Annotation of imach/src/imach.c, revision 1.163
1.163 ! brouard 1: /* $Id: imach.c,v 1.162 2014/09/25 11:43:39 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 ! brouard 3: $Log: imach.c,v $
! 4: Revision 1.162 2014/09/25 11:43:39 brouard
! 5: Summary: temporary backup 0.99!
! 6:
1.162 brouard 7: Revision 1.1 2014/09/16 11:06:58 brouard
8: Summary: With some code (wrong) for nlopt
9:
10: Author:
11:
12: Revision 1.161 2014/09/15 20:41:41 brouard
13: Summary: Problem with macro SQR on Intel compiler
14:
1.161 brouard 15: Revision 1.160 2014/09/02 09:24:05 brouard
16: *** empty log message ***
17:
1.160 brouard 18: Revision 1.159 2014/09/01 10:34:10 brouard
19: Summary: WIN32
20: Author: Brouard
21:
1.159 brouard 22: Revision 1.158 2014/08/27 17:11:51 brouard
23: *** empty log message ***
24:
1.158 brouard 25: Revision 1.157 2014/08/27 16:26:55 brouard
26: Summary: Preparing windows Visual studio version
27: Author: Brouard
28:
29: In order to compile on Visual studio, time.h is now correct and time_t
30: and tm struct should be used. difftime should be used but sometimes I
31: just make the differences in raw time format (time(&now).
32: Trying to suppress #ifdef LINUX
33: Add xdg-open for __linux in order to open default browser.
34:
1.157 brouard 35: Revision 1.156 2014/08/25 20:10:10 brouard
36: *** empty log message ***
37:
1.156 brouard 38: Revision 1.155 2014/08/25 18:32:34 brouard
39: Summary: New compile, minor changes
40: Author: Brouard
41:
1.155 brouard 42: Revision 1.154 2014/06/20 17:32:08 brouard
43: Summary: Outputs now all graphs of convergence to period prevalence
44:
1.154 brouard 45: Revision 1.153 2014/06/20 16:45:46 brouard
46: Summary: If 3 live state, convergence to period prevalence on same graph
47: Author: Brouard
48:
1.153 brouard 49: Revision 1.152 2014/06/18 17:54:09 brouard
50: Summary: open browser, use gnuplot on same dir than imach if not found in the path
51:
1.152 brouard 52: Revision 1.151 2014/06/18 16:43:30 brouard
53: *** empty log message ***
54:
1.151 brouard 55: Revision 1.150 2014/06/18 16:42:35 brouard
56: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
57: Author: brouard
58:
1.150 brouard 59: Revision 1.149 2014/06/18 15:51:14 brouard
60: Summary: Some fixes in parameter files errors
61: Author: Nicolas Brouard
62:
1.149 brouard 63: Revision 1.148 2014/06/17 17:38:48 brouard
64: Summary: Nothing new
65: Author: Brouard
66:
67: Just a new packaging for OS/X version 0.98nS
68:
1.148 brouard 69: Revision 1.147 2014/06/16 10:33:11 brouard
70: *** empty log message ***
71:
1.147 brouard 72: Revision 1.146 2014/06/16 10:20:28 brouard
73: Summary: Merge
74: Author: Brouard
75:
76: Merge, before building revised version.
77:
1.146 brouard 78: Revision 1.145 2014/06/10 21:23:15 brouard
79: Summary: Debugging with valgrind
80: Author: Nicolas Brouard
81:
82: Lot of changes in order to output the results with some covariates
83: After the Edimburgh REVES conference 2014, it seems mandatory to
84: improve the code.
85: No more memory valgrind error but a lot has to be done in order to
86: continue the work of splitting the code into subroutines.
87: Also, decodemodel has been improved. Tricode is still not
88: optimal. nbcode should be improved. Documentation has been added in
89: the source code.
90:
1.144 brouard 91: Revision 1.143 2014/01/26 09:45:38 brouard
92: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
93:
94: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
95: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
96:
1.143 brouard 97: Revision 1.142 2014/01/26 03:57:36 brouard
98: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
99:
100: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
101:
1.142 brouard 102: Revision 1.141 2014/01/26 02:42:01 brouard
103: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
104:
1.141 brouard 105: Revision 1.140 2011/09/02 10:37:54 brouard
106: Summary: times.h is ok with mingw32 now.
107:
1.140 brouard 108: Revision 1.139 2010/06/14 07:50:17 brouard
109: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
110: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
111:
1.139 brouard 112: Revision 1.138 2010/04/30 18:19:40 brouard
113: *** empty log message ***
114:
1.138 brouard 115: Revision 1.137 2010/04/29 18:11:38 brouard
116: (Module): Checking covariates for more complex models
117: than V1+V2. A lot of change to be done. Unstable.
118:
1.137 brouard 119: Revision 1.136 2010/04/26 20:30:53 brouard
120: (Module): merging some libgsl code. Fixing computation
121: of likelione (using inter/intrapolation if mle = 0) in order to
122: get same likelihood as if mle=1.
123: Some cleaning of code and comments added.
