality of this covariate Vj*/
1.145 brouard 2709: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2710: * If product of Vn*Vm, still boolean *:
2711: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2712: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2713: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2714: modality of the nth covariate of individual i. */
1.145 brouard 2715: if (ij > modmaxcovj)
2716: modmaxcovj=ij;
2717: else if (ij < modmincovj)
2718: modmincovj=ij;
2719: if ((ij < -1) && (ij > NCOVMAX)){
2720: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2721: exit(1);
2722: }else
1.136 brouard 2723: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 2724: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2725: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2726: /* getting the maximum value of the modality of the covariate
2727: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2728: female is 1, then modmaxcovj=1.*/
1.126 brouard 2729: }
1.145 brouard 2730: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2731: cptcode=modmaxcovj;
1.137 brouard 2732: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 2733: /*for (i=0; i<=cptcode; i++) {*/
2734: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2735: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2736: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2737: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2738: }
2739: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2740: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 2741: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2742:
1.136 brouard 2743: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 2744: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2745: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2746: modmincovj=3; modmaxcovj = 7;
2747: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2748: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2749: variables V1_1 and V1_2.
2750: nbcode[Tvar[j]][ij]=k;
2751: nbcode[Tvar[j]][1]=0;
2752: nbcode[Tvar[j]][2]=1;
2753: nbcode[Tvar[j]][3]=2;
2754: */
2755: ij=1; /* ij is similar to i but can jumps over null modalities */
2756: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2757: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2758: /*recode from 0 */
1.131 brouard 2759: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2760: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2761: k is a modality. If we have model=V1+V1*sex
2762: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2763: ij++;
2764: }
2765: if (ij > ncodemax[j]) break;
1.137 brouard 2766: } /* end of loop on */
2767: } /* end of loop on modality */
2768: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2769:
1.145 brouard 2770: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 2771:
1.145 brouard 2772: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2773: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2774: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2775: Ndum[ij]++;
2776: }
1.126 brouard 2777:
2778: ij=1;
1.145 brouard 2779: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2780: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 2781: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 2782: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2783: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 2784: ij++;
1.145 brouard 2785: }else
2786: Tvaraff[ij]=0;
1.126 brouard 2787: }
1.131 brouard 2788: ij--;
1.144 brouard 2789: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 2790:
1.126 brouard 2791: }
2792:
1.145 brouard 2793:
1.126 brouard 2794: /*********** Health Expectancies ****************/
2795:
1.127 brouard 2796: 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 2797:
2798: {
2799: /* Health expectancies, no variances */
2800: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2801: int nhstepma, nstepma; /* Decreasing with age */
2802: double age, agelim, hf;
2803: double ***p3mat;
2804: double eip;
2805:
2806: pstamp(ficreseij);
2807: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
2808: fprintf(ficreseij,"# Age");
2809: for(i=1; i<=nlstate;i++){
2810: for(j=1; j<=nlstate;j++){
2811: fprintf(ficreseij," e%1d%1d ",i,j);
2812: }
2813: fprintf(ficreseij," e%1d. ",i);
2814: }
2815: fprintf(ficreseij,"\n");
2816:
2817:
2818: if(estepm < stepm){
2819: printf ("Problem %d lower than %d\n",estepm, stepm);
2820: }
2821: else hstepm=estepm;
2822: /* We compute the life expectancy from trapezoids spaced every estepm months
2823: * This is mainly to measure the difference between two models: for example
2824: * if stepm=24 months pijx are given only every 2 years and by summing them
2825: * we are calculating an estimate of the Life Expectancy assuming a linear
2826: * progression in between and thus overestimating or underestimating according
2827: * to the curvature of the survival function. If, for the same date, we
2828: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2829: * to compare the new estimate of Life expectancy with the same linear
2830: * hypothesis. A more precise result, taking into account a more precise
2831: * curvature will be obtained if estepm is as small as stepm. */
2832:
2833: /* For example we decided to compute the life expectancy with the smallest unit */
2834: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2835: nhstepm is the number of hstepm from age to agelim
2836: nstepm is the number of stepm from age to agelin.
2837: Look at hpijx to understand the reason of that which relies in memory size
2838: and note for a fixed period like estepm months */
2839: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2840: survival function given by stepm (the optimization length). Unfortunately it
2841: means that if the survival funtion is printed only each two years of age and if
2842: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2843: results. So we changed our mind and took the option of the best precision.
2844: */
2845: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2846:
2847: agelim=AGESUP;
2848: /* If stepm=6 months */
2849: /* Computed by stepm unit matrices, product of hstepm matrices, stored
2850: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
2851:
2852: /* nhstepm age range expressed in number of stepm */
2853: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2854: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2855: /* if (stepm >= YEARM) hstepm=1;*/
2856: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2857: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2858:
2859: for (age=bage; age<=fage; age ++){
2860: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2861: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2862: /* if (stepm >= YEARM) hstepm=1;*/
2863: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
2864:
2865: /* If stepm=6 months */
2866: /* Computed by stepm unit matrices, product of hstepma matrices, stored
2867: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
2868:
2869: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
2870:
2871: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
2872:
2873: printf("%d|",(int)age);fflush(stdout);
2874: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
2875:
2876: /* Computing expectancies */
2877: for(i=1; i<=nlstate;i++)
2878: for(j=1; j<=nlstate;j++)
2879: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
2880: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
2881:
2882: /* 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]);*/
2883:
2884: }
2885:
2886: fprintf(ficreseij,"%3.0f",age );
2887: for(i=1; i<=nlstate;i++){
2888: eip=0;
2889: for(j=1; j<=nlstate;j++){
2890: eip +=eij[i][j][(int)age];
2891: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
2892: }
2893: fprintf(ficreseij,"%9.4f", eip );
2894: }
2895: fprintf(ficreseij,"\n");
2896:
2897: }
2898: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2899: printf("\n");
2900: fprintf(ficlog,"\n");
2901:
2902: }
2903:
1.127 brouard 2904: 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 2905:
2906: {
2907: /* Covariances of health expectancies eij and of total life expectancies according
2908: to initial status i, ei. .
2909: */
2910: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
2911: int nhstepma, nstepma; /* Decreasing with age */
2912: double age, agelim, hf;
2913: double ***p3matp, ***p3matm, ***varhe;
2914: double **dnewm,**doldm;
2915: double *xp, *xm;
2916: double **gp, **gm;
2917: double ***gradg, ***trgradg;
2918: int theta;
2919:
2920: double eip, vip;
2921:
2922: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
2923: xp=vector(1,npar);
2924: xm=vector(1,npar);
2925: dnewm=matrix(1,nlstate*nlstate,1,npar);
2926: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
2927:
2928: pstamp(ficresstdeij);
2929: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
2930: fprintf(ficresstdeij,"# Age");
2931: for(i=1; i<=nlstate;i++){
2932: for(j=1; j<=nlstate;j++)
2933: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
2934: fprintf(ficresstdeij," e%1d. ",i);
2935: }
2936: fprintf(ficresstdeij,"\n");
2937:
2938: pstamp(ficrescveij);
2939: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
2940: fprintf(ficrescveij,"# Age");
2941: for(i=1; i<=nlstate;i++)
2942: for(j=1; j<=nlstate;j++){
2943: cptj= (j-1)*nlstate+i;
2944: for(i2=1; i2<=nlstate;i2++)
2945: for(j2=1; j2<=nlstate;j2++){
2946: cptj2= (j2-1)*nlstate+i2;
2947: if(cptj2 <= cptj)
2948: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
2949: }
2950: }
2951: fprintf(ficrescveij,"\n");
2952:
2953: if(estepm < stepm){
2954: printf ("Problem %d lower than %d\n",estepm, stepm);
2955: }
2956: else hstepm=estepm;
2957: /* We compute the life expectancy from trapezoids spaced every estepm months
2958: * This is mainly to measure the difference between two models: for example
2959: * if stepm=24 months pijx are given only every 2 years and by summing them
2960: * we are calculating an estimate of the Life Expectancy assuming a linear
2961: * progression in between and thus overestimating or underestimating according
2962: * to the curvature of the survival function. If, for the same date, we
2963: * estimate the model with stepm=1 month, we can keep estepm to 24 months
2964: * to compare the new estimate of Life expectancy with the same linear
2965: * hypothesis. A more precise result, taking into account a more precise
2966: * curvature will be obtained if estepm is as small as stepm. */
2967:
2968: /* For example we decided to compute the life expectancy with the smallest unit */
2969: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
2970: nhstepm is the number of hstepm from age to agelim
2971: nstepm is the number of stepm from age to agelin.
2972: Look at hpijx to understand the reason of that which relies in memory size
2973: and note for a fixed period like estepm months */
2974: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
2975: survival function given by stepm (the optimization length). Unfortunately it
2976: means that if the survival funtion is printed only each two years of age and if
2977: you sum them up and add 1 year (area under the trapezoids) you won't get the same
2978: results. So we changed our mind and took the option of the best precision.
2979: */
2980: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
2981:
2982: /* If stepm=6 months */
2983: /* nhstepm age range expressed in number of stepm */
2984: agelim=AGESUP;
2985: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
2986: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
2987: /* if (stepm >= YEARM) hstepm=1;*/
2988: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
2989:
2990: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2991: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
2992: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
2993: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
2994: gp=matrix(0,nhstepm,1,nlstate*nlstate);
2995: gm=matrix(0,nhstepm,1,nlstate*nlstate);
2996:
2997: for (age=bage; age<=fage; age ++){
2998: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
2999: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3000: /* if (stepm >= YEARM) hstepm=1;*/
3001: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3002:
3003: /* If stepm=6 months */
3004: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3005: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3006:
3007: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3008:
3009: /* Computing Variances of health expectancies */
3010: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3011: decrease memory allocation */
3012: for(theta=1; theta <=npar; theta++){
3013: for(i=1; i<=npar; i++){
3014: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3015: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3016: }
3017: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3018: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3019:
3020: for(j=1; j<= nlstate; j++){
3021: for(i=1; i<=nlstate; i++){
3022: for(h=0; h<=nhstepm-1; h++){
3023: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3024: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3025: }
3026: }
3027: }
3028:
3029: for(ij=1; ij<= nlstate*nlstate; ij++)
3030: for(h=0; h<=nhstepm-1; h++){
3031: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3032: }
3033: }/* End theta */
3034:
3035:
3036: for(h=0; h<=nhstepm-1; h++)
3037: for(j=1; j<=nlstate*nlstate;j++)
3038: for(theta=1; theta <=npar; theta++)
3039: trgradg[h][j][theta]=gradg[h][theta][j];
3040:
3041:
3042: for(ij=1;ij<=nlstate*nlstate;ij++)
3043: for(ji=1;ji<=nlstate*nlstate;ji++)
3044: varhe[ij][ji][(int)age] =0.;
3045:
3046: printf("%d|",(int)age);fflush(stdout);
3047: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3048: for(h=0;h<=nhstepm-1;h++){
3049: for(k=0;k<=nhstepm-1;k++){
3050: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3051: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3052: for(ij=1;ij<=nlstate*nlstate;ij++)
3053: for(ji=1;ji<=nlstate*nlstate;ji++)
3054: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3055: }
3056: }
3057:
3058: /* Computing expectancies */
3059: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3060: for(i=1; i<=nlstate;i++)
3061: for(j=1; j<=nlstate;j++)
3062: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3063: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3064:
3065: /* 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]);*/
3066:
3067: }
3068:
3069: fprintf(ficresstdeij,"%3.0f",age );
3070: for(i=1; i<=nlstate;i++){
3071: eip=0.;
3072: vip=0.;
3073: for(j=1; j<=nlstate;j++){
3074: eip += eij[i][j][(int)age];
3075: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3076: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3077: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3078: }
3079: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3080: }
3081: fprintf(ficresstdeij,"\n");
3082:
3083: fprintf(ficrescveij,"%3.0f",age );
3084: for(i=1; i<=nlstate;i++)
3085: for(j=1; j<=nlstate;j++){
3086: cptj= (j-1)*nlstate+i;
3087: for(i2=1; i2<=nlstate;i2++)
3088: for(j2=1; j2<=nlstate;j2++){
3089: cptj2= (j2-1)*nlstate+i2;
3090: if(cptj2 <= cptj)
3091: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3092: }
3093: }
3094: fprintf(ficrescveij,"\n");
3095:
3096: }
3097: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3098: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3099: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3100: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3101: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3102: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3103: printf("\n");
3104: fprintf(ficlog,"\n");
3105:
3106: free_vector(xm,1,npar);
3107: free_vector(xp,1,npar);
3108: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3109: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3110: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3111: }
3112:
3113: /************ Variance ******************/
3114: 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[])
3115: {
3116: /* Variance of health expectancies */
3117: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3118: /* double **newm;*/
3119: double **dnewm,**doldm;
3120: double **dnewmp,**doldmp;
3121: int i, j, nhstepm, hstepm, h, nstepm ;
3122: int k, cptcode;
3123: double *xp;
3124: double **gp, **gm; /* for var eij */
3125: double ***gradg, ***trgradg; /*for var eij */
3126: double **gradgp, **trgradgp; /* for var p point j */
3127: double *gpp, *gmp; /* for var p point j */
3128: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3129: double ***p3mat;
3130: double age,agelim, hf;
3131: double ***mobaverage;
3132: int theta;
3133: char digit[4];
3134: char digitp[25];
3135:
3136: char fileresprobmorprev[FILENAMELENGTH];
3137:
3138: if(popbased==1){
3139: if(mobilav!=0)
3140: strcpy(digitp,"-populbased-mobilav-");
3141: else strcpy(digitp,"-populbased-nomobil-");
3142: }
3143: else
3144: strcpy(digitp,"-stablbased-");
3145:
3146: if (mobilav!=0) {
3147: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3148: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3149: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3150: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3151: }
3152: }
3153:
3154: strcpy(fileresprobmorprev,"prmorprev");
3155: sprintf(digit,"%-d",ij);
3156: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3157: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3158: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3159: strcat(fileresprobmorprev,fileres);
3160: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3161: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3162: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3163: }
3164: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3165:
3166: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3167: pstamp(ficresprobmorprev);
3168: 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);
3169: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3170: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3171: fprintf(ficresprobmorprev," p.%-d SE",j);
3172: for(i=1; i<=nlstate;i++)
3173: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3174: }
3175: fprintf(ficresprobmorprev,"\n");
3176: fprintf(ficgp,"\n# Routine varevsij");
3177: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3178: 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");
3179: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3180: /* } */
3181: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3182: pstamp(ficresvij);
3183: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3184: if(popbased==1)
1.128 brouard 3185: 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 3186: else
3187: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3188: fprintf(ficresvij,"# Age");
3189: for(i=1; i<=nlstate;i++)
3190: for(j=1; j<=nlstate;j++)
3191: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3192: fprintf(ficresvij,"\n");
3193:
3194: xp=vector(1,npar);
3195: dnewm=matrix(1,nlstate,1,npar);
3196: doldm=matrix(1,nlstate,1,nlstate);
3197: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3198: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3199:
3200: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3201: gpp=vector(nlstate+1,nlstate+ndeath);
3202: gmp=vector(nlstate+1,nlstate+ndeath);
3203: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3204:
3205: if(estepm < stepm){
3206: printf ("Problem %d lower than %d\n",estepm, stepm);
3207: }
3208: else hstepm=estepm;
3209: /* For example we decided to compute the life expectancy with the smallest unit */
3210: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3211: nhstepm is the number of hstepm from age to agelim
3212: nstepm is the number of stepm from age to agelin.