124:
1.136 brouard 125: Revision 1.135 2009/10/29 15:33:14 brouard
126: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
127:
1.135 brouard 128: Revision 1.134 2009/10/29 13:18:53 brouard
129: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
130:
1.134 brouard 131: Revision 1.133 2009/07/06 10:21:25 brouard
132: just nforces
133:
1.133 brouard 134: Revision 1.132 2009/07/06 08:22:05 brouard
135: Many tings
136:
1.132 brouard 137: Revision 1.131 2009/06/20 16:22:47 brouard
138: Some dimensions resccaled
139:
1.131 brouard 140: Revision 1.130 2009/05/26 06:44:34 brouard
141: (Module): Max Covariate is now set to 20 instead of 8. A
142: lot of cleaning with variables initialized to 0. Trying to make
143: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
144:
1.130 brouard 145: Revision 1.129 2007/08/31 13:49:27 lievre
146: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
147:
1.129 lievre 148: Revision 1.128 2006/06/30 13:02:05 brouard
149: (Module): Clarifications on computing e.j
150:
1.128 brouard 151: Revision 1.127 2006/04/28 18:11:50 brouard
152: (Module): Yes the sum of survivors was wrong since
153: imach-114 because nhstepm was no more computed in the age
154: loop. Now we define nhstepma in the age loop.
155: (Module): In order to speed up (in case of numerous covariates) we
156: compute health expectancies (without variances) in a first step
157: and then all the health expectancies with variances or standard
158: deviation (needs data from the Hessian matrices) which slows the
159: computation.
160: In the future we should be able to stop the program is only health
161: expectancies and graph are needed without standard deviations.
162:
1.127 brouard 163: Revision 1.126 2006/04/28 17:23:28 brouard
164: (Module): Yes the sum of survivors was wrong since
165: imach-114 because nhstepm was no more computed in the age
166: loop. Now we define nhstepma in the age loop.
167: Version 0.98h
168:
1.126 brouard 169: Revision 1.125 2006/04/04 15:20:31 lievre
170: Errors in calculation of health expectancies. Age was not initialized.
171: Forecasting file added.
172:
173: Revision 1.124 2006/03/22 17:13:53 lievre
174: Parameters are printed with %lf instead of %f (more numbers after the comma).
175: The log-likelihood is printed in the log file
176:
177: Revision 1.123 2006/03/20 10:52:43 brouard
178: * imach.c (Module): <title> changed, corresponds to .htm file
179: name. <head> headers where missing.
180:
181: * imach.c (Module): Weights can have a decimal point as for
182: English (a comma might work with a correct LC_NUMERIC environment,
183: otherwise the weight is truncated).
184: Modification of warning when the covariates values are not 0 or
185: 1.
186: Version 0.98g
187:
188: Revision 1.122 2006/03/20 09:45:41 brouard
189: (Module): Weights can have a decimal point as for
190: English (a comma might work with a correct LC_NUMERIC environment,
191: otherwise the weight is truncated).
192: Modification of warning when the covariates values are not 0 or
193: 1.
194: Version 0.98g
195:
196: Revision 1.121 2006/03/16 17:45:01 lievre
197: * imach.c (Module): Comments concerning covariates added
198:
199: * imach.c (Module): refinements in the computation of lli if
200: status=-2 in order to have more reliable computation if stepm is
201: not 1 month. Version 0.98f
202:
203: Revision 1.120 2006/03/16 15:10:38 lievre
204: (Module): refinements in the computation of lli if
205: status=-2 in order to have more reliable computation if stepm is
206: not 1 month. Version 0.98f
207:
208: Revision 1.119 2006/03/15 17:42:26 brouard
209: (Module): Bug if status = -2, the loglikelihood was
210: computed as likelihood omitting the logarithm. Version O.98e
211:
212: Revision 1.118 2006/03/14 18:20:07 brouard
213: (Module): varevsij Comments added explaining the second
214: table of variances if popbased=1 .
215: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
216: (Module): Function pstamp added
217: (Module): Version 0.98d
218:
219: Revision 1.117 2006/03/14 17:16:22 brouard
220: (Module): varevsij Comments added explaining the second
221: table of variances if popbased=1 .
222: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
223: (Module): Function pstamp added
224: (Module): Version 0.98d
225:
226: Revision 1.116 2006/03/06 10:29:27 brouard
227: (Module): Variance-covariance wrong links and
228: varian-covariance of ej. is needed (Saito).
229:
230: Revision 1.115 2006/02/27 12:17:45 brouard
231: (Module): One freematrix added in mlikeli! 0.98c
232:
233: Revision 1.114 2006/02/26 12:57:58 brouard
234: (Module): Some improvements in processing parameter
235: filename with strsep.
236:
237: Revision 1.113 2006/02/24 14:20:24 brouard
238: (Module): Memory leaks checks with valgrind and:
239: datafile was not closed, some imatrix were not freed and on matrix
240: allocation too.
241:
242: Revision 1.112 2006/01/30 09:55:26 brouard
243: (Module): Back to gnuplot.exe instead of wgnuplot.exe
244:
245: Revision 1.111 2006/01/25 20:38:18 brouard
246: (Module): Lots of cleaning and bugs added (Gompertz)
247: (Module): Comments can be added in data file. Missing date values
248: can be a simple dot '.'.
249:
250: Revision 1.110 2006/01/25 00:51:50 brouard
251: (Module): Lots of cleaning and bugs added (Gompertz)
252:
253: Revision 1.109 2006/01/24 19:37:15 brouard
254: (Module): Comments (lines starting with a #) are allowed in data.
255:
256: Revision 1.108 2006/01/19 18:05:42 lievre
257: Gnuplot problem appeared...
258: To be fixed
259:
260: Revision 1.107 2006/01/19 16:20:37 brouard
261: Test existence of gnuplot in imach path
262:
263: Revision 1.106 2006/01/19 13:24:36 brouard
264: Some cleaning and links added in html output
265:
266: Revision 1.105 2006/01/05 20:23:19 lievre
267: *** empty log message ***
268:
269: Revision 1.104 2005/09/30 16:11:43 lievre
270: (Module): sump fixed, loop imx fixed, and simplifications.