1.128 brouard 3213: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3214: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3215: survival function given by stepm (the optimization length). Unfortunately it
3216: means that if the survival funtion is printed every two years of age and if
3217: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3218: results. So we changed our mind and took the option of the best precision.
3219: */
3220: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3221: agelim = AGESUP;
3222: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3223: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3224: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3225: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3226: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3227: gp=matrix(0,nhstepm,1,nlstate);
3228: gm=matrix(0,nhstepm,1,nlstate);
3229:
3230:
3231: for(theta=1; theta <=npar; theta++){
3232: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3233: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3234: }
3235: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3236: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3237:
3238: if (popbased==1) {
3239: if(mobilav ==0){
3240: for(i=1; i<=nlstate;i++)
3241: prlim[i][i]=probs[(int)age][i][ij];
3242: }else{ /* mobilav */
3243: for(i=1; i<=nlstate;i++)
3244: prlim[i][i]=mobaverage[(int)age][i][ij];
3245: }
3246: }
3247:
3248: for(j=1; j<= nlstate; j++){
3249: for(h=0; h<=nhstepm; h++){
3250: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3251: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3252: }
3253: }
3254: /* This for computing probability of death (h=1 means
3255: computed over hstepm matrices product = hstepm*stepm months)
3256: as a weighted average of prlim.
3257: */
3258: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3259: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3260: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3261: }
3262: /* end probability of death */
3263:
3264: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3265: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3266: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3267: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3268:
3269: if (popbased==1) {
3270: if(mobilav ==0){
3271: for(i=1; i<=nlstate;i++)
3272: prlim[i][i]=probs[(int)age][i][ij];
3273: }else{ /* mobilav */
3274: for(i=1; i<=nlstate;i++)
3275: prlim[i][i]=mobaverage[(int)age][i][ij];
3276: }
3277: }
3278:
1.128 brouard 3279: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3280: for(h=0; h<=nhstepm; h++){
3281: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3282: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3283: }
3284: }
3285: /* This for computing probability of death (h=1 means
3286: computed over hstepm matrices product = hstepm*stepm months)
3287: as a weighted average of prlim.
3288: */
3289: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3290: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3291: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3292: }
3293: /* end probability of death */
3294:
3295: for(j=1; j<= nlstate; j++) /* vareij */
3296: for(h=0; h<=nhstepm; h++){
3297: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3298: }
3299:
3300: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3301: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3302: }
3303:
3304: } /* End theta */
3305:
3306: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3307:
3308: for(h=0; h<=nhstepm; h++) /* veij */
3309: for(j=1; j<=nlstate;j++)
3310: for(theta=1; theta <=npar; theta++)
3311: trgradg[h][j][theta]=gradg[h][theta][j];
3312:
3313: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3314: for(theta=1; theta <=npar; theta++)
3315: trgradgp[j][theta]=gradgp[theta][j];
3316:
3317:
3318: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3319: for(i=1;i<=nlstate;i++)
3320: for(j=1;j<=nlstate;j++)
3321: vareij[i][j][(int)age] =0.;
3322:
3323: for(h=0;h<=nhstepm;h++){
3324: for(k=0;k<=nhstepm;k++){
3325: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3326: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3327: for(i=1;i<=nlstate;i++)
3328: for(j=1;j<=nlstate;j++)
3329: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3330: }
3331: }
3332:
3333: /* pptj */
3334: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3335: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3336: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3337: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3338: varppt[j][i]=doldmp[j][i];
3339: /* end ppptj */
3340: /* x centered again */
3341: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3342: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3343:
3344: if (popbased==1) {
3345: if(mobilav ==0){
3346: for(i=1; i<=nlstate;i++)
3347: prlim[i][i]=probs[(int)age][i][ij];
3348: }else{ /* mobilav */
3349: for(i=1; i<=nlstate;i++)
3350: prlim[i][i]=mobaverage[(int)age][i][ij];
3351: }
3352: }
3353:
3354: /* This for computing probability of death (h=1 means
3355: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3356: as a weighted average of prlim.
3357: */
3358: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3359: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3360: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3361: }
3362: /* end probability of death */
3363:
3364: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3365: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3366: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3367: for(i=1; i<=nlstate;i++){
3368: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3369: }
3370: }
3371: fprintf(ficresprobmorprev,"\n");
3372:
3373: fprintf(ficresvij,"%.0f ",age );
3374: for(i=1; i<=nlstate;i++)
3375: for(j=1; j<=nlstate;j++){
3376: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3377: }
3378: fprintf(ficresvij,"\n");
3379: free_matrix(gp,0,nhstepm,1,nlstate);
3380: free_matrix(gm,0,nhstepm,1,nlstate);
3381: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3382: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3383: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3384: } /* End age */
3385: free_vector(gpp,nlstate+1,nlstate+ndeath);
3386: free_vector(gmp,nlstate+1,nlstate+ndeath);
3387: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3388: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3389: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3390: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3391: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3392: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3393: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3394: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3395: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3396: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3397: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3398: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3399: 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);
3400: /* 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);
3401: */
3402: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3403: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3404:
3405: free_vector(xp,1,npar);
3406: free_matrix(doldm,1,nlstate,1,nlstate);
3407: free_matrix(dnewm,1,nlstate,1,npar);
3408: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3409: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3410: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3411: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3412: fclose(ficresprobmorprev);
3413: fflush(ficgp);
3414: fflush(fichtm);
3415: } /* end varevsij */
3416:
3417: /************ Variance of prevlim ******************/
3418: 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[])
3419: {
3420: /* Variance of prevalence limit */
3421: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3422: double **newm;
3423: double **dnewm,**doldm;
3424: int i, j, nhstepm, hstepm;
3425: int k, cptcode;
3426: double *xp;
3427: double *gp, *gm;
3428: double **gradg, **trgradg;
3429: double age,agelim;
3430: int theta;
3431:
3432: pstamp(ficresvpl);
3433: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3434: fprintf(ficresvpl,"# Age");
3435: for(i=1; i<=nlstate;i++)
3436: fprintf(ficresvpl," %1d-%1d",i,i);
3437: fprintf(ficresvpl,"\n");
3438:
3439: xp=vector(1,npar);
3440: dnewm=matrix(1,nlstate,1,npar);
3441: doldm=matrix(1,nlstate,1,nlstate);
3442:
3443: hstepm=1*YEARM; /* Every year of age */
3444: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3445: agelim = AGESUP;
3446: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3447: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3448: if (stepm >= YEARM) hstepm=1;
3449: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3450: gradg=matrix(1,npar,1,nlstate);
3451: gp=vector(1,nlstate);
3452: gm=vector(1,nlstate);
3453:
3454: for(theta=1; theta <=npar; theta++){
3455: for(i=1; i<=npar; i++){ /* Computes gradient */
3456: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3457: }
3458: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3459: for(i=1;i<=nlstate;i++)
3460: gp[i] = prlim[i][i];
3461:
3462: for(i=1; i<=npar; i++) /* Computes gradient */
3463: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3464: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3465: for(i=1;i<=nlstate;i++)
3466: gm[i] = prlim[i][i];
3467:
3468: for(i=1;i<=nlstate;i++)
3469: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3470: } /* End theta */
3471:
3472: trgradg =matrix(1,nlstate,1,npar);
3473:
3474: for(j=1; j<=nlstate;j++)
3475: for(theta=1; theta <=npar; theta++)
3476: trgradg[j][theta]=gradg[theta][j];
3477:
3478: for(i=1;i<=nlstate;i++)
3479: varpl[i][(int)age] =0.;
3480: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3481: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3482: for(i=1;i<=nlstate;i++)
3483: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3484:
3485: fprintf(ficresvpl,"%.0f ",age );
3486: for(i=1; i<=nlstate;i++)
3487: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3488: fprintf(ficresvpl,"\n");
3489: free_vector(gp,1,nlstate);
3490: free_vector(gm,1,nlstate);
3491: free_matrix(gradg,1,npar,1,nlstate);
3492: free_matrix(trgradg,1,nlstate,1,npar);
3493: } /* End age */
3494:
3495: free_vector(xp,1,npar);
3496: free_matrix(doldm,1,nlstate,1,npar);
3497: free_matrix(dnewm,1,nlstate,1,nlstate);
3498:
3499: }
3500:
3501: /************ Variance of one-step probabilities ******************/
3502: 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[])
3503: {
3504: int i, j=0, i1, k1, l1, t, tj;
3505: int k2, l2, j1, z1;
3506: int k=0,l, cptcode;
1.145 brouard 3507: int first=1, first1, first2;
1.126 brouard 3508: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3509: double **dnewm,**doldm;
3510: double *xp;
3511: double *gp, *gm;
3512: double **gradg, **trgradg;
3513: double **mu;
1.145 brouard 3514: double age,agelim, cov[NCOVMAX+1];
1.126 brouard 3515: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3516: int theta;
3517: char fileresprob[FILENAMELENGTH];
3518: char fileresprobcov[FILENAMELENGTH];
3519: char fileresprobcor[FILENAMELENGTH];
3520: double ***varpij;
3521:
3522: strcpy(fileresprob,"prob");
3523: strcat(fileresprob,fileres);
3524: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3525: printf("Problem with resultfile: %s\n", fileresprob);
3526: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3527: }
3528: strcpy(fileresprobcov,"probcov");
3529: strcat(fileresprobcov,fileres);
3530: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3531: printf("Problem with resultfile: %s\n", fileresprobcov);
3532: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3533: }
3534: strcpy(fileresprobcor,"probcor");
3535: strcat(fileresprobcor,fileres);
3536: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3537: printf("Problem with resultfile: %s\n", fileresprobcor);
3538: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3539: }
3540: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3541: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3542: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3543: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3544: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3545: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3546: pstamp(ficresprob);
3547: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3548: fprintf(ficresprob,"# Age");
3549: pstamp(ficresprobcov);
3550: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3551: fprintf(ficresprobcov,"# Age");
3552: pstamp(ficresprobcor);
3553: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3554: fprintf(ficresprobcor,"# Age");
3555:
3556:
3557: for(i=1; i<=nlstate;i++)
3558: for(j=1; j<=(nlstate+ndeath);j++){
3559: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3560: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3561: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3562: }
3563: /* fprintf(ficresprob,"\n");
3564: fprintf(ficresprobcov,"\n");
3565: fprintf(ficresprobcor,"\n");
3566: */
1.131 brouard 3567: xp=vector(1,npar);
1.126 brouard 3568: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3569: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3570: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3571: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3572: first=1;
3573: fprintf(ficgp,"\n# Routine varprob");
3574: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3575: fprintf(fichtm,"\n");
3576:
3577: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3578: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3579: file %s<br>\n",optionfilehtmcov);
3580: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3581: and drawn. It helps understanding how is the covariance between two incidences.\
3582: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3583: 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. \
3584: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3585: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3586: standard deviations wide on each axis. <br>\
3587: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3588: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3589: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3590:
3591: cov[1]=1;
1.145 brouard 3592: /* tj=cptcoveff; */
3593: tj = (int) pow(2,cptcoveff);
1.126 brouard 3594: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3595: j1=0;
1.145 brouard 3596: for(j1=1; j1<=tj;j1++){
3597: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3598: /*j1++;*/
1.126 brouard 3599: if (cptcovn>0) {
3600: fprintf(ficresprob, "\n#********** Variable ");
3601: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3602: fprintf(ficresprob, "**********\n#\n");
3603: fprintf(ficresprobcov, "\n#********** Variable ");
3604: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3605: fprintf(ficresprobcov, "**********\n#\n");
3606:
3607: fprintf(ficgp, "\n#********** Variable ");
3608: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3609: fprintf(ficgp, "**********\n#\n");
3610:
3611:
3612: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3613: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3614: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3615:
3616: fprintf(ficresprobcor, "\n#********** Variable ");
3617: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3618: fprintf(ficresprobcor, "**********\n#");
3619: }
3620:
1.145 brouard 3621: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3622: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3623: gp=vector(1,(nlstate)*(nlstate+ndeath));
3624: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3625: for (age=bage; age<=fage; age ++){
3626: cov[2]=age;
3627: for (k=1; k<=cptcovn;k++) {
1.145 brouard 3628: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3629: * 1 1 1 1 1
3630: * 2 2 1 1 1
3631: * 3 1 2 1 1
3632: */
3633: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3634: }
3635: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3636: for (k=1; k<=cptcovprod;k++)
3637: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3638:
3639:
3640: for(theta=1; theta <=npar; theta++){
3641: for(i=1; i<=npar; i++)
3642: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3643:
3644: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3645:
3646: k=0;
3647: for(i=1; i<= (nlstate); i++){
3648: for(j=1; j<=(nlstate+ndeath);j++){
3649: k=k+1;
3650: gp[k]=pmmij[i][j];
3651: }
3652: }
3653:
3654: for(i=1; i<=npar; i++)
3655: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3656:
3657: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3658: k=0;
3659: for(i=1; i<=(nlstate); i++){
3660: for(j=1; j<=(nlstate+ndeath);j++){
3661: k=k+1;
3662: gm[k]=pmmij[i][j];
3663: }
3664: }
3665:
3666: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3667: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3668: }
3669:
3670: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3671: for(theta=1; theta <=npar; theta++)
3672: trgradg[j][theta]=gradg[theta][j];
3673:
3674: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3675: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3676:
3677: pmij(pmmij,cov,ncovmodel,x,nlstate);
3678:
3679: k=0;
3680: for(i=1; i<=(nlstate); i++){
3681: for(j=1; j<=(nlstate+ndeath);j++){
3682: k=k+1;
3683: mu[k][(int) age]=pmmij[i][j];
3684: }
3685: }
3686: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3687: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3688: varpij[i][j][(int)age] = doldm[i][j];
3689:
3690: /*printf("\n%d ",(int)age);
3691: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3692: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3693: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3694: }*/
3695:
3696: fprintf(ficresprob,"\n%d ",(int)age);
3697: fprintf(ficresprobcov,"\n%d ",(int)age);
3698: fprintf(ficresprobcor,"\n%d ",(int)age);
3699:
3700: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3701: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3702: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3703: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3704: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3705: }
3706: i=0;
3707: for (k=1; k<=(nlstate);k++){
3708: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 3709: i++;
1.126 brouard 3710: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3711: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3712: for (j=1; j<=i;j++){
1.145 brouard 3713: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3714: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3715: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3716: }
3717: }
3718: }/* end of loop for state */
3719: } /* end of loop for age */
1.145 brouard 3720: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3721: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3722: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3723: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3724:
1.126 brouard 3725: /* Confidence intervalle of pij */
3726: /*