271: (Module): If the status is missing at the last wave but we know
272: that the person is alive, then we can code his/her status as -2
273: (instead of missing=-1 in earlier versions) and his/her
274: contributions to the likelihood is 1 - Prob of dying from last
275: health status (= 1-p13= p11+p12 in the easiest case of somebody in
276: the healthy state at last known wave). Version is 0.98
277:
278: Revision 1.103 2005/09/30 15:54:49 lievre
279: (Module): sump fixed, loop imx fixed, and simplifications.
280:
281: Revision 1.102 2004/09/15 17:31:30 brouard
282: Add the possibility to read data file including tab characters.
283:
284: Revision 1.101 2004/09/15 10:38:38 brouard
285: Fix on curr_time
286:
287: Revision 1.100 2004/07/12 18:29:06 brouard
288: Add version for Mac OS X. Just define UNIX in Makefile
289:
290: Revision 1.99 2004/06/05 08:57:40 brouard
291: *** empty log message ***
292:
293: Revision 1.98 2004/05/16 15:05:56 brouard
294: New version 0.97 . First attempt to estimate force of mortality
295: directly from the data i.e. without the need of knowing the health
296: state at each age, but using a Gompertz model: log u =a + b*age .
297: This is the basic analysis of mortality and should be done before any
298: other analysis, in order to test if the mortality estimated from the
299: cross-longitudinal survey is different from the mortality estimated
300: from other sources like vital statistic data.
301:
302: The same imach parameter file can be used but the option for mle should be -3.
303:
1.133 brouard 304: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 305: former routines in order to include the new code within the former code.
306:
307: The output is very simple: only an estimate of the intercept and of
308: the slope with 95% confident intervals.
309:
310: Current limitations:
311: A) Even if you enter covariates, i.e. with the
312: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
313: B) There is no computation of Life Expectancy nor Life Table.
314:
315: Revision 1.97 2004/02/20 13:25:42 lievre
316: Version 0.96d. Population forecasting command line is (temporarily)
317: suppressed.
318:
319: Revision 1.96 2003/07/15 15:38:55 brouard
320: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
321: rewritten within the same printf. Workaround: many printfs.
322:
323: Revision 1.95 2003/07/08 07:54:34 brouard
324: * imach.c (Repository):
325: (Repository): Using imachwizard code to output a more meaningful covariance
326: matrix (cov(a12,c31) instead of numbers.
327:
328: Revision 1.94 2003/06/27 13:00:02 brouard
329: Just cleaning
330:
331: Revision 1.93 2003/06/25 16:33:55 brouard
332: (Module): On windows (cygwin) function asctime_r doesn't
333: exist so I changed back to asctime which exists.
334: (Module): Version 0.96b
335:
336: Revision 1.92 2003/06/25 16:30:45 brouard
337: (Module): On windows (cygwin) function asctime_r doesn't
338: exist so I changed back to asctime which exists.
339:
340: Revision 1.91 2003/06/25 15:30:29 brouard
341: * imach.c (Repository): Duplicated warning errors corrected.
342: (Repository): Elapsed time after each iteration is now output. It
343: helps to forecast when convergence will be reached. Elapsed time
344: is stamped in powell. We created a new html file for the graphs
345: concerning matrix of covariance. It has extension -cov.htm.
346:
347: Revision 1.90 2003/06/24 12:34:15 brouard
348: (Module): Some bugs corrected for windows. Also, when
349: mle=-1 a template is output in file "or"mypar.txt with the design
350: of the covariance matrix to be input.
351:
352: Revision 1.89 2003/06/24 12:30:52 brouard
353: (Module): Some bugs corrected for windows. Also, when
354: mle=-1 a template is output in file "or"mypar.txt with the design
355: of the covariance matrix to be input.
356:
357: Revision 1.88 2003/06/23 17:54:56 brouard
358: * 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.
359:
360: Revision 1.87 2003/06/18 12:26:01 brouard
361: Version 0.96
362:
363: Revision 1.86 2003/06/17 20:04:08 brouard
364: (Module): Change position of html and gnuplot routines and added
365: routine fileappend.
366:
367: Revision 1.85 2003/06/17 13:12:43 brouard
368: * imach.c (Repository): Check when date of death was earlier that
369: current date of interview. It may happen when the death was just
370: prior to the death. In this case, dh was negative and likelihood
371: was wrong (infinity). We still send an "Error" but patch by
372: assuming that the date of death was just one stepm after the
373: interview.
374: (Repository): Because some people have very long ID (first column)
375: we changed int to long in num[] and we added a new lvector for
376: memory allocation. But we also truncated to 8 characters (left
377: truncation)
378: (Repository): No more line truncation errors.
379:
380: Revision 1.84 2003/06/13 21:44:43 brouard
381: * imach.c (Repository): Replace "freqsummary" at a correct
382: place. It differs from routine "prevalence" which may be called
383: many times. Probs is memory consuming and must be used with
384: parcimony.
385: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
386:
387: Revision 1.83 2003/06/10 13:39:11 lievre
388: *** empty log message ***
389:
390: Revision 1.82 2003/06/05 15:57:20 brouard
391: Add log in imach.c and fullversion number is now printed.
392:
393: */
394: /*
395: Interpolated Markov Chain
396:
397: Short summary of the programme:
398:
399: This program computes Healthy Life Expectancies from
400: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
401: first survey ("cross") where individuals from different ages are
402: interviewed on their health status or degree of disability (in the
403: case of a health survey which is our main interest) -2- at least a
404: second wave of interviews ("longitudinal") which measure each change
405: (if any) in individual health status. Health expectancies are
406: computed from the time spent in each health state according to a
407: model. More health states you consider, more time is necessary to reach the
408: Maximum Likelihood of the parameters involved in the model. The
409: simplest model is the multinomial logistic model where pij is the
410: probability to be observed in state j at the second wave
411: conditional to be observed in state i at the first wave. Therefore
412: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
413: 'age' is age and 'sex' is a covariate. If you want to have a more
414: complex model than "constant and age", you should modify the program
415: where the markup *Covariates have to be included here again* invites
416: you to do it. More covariates you add, slower the
417: convergence.
418:
419: The advantage of this computer programme, compared to a simple
420: multinomial logistic model, is clear when the delay between waves is not
421: identical for each individual. Also, if a individual missed an
422: intermediate interview, the information is lost, but taken into
423: account using an interpolation or extrapolation.
424:
425: hPijx is the probability to be observed in state i at age x+h
426: conditional to the observed state i at age x. The delay 'h' can be
427: split into an exact number (nh*stepm) of unobserved intermediate
428: states. This elementary transition (by month, quarter,
429: semester or year) is modelled as a multinomial logistic. The hPx
430: matrix is simply the matrix product of nh*stepm elementary matrices
431: and the contribution of each individual to the likelihood is simply
432: hPijx.
433:
434: Also this programme outputs the covariance matrix of the parameters but also
435: of the life expectancies. It also computes the period (stable) prevalence.
436:
1.133 brouard 437: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
438: Institut national d'études démographiques, Paris.
1.126 brouard 439: This software have been partly granted by Euro-REVES, a concerted action
440: from the European Union.
441: It is copyrighted identically to a GNU software product, ie programme and
442: software can be distributed freely for non commercial use. Latest version
443: can be accessed at http://euroreves.ined.fr/imach .
444:
445: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
446: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
447:
448: **********************************************************************/
449: /*
450: main
451: read parameterfile
452: read datafile
453: concatwav
454: freqsummary
455: if (mle >= 1)
456: mlikeli
457: print results files
458: if mle==1
459: computes hessian
460: read end of parameter file: agemin, agemax, bage, fage, estepm
461: begin-prev-date,...
462: open gnuplot file
463: open html file
1.145 brouard 464: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
465: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
466: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
467: freexexit2 possible for memory heap.
468:
469: h Pij x | pij_nom ficrestpij
470: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
471: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
472: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
473:
474: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
475: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
476: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
477: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
478: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
479:
1.126 brouard 480: forecasting if prevfcast==1 prevforecast call prevalence()
481: health expectancies
482: Variance-covariance of DFLE
483: prevalence()
484: movingaverage()
485: varevsij()
486: if popbased==1 varevsij(,popbased)
487: total life expectancies
488: Variance of period (stable) prevalence
489: end
490: */
491:
492:
493:
494:
495: #include <math.h>
496: #include <stdio.h>
497: #include <stdlib.h>
498: #include <string.h>
1.159 brouard 499:
500: #ifdef _WIN32
501: #include <io.h>
502: #else
1.126 brouard 503: #include <unistd.h>
1.159 brouard 504: #endif
1.126 brouard 505:
506: #include <limits.h>
507: #include <sys/types.h>
508: #include <sys/stat.h>
509: #include <errno.h>
1.159 brouard 510: /* extern int errno; */
1.126 brouard 511:
1.157 brouard 512: /* #ifdef LINUX */
513: /* #include <time.h> */
514: /* #include "timeval.h" */
515: /* #else */
516: /* #include <sys/time.h> */
517: /* #endif */
518:
1.126 brouard 519: #include <time.h>
520:
1.136 brouard 521: #ifdef GSL
522: #include <gsl/gsl_errno.h>
523: #include <gsl/gsl_multimin.h>
524: #endif
525:
1.162 brouard 526: #ifdef NLOPT
527: #include <nlopt.h>
528: typedef struct {
529: double (* function)(double [] );
530: } myfunc_data ;
531: #endif
532:
1.126 brouard 533: /* #include <libintl.h> */
534: /* #define _(String) gettext (String) */
535:
1.141 brouard 536: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 537:
538: #define GNUPLOTPROGRAM "gnuplot"
539: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
540: #define FILENAMELENGTH 132
541:
542: #define GLOCK_ERROR_NOPATH -1 /* empty path */
543: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
544:
1.144 brouard 545: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
546: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 547:
548: #define NINTERVMAX 8
1.144 brouard 549: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
550: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