1.131 brouard 3727: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3728: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3729: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3730: 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);
3731: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3732: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3733: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3734: */
3735:
3736: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 3737: first1=1;first2=2;
1.126 brouard 3738: for (k2=1; k2<=(nlstate);k2++){
3739: for (l2=1; l2<=(nlstate+ndeath);l2++){
3740: if(l2==k2) continue;
3741: j=(k2-1)*(nlstate+ndeath)+l2;
3742: for (k1=1; k1<=(nlstate);k1++){
3743: for (l1=1; l1<=(nlstate+ndeath);l1++){
3744: if(l1==k1) continue;
3745: i=(k1-1)*(nlstate+ndeath)+l1;
3746: if(i<=j) continue;
3747: for (age=bage; age<=fage; age ++){
3748: if ((int)age %5==0){
3749: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3750: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3751: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3752: mu1=mu[i][(int) age]/stepm*YEARM ;
3753: mu2=mu[j][(int) age]/stepm*YEARM;
3754: c12=cv12/sqrt(v1*v2);
3755: /* Computing eigen value of matrix of covariance */
3756: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3757: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3758: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 3759: if(first2==1){
3760: first1=0;
3761: printf("Strange: j1=%d 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. Probably WRONG RESULTS. See log file for details...\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);
3762: }
3763: fprintf(ficlog,"Strange: j1=%d 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. Probably WRONG RESULTS.\n", j1, lc1, lc2, v1, v2, cv12, i, j, (int)age,fileresprobcov, fileresprobcor);fflush(ficlog);
3764: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3765: /* lc2=fabs(lc2); */
1.135 brouard 3766: }
3767:
1.126 brouard 3768: /* Eigen vectors */
3769: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3770: /*v21=sqrt(1.-v11*v11); *//* error */
3771: v21=(lc1-v1)/cv12*v11;
3772: v12=-v21;
3773: v22=v11;
3774: tnalp=v21/v11;
3775: if(first1==1){
3776: first1=0;
3777: 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);
3778: }
3779: 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);
3780: /*printf(fignu*/
3781: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3782: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3783: if(first==1){
3784: first=0;
3785: fprintf(ficgp,"\nset parametric;unset label");
3786: 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);
1.145 brouard 3787: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 3788: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3789: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3790: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3791: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3792: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3793: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3794: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3795: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3796: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3797: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3798: 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",\
3799: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3800: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3801: }else{
3802: first=0;
3803: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3804: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3805: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3806: 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",\
3807: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3808: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3809: }/* if first */
3810: } /* age mod 5 */
3811: } /* end loop age */
3812: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3813: first=1;
3814: } /*l12 */
3815: } /* k12 */
3816: } /*l1 */
3817: }/* k1 */
1.145 brouard 3818: /* } /* loop covariates */
1.126 brouard 3819: }
3820: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
3821: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
3822: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3823: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
3824: free_vector(xp,1,npar);
3825: fclose(ficresprob);
3826: fclose(ficresprobcov);
3827: fclose(ficresprobcor);
3828: fflush(ficgp);
3829: fflush(fichtmcov);
3830: }
3831:
3832:
3833: /******************* Printing html file ***********/
3834: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
3835: int lastpass, int stepm, int weightopt, char model[],\
3836: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
3837: int popforecast, int estepm ,\
3838: double jprev1, double mprev1,double anprev1, \
3839: double jprev2, double mprev2,double anprev2){
3840: int jj1, k1, i1, cpt;
3841:
3842: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
3843: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
3844: </ul>");
3845: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
3846: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
3847: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
3848: fprintf(fichtm,"\
3849: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
3850: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
3851: fprintf(fichtm,"\
3852: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
3853: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
3854: fprintf(fichtm,"\
1.128 brouard 3855: - (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 3856: <a href=\"%s\">%s</a> <br>\n",
3857: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
3858: fprintf(fichtm,"\
3859: - Population projections by age and states: \
3860: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
3861:
3862: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
3863:
1.145 brouard 3864: m=pow(2,cptcoveff);
1.126 brouard 3865: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3866:
3867: jj1=0;
3868: for(k1=1; k1<=m;k1++){
3869: for(i1=1; i1<=ncodemax[k1];i1++){
3870: jj1++;
3871: if (cptcovn > 0) {
3872: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3873: for (cpt=1; cpt<=cptcoveff;cpt++)
3874: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3875: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3876: }
3877: /* Pij */
1.145 brouard 3878: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d_1.png\">%s%d_1.png</a><br> \
3879: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 3880: /* Quasi-incidences */
3881: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 3882: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d_2.png\">%s%d_2.png</a><br> \
3883: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 3884: /* Period (stable) prevalence in each health state */
3885: for(cpt=1; cpt<nlstate;cpt++){
1.145 brouard 3886: fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
3887: <img src=\"%s%d_%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 3888: }
3889: for(cpt=1; cpt<=nlstate;cpt++) {
3890: 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> \
3891: <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
3892: }
3893: } /* end i1 */
3894: }/* End k1 */
3895: fprintf(fichtm,"</ul>");
3896:
3897:
3898: fprintf(fichtm,"\
3899: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
3900: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
3901:
3902: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3903: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
3904: fprintf(fichtm,"\
3905: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3906: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
3907:
3908: fprintf(fichtm,"\
3909: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
3910: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
3911: fprintf(fichtm,"\
3912: - 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): \
3913: <a href=\"%s\">%s</a> <br>\n</li>",
3914: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
3915: fprintf(fichtm,"\
3916: - (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): \
3917: <a href=\"%s\">%s</a> <br>\n</li>",
3918: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
3919: fprintf(fichtm,"\
1.128 brouard 3920: - 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 3921: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
3922: fprintf(fichtm,"\
1.128 brouard 3923: - 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",
3924: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 3925: fprintf(fichtm,"\
3926: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
3927: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
3928:
3929: /* if(popforecast==1) fprintf(fichtm,"\n */
3930: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
3931: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
3932: /* <br>",fileres,fileres,fileres,fileres); */
3933: /* else */
3934: /* 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); */
3935: fflush(fichtm);
3936: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
3937:
1.145 brouard 3938: m=pow(2,cptcoveff);
1.126 brouard 3939: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
3940:
3941: jj1=0;
3942: for(k1=1; k1<=m;k1++){
3943: for(i1=1; i1<=ncodemax[k1];i1++){
3944: jj1++;
3945: if (cptcovn > 0) {
3946: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
3947: for (cpt=1; cpt<=cptcoveff;cpt++)
3948: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
3949: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
3950: }
3951: for(cpt=1; cpt<=nlstate;cpt++) {
3952: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 3953: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
3954: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 3955: }
3956: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 3957: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
3958: true period expectancies (those weighted with period prevalences are also\
3959: drawn in addition to the population based expectancies computed using\
3960: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 3961: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
3962: } /* end i1 */
3963: }/* End k1 */
3964: fprintf(fichtm,"</ul>");
3965: fflush(fichtm);
3966: }
3967:
3968: /******************* Gnuplot file **************/
3969: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
3970:
3971: char dirfileres[132],optfileres[132];
1.130 brouard 3972: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
3973: int ng=0;
1.126 brouard 3974: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
3975: /* printf("Problem with file %s",optionfilegnuplot); */
3976: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
3977: /* } */
3978:
3979: /*#ifdef windows */
3980: fprintf(ficgp,"cd \"%s\" \n",pathc);
3981: /*#endif */
3982: m=pow(2,cptcoveff);
3983:
3984: strcpy(dirfileres,optionfilefiname);
3985: strcpy(optfileres,"vpl");
3986: /* 1eme*/
3987: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 3988: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
3989: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
3990: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 3991: fprintf(ficgp,"set xlabel \"Age\" \n\
3992: set ylabel \"Probability\" \n\
1.145 brouard 3993: set ter png small size 320, 240\n\
1.126 brouard 3994: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
3995:
3996: for (i=1; i<= nlstate ; i ++) {
3997: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 3998: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 3999: }
1.145 brouard 4000: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4001: for (i=1; i<= nlstate ; i ++) {
4002: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4003: else fprintf(ficgp," \%%*lf (\%%*lf)");
4004: }
1.145 brouard 4005: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4006: for (i=1; i<= nlstate ; i ++) {
4007: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4008: else fprintf(ficgp," \%%*lf (\%%*lf)");
4009: }
1.145 brouard 4010: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4011: }
4012: }
4013: /*2 eme*/
4014:
4015: for (k1=1; k1<= m ; k1 ++) {
4016: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4017: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4018:
4019: for (i=1; i<= nlstate+1 ; i ++) {
4020: k=2*i;
4021: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4022: for (j=1; j<= nlstate+1 ; j ++) {
4023: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4024: else fprintf(ficgp," \%%*lf (\%%*lf)");
4025: }
4026: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4027: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4028: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4029: for (j=1; j<= nlstate+1 ; j ++) {
4030: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4031: else fprintf(ficgp," \%%*lf (\%%*lf)");
4032: }
1.145 brouard 4033: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4034: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4035: for (j=1; j<= nlstate+1 ; j ++) {
4036: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4037: else fprintf(ficgp," \%%*lf (\%%*lf)");
4038: }
1.145 brouard 4039: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4040: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4041: }
4042: }
4043:
4044: /*3eme*/
4045:
4046: for (k1=1; k1<= m ; k1 ++) {
4047: for (cpt=1; cpt<= nlstate ; cpt ++) {
4048: /* k=2+nlstate*(2*cpt-2); */
4049: k=2+(nlstate+1)*(cpt-1);
4050: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4051: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4052: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4053: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4054: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4055: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4056: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4057: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4058: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4059:
4060: */
4061: for (i=1; i< nlstate ; i ++) {
4062: 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);
4063: /* 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);*/
4064:
4065: }
4066: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4067: }
4068: }
4069:
4070: /* CV preval stable (period) */
4071: for (k1=1; k1<= m ; k1 ++) {
4072: for (cpt=1; cpt<=nlstate ; cpt ++) {
4073: k=3;
1.145 brouard 4074: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4075: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4076: set ter png small size 320, 240\n\
1.126 brouard 4077: unset log y\n\
4078: plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
4079:
4080: for (i=1; i< nlstate ; i ++)
4081: fprintf(ficgp,"+$%d",k+i+1);
4082: fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
4083:
4084: l=3+(nlstate+ndeath)*cpt;
4085: fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
4086: for (i=1; i< nlstate ; i ++) {
4087: l=3+(nlstate+ndeath)*cpt;
4088: fprintf(ficgp,"+$%d",l+i+1);
4089: }
4090: fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
4091: }
4092: }
4093:
4094: /* proba elementaires */
4095: for(i=1,jk=1; i <=nlstate; i++){
4096: for(k=1; k <=(nlstate+ndeath); k++){
4097: if (k != i) {
4098: for(j=1; j <=ncovmodel; j++){
4099: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4100: jk++;
4101: fprintf(ficgp,"\n");
4102: }
4103: }
4104: }
4105: }
1.145 brouard 4106: /*goto avoid;*/
1.126 brouard 4107: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4108: for(jk=1; jk <=m; jk++) {
1.145 brouard 4109: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4110: if (ng==2)
4111: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4112: else
4113: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4114: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4115: i=1;
4116: for(k2=1; k2<=nlstate; k2++) {
4117: k3=i;
4118: for(k=1; k<=(nlstate+ndeath); k++) {
4119: if (k != k2){
4120: if(ng==2)
4121: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4122: else
4123: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4124: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4125: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4126: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4127: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4128: /* ij++; */
4129: /* } */
4130: /* else */
1.126 brouard 4131: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4132: }
4133: fprintf(ficgp,")/(1");
4134:
4135: for(k1=1; k1 <=nlstate; k1++){
4136: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4137: ij=1;
4138: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4139: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4140: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4141: /* ij++; */
4142: /* } */
4143: /* else */
1.126 brouard 4144: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4145: }
4146: fprintf(ficgp,")");
4147: }
4148: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4149: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4150: i=i+ncovmodel;
4151: }
4152: } /* end k */
4153: } /* end k2 */
4154: } /* end jk */
4155: } /* end ng */
1.145 brouard 4156: avoid:
1.126 brouard 4157: fflush(ficgp);
4158: } /* end gnuplot */
4159:
4160:
4161: /*************** Moving average **************/
4162: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4163:
4164: int i, cpt, cptcod;
4165: int modcovmax =1;
4166: int mobilavrange, mob;
4167: double age;
4168:
4169: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4170: a covariate has 2 modalities */
4171: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4172:
4173: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4174: if(mobilav==1) mobilavrange=5; /* default */
4175: else mobilavrange=mobilav;
4176: for (age=bage; age<=fage; age++)
4177: for (i=1; i<=nlstate;i++)
4178: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4179: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4180: /* We keep the original values on the extreme ages bage, fage and for
4181: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4182: we use a 5 terms etc. until the borders are no more concerned.
4183: */
4184: for (mob=3;mob <=mobilavrange;mob=mob+2){
4185: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4186: for (i=1; i<=nlstate;i++){
4187: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4188: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4189: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4190: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4191: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4192: }
4193: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4194: }
4195: }
4196: }/* end age */
4197: }/* end mob */
4198: }else return -1;
4199: return 0;
4200: }/* End movingaverage */
4201:
4202:
4203: /************** Forecasting ******************/
4204: 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){
4205: /* proj1, year, month, day of starting projection
4206: agemin, agemax range of age
4207: dateprev1 dateprev2 range of dates during which prevalence is computed
4208: anproj2 year of en of projection (same day and month as proj1).
4209: */
4210: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4211: int *popage;
4212: double agec; /* generic age */
4213: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4214: double *popeffectif,*popcount;
4215: double ***p3mat;
4216: double ***mobaverage;
4217: char fileresf[FILENAMELENGTH];
4218:
4219: agelim=AGESUP;
4220: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4221:
4222: strcpy(fileresf,"f");
4223: strcat(fileresf,fileres);
4224: if((ficresf=fopen(fileresf,"w"))==NULL) {
4225: printf("Problem with forecast resultfile: %s\n", fileresf);
4226: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4227: }
4228: printf("Computing forecasting: result on file '%s' \n", fileresf);
4229: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4230:
4231: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4232:
4233: if (mobilav!=0) {
4234: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4235: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4236: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4237: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4238: }
4239: }
4240:
4241: stepsize=(int) (stepm+YEARM-1)/YEARM;
4242: if (stepm<=12) stepsize=1;
4243: if(estepm < stepm){
4244: printf ("Problem %d lower than %d\n",estepm, stepm);
4245: }
4246: else hstepm=estepm;
4247:
4248: hstepm=hstepm/stepm;
4249: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4250: fractional in yp1 */
4251: anprojmean=yp;
4252: yp2=modf((yp1*12),&yp);
4253: mprojmean=yp;
4254: yp1=modf((yp2*30.5),&yp);
4255: jprojmean=yp;
4256: if(jprojmean==0) jprojmean=1;
4257: if(mprojmean==0) jprojmean=1;
4258:
4259: i1=cptcoveff;
4260: if (cptcovn < 1){i1=1;}
4261:
4262: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4263:
4264: fprintf(ficresf,"#****** Routine prevforecast **\n");
4265:
4266: /* if (h==(int)(YEARM*yearp)){ */
4267: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4268: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4269: k=k+1;
4270: fprintf(ficresf,"\n#******");
4271: for(j=1;j<=cptcoveff;j++) {
4272: 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]]);
4273: }
4274: fprintf(ficresf,"******\n");
4275: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4276: for(j=1; j<=nlstate+ndeath;j++){
4277: for(i=1; i<=nlstate;i++)
4278: fprintf(ficresf," p%d%d",i,j);
4279: fprintf(ficresf," p.%d",j);
4280: }
4281: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4282: fprintf(ficresf,"\n");
4283: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4284:
4285: for (agec=fage; agec>=(ageminpar-1); agec--){
4286: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4287: nhstepm = nhstepm/hstepm;
4288: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4289: oldm=oldms;savm=savms;
4290: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4291:
4292: for (h=0; h<=nhstepm; h++){
4293: if (h*hstepm/YEARM*stepm ==yearp) {
4294: fprintf(ficresf,"\n");
4295: for(j=1;j<=cptcoveff;j++)
4296: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4297: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4298: }
4299: for(j=1; j<=nlstate+ndeath;j++) {
4300: ppij=0.;
4301: for(i=1; i<=nlstate;i++) {
4302: if (mobilav==1)
4303: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4304: else {
4305: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4306: }
4307: if (h*hstepm/YEARM*stepm== yearp) {
4308: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4309: }
4310: } /* end i */
4311: if (h*hstepm/YEARM*stepm==yearp) {
4312: fprintf(ficresf," %.3f", ppij);
4313: }
4314: }/* end j */
4315: } /* end h */
4316: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4317: } /* end agec */
4318: } /* end yearp */
4319: } /* end cptcod */
4320: } /* end cptcov */
4321:
4322: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4323:
4324: fclose(ficresf);
4325: }
4326:
4327: /************** Forecasting *****not tested NB*************/
4328: 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){
4329:
4330: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4331: int *popage;
4332: double calagedatem, agelim, kk1, kk2;
4333: double *popeffectif,*popcount;
4334: double ***p3mat,***tabpop,***tabpopprev;
4335: double ***mobaverage;
4336: char filerespop[FILENAMELENGTH];
4337:
4338: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4339: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4340: agelim=AGESUP;
4341: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4342:
4343: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4344:
4345:
4346: strcpy(filerespop,"pop");
4347: strcat(filerespop,fileres);
4348: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4349: printf("Problem with forecast resultfile: %s\n", filerespop);
4350: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4351: }
4352: printf("Computing forecasting: result on file '%s' \n", filerespop);
4353: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4354:
4355: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4356:
4357: if (mobilav!=0) {
4358: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4359: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4360: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4361: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4362: }
4363: }
4364:
4365: stepsize=(int) (stepm+YEARM-1)/YEARM;
4366: if (stepm<=12) stepsize=1;
4367:
4368: agelim=AGESUP;
4369:
4370: hstepm=1;
4371: hstepm=hstepm/stepm;
4372:
4373: if (popforecast==1) {
4374: if((ficpop=fopen(popfile,"r"))==NULL) {
4375: printf("Problem with population file : %s\n",popfile);exit(0);
4376: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4377: }
4378: popage=ivector(0,AGESUP);
4379: popeffectif=vector(0,AGESUP);
4380: popcount=vector(0,AGESUP);
4381:
4382: i=1;
4383: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4384:
4385: imx=i;
4386: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4387: }
4388:
4389: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4390: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4391: k=k+1;
4392: fprintf(ficrespop,"\n#******");
4393: for(j=1;j<=cptcoveff;j++) {
4394: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4395: }
4396: fprintf(ficrespop,"******\n");
4397: fprintf(ficrespop,"# Age");
4398: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4399: if (popforecast==1) fprintf(ficrespop," [Population]");
4400:
4401: for (cpt=0; cpt<=0;cpt++) {
4402: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4403:
4404: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4405: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4406: nhstepm = nhstepm/hstepm;
4407:
4408: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4409: oldm=oldms;savm=savms;
4410: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4411:
4412: for (h=0; h<=nhstepm; h++){
4413: if (h==(int) (calagedatem+YEARM*cpt)) {
4414: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4415: }
4416: for(j=1; j<=nlstate+ndeath;j++) {
4417: kk1=0.;kk2=0;
4418: for(i=1; i<=nlstate;i++) {
4419: if (mobilav==1)
4420: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4421: else {
4422: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4423: }
4424: }
4425: if (h==(int)(calagedatem+12*cpt)){
4426: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4427: /*fprintf(ficrespop," %.3f", kk1);
4428: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4429: }
4430: }
4431: for(i=1; i<=nlstate;i++){
4432: kk1=0.;
4433: for(j=1; j<=nlstate;j++){
4434: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4435: }
4436: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4437: }
4438:
4439: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4440: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4441: }
4442: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4443: }
4444: }
4445:
4446: /******/
4447:
4448: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4449: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4450: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4451: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4452: nhstepm = nhstepm/hstepm;
4453:
4454: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4455: oldm=oldms;savm=savms;
4456: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4457: for (h=0; h<=nhstepm; h++){
4458: if (h==(int) (calagedatem+YEARM*cpt)) {
4459: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4460: }
4461: for(j=1; j<=nlstate+ndeath;j++) {
4462: kk1=0.;kk2=0;
4463: for(i=1; i<=nlstate;i++) {
4464: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4465: }
4466: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4467: }
4468: }
4469: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4470: }
4471: }
4472: }
4473: }
4474:
4475: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4476:
4477: if (popforecast==1) {
4478: free_ivector(popage,0,AGESUP);
4479: free_vector(popeffectif,0,AGESUP);
4480: free_vector(popcount,0,AGESUP);
4481: }
4482: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4483: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4484: fclose(ficrespop);
4485: } /* End of popforecast */
4486:
4487: int fileappend(FILE *fichier, char *optionfich)
4488: {
4489: if((fichier=fopen(optionfich,"a"))==NULL) {
4490: printf("Problem with file: %s\n", optionfich);
4491: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4492: return (0);
4493: }
4494: fflush(fichier);
4495: return (1);
4496: }
4497:
4498:
4499: /**************** function prwizard **********************/
4500: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4501: {
4502:
4503: /* Wizard to print covariance matrix template */
4504:
4505: char ca[32], cb[32], cc[32];
4506: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4507: int numlinepar;
4508:
4509: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4510: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4511: for(i=1; i <=nlstate; i++){
4512: jj=0;
4513: for(j=1; j <=nlstate+ndeath; j++){
4514: if(j==i) continue;
4515: jj++;
4516: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4517: printf("%1d%1d",i,j);
4518: fprintf(ficparo,"%1d%1d",i,j);
4519: for(k=1; k<=ncovmodel;k++){
4520: /* printf(" %lf",param[i][j][k]); */
4521: /* fprintf(ficparo," %lf",param[i][j][k]); */
4522: printf(" 0.");
4523: fprintf(ficparo," 0.");
4524: }
4525: printf("\n");
4526: fprintf(ficparo,"\n");
4527: }
4528: }
4529: printf("# Scales (for hessian or gradient estimation)\n");
4530: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4531: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4532: for(i=1; i <=nlstate; i++){
4533: jj=0;
4534: for(j=1; j <=nlstate+ndeath; j++){
4535: if(j==i) continue;
4536: jj++;
4537: fprintf(ficparo,"%1d%1d",i,j);
4538: printf("%1d%1d",i,j);
4539: fflush(stdout);
4540: for(k=1; k<=ncovmodel;k++){
4541: /* printf(" %le",delti3[i][j][k]); */
4542: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4543: printf(" 0.");
4544: fprintf(ficparo," 0.");
4545: }
4546: numlinepar++;
4547: printf("\n");
4548: fprintf(ficparo,"\n");
4549: }
4550: }
4551: printf("# Covariance matrix\n");
4552: /* # 121 Var(a12)\n\ */
4553: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4554: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4555: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4556: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4557: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4558: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4559: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4560: fflush(stdout);
4561: fprintf(ficparo,"# Covariance matrix\n");
4562: /* # 121 Var(a12)\n\ */
4563: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4564: /* # ...\n\ */
4565: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4566:
4567: for(itimes=1;itimes<=2;itimes++){
4568: jj=0;
4569: for(i=1; i <=nlstate; i++){
4570: for(j=1; j <=nlstate+ndeath; j++){
4571: if(j==i) continue;
4572: for(k=1; k<=ncovmodel;k++){
4573: jj++;
4574: ca[0]= k+'a'-1;ca[1]='\0';
4575: if(itimes==1){
4576: printf("#%1d%1d%d",i,j,k);
4577: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4578: }else{
4579: printf("%1d%1d%d",i,j,k);
4580: fprintf(ficparo,"%1d%1d%d",i,j,k);
4581: /* printf(" %.5le",matcov[i][j]); */
4582: }
4583: ll=0;
4584: for(li=1;li <=nlstate; li++){
4585: for(lj=1;lj <=nlstate+ndeath; lj++){
4586: if(lj==li) continue;
4587: for(lk=1;lk<=ncovmodel;lk++){
4588: ll++;
4589: if(ll<=jj){
4590: cb[0]= lk +'a'-1;cb[1]='\0';
4591: if(ll<jj){
4592: if(itimes==1){
4593: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4594: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4595: }else{
4596: printf(" 0.");
4597: fprintf(ficparo," 0.");
4598: }
4599: }else{
4600: if(itimes==1){
4601: printf(" Var(%s%1d%1d)",ca,i,j);
4602: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4603: }else{
4604: printf(" 0.");
4605: fprintf(ficparo," 0.");
4606: }
4607: }
4608: }
4609: } /* end lk */
4610: } /* end lj */
4611: } /* end li */
4612: printf("\n");
4613: fprintf(ficparo,"\n");
4614: numlinepar++;
4615: } /* end k*/
4616: } /*end j */
4617: } /* end i */
4618: } /* end itimes */
4619:
4620: } /* end of prwizard */
4621: /******************* Gompertz Likelihood ******************************/
4622: double gompertz(double x[])
4623: {
4624: double A,B,L=0.0,sump=0.,num=0.;
4625: int i,n=0; /* n is the size of the sample */
4626:
4627: for (i=0;i<=imx-1 ; i++) {
4628: sump=sump+weight[i];
4629: /* sump=sump+1;*/
4630: num=num+1;
4631: }
4632:
4633:
4634: /* for (i=0; i<=imx; i++)
4635: 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]);*/
4636:
4637: for (i=1;i<=imx ; i++)
4638: {
4639: if (cens[i] == 1 && wav[i]>1)
4640: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4641:
4642: if (cens[i] == 0 && wav[i]>1)
4643: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4644: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4645:
4646: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4647: if (wav[i] > 1 ) { /* ??? */
4648: L=L+A*weight[i];
4649: /* 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]);*/
4650: }
4651: }
4652:
4653: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4654:
4655: return -2*L*num/sump;
4656: }
4657:
1.136 brouard 4658: #ifdef GSL
4659: /******************* Gompertz_f Likelihood ******************************/
4660: double gompertz_f(const gsl_vector *v, void *params)
4661: {
4662: double A,B,LL=0.0,sump=0.,num=0.;
4663: double *x= (double *) v->data;
4664: int i,n=0; /* n is the size of the sample */
4665:
4666: for (i=0;i<=imx-1 ; i++) {
4667: sump=sump+weight[i];
4668: /* sump=sump+1;*/
4669: num=num+1;
4670: }
4671:
4672:
4673: /* for (i=0; i<=imx; i++)
4674: 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]);*/
4675: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4676: for (i=1;i<=imx ; i++)
4677: {
4678: if (cens[i] == 1 && wav[i]>1)
4679: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4680:
4681: if (cens[i] == 0 && wav[i]>1)
4682: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4683: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4684:
4685: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4686: if (wav[i] > 1 ) { /* ??? */
4687: LL=LL+A*weight[i];
4688: /* 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]);*/
4689: }
4690: }
4691:
4692: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4693: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4694:
4695: return -2*LL*num/sump;
4696: }
4697: #endif
4698:
1.126 brouard 4699: /******************* Printing html file ***********/
4700: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4701: int lastpass, int stepm, int weightopt, char model[],\
4702: int imx, double p[],double **matcov,double agemortsup){
4703: int i,k;
4704:
4705: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4706: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4707: for (i=1;i<=2;i++)
4708: 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]));
4709: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4710: fprintf(fichtm,"</ul>");
4711:
4712: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4713:
4714: 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>");
4715:
4716: for (k=agegomp;k<(agemortsup-2);k++)
4717: 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]);
4718:
4719:
4720: fflush(fichtm);
4721: }
4722:
4723: /******************* Gnuplot file **************/
4724: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4725:
4726: char dirfileres[132],optfileres[132];
4727: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4728: int ng;
4729:
4730:
4731: /*#ifdef windows */
4732: fprintf(ficgp,"cd \"%s\" \n",pathc);
4733: /*#endif */
4734:
4735:
4736: strcpy(dirfileres,optionfilefiname);
4737: strcpy(optfileres,"vpl");
4738: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4739: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 4740: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4741: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 4742: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4743:
4744: }
4745:
1.136 brouard 4746: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4747: {
1.126 brouard 4748:
1.136 brouard 4749: /*-------- data file ----------*/
4750: FILE *fic;
4751: char dummy[]=" ";
4752: int i, j, n;
4753: int linei, month, year,iout;
4754: char line[MAXLINE], linetmp[MAXLINE];
4755: char stra[80], strb[80];
4756: char *stratrunc;
4757: int lstra;
1.126 brouard 4758:
4759:
1.136 brouard 4760: if((fic=fopen(datafile,"r"))==NULL) {
4761: printf("Problem while opening datafile: %s\n", datafile);return 1;
4762: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4763: }
1.126 brouard 4764:
1.136 brouard 4765: i=1;
4766: linei=0;
4767: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4768: linei=linei+1;
4769: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4770: if(line[j] == '\t')
4771: line[j] = ' ';
4772: }
4773: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4774: ;
4775: };
4776: line[j+1]=0; /* Trims blanks at end of line */
4777: if(line[0]=='#'){
4778: fprintf(ficlog,"Comment line\n%s\n",line);
4779: printf("Comment line\n%s\n",line);
4780: continue;
4781: }
4782: trimbb(linetmp,line); /* Trims multiple blanks in line */
4783: for (j=0; line[j]!='\0';j++){
4784: line[j]=linetmp[j];
4785: }
4786:
1.126 brouard 4787:
1.136 brouard 4788: for (j=maxwav;j>=1;j--){
1.137 brouard 4789: cutv(stra, strb, line, ' ');
1.136 brouard 4790: if(strb[0]=='.') { /* Missing status */
4791: lval=-1;
4792: }else{
4793: errno=0;
4794: lval=strtol(strb,&endptr,10);
4795: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4796: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4797: printf("Error reading data around '%s' at line number %d 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);
4798: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
1.136 brouard 4799: return 1;
4800: }
4801: }
4802: s[j][i]=lval;
4803:
4804: strcpy(line,stra);
4805: cutv(stra, strb,line,' ');
4806: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4807: }
1.145 brouard 4808: else if(iout=sscanf(strb,"%s.",dummy) != 0){
1.136 brouard 4809: month=99;
4810: year=9999;
4811: }else{
1.141 brouard 4812: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
4813: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
1.136 brouard 4814: return 1;
4815: }
4816: anint[j][i]= (double) year;
4817: mint[j][i]= (double)month;
4818: strcpy(line,stra);
4819: } /* ENd Waves */
4820:
4821: cutv(stra, strb,line,' ');
4822: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4823: }
4824: else if(iout=sscanf(strb,"%s.",dummy) != 0){
4825: month=99;
4826: year=9999;
4827: }else{
1.141 brouard 4828: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4829: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 4830: return 1;
4831: }
4832: andc[i]=(double) year;
4833: moisdc[i]=(double) month;
4834: strcpy(line,stra);
4835:
4836: cutv(stra, strb,line,' ');
4837: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
4838: }
1.145 brouard 4839: else if(iout=sscanf(strb,"%s.", dummy) != 0){
1.136 brouard 4840: month=99;
4841: year=9999;
4842: }else{
1.141 brouard 4843: printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
4844: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 4845: return 1;
4846: }
4847: if (year==9999) {
1.141 brouard 4848: printf("Error reading data around '%s' at line number %d 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);
4849: fprintf(ficlog,"Error reading data around '%s' at line number %d 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);
1.136 brouard 4850: return 1;
1.126 brouard 4851:
1.136 brouard 4852: }
4853: annais[i]=(double)(year);
4854: moisnais[i]=(double)(month);
4855: strcpy(line,stra);
4856:
4857: cutv(stra, strb,line,' ');
4858: errno=0;
4859: dval=strtod(strb,&endptr);
4860: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4861: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
4862: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 4863: fflush(ficlog);
4864: return 1;
4865: }
4866: weight[i]=dval;
4867: strcpy(line,stra);
4868:
4869: for (j=ncovcol;j>=1;j--){
4870: cutv(stra, strb,line,' ');
4871: if(strb[0]=='.') { /* Missing status */
4872: lval=-1;
4873: }else{
4874: errno=0;
4875: lval=strtol(strb,&endptr,10);
4876: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4877: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
4878: fprintf(ficlog,"Error reading data around '%ld' at line number %d 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);
1.136 brouard 4879: return 1;
4880: }
4881: }
4882: if(lval <-1 || lval >1){
1.141 brouard 4883: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4884: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4885: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4886: For example, for multinomial values like 1, 2 and 3,\n \
4887: build V1=0 V2=0 for the reference value (1),\n \
4888: V1=1 V2=0 for (2) \n \
4889: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4890: output of IMaCh is often meaningless.\n \
4891: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 4892: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 4893: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
4894: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
4895: For example, for multinomial values like 1, 2 and 3,\n \
4896: build V1=0 V2=0 for the reference value (1),\n \
4897: V1=1 V2=0 for (2) \n \
4898: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
4899: output of IMaCh is often meaningless.\n \
4900: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
4901: return 1;
4902: }
4903: covar[j][i]=(double)(lval);
4904: strcpy(line,stra);
4905: }
4906: lstra=strlen(stra);
4907:
4908: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
4909: stratrunc = &(stra[lstra-9]);
4910: num[i]=atol(stratrunc);
4911: }
4912: else
4913: num[i]=atol(stra);
4914: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
4915: 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;}*/
4916:
4917: i=i+1;
4918: } /* End loop reading data */
1.126 brouard 4919:
1.136 brouard 4920: *imax=i-1; /* Number of individuals */
4921: fclose(fic);
4922:
4923: return (0);
4924: endread:
4925: printf("Exiting readdata: ");
4926: fclose(fic);
4927: return (1);
1.126 brouard 4928:
4929:
4930:
1.136 brouard 4931: }
1.145 brouard 4932: void removespace(char *str) {
4933: char *p1 = str, *p2 = str;
4934: do
4935: while (*p2 == ' ')
4936: p2++;
4937: while (*p1++ = *p2++);
4938: }
4939:
4940: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
4941: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
4942: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
4943: * - cptcovn or number of covariates k of the models excluding age*products =6
4944: * - cptcovage number of covariates with age*products =2
4945: * - cptcovs number of simple covariates
4946: * - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
4947: * which is a new column after the 9 (ncovcol) variables.
4948: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
4949: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
4950: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
4951: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
4952: */
1.136 brouard 4953: {
1.145 brouard 4954: int i, j, k, ks;
1.136 brouard 4955: int i1, j1, k1, k2;
4956: char modelsav[80];
1.145 brouard 4957: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 4958:
1.145 brouard 4959: /*removespace(model);*/
1.136 brouard 4960: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 4961: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
4962: j=nbocc(model,'+'); /**< j=Number of '+' */
4963: j1=nbocc(model,'*'); /**< j1=Number of '*' */
4964: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
4965: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
4966: /* including age products which are counted in cptcovage.
4967: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
4968: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
4969: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 4970: strcpy(modelsav,model);
1.137 brouard 4971: if (strstr(model,"AGE") !=0){
4972: printf("Error. AGE must be in lower case 'age' model=%s ",model);
4973: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 4974: return 1;
4975: }
1.141 brouard 4976: if (strstr(model,"v") !=0){
4977: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
4978: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
4979: return 1;
4980: }
1.136 brouard 4981:
1.145 brouard 4982: /* Design
4983: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
4984: * < ncovcol=8 >
4985: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
4986: * k= 1 2 3 4 5 6 7 8
4987: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
4988: * covar[k,i], value of kth covariate if not including age for individual i:
4989: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
4990: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
4991: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
4992: * Tage[++cptcovage]=k
4993: * if products, new covar are created after ncovcol with k1
4994: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
4995: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
4996: * Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
4997: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
4998: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
4999: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5000: * < ncovcol=8 >
5001: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5002: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5003: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5004: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5005: * p Tprod[1]@2={ 6, 5}
5006: *p Tvard[1][1]@4= {7, 8, 5, 6}
5007: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5008: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5009: *How to reorganize?
5010: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5011: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5012: * {2, 1, 4, 8, 5, 6, 3, 7}
5013: * Struct []
5014: */
5015:
1.136 brouard 5016: /* This loop fills the array Tvar from the string 'model'.*/
5017: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5018: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5019: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5020: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5021: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5022: /* k=1 Tvar[1]=2 (from V2) */
5023: /* k=5 Tvar[5] */
5024: /* for (k=1; k<=cptcovn;k++) { */
5025: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5026: /* } */
5027: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5028: /*
5029: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5030: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5031: Tvar[k]=0;
5032: cptcovage=0;
5033: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5034: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5035: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5036: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5037: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5038: /*scanf("%d",i);*/
1.145 brouard 5039: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5040: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5041: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5042: /* covar is not filled and then is empty */
1.136 brouard 5043: cptcovprod--;
1.145 brouard 5044: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5045: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5046: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5047: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5048: /*printf("stre=%s ", stre);*/
1.137 brouard 5049: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5050: cptcovprod--;
1.145 brouard 5051: cutl(stre,strb,strc,'V');
1.136 brouard 5052: Tvar[k]=atoi(stre);
5053: cptcovage++;
5054: Tage[cptcovage]=k;
1.137 brouard 5055: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5056: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5057: cptcovn++;
5058: cptcovprodnoage++;k1++;
5059: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5060: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5061: because this model-covariate is a construction we invent a new column
5062: ncovcol + k1
5063: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5064: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5065: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5066: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5067: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5068: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5069: k2=k2+2;
5070: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5071: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5072: for (i=1; i<=lastobs;i++){
5073: /* Computes the new covariate which is a product of
1.145 brouard 5074: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5075: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5076: }
5077: } /* End age is not in the model */
5078: } /* End if model includes a product */
1.136 brouard 5079: else { /* no more sum */
5080: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5081: /* scanf("%d",i);*/
1.145 brouard 5082: cutl(strd,strc,strb,'V');
5083: ks++; /**< Number of simple covariates */
5084: cptcovn++;
5085: Tvar[k]=atoi(strd);
1.136 brouard 5086: }
1.137 brouard 5087: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5088: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5089: scanf("%d",i);*/
5090: } /* end of loop + */
5091: } /* end model */
5092:
5093: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5094: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5095:
5096: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5097: printf("cptcovprod=%d ", cptcovprod);
5098: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5099:
5100: scanf("%d ",i);*/
5101:
5102:
1.137 brouard 5103: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.136 brouard 5104: endread:
5105: printf("Exiting decodemodel: ");
5106: return (1);
5107: }
5108:
5109: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5110: {
5111: int i, m;
5112:
5113: for (i=1; i<=imx; i++) {
5114: for(m=2; (m<= maxwav); m++) {
5115: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5116: anint[m][i]=9999;
5117: s[m][i]=-1;
5118: }
5119: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5120: *nberr++;
5121: 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);
5122: 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);
5123: s[m][i]=-1;
5124: }
5125: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5126: *nberr++;
5127: 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]);
5128: 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]);
5129: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5130: }
5131: }
5132: }
5133:
5134: for (i=1; i<=imx; i++) {
5135: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5136: for(m=firstpass; (m<= lastpass); m++){
5137: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5138: if (s[m][i] >= nlstate+1) {
5139: if(agedc[i]>0)
5140: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5141: agev[m][i]=agedc[i];
5142: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5143: else {
5144: if ((int)andc[i]!=9999){
5145: nbwarn++;
5146: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5147: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5148: agev[m][i]=-1;
5149: }
5150: }
5151: }
5152: else if(s[m][i] !=9){ /* Standard case, age in fractional
5153: years but with the precision of a month */
5154: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5155: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5156: agev[m][i]=1;
5157: else if(agev[m][i] < *agemin){
5158: *agemin=agev[m][i];
5159: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5160: }
5161: else if(agev[m][i] >*agemax){
5162: *agemax=agev[m][i];
1.139 brouard 5163: printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);
1.136 brouard 5164: }
5165: /*agev[m][i]=anint[m][i]-annais[i];*/
5166: /* agev[m][i] = age[i]+2*m;*/
5167: }
5168: else { /* =9 */
5169: agev[m][i]=1;
5170: s[m][i]=-1;
5171: }
5172: }
5173: else /*= 0 Unknown */
5174: agev[m][i]=1;
5175: }
5176:
5177: }
5178: for (i=1; i<=imx; i++) {
5179: for(m=firstpass; (m<=lastpass); m++){
5180: if (s[m][i] > (nlstate+ndeath)) {
5181: *nberr++;
5182: 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);
5183: 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);
5184: return 1;
5185: }
5186: }
5187: }
5188:
5189: /*for (i=1; i<=imx; i++){
5190: for (m=firstpass; (m<lastpass); m++){
5191: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5192: }
5193:
5194: }*/
5195:
5196:
1.139 brouard 5197: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5198: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5199:
5200: return (0);
5201: endread:
5202: printf("Exiting calandcheckages: ");
5203: return (1);
5204: }
5205:
5206:
5207: /***********************************************/
5208: /**************** Main Program *****************/