551: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.145 brouard 552: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
1.126 brouard 553: #define MAXN 20000
1.144 brouard 554: #define YEARM 12. /**< Number of months per year */
1.126 brouard 555: #define AGESUP 130
556: #define AGEBASE 40
1.144 brouard 557: #define AGEGOMP 10. /**< Minimal age for Gompertz adjustment */
1.157 brouard 558: #ifdef _WIN32
559: #define DIRSEPARATOR '\\'
560: #define CHARSEPARATOR "\\"
561: #define ODIRSEPARATOR '/'
562: #else
1.126 brouard 563: #define DIRSEPARATOR '/'
564: #define CHARSEPARATOR "/"
565: #define ODIRSEPARATOR '\\'
566: #endif
567:
1.163 ! brouard 568: /* $Id: imach.c,v 1.162 2014/09/25 11:43:39 brouard Exp $ */
1.126 brouard 569: /* $State: Exp $ */
570:
1.162 brouard 571: char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
1.163 ! brouard 572: char fullversion[]="$Revision: 1.162 $ $Date: 2014/09/25 11:43:39 $";
1.126 brouard 573: char strstart[80];
574: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 575: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.133 brouard 576: int nvar=0, nforce=0; /* Number of variables, number of forces */
1.145 brouard 577: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
578: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
579: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
580: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
581: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
582: int cptcovprodnoage=0; /**< Number of covariate products without age */
583: int cptcoveff=0; /* Total number of covariates to vary for printing results */
584: int cptcov=0; /* Working variable */
1.126 brouard 585: int npar=NPARMAX;
586: int nlstate=2; /* Number of live states */
587: int ndeath=1; /* Number of dead states */
1.130 brouard 588: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 589: int popbased=0;
590:
591: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 592: int maxwav=0; /* Maxim number of waves */
593: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
594: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
595: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 596: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 597: int mle=1, weightopt=0;
1.126 brouard 598: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
599: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
600: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
601: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 602: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 603: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 604: double **matprod2(); /* test */
1.126 brouard 605: double **oldm, **newm, **savm; /* Working pointers to matrices */
606: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 607: /*FILE *fic ; */ /* Used in readdata only */
608: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 609: FILE *ficlog, *ficrespow;
1.130 brouard 610: int globpr=0; /* Global variable for printing or not */
1.126 brouard 611: double fretone; /* Only one call to likelihood */
1.130 brouard 612: long ipmx=0; /* Number of contributions */
1.126 brouard 613: double sw; /* Sum of weights */
614: char filerespow[FILENAMELENGTH];
615: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
616: FILE *ficresilk;
617: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
618: FILE *ficresprobmorprev;
619: FILE *fichtm, *fichtmcov; /* Html File */
620: FILE *ficreseij;
621: char filerese[FILENAMELENGTH];
622: FILE *ficresstdeij;
623: char fileresstde[FILENAMELENGTH];
624: FILE *ficrescveij;
625: char filerescve[FILENAMELENGTH];
626: FILE *ficresvij;
627: char fileresv[FILENAMELENGTH];
628: FILE *ficresvpl;
629: char fileresvpl[FILENAMELENGTH];
630: char title[MAXLINE];
631: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
632: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
633: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
634: char command[FILENAMELENGTH];
635: int outcmd=0;
636:
637: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
638:
639: char filelog[FILENAMELENGTH]; /* Log file */
640: char filerest[FILENAMELENGTH];
641: char fileregp[FILENAMELENGTH];
642: char popfile[FILENAMELENGTH];
643:
644: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
645:
1.157 brouard 646: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
647: /* struct timezone tzp; */
648: /* extern int gettimeofday(); */
649: struct tm tml, *gmtime(), *localtime();
650:
651: extern time_t time();
652:
653: struct tm start_time, end_time, curr_time, last_time, forecast_time;
654: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
655: struct tm tm;
656:
1.126 brouard 657: char strcurr[80], strfor[80];
658:
659: char *endptr;
660: long lval;
661: double dval;
662:
663: #define NR_END 1
664: #define FREE_ARG char*
665: #define FTOL 1.0e-10
666:
667: #define NRANSI
668: #define ITMAX 200
669:
670: #define TOL 2.0e-4
671:
672: #define CGOLD 0.3819660
673: #define ZEPS 1.0e-10
674: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
675:
676: #define GOLD 1.618034
677: #define GLIMIT 100.0
678: #define TINY 1.0e-20
679:
680: static double maxarg1,maxarg2;
681: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
682: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
683:
684: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
685: #define rint(a) floor(a+0.5)
686:
687: static double sqrarg;
688: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
689: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
690: int agegomp= AGEGOMP;
691:
692: int imx;
693: int stepm=1;
694: /* Stepm, step in month: minimum step interpolation*/
695:
696: int estepm;
697: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
698:
699: int m,nb;
700: long *num;
701: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
702: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
703: double **pmmij, ***probs;
704: double *ageexmed,*agecens;
705: double dateintmean=0;
706:
707: double *weight;
708: int **s; /* Status */