5209: /***********************************************/
5210:
5211: int main(int argc, char *argv[])
5212: {
5213: #ifdef GSL
5214: const gsl_multimin_fminimizer_type *T;
5215: size_t iteri = 0, it;
5216: int rval = GSL_CONTINUE;
5217: int status = GSL_SUCCESS;
5218: double ssval;
5219: #endif
5220: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5221: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5222: int linei, month, year,iout;
5223: int jj, ll, li, lj, lk, imk;
5224: int numlinepar=0; /* Current linenumber of parameter file */
5225: int itimes;
5226: int NDIM=2;
5227: int vpopbased=0;
5228:
5229: char ca[32], cb[32], cc[32];
5230: /* FILE *fichtm; *//* Html File */
5231: /* FILE *ficgp;*/ /*Gnuplot File */
5232: struct stat info;
5233: double agedeb, agefin,hf;
5234: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5235:
5236: double fret;
5237: double **xi,tmp,delta;
5238:
5239: double dum; /* Dummy variable */
5240: double ***p3mat;
5241: double ***mobaverage;
5242: int *indx;
5243: char line[MAXLINE], linepar[MAXLINE];
5244: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5245: char pathr[MAXLINE], pathimach[MAXLINE];
5246: char **bp, *tok, *val; /* pathtot */
5247: int firstobs=1, lastobs=10;
5248: int sdeb, sfin; /* Status at beginning and end */
5249: int c, h , cpt,l;
5250: int ju,jl, mi;
5251: int i1,j1, jk,aa,bb, stepsize, ij;
5252: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5253: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5254: int mobilav=0,popforecast=0;
5255: int hstepm, nhstepm;
5256: int agemortsup;
5257: float sumlpop=0.;
5258: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5259: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5260:
5261: double bage, fage, age, agelim, agebase;
5262: double ftolpl=FTOL;
5263: double **prlim;
5264: double ***param; /* Matrix of parameters */
5265: double *p;
5266: double **matcov; /* Matrix of covariance */
5267: double ***delti3; /* Scale */
5268: double *delti; /* Scale */
5269: double ***eij, ***vareij;
5270: double **varpl; /* Variances of prevalence limits by age */
5271: double *epj, vepp;
5272: double kk1, kk2;
5273: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5274: double **ximort;
1.145 brouard 5275: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5276: int *dcwave;
5277:
5278: char z[1]="c", occ;
5279:
5280: /*char *strt;*/
5281: char strtend[80];
1.126 brouard 5282:
5283: long total_usecs;
5284:
5285: /* setlocale (LC_ALL, ""); */
5286: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5287: /* textdomain (PACKAGE); */
5288: /* setlocale (LC_CTYPE, ""); */
5289: /* setlocale (LC_MESSAGES, ""); */
5290:
5291: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5292: (void) gettimeofday(&start_time,&tzp);
5293: curr_time=start_time;
5294: tm = *localtime(&start_time.tv_sec);
5295: tmg = *gmtime(&start_time.tv_sec);
5296: strcpy(strstart,asctime(&tm));
5297:
5298: /* printf("Localtime (at start)=%s",strstart); */
5299: /* tp.tv_sec = tp.tv_sec +86400; */
5300: /* tm = *localtime(&start_time.tv_sec); */
5301: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5302: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5303: /* tmg.tm_hour=tmg.tm_hour + 1; */
5304: /* tp.tv_sec = mktime(&tmg); */
5305: /* strt=asctime(&tmg); */
5306: /* printf("Time(after) =%s",strstart); */
5307: /* (void) time (&time_value);
5308: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5309: * tm = *localtime(&time_value);
5310: * strstart=asctime(&tm);
5311: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5312: */
5313:
5314: nberr=0; /* Number of errors and warnings */
5315: nbwarn=0;
5316: getcwd(pathcd, size);
5317:
5318: printf("\n%s\n%s",version,fullversion);
5319: if(argc <=1){
5320: printf("\nEnter the parameter file name: ");
5321: fgets(pathr,FILENAMELENGTH,stdin);
5322: i=strlen(pathr);
5323: if(pathr[i-1]=='\n')
5324: pathr[i-1]='\0';
5325: for (tok = pathr; tok != NULL; ){
5326: printf("Pathr |%s|\n",pathr);
5327: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5328: printf("val= |%s| pathr=%s\n",val,pathr);
5329: strcpy (pathtot, val);
5330: if(pathr[0] == '\0') break; /* Dirty */
5331: }
5332: }
5333: else{
5334: strcpy(pathtot,argv[1]);
5335: }
5336: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5337: /*cygwin_split_path(pathtot,path,optionfile);
5338: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5339: /* cutv(path,optionfile,pathtot,'\\');*/
5340:
5341: /* Split argv[0], imach program to get pathimach */
5342: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5343: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5344: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5345: /* strcpy(pathimach,argv[0]); */
5346: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5347: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5348: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5349: chdir(path); /* Can be a relative path */
5350: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5351: printf("Current directory %s!\n",pathcd);
5352: strcpy(command,"mkdir ");
5353: strcat(command,optionfilefiname);
5354: if((outcmd=system(command)) != 0){
5355: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5356: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5357: /* fclose(ficlog); */
5358: /* exit(1); */
5359: }
5360: /* if((imk=mkdir(optionfilefiname))<0){ */
5361: /* perror("mkdir"); */
5362: /* } */
5363:
5364: /*-------- arguments in the command line --------*/
5365:
5366: /* Log file */
5367: strcat(filelog, optionfilefiname);
5368: strcat(filelog,".log"); /* */
5369: if((ficlog=fopen(filelog,"w"))==NULL) {
5370: printf("Problem with logfile %s\n",filelog);
5371: goto end;
5372: }
5373: fprintf(ficlog,"Log filename:%s\n",filelog);
5374: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5375: fprintf(ficlog,"\nEnter the parameter file name: \n");
5376: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5377: path=%s \n\
5378: optionfile=%s\n\
5379: optionfilext=%s\n\
5380: optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5381:
5382: printf("Local time (at start):%s",strstart);
5383: fprintf(ficlog,"Local time (at start): %s",strstart);
5384: fflush(ficlog);
5385: /* (void) gettimeofday(&curr_time,&tzp); */
5386: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
5387:
5388: /* */
5389: strcpy(fileres,"r");
5390: strcat(fileres, optionfilefiname);
5391: strcat(fileres,".txt"); /* Other files have txt extension */
5392:
5393: /*---------arguments file --------*/
5394:
5395: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.149 brouard 5396: printf("Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
5397: fprintf(ficlog,"Problem with optionfile %s with errno=%s\n",optionfile,strerror(errno));
1.126 brouard 5398: fflush(ficlog);
1.149 brouard 5399: /* goto end; */
5400: exit(70);
1.126 brouard 5401: }
5402:
5403:
5404:
5405: strcpy(filereso,"o");
5406: strcat(filereso,fileres);
5407: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5408: printf("Problem with Output resultfile: %s\n", filereso);
5409: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5410: fflush(ficlog);
5411: goto end;
5412: }
5413:
5414: /* Reads comments: lines beginning with '#' */
5415: numlinepar=0;
5416: while((c=getc(ficpar))=='#' && c!= EOF){
5417: ungetc(c,ficpar);
5418: fgets(line, MAXLINE, ficpar);
5419: numlinepar++;
1.141 brouard 5420: fputs(line,stdout);
1.126 brouard 5421: fputs(line,ficparo);
5422: fputs(line,ficlog);
5423: }
5424: ungetc(c,ficpar);
5425:
5426: 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);
5427: numlinepar++;
5428: 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);
5429: 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);
5430: 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);
5431: fflush(ficlog);
5432: while((c=getc(ficpar))=='#' && c!= EOF){
5433: ungetc(c,ficpar);
5434: fgets(line, MAXLINE, ficpar);
5435: numlinepar++;
1.141 brouard 5436: fputs(line, stdout);
5437: //puts(line);
1.126 brouard 5438: fputs(line,ficparo);
5439: fputs(line,ficlog);
5440: }
5441: ungetc(c,ficpar);
5442:
5443:
1.145 brouard 5444: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5445: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5446: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5447: v1+v2*age+v2*v3 makes cptcovn = 3
5448: */
5449: if (strlen(model)>1)
1.145 brouard 5450: ncovmodel=2+nbocc(model,'+')+1; /*Number of variables including intercept and age = cptcovn + intercept + age : v1+v2+v3+v2*v4+v5*age makes 5+2=7*/
5451: else
5452: ncovmodel=2;
1.126 brouard 5453: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5454: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5455: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5456: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5457: 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);
5458: 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);
5459: fflush(stdout);
5460: fclose (ficlog);
5461: goto end;
5462: }
1.126 brouard 5463: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5464: delti=delti3[1][1];
5465: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5466: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5467: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5468: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5469: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5470: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5471: fclose (ficparo);
5472: fclose (ficlog);
5473: goto end;
5474: exit(0);
5475: }
5476: else if(mle==-3) {
5477: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5478: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5479: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5480: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5481: matcov=matrix(1,npar,1,npar);
5482: }
5483: else{
1.145 brouard 5484: /* Read guessed parameters */
1.126 brouard 5485: /* Reads comments: lines beginning with '#' */
5486: while((c=getc(ficpar))=='#' && c!= EOF){
5487: ungetc(c,ficpar);
5488: fgets(line, MAXLINE, ficpar);
5489: numlinepar++;
1.141 brouard 5490: fputs(line,stdout);
1.126 brouard 5491: fputs(line,ficparo);
5492: fputs(line,ficlog);
5493: }
5494: ungetc(c,ficpar);
5495:
5496: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5497: for(i=1; i <=nlstate; i++){
5498: j=0;
5499: for(jj=1; jj <=nlstate+ndeath; jj++){
5500: if(jj==i) continue;
5501: j++;
5502: fscanf(ficpar,"%1d%1d",&i1,&j1);
5503: if ((i1 != i) && (j1 != j)){
5504: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5505: It might be a problem of design; if ncovcol and the model are correct\n \
5506: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5507: exit(1);
5508: }
5509: fprintf(ficparo,"%1d%1d",i1,j1);
5510: if(mle==1)
5511: printf("%1d%1d",i,j);
5512: fprintf(ficlog,"%1d%1d",i,j);
5513: for(k=1; k<=ncovmodel;k++){
5514: fscanf(ficpar," %lf",¶m[i][j][k]);
5515: if(mle==1){
5516: printf(" %lf",param[i][j][k]);
5517: fprintf(ficlog," %lf",param[i][j][k]);
5518: }
5519: else
5520: fprintf(ficlog," %lf",param[i][j][k]);
5521: fprintf(ficparo," %lf",param[i][j][k]);
5522: }
5523: fscanf(ficpar,"\n");
5524: numlinepar++;
5525: if(mle==1)
5526: printf("\n");
5527: fprintf(ficlog,"\n");
5528: fprintf(ficparo,"\n");
5529: }
5530: }
5531: fflush(ficlog);
5532:
1.145 brouard 5533: /* Reads scales values */
1.126 brouard 5534: p=param[1][1];
5535:
5536: /* Reads comments: lines beginning with '#' */
5537: while((c=getc(ficpar))=='#' && c!= EOF){
5538: ungetc(c,ficpar);
5539: fgets(line, MAXLINE, ficpar);
5540: numlinepar++;
1.141 brouard 5541: fputs(line,stdout);
1.126 brouard 5542: fputs(line,ficparo);
5543: fputs(line,ficlog);
5544: }
5545: ungetc(c,ficpar);
5546:
5547: for(i=1; i <=nlstate; i++){
5548: for(j=1; j <=nlstate+ndeath-1; j++){
5549: fscanf(ficpar,"%1d%1d",&i1,&j1);
5550: if ((i1-i)*(j1-j)!=0){
5551: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5552: exit(1);
5553: }
5554: printf("%1d%1d",i,j);
5555: fprintf(ficparo,"%1d%1d",i1,j1);
5556: fprintf(ficlog,"%1d%1d",i1,j1);
5557: for(k=1; k<=ncovmodel;k++){
5558: fscanf(ficpar,"%le",&delti3[i][j][k]);
5559: printf(" %le",delti3[i][j][k]);
5560: fprintf(ficparo," %le",delti3[i][j][k]);
5561: fprintf(ficlog," %le",delti3[i][j][k]);
5562: }
5563: fscanf(ficpar,"\n");
5564: numlinepar++;
5565: printf("\n");
5566: fprintf(ficparo,"\n");
5567: fprintf(ficlog,"\n");
5568: }
5569: }
5570: fflush(ficlog);
5571:
1.145 brouard 5572: /* Reads covariance matrix */
1.126 brouard 5573: delti=delti3[1][1];
5574:
5575:
5576: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5577:
5578: /* Reads comments: lines beginning with '#' */
5579: while((c=getc(ficpar))=='#' && c!= EOF){
5580: ungetc(c,ficpar);
5581: fgets(line, MAXLINE, ficpar);
5582: numlinepar++;
1.141 brouard 5583: fputs(line,stdout);
1.126 brouard 5584: fputs(line,ficparo);
5585: fputs(line,ficlog);
5586: }
5587: ungetc(c,ficpar);
5588:
5589: matcov=matrix(1,npar,1,npar);
1.131 brouard 5590: for(i=1; i <=npar; i++)
5591: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5592:
1.126 brouard 5593: for(i=1; i <=npar; i++){
1.145 brouard 5594: fscanf(ficpar,"%s",str);
1.126 brouard 5595: if(mle==1)
5596: printf("%s",str);
5597: fprintf(ficlog,"%s",str);
5598: fprintf(ficparo,"%s",str);
5599: for(j=1; j <=i; j++){
5600: fscanf(ficpar," %le",&matcov[i][j]);
5601: if(mle==1){
5602: printf(" %.5le",matcov[i][j]);
5603: }
5604: fprintf(ficlog," %.5le",matcov[i][j]);
5605: fprintf(ficparo," %.5le",matcov[i][j]);
5606: }
5607: fscanf(ficpar,"\n");
5608: numlinepar++;
5609: if(mle==1)
5610: printf("\n");
5611: fprintf(ficlog,"\n");
5612: fprintf(ficparo,"\n");
5613: }
5614: for(i=1; i <=npar; i++)
5615: for(j=i+1;j<=npar;j++)
5616: matcov[i][j]=matcov[j][i];
5617:
5618: if(mle==1)
5619: printf("\n");
5620: fprintf(ficlog,"\n");
5621:
5622: fflush(ficlog);
5623:
5624: /*-------- Rewriting parameter file ----------*/
5625: strcpy(rfileres,"r"); /* "Rparameterfile */
5626: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5627: strcat(rfileres,"."); /* */
5628: strcat(rfileres,optionfilext); /* Other files have txt extension */
5629: if((ficres =fopen(rfileres,"w"))==NULL) {
5630: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5631: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5632: }
5633: fprintf(ficres,"#%s\n",version);
5634: } /* End of mle != -3 */
5635:
5636:
5637: n= lastobs;
5638: num=lvector(1,n);
5639: moisnais=vector(1,n);
5640: annais=vector(1,n);
5641: moisdc=vector(1,n);
5642: andc=vector(1,n);
5643: agedc=vector(1,n);
5644: cod=ivector(1,n);
5645: weight=vector(1,n);
5646: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5647: mint=matrix(1,maxwav,1,n);
5648: anint=matrix(1,maxwav,1,n);
1.131 brouard 5649: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5650: tab=ivector(1,NCOVMAX);
1.144 brouard 5651: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5652:
1.136 brouard 5653: /* Reads data from file datafile */
5654: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5655: goto end;
5656:
5657: /* Calculation of the number of parameters from char model */
1.137 brouard 5658: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5659: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5660: k=3 V4 Tvar[k=3]= 4 (from V4)
5661: k=2 V1 Tvar[k=2]= 1 (from V1)
5662: k=1 Tvar[1]=2 (from V2)
5663: */
5664: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5665: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5666: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5667: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5668: */
5669: /* For model-covariate k tells which data-covariate to use but
5670: because this model-covariate is a construction we invent a new column
5671: ncovcol + k1
5672: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5673: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 5674: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 5675: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5676: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5677: */
1.145 brouard 5678: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5679: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 5680: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5681: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 5682: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 5683: 4 covariates (3 plus signs)
5684: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5685: */
1.136 brouard 5686:
5687: if(decodemodel(model, lastobs) == 1)
5688: goto end;
5689:
1.137 brouard 5690: if((double)(lastobs-imx)/(double)imx > 1.10){
5691: nbwarn++;
5692: printf("Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5693: fprintf(ficlog,"Warning: The value of parameter lastobs=%d is big compared to the \n effective number of cases imx=%d, please adjust, \n otherwise you are allocating more memory than necessary.\n",lastobs, imx);
5694: }
1.136 brouard 5695: /* if(mle==1){*/