1.141 brouard 709: double *agedc;
1.145 brouard 710: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 711: * covar=matrix(0,NCOVMAX,1,n);
712: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
713: double idx;
714: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.145 brouard 715: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 716: int **codtab; /**< codtab=imatrix(1,100,1,10); */
717: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 718: double *lsurv, *lpop, *tpop;
719:
1.143 brouard 720: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
721: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 722:
723: /**************** split *************************/
724: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
725: {
726: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
727: the name of the file (name), its extension only (ext) and its first part of the name (finame)
728: */
729: char *ss; /* pointer */
730: int l1, l2; /* length counters */
731:
732: l1 = strlen(path ); /* length of path */
733: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
734: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
735: if ( ss == NULL ) { /* no directory, so determine current directory */
736: strcpy( name, path ); /* we got the fullname name because no directory */
737: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
738: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
739: /* get current working directory */
740: /* extern char* getcwd ( char *buf , int len);*/
741: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
742: return( GLOCK_ERROR_GETCWD );
743: }
744: /* got dirc from getcwd*/
745: printf(" DIRC = %s \n",dirc);
746: } else { /* strip direcotry from path */
747: ss++; /* after this, the filename */
748: l2 = strlen( ss ); /* length of filename */
749: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
750: strcpy( name, ss ); /* save file name */
751: strncpy( dirc, path, l1 - l2 ); /* now the directory */
752: dirc[l1-l2] = 0; /* add zero */
753: printf(" DIRC2 = %s \n",dirc);
754: }
755: /* We add a separator at the end of dirc if not exists */
756: l1 = strlen( dirc ); /* length of directory */
757: if( dirc[l1-1] != DIRSEPARATOR ){
758: dirc[l1] = DIRSEPARATOR;
759: dirc[l1+1] = 0;
760: printf(" DIRC3 = %s \n",dirc);
761: }
762: ss = strrchr( name, '.' ); /* find last / */
763: if (ss >0){
764: ss++;
765: strcpy(ext,ss); /* save extension */
766: l1= strlen( name);
767: l2= strlen(ss)+1;
768: strncpy( finame, name, l1-l2);
769: finame[l1-l2]= 0;
770: }
771:
772: return( 0 ); /* we're done */
773: }
774:
775:
776: /******************************************/
777:
778: void replace_back_to_slash(char *s, char*t)
779: {
780: int i;
781: int lg=0;
782: i=0;
783: lg=strlen(t);
784: for(i=0; i<= lg; i++) {
785: (s[i] = t[i]);
786: if (t[i]== '\\') s[i]='/';
787: }
788: }
789:
1.132 brouard 790: char *trimbb(char *out, char *in)
1.137 brouard 791: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 792: char *s;
793: s=out;
794: while (*in != '\0'){
1.137 brouard 795: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 796: in++;
797: }
798: *out++ = *in++;
799: }
800: *out='\0';
801: return s;
802: }
803:
1.145 brouard 804: char *cutl(char *blocc, char *alocc, char *in, char occ)
805: {
806: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
807: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
808: gives blocc="abcdef2ghi" and alocc="j".
809: If occ is not found blocc is null and alocc is equal to in. Returns blocc
810: */
1.160 brouard 811: char *s, *t;
1.145 brouard 812: t=in;s=in;
813: while ((*in != occ) && (*in != '\0')){
814: *alocc++ = *in++;
815: }
816: if( *in == occ){
817: *(alocc)='\0';
818: s=++in;
819: }
820:
821: if (s == t) {/* occ not found */
822: *(alocc-(in-s))='\0';
823: in=s;
824: }
825: while ( *in != '\0'){
826: *blocc++ = *in++;
827: }
828:
829: *blocc='\0';
830: return t;
831: }
1.137 brouard 832: char *cutv(char *blocc, char *alocc, char *in, char occ)
833: {
834: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
835: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
836: gives blocc="abcdef2ghi" and alocc="j".
837: If occ is not found blocc is null and alocc is equal to in. Returns alocc
838: */
839: char *s, *t;
840: t=in;s=in;
841: while (*in != '\0'){
842: while( *in == occ){
843: *blocc++ = *in++;
844: s=in;
845: }
846: *blocc++ = *in++;
847: }
848: if (s == t) /* occ not found */
849: *(blocc-(in-s))='\0';
850: else
851: *(blocc-(in-s)-1)='\0';
852: in=s;
853: while ( *in != '\0'){
854: *alocc++ = *in++;
855: }
856:
857: *alocc='\0';
858: return s;
859: }
860:
1.126 brouard 861: int nbocc(char *s, char occ)
862: {
863: int i,j=0;
864: int lg=20;
865: i=0;
866: lg=strlen(s);
867: for(i=0; i<= lg; i++) {
868: if (s[i] == occ ) j++;
869: }
870: return j;
871: }
872:
1.137 brouard 873: /* void cutv(char *u,char *v, char*t, char occ) */
874: /* { */
875: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
876: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
877: /* gives u="abcdef2ghi" and v="j" *\/ */
878: /* int i,lg,j,p=0; */
879: /* i=0; */
880: /* lg=strlen(t); */
881: /* for(j=0; j<=lg-1; j++) { */
882: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
883: /* } */
1.126 brouard 884:
1.137 brouard 885: /* for(j=0; j<p; j++) { */
886: /* (u[j] = t[j]); */
887: /* } */
888: /* u[p]='\0'; */
1.126 brouard 889:
1.137 brouard 890: /* for(j=0; j<= lg; j++) { */
891: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
892: /* } */
893: /* } */
1.126 brouard 894:
1.160 brouard 895: #ifdef _WIN32
896: char * strsep(char **pp, const char *delim)
897: {
898: char *p, *q;
899:
900: if ((p = *pp) == NULL)
901: return 0;
902: if ((q = strpbrk (p, delim)) != NULL)
903: {
904: *pp = q + 1;
905: *q = '\0';
906: }
907: else
908: *pp = 0;
909: return p;
910: }
911: #endif
912:
1.126 brouard 913: /********************** nrerror ********************/
914:
915: void nrerror(char error_text[])
916: {
917: fprintf(stderr,"ERREUR ...\n");
918: fprintf(stderr,"%s\n",error_text);
919: exit(EXIT_FAILURE);
920: }
921: /*********************** vector *******************/
922: double *vector(int nl, int nh)
923: {
924: double *v;
925: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
926: if (!v) nrerror("allocation failure in vector");
927: return v-nl+NR_END;
928: }
929:
930: /************************ free vector ******************/
931: void free_vector(double*v, int nl, int nh)
932: {
933: free((FREE_ARG)(v+nl-NR_END));
934: }
935:
936: /************************ivector *******************************/
937: int *ivector(long nl,long nh)
938: {
939: int *v;
940: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
941: if (!v) nrerror("allocation failure in ivector");
942: return v-nl+NR_END;
943: }
944:
945: /******************free ivector **************************/
946: void free_ivector(int *v, long nl, long nh)
947: {
948: free((FREE_ARG)(v+nl-NR_END));
949: }
950:
951: /************************lvector *******************************/
952: long *lvector(long nl,long nh)
953: {
954: long *v;
955: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
956: if (!v) nrerror("allocation failure in ivector");
957: return v-nl+NR_END;
958: }
959:
960: /******************free lvector **************************/
961: void free_lvector(long *v, long nl, long nh)
962: {
963: free((FREE_ARG)(v+nl-NR_END));
964: }
965:
966: /******************* imatrix *******************************/
967: int **imatrix(long nrl, long nrh, long ncl, long nch)
968: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
969: {
970: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
971: int **m;
972:
973: /* allocate pointers to rows */
974: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
975: if (!m) nrerror("allocation failure 1 in matrix()");
976: m += NR_END;
977: m -= nrl;
978:
979:
980: /* allocate rows and set pointers to them */
981: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
982: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
983: m[nrl] += NR_END;
984: m[nrl] -= ncl;
985:
986: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
987:
988: /* return pointer to array of pointers to rows */
989: return m;
990: }
991:
992: /****************** free_imatrix *************************/
993: void free_imatrix(m,nrl,nrh,ncl,nch)
994: int **m;
995: long nch,ncl,nrh,nrl;
996: /* free an int matrix allocated by imatrix() */
997: {
998: free((FREE_ARG) (m[nrl]+ncl-NR_END));
999: free((FREE_ARG) (m+nrl-NR_END));
1000: }
1001:
1002: /******************* matrix *******************************/
1003: double **matrix(long nrl, long nrh, long ncl, long nch)
1004: {
1005: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1006: double **m;
1007:
1008: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1009: if (!m) nrerror("allocation failure 1 in matrix()");
1010: m += NR_END;
1011: m -= nrl;
1012:
1013: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1014: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1015: m[nrl] += NR_END;
1016: m[nrl] -= ncl;
1017:
1018: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1019: return m;
1.145 brouard 1020: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1021: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1022: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1023: */
1024: }
1025:
1026: /*************************free matrix ************************/
1027: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1028: {
1029: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1030: free((FREE_ARG)(m+nrl-NR_END));
1031: }
1032:
1033: /******************* ma3x *******************************/
1034: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1035: {
1036: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1037: double ***m;
1038:
1039: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1040: if (!m) nrerror("allocation failure 1 in matrix()");
1041: m += NR_END;
1042: m -= nrl;
1043:
1044: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1045: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1046: m[nrl] += NR_END;
1047: m[nrl] -= ncl;
1048:
1049: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1050:
1051: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1052: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1053: m[nrl][ncl] += NR_END;
1054: m[nrl][ncl] -= nll;
1055: for (j=ncl+1; j<=nch; j++)
1056: m[nrl][j]=m[nrl][j-1]+nlay;
1057:
1058: for (i=nrl+1; i<=nrh; i++) {
1059: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1060: for (j=ncl+1; j<=nch; j++)
1061: m[i][j]=m[i][j-1]+nlay;
1062: }
1063: return m;
1064: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1065: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1066: */
1067: }
1068:
1069: /*************************free ma3x ************************/
1070: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1071: {
1072: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1073: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1074: free((FREE_ARG)(m+nrl-NR_END));
1075: }
1076:
1077: /*************** function subdirf ***********/
1078: char *subdirf(char fileres[])
1079: {
1080: /* Caution optionfilefiname is hidden */
1081: strcpy(tmpout,optionfilefiname);
1082: strcat(tmpout,"/"); /* Add to the right */
1083: strcat(tmpout,fileres);
1084: return tmpout;
1085: }
1086:
1087: /*************** function subdirf2 ***********/
1088: char *subdirf2(char fileres[], char *preop)
1089: {
1090:
1091: /* Caution optionfilefiname is hidden */
1092: strcpy(tmpout,optionfilefiname);
1093: strcat(tmpout,"/");
1094: strcat(tmpout,preop);
1095: strcat(tmpout,fileres);
1096: return tmpout;
1097: }
1098:
1099: /*************** function subdirf3 ***********/
1100: char *subdirf3(char fileres[], char *preop, char *preop2)
1101: {
1102:
1103: /* Caution optionfilefiname is hidden */
1104: strcpy(tmpout,optionfilefiname);
1105: strcat(tmpout,"/");
1106: strcat(tmpout,preop);
1107: strcat(tmpout,preop2);
1108: strcat(tmpout,fileres);
1109: return tmpout;
1110: }
1111:
1.162 brouard 1112: char *asc_diff_time(long time_sec, char ascdiff[])