1.137 brouard 5696: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5697: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 5698: }
5699:
5700: /*-calculation of age at interview from date of interview and age at death -*/
5701: agev=matrix(1,maxwav,1,imx);
5702:
5703: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5704: goto end;
5705:
1.126 brouard 5706:
1.136 brouard 5707: agegomp=(int)agemin;
5708: free_vector(moisnais,1,n);
5709: free_vector(annais,1,n);
1.126 brouard 5710: /* free_matrix(mint,1,maxwav,1,n);
5711: free_matrix(anint,1,maxwav,1,n);*/
5712: free_vector(moisdc,1,n);
5713: free_vector(andc,1,n);
1.145 brouard 5714: /* */
5715:
1.126 brouard 5716: wav=ivector(1,imx);
5717: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5718: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5719: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5720:
5721: /* Concatenates waves */
5722: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 5723: /* */
5724:
1.126 brouard 5725: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5726:
5727: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5728: ncodemax[1]=1;
1.145 brouard 5729: Ndum =ivector(-1,NCOVMAX);
5730: if (ncovmodel > 2)
5731: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5732:
5733: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5734: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5735: h=0;
5736:
5737:
5738: /*if (cptcovn > 0) */
1.126 brouard 5739:
1.145 brouard 5740:
1.126 brouard 5741: m=pow(2,cptcoveff);
5742:
1.131 brouard 5743: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 5744: for(i=1; i <=pow(2,cptcoveff-k);i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
5745: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5746: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
1.126 brouard 5747: h++;
1.141 brouard 5748: if (h>m)
1.136 brouard 5749: h=1;
1.144 brouard 5750: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 5751: * h 1 2 3 4
5752: *______________________________
5753: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5754: * 2 2 1 1 1
5755: * 3 i=2 1 2 1 1
5756: * 4 2 2 1 1
5757: * 5 i=3 1 i=2 1 2 1
5758: * 6 2 1 2 1
5759: * 7 i=4 1 2 2 1
5760: * 8 2 2 2 1
5761: * 9 i=5 1 i=3 1 i=2 1 1
5762: * 10 2 1 1 1
5763: * 11 i=6 1 2 1 1
5764: * 12 2 2 1 1
5765: * 13 i=7 1 i=4 1 2 1
5766: * 14 2 1 2 1
5767: * 15 i=8 1 2 2 1
5768: * 16 2 2 2 1
5769: */
1.141 brouard 5770: codtab[h][k]=j;
1.145 brouard 5771: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 5772: 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 5773: }
5774: }
5775: }
5776: }
5777: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5778: codtab[1][2]=1;codtab[2][2]=2; */
5779: /* for(i=1; i <=m ;i++){
5780: for(k=1; k <=cptcovn; k++){
1.131 brouard 5781: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5782: }
5783: printf("\n");
5784: }
5785: scanf("%d",i);*/
1.145 brouard 5786:
5787: free_ivector(Ndum,-1,NCOVMAX);
5788:
5789:
1.126 brouard 5790:
5791: /*------------ gnuplot -------------*/
5792: strcpy(optionfilegnuplot,optionfilefiname);
5793: if(mle==-3)
5794: strcat(optionfilegnuplot,"-mort");
5795: strcat(optionfilegnuplot,".gp");
5796:
5797: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
5798: printf("Problem with file %s",optionfilegnuplot);
5799: }
5800: else{
5801: fprintf(ficgp,"\n# %s\n", version);
5802: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 5803: //fprintf(ficgp,"set missing 'NaNq'\n");
5804: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 5805: }
5806: /* fclose(ficgp);*/
5807: /*--------- index.htm --------*/
5808:
5809: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
5810: if(mle==-3)
5811: strcat(optionfilehtm,"-mort");
5812: strcat(optionfilehtm,".htm");
5813: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 5814: printf("Problem with %s \n",optionfilehtm);
5815: exit(0);
1.126 brouard 5816: }
5817:
5818: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
5819: strcat(optionfilehtmcov,"-cov.htm");
5820: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
5821: printf("Problem with %s \n",optionfilehtmcov), exit(0);
5822: }
5823: else{
5824: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5825: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5826: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
5827: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
5828: }
5829:
5830: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
5831: <hr size=\"2\" color=\"#EC5E5E\"> \n\
5832: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
5833: \n\
5834: <hr size=\"2\" color=\"#EC5E5E\">\
5835: <ul><li><h4>Parameter files</h4>\n\
5836: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
5837: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
5838: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
5839: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
5840: - Date and time at start: %s</ul>\n",\
5841: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
5842: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
5843: fileres,fileres,\
5844: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
5845: fflush(fichtm);
5846:
5847: strcpy(pathr,path);
5848: strcat(pathr,optionfilefiname);
5849: chdir(optionfilefiname); /* Move to directory named optionfile */
5850:
5851: /* Calculates basic frequencies. Computes observed prevalence at single age
5852: and prints on file fileres'p'. */
5853: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
5854:
5855: fprintf(fichtm,"\n");
5856: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
5857: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
5858: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
5859: imx,agemin,agemax,jmin,jmax,jmean);
5860: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5861: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5862: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5863: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
5864: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
5865:
5866:
5867: /* For Powell, parameters are in a vector p[] starting at p[1]
5868: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
5869: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
5870:
5871: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
5872:
5873: if (mle==-3){
1.136 brouard 5874: ximort=matrix(1,NDIM,1,NDIM);
5875: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 5876: cens=ivector(1,n);
5877: ageexmed=vector(1,n);
5878: agecens=vector(1,n);
5879: dcwave=ivector(1,n);
5880:
5881: for (i=1; i<=imx; i++){
5882: dcwave[i]=-1;
5883: for (m=firstpass; m<=lastpass; m++)
5884: if (s[m][i]>nlstate) {
5885: dcwave[i]=m;
5886: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
5887: break;
5888: }
5889: }
5890:
5891: for (i=1; i<=imx; i++) {
5892: if (wav[i]>0){
5893: ageexmed[i]=agev[mw[1][i]][i];
5894: j=wav[i];
5895: agecens[i]=1.;
5896:
5897: if (ageexmed[i]> 1 && wav[i] > 0){
5898: agecens[i]=agev[mw[j][i]][i];
5899: cens[i]= 1;
5900: }else if (ageexmed[i]< 1)
5901: cens[i]= -1;
5902: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
5903: cens[i]=0 ;
5904: }
5905: else cens[i]=-1;
5906: }
5907:
5908: for (i=1;i<=NDIM;i++) {
5909: for (j=1;j<=NDIM;j++)
5910: ximort[i][j]=(i == j ? 1.0 : 0.0);
5911: }
5912:
1.145 brouard 5913: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 5914: /*printf("%lf %lf", p[1], p[2]);*/
5915:
5916:
1.136 brouard 5917: #ifdef GSL
5918: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
5919: #elsedef
1.126 brouard 5920: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 5921: #endif
1.126 brouard 5922: strcpy(filerespow,"pow-mort");
5923: strcat(filerespow,fileres);
5924: if((ficrespow=fopen(filerespow,"w"))==NULL) {
5925: printf("Problem with resultfile: %s\n", filerespow);
5926: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
5927: }
1.136 brouard 5928: #ifdef GSL
5929: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
5930: #elsedef
1.126 brouard 5931: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 5932: #endif
1.126 brouard 5933: /* for (i=1;i<=nlstate;i++)
5934: for(j=1;j<=nlstate+ndeath;j++)
5935: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
5936: */
5937: fprintf(ficrespow,"\n");
1.136 brouard 5938: #ifdef GSL
5939: /* gsl starts here */
5940: T = gsl_multimin_fminimizer_nmsimplex;
5941: gsl_multimin_fminimizer *sfm = NULL;
5942: gsl_vector *ss, *x;
5943: gsl_multimin_function minex_func;
5944:
5945: /* Initial vertex size vector */
5946: ss = gsl_vector_alloc (NDIM);
5947:
5948: if (ss == NULL){
5949: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
5950: }
5951: /* Set all step sizes to 1 */
5952: gsl_vector_set_all (ss, 0.001);
5953:
5954: /* Starting point */
1.126 brouard 5955:
1.136 brouard 5956: x = gsl_vector_alloc (NDIM);
5957:
5958: if (x == NULL){
5959: gsl_vector_free(ss);
5960: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
5961: }
5962:
5963: /* Initialize method and iterate */
5964: /* p[1]=0.0268; p[NDIM]=0.083; */
5965: /* gsl_vector_set(x, 0, 0.0268); */
5966: /* gsl_vector_set(x, 1, 0.083); */
5967: gsl_vector_set(x, 0, p[1]);
5968: gsl_vector_set(x, 1, p[2]);
5969:
5970: minex_func.f = &gompertz_f;
5971: minex_func.n = NDIM;
5972: minex_func.params = (void *)&p; /* ??? */
5973:
5974: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
5975: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
5976:
5977: printf("Iterations beginning .....\n\n");
5978: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
5979:
5980: iteri=0;
5981: while (rval == GSL_CONTINUE){
5982: iteri++;
5983: status = gsl_multimin_fminimizer_iterate(sfm);
5984:
5985: if (status) printf("error: %s\n", gsl_strerror (status));
5986: fflush(0);
5987:
5988: if (status)
5989: break;
5990:
5991: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
5992: ssval = gsl_multimin_fminimizer_size (sfm);
5993:
5994: if (rval == GSL_SUCCESS)
5995: printf ("converged to a local maximum at\n");
5996:
5997: printf("%5d ", iteri);
5998: for (it = 0; it < NDIM; it++){
5999: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6000: }
6001: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6002: }
6003:
6004: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6005:
6006: gsl_vector_free(x); /* initial values */
6007: gsl_vector_free(ss); /* inital step size */
6008: for (it=0; it<NDIM; it++){
6009: p[it+1]=gsl_vector_get(sfm->x,it);
6010: fprintf(ficrespow," %.12lf", p[it]);
6011: }
6012: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6013: #endif
6014: #ifdef POWELL
6015: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6016: #endif
1.126 brouard 6017: fclose(ficrespow);
6018:
6019: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6020:
6021: for(i=1; i <=NDIM; i++)
6022: for(j=i+1;j<=NDIM;j++)
6023: matcov[i][j]=matcov[j][i];
6024:
6025: printf("\nCovariance matrix\n ");
6026: for(i=1; i <=NDIM; i++) {
6027: for(j=1;j<=NDIM;j++){
6028: printf("%f ",matcov[i][j]);
6029: }
6030: printf("\n ");
6031: }
6032:
6033: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6034: for (i=1;i<=NDIM;i++)
6035: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6036:
6037: lsurv=vector(1,AGESUP);
6038: lpop=vector(1,AGESUP);
6039: tpop=vector(1,AGESUP);
6040: lsurv[agegomp]=100000;
6041:
6042: for (k=agegomp;k<=AGESUP;k++) {
6043: agemortsup=k;
6044: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6045: }
6046:
6047: for (k=agegomp;k<agemortsup;k++)
6048: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6049:
6050: for (k=agegomp;k<agemortsup;k++){
6051: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6052: sumlpop=sumlpop+lpop[k];
6053: }
6054:
6055: tpop[agegomp]=sumlpop;
6056: for (k=agegomp;k<(agemortsup-3);k++){
6057: /* tpop[k+1]=2;*/
6058: tpop[k+1]=tpop[k]-lpop[k];
6059: }
6060:
6061:
6062: printf("\nAge lx qx dx Lx Tx e(x)\n");
6063: for (k=agegomp;k<(agemortsup-2);k++)
6064: 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]);
6065:
6066:
6067: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6068: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6069:
6070: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6071: stepm, weightopt,\
6072: model,imx,p,matcov,agemortsup);
6073:
6074: free_vector(lsurv,1,AGESUP);
6075: free_vector(lpop,1,AGESUP);
6076: free_vector(tpop,1,AGESUP);
1.136 brouard 6077: #ifdef GSL
6078: free_ivector(cens,1,n);
6079: free_vector(agecens,1,n);
6080: free_ivector(dcwave,1,n);
6081: free_matrix(ximort,1,NDIM,1,NDIM);
6082: #endif
1.126 brouard 6083: } /* Endof if mle==-3 */
6084:
6085: else{ /* For mle >=1 */
1.132 brouard 6086: globpr=0;/* debug */
6087: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6088: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6089: for (k=1; k<=npar;k++)
6090: printf(" %d %8.5f",k,p[k]);
6091: printf("\n");
6092: globpr=1; /* to print the contributions */
6093: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6094: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6095: for (k=1; k<=npar;k++)
6096: printf(" %d %8.5f",k,p[k]);
6097: printf("\n");
6098: if(mle>=1){ /* Could be 1 or 2 */
6099: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6100: }
6101:
6102: /*--------- results files --------------*/
6103: 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);
6104:
6105:
6106: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6107: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6108: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6109: for(i=1,jk=1; i <=nlstate; i++){
6110: for(k=1; k <=(nlstate+ndeath); k++){
6111: if (k != i) {
6112: printf("%d%d ",i,k);
6113: fprintf(ficlog,"%d%d ",i,k);
6114: fprintf(ficres,"%1d%1d ",i,k);
6115: for(j=1; j <=ncovmodel; j++){
6116: printf("%lf ",p[jk]);
6117: fprintf(ficlog,"%lf ",p[jk]);
6118: fprintf(ficres,"%lf ",p[jk]);
6119: jk++;
6120: }
6121: printf("\n");
6122: fprintf(ficlog,"\n");
6123: fprintf(ficres,"\n");
6124: }
6125: }
6126: }
6127: if(mle!=0){
6128: /* Computing hessian and covariance matrix */
6129: ftolhess=ftol; /* Usually correct */
6130: hesscov(matcov, p, npar, delti, ftolhess, func);
6131: }
6132: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6133: printf("# Scales (for hessian or gradient estimation)\n");
6134: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6135: for(i=1,jk=1; i <=nlstate; i++){
6136: for(j=1; j <=nlstate+ndeath; j++){
6137: if (j!=i) {
6138: fprintf(ficres,"%1d%1d",i,j);
6139: printf("%1d%1d",i,j);
6140: fprintf(ficlog,"%1d%1d",i,j);
6141: for(k=1; k<=ncovmodel;k++){
6142: printf(" %.5e",delti[jk]);
6143: fprintf(ficlog," %.5e",delti[jk]);
6144: fprintf(ficres," %.5e",delti[jk]);
6145: jk++;
6146: }
6147: printf("\n");
6148: fprintf(ficlog,"\n");
6149: fprintf(ficres,"\n");
6150: }
6151: }
6152: }
6153:
6154: 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");
6155: if(mle>=1)
6156: 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");
6157: 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");
6158: /* # 121 Var(a12)\n\ */
6159: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6160: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6161: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6162: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6163: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6164: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6165: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6166:
6167:
6168: /* Just to have a covariance matrix which will be more understandable
6169: even is we still don't want to manage dictionary of variables
6170: */
6171: for(itimes=1;itimes<=2;itimes++){
6172: jj=0;
6173: for(i=1; i <=nlstate; i++){
6174: for(j=1; j <=nlstate+ndeath; j++){
6175: if(j==i) continue;
6176: for(k=1; k<=ncovmodel;k++){
6177: jj++;
6178: ca[0]= k+'a'-1;ca[1]='\0';
6179: if(itimes==1){
6180: if(mle>=1)
6181: printf("#%1d%1d%d",i,j,k);
6182: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6183: fprintf(ficres,"#%1d%1d%d",i,j,k);
6184: }else{
6185: if(mle>=1)
6186: printf("%1d%1d%d",i,j,k);
6187: fprintf(ficlog,"%1d%1d%d",i,j,k);
6188: fprintf(ficres,"%1d%1d%d",i,j,k);
6189: }
6190: ll=0;
6191: for(li=1;li <=nlstate; li++){
6192: for(lj=1;lj <=nlstate+ndeath; lj++){
6193: if(lj==li) continue;
6194: for(lk=1;lk<=ncovmodel;lk++){
6195: ll++;
6196: if(ll<=jj){
6197: cb[0]= lk +'a'-1;cb[1]='\0';
6198: if(ll<jj){
6199: if(itimes==1){
6200: if(mle>=1)
6201: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6202: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6203: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6204: }else{
6205: if(mle>=1)
6206: printf(" %.5e",matcov[jj][ll]);
6207: fprintf(ficlog," %.5e",matcov[jj][ll]);
6208: fprintf(ficres," %.5e",matcov[jj][ll]);
6209: }
6210: }else{
6211: if(itimes==1){
6212: if(mle>=1)
6213: printf(" Var(%s%1d%1d)",ca,i,j);
6214: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6215: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6216: }else{
6217: if(mle>=1)
6218: printf(" %.5e",matcov[jj][ll]);
6219: fprintf(ficlog," %.5e",matcov[jj][ll]);
6220: fprintf(ficres," %.5e",matcov[jj][ll]);
6221: }
6222: }
6223: }
6224: } /* end lk */
6225: } /* end lj */
6226: } /* end li */
6227: if(mle>=1)
6228: printf("\n");
6229: fprintf(ficlog,"\n");
6230: fprintf(ficres,"\n");
6231: numlinepar++;
6232: } /* end k*/
6233: } /*end j */
6234: } /* end i */
6235: } /* end itimes */
6236:
6237: fflush(ficlog);
6238: fflush(ficres);
6239:
6240: while((c=getc(ficpar))=='#' && c!= EOF){
6241: ungetc(c,ficpar);
6242: fgets(line, MAXLINE, ficpar);
1.141 brouard 6243: fputs(line,stdout);
1.126 brouard 6244: fputs(line,ficparo);
6245: }
6246: ungetc(c,ficpar);
6247:
6248: estepm=0;
6249: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6250: if (estepm==0 || estepm < stepm) estepm=stepm;
6251: if (fage <= 2) {
6252: bage = ageminpar;
6253: fage = agemaxpar;
6254: }
6255:
6256: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6257: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6258: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6259:
6260: while((c=getc(ficpar))=='#' && c!= EOF){
6261: ungetc(c,ficpar);
6262: fgets(line, MAXLINE, ficpar);
1.141 brouard 6263: fputs(line,stdout);
1.126 brouard 6264: fputs(line,ficparo);
6265: }
6266: ungetc(c,ficpar);
6267:
6268: 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);
6269: 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);
6270: 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);
6271: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6272: 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);
6273:
6274: while((c=getc(ficpar))=='#' && c!= EOF){
6275: ungetc(c,ficpar);
6276: fgets(line, MAXLINE, ficpar);
1.141 brouard 6277: fputs(line,stdout);
1.126 brouard 6278: fputs(line,ficparo);
6279: }
6280: ungetc(c,ficpar);
6281:
6282:
6283: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6284: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6285:
6286: fscanf(ficpar,"pop_based=%d\n",&popbased);
6287: fprintf(ficparo,"pop_based=%d\n",popbased);
6288: fprintf(ficres,"pop_based=%d\n",popbased);
6289:
6290: while((c=getc(ficpar))=='#' && c!= EOF){
6291: ungetc(c,ficpar);
6292: fgets(line, MAXLINE, ficpar);
1.141 brouard 6293: fputs(line,stdout);
1.126 brouard 6294: fputs(line,ficparo);
6295: }
6296: ungetc(c,ficpar);
6297:
6298: 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);
6299: 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);
6300: 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);
6301: 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);
6302: 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);
6303: /* day and month of proj2 are not used but only year anproj2.*/
6304:
6305:
6306:
1.145 brouard 6307: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6308: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6309:
6310: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6311: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6312:
6313: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6314: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6315: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6316:
6317: /*------------ free_vector -------------*/
6318: /* chdir(path); */
6319:
6320: free_ivector(wav,1,imx);
6321: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6322: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6323: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6324: free_lvector(num,1,n);
6325: free_vector(agedc,1,n);
6326: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6327: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6328: fclose(ficparo);
6329: fclose(ficres);
6330:
6331:
6332: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 brouard 6333: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6334: fclose(ficrespl);
6335:
1.145 brouard 6336: #ifdef FREEEXIT2
6337: #include "freeexit2.h"
6338: #endif
6339:
1.126 brouard 6340: /*------------- h Pij x at various ages ------------*/
1.145 brouard 6341: #include "hpijx.h"
6342: fclose(ficrespij);
1.126 brouard 6343:
1.145 brouard 6344: /*-------------- Variance of one-step probabilities---*/
6345: k=1;
1.126 brouard 6346: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6347:
6348:
6349: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6350: for(i=1;i<=AGESUP;i++)
6351: for(j=1;j<=NCOVMAX;j++)
6352: for(k=1;k<=NCOVMAX;k++)
6353: probs[i][j][k]=0.;
6354:
6355: /*---------- Forecasting ------------------*/
6356: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6357: if(prevfcast==1){
6358: /* if(stepm ==1){*/
6359: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6360: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6361: /* } */
6362: /* else{ */
6363: /* erreur=108; */
6364: /* 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); */
6365: /* 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); */
6366: /* } */
6367: }
6368:
6369:
1.127 brouard 6370: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6371:
6372: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6373: /* 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",\
6374: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6375: */
1.126 brouard 6376:
1.127 brouard 6377: if (mobilav!=0) {
6378: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6379: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6380: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6381: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6382: }
1.126 brouard 6383: }
6384:
6385:
1.127 brouard 6386: /*---------- Health expectancies, no variances ------------*/
6387:
1.126 brouard 6388: strcpy(filerese,"e");
6389: strcat(filerese,fileres);
6390: if((ficreseij=fopen(filerese,"w"))==NULL) {
6391: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6392: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6393: }
6394: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6395: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 6396: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6397: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6398:
6399: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6400: fprintf(ficreseij,"\n#****** ");
6401: for(j=1;j<=cptcoveff;j++) {
6402: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6403: }
6404: fprintf(ficreseij,"******\n");
6405:
6406: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6407: oldm=oldms;savm=savms;
6408: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6409:
6410: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6411: /*}*/
1.127 brouard 6412: }
6413: fclose(ficreseij);
6414:
6415:
6416: /*---------- Health expectancies and variances ------------*/
6417:
6418:
6419: strcpy(filerest,"t");
6420: strcat(filerest,fileres);
6421: if((ficrest=fopen(filerest,"w"))==NULL) {
6422: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6423: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6424: }
6425: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6426: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6427:
1.126 brouard 6428:
6429: strcpy(fileresstde,"stde");
6430: strcat(fileresstde,fileres);
6431: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6432: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6433: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6434: }
6435: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6436: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6437:
6438: strcpy(filerescve,"cve");
6439: strcat(filerescve,fileres);
6440: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6441: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6442: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6443: }
6444: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6445: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6446:
6447: strcpy(fileresv,"v");
6448: strcat(fileresv,fileres);
6449: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6450: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6451: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6452: }
6453: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6454: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6455:
1.145 brouard 6456: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6457: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6458:
6459: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6460: fprintf(ficrest,"\n#****** ");
1.126 brouard 6461: for(j=1;j<=cptcoveff;j++)
6462: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6463: fprintf(ficrest,"******\n");
6464:
6465: fprintf(ficresstdeij,"\n#****** ");
6466: fprintf(ficrescveij,"\n#****** ");
6467: for(j=1;j<=cptcoveff;j++) {
6468: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6469: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6470: }
6471: fprintf(ficresstdeij,"******\n");
6472: fprintf(ficrescveij,"******\n");
6473:
6474: fprintf(ficresvij,"\n#****** ");
6475: for(j=1;j<=cptcoveff;j++)
6476: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6477: fprintf(ficresvij,"******\n");
6478:
6479: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6480: oldm=oldms;savm=savms;
1.127 brouard 6481: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 6482: /*
6483: */
6484: /* goto endfree; */
1.126 brouard 6485:
6486: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6487: pstamp(ficrest);
1.145 brouard 6488:
6489:
1.128 brouard 6490: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 6491: oldm=oldms;savm=savms; /* Segmentation fault */
6492: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);
6493: 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 ");
1.128 brouard 6494: if(vpopbased==1)
6495: 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);
6496: else
6497: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6498: fprintf(ficrest,"# Age e.. (std) ");
6499: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6500: fprintf(ficrest,"\n");
1.126 brouard 6501:
1.128 brouard 6502: epj=vector(1,nlstate+1);
6503: for(age=bage; age <=fage ;age++){
6504: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6505: if (vpopbased==1) {
6506: if(mobilav ==0){
6507: for(i=1; i<=nlstate;i++)
6508: prlim[i][i]=probs[(int)age][i][k];
6509: }else{ /* mobilav */
6510: for(i=1; i<=nlstate;i++)
6511: prlim[i][i]=mobaverage[(int)age][i][k];
6512: }
1.126 brouard 6513: }
6514:
1.128 brouard 6515: fprintf(ficrest," %4.0f",age);
6516: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6517: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6518: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6519: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6520: }
6521: epj[nlstate+1] +=epj[j];
1.126 brouard 6522: }
6523:
1.128 brouard 6524: for(i=1, vepp=0.;i <=nlstate;i++)
6525: for(j=1;j <=nlstate;j++)
6526: vepp += vareij[i][j][(int)age];
6527: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6528: for(j=1;j <=nlstate;j++){
6529: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6530: }
6531: fprintf(ficrest,"\n");
1.126 brouard 6532: }
6533: }
6534: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6535: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6536: free_vector(epj,1,nlstate+1);
1.145 brouard 6537: /*}*/
1.126 brouard 6538: }
6539: free_vector(weight,1,n);
1.145 brouard 6540: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6541: free_imatrix(s,1,maxwav+1,1,n);
6542: free_matrix(anint,1,maxwav,1,n);
6543: free_matrix(mint,1,maxwav,1,n);
6544: free_ivector(cod,1,n);
6545: free_ivector(tab,1,NCOVMAX);
6546: fclose(ficresstdeij);
6547: fclose(ficrescveij);
6548: fclose(ficresvij);
6549: fclose(ficrest);
6550: fclose(ficpar);
6551:
6552: /*------- Variance of period (stable) prevalence------*/
6553:
6554: strcpy(fileresvpl,"vpl");
6555: strcat(fileresvpl,fileres);
6556: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6557: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6558: exit(0);
6559: }
6560: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6561:
1.145 brouard 6562: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6563: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6564:
6565: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6566: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6567: for(j=1;j<=cptcoveff;j++)
6568: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6569: fprintf(ficresvpl,"******\n");
6570:
6571: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6572: oldm=oldms;savm=savms;
6573: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6574: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6575: /*}*/
1.126 brouard 6576: }
6577:
6578: fclose(ficresvpl);
6579:
6580: /*---------- End : free ----------------*/
6581: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6582: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6583: } /* mle==-3 arrives here for freeing */
1.131 brouard 6584: endfree:
1.141 brouard 6585: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6586: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6587: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6588: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6589: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6590: free_matrix(covar,0,NCOVMAX,1,n);
6591: free_matrix(matcov,1,npar,1,npar);
6592: /*free_vector(delti,1,npar);*/
6593: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6594: free_matrix(agev,1,maxwav,1,imx);
6595: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6596:
1.145 brouard 6597: free_ivector(ncodemax,1,NCOVMAX);
6598: free_ivector(Tvar,1,NCOVMAX);
6599: free_ivector(Tprod,1,NCOVMAX);
6600: free_ivector(Tvaraff,1,NCOVMAX);
6601: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 6602:
6603: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6604: free_imatrix(codtab,1,100,1,10);
6605: fflush(fichtm);
6606: fflush(ficgp);
6607:
6608:
6609: if((nberr >0) || (nbwarn>0)){
6610: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6611: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6612: }else{
6613: printf("End of Imach\n");
6614: fprintf(ficlog,"End of Imach\n");
6615: }
6616: printf("See log file on %s\n",filelog);
6617: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6618: (void) gettimeofday(&end_time,&tzp);
6619: tm = *localtime(&end_time.tv_sec);
6620: tmg = *gmtime(&end_time.tv_sec);
6621: strcpy(strtend,asctime(&tm));
6622: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6623: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6624: printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
6625:
1.141 brouard 6626: printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6627: fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
1.141 brouard 6628: fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);
1.126 brouard 6629: /* printf("Total time was %d uSec.\n", total_usecs);*/
6630: /* if(fileappend(fichtm,optionfilehtm)){ */
6631: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6632: fclose(fichtm);
6633: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6634: fclose(fichtmcov);
6635: fclose(ficgp);
6636: fclose(ficlog);
6637: /*------ End -----------*/
6638:
6639:
6640: printf("Before Current directory %s!\n",pathcd);
6641: if(chdir(pathcd) != 0)
6642: printf("Can't move to directory %s!\n",path);
6643: if(getcwd(pathcd,MAXLINE) > 0)
6644: printf("Current directory %s!\n",pathcd);
6645: /*strcat(plotcmd,CHARSEPARATOR);*/
6646: sprintf(plotcmd,"gnuplot");
6647: #ifndef UNIX
6648: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6649: #endif
6650: if(!stat(plotcmd,&info)){
6651: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6652: if(!stat(getenv("GNUPLOTBIN"),&info)){
6653: printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6654: }else
6655: strcpy(pplotcmd,plotcmd);
6656: #ifdef UNIX
6657: strcpy(plotcmd,GNUPLOTPROGRAM);
6658: if(!stat(plotcmd,&info)){
6659: printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
6660: }else
6661: strcpy(pplotcmd,plotcmd);
6662: #endif
6663: }else
6664: strcpy(pplotcmd,plotcmd);
6665:
6666: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
6667: printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
6668:
6669: if((outcmd=system(plotcmd)) != 0){
1.151 ! brouard 6670: printf("\n Problem with gnuplot command %s\n", plotcmd);
1.150 brouard 6671: printf("\n Trying on same directory\n");
6672: sprintf(plotcmd,"./gnuplot %s", optionfilegnuplot);
6673: if((outcmd=system(plotcmd)) != 0)
6674: printf("\n Still a problem with gnuplot command %s\n", plotcmd);
1.126 brouard 6675: }
6676: printf(" Wait...");
6677: while (z[0] != 'q') {
6678: /* chdir(path); */
6679: printf("\nType e to edit output files, g to graph again and q for exiting: ");
6680: scanf("%s",z);
6681: /* if (z[0] == 'c') system("./imach"); */
6682: if (z[0] == 'e') {
6683: printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
6684: system(optionfilehtm);
6685: }
6686: else if (z[0] == 'g') system(plotcmd);
6687: else if (z[0] == 'q') exit(0);
6688: }
6689: end:
6690: while (z[0] != 'q') {
6691: printf("\nType q for exiting: ");
6692: scanf("%s",z);
6693: }
6694: }
6695:
6696:
6697:
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