1113: {
1114: long sec_left, days, hours, minutes;
1115: days = (time_sec) / (60*60*24);
1116: sec_left = (time_sec) % (60*60*24);
1117: hours = (sec_left) / (60*60) ;
1118: sec_left = (sec_left) %(60*60);
1119: minutes = (sec_left) /60;
1120: sec_left = (sec_left) % (60);
1121: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1122: return ascdiff;
1123: }
1124:
1.126 brouard 1125: /***************** f1dim *************************/
1126: extern int ncom;
1127: extern double *pcom,*xicom;
1128: extern double (*nrfunc)(double []);
1129:
1130: double f1dim(double x)
1131: {
1132: int j;
1133: double f;
1134: double *xt;
1135:
1136: xt=vector(1,ncom);
1137: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1138: f=(*nrfunc)(xt);
1139: free_vector(xt,1,ncom);
1140: return f;
1141: }
1142:
1143: /*****************brent *************************/
1144: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1145: {
1146: int iter;
1147: double a,b,d,etemp;
1.159 brouard 1148: double fu=0,fv,fw,fx;
1.126 brouard 1149: double ftemp;
1150: double p,q,r,tol1,tol2,u,v,w,x,xm;
1151: double e=0.0;
1152:
1153: a=(ax < cx ? ax : cx);
1154: b=(ax > cx ? ax : cx);
1155: x=w=v=bx;
1156: fw=fv=fx=(*f)(x);
1157: for (iter=1;iter<=ITMAX;iter++) {
1158: xm=0.5*(a+b);
1159: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1160: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1161: printf(".");fflush(stdout);
1162: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1163: #ifdef DEBUGBRENT
1.126 brouard 1164: 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);
1165: 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);
1166: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1167: #endif
1168: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1169: *xmin=x;
1170: return fx;
1171: }
1172: ftemp=fu;
1173: if (fabs(e) > tol1) {
1174: r=(x-w)*(fx-fv);
1175: q=(x-v)*(fx-fw);
1176: p=(x-v)*q-(x-w)*r;
1177: q=2.0*(q-r);
1178: if (q > 0.0) p = -p;
1179: q=fabs(q);
1180: etemp=e;
1181: e=d;
1182: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1183: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1184: else {
1185: d=p/q;
1186: u=x+d;
1187: if (u-a < tol2 || b-u < tol2)
1188: d=SIGN(tol1,xm-x);
1189: }
1190: } else {
1191: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1192: }
1193: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1194: fu=(*f)(u);
1195: if (fu <= fx) {
1196: if (u >= x) a=x; else b=x;
1197: SHFT(v,w,x,u)
1198: SHFT(fv,fw,fx,fu)
1199: } else {
1200: if (u < x) a=u; else b=u;
1201: if (fu <= fw || w == x) {
1202: v=w;
1203: w=u;
1204: fv=fw;
1205: fw=fu;
1206: } else if (fu <= fv || v == x || v == w) {
1207: v=u;
1208: fv=fu;
1209: }
1210: }
1211: }
1212: nrerror("Too many iterations in brent");
1213: *xmin=x;
1214: return fx;
1215: }
1216:
1217: /****************** mnbrak ***********************/
1218:
1219: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1220: double (*func)(double))
1221: {
1222: double ulim,u,r,q, dum;
1223: double fu;
1224:
1225: *fa=(*func)(*ax);
1226: *fb=(*func)(*bx);
1227: if (*fb > *fa) {
1228: SHFT(dum,*ax,*bx,dum)
1229: SHFT(dum,*fb,*fa,dum)
1230: }
1231: *cx=(*bx)+GOLD*(*bx-*ax);
1232: *fc=(*func)(*cx);
1.162 brouard 1233: while (*fb > *fc) { /* Declining fa, fb, fc */
1.126 brouard 1234: r=(*bx-*ax)*(*fb-*fc);
1235: q=(*bx-*cx)*(*fb-*fa);
1236: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.162 brouard 1237: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1238: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1239: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1.126 brouard 1240: fu=(*func)(u);
1.163 ! brouard 1241: #ifdef DEBUG
! 1242: /* f(x)=A(x-u)**2+f(u) */
! 1243: double A, fparabu;
! 1244: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
! 1245: fparabu= *fa - A*(*ax-u)*(*ax-u);
! 1246: printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
! 1247: fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
! 1248: #endif
1.162 brouard 1249: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.126 brouard 1250: fu=(*func)(u);
1251: if (fu < *fc) {
1252: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1253: SHFT(*fb,*fc,fu,(*func)(u))
1254: }
1.162 brouard 1255: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.126 brouard 1256: u=ulim;
1257: fu=(*func)(u);
1258: } else {
1259: u=(*cx)+GOLD*(*cx-*bx);
1260: fu=(*func)(u);
1261: }
1262: SHFT(*ax,*bx,*cx,u)
1263: SHFT(*fa,*fb,*fc,fu)
1264: }
1265: }
1266:
1267: /*************** linmin ************************/
1.162 brouard 1268: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1269: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1270: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1271: the value of func at the returned location p . This is actually all accomplished by calling the
1272: routines mnbrak and brent .*/
1.126 brouard 1273: int ncom;
1274: double *pcom,*xicom;
1275: double (*nrfunc)(double []);
1276:
1277: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1278: {
1279: double brent(double ax, double bx, double cx,
1280: double (*f)(double), double tol, double *xmin);
1281: double f1dim(double x);
1282: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1283: double *fc, double (*func)(double));
1284: int j;
1285: double xx,xmin,bx,ax;
1286: double fx,fb,fa;
1287:
1288: ncom=n;
1289: pcom=vector(1,n);
1290: xicom=vector(1,n);
1291: nrfunc=func;
1292: for (j=1;j<=n;j++) {
1293: pcom[j]=p[j];
1294: xicom[j]=xi[j];
1295: }
1296: ax=0.0;
1297: xx=1.0;
1.162 brouard 1298: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1299: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1.126 brouard 1300: #ifdef DEBUG
1301: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1302: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1303: #endif
1304: for (j=1;j<=n;j++) {
1305: xi[j] *= xmin;
1306: p[j] += xi[j];
1307: }
1308: free_vector(xicom,1,n);
1309: free_vector(pcom,1,n);
1310: }
1311:
1312:
1313: /*************** powell ************************/
1.162 brouard 1314: /*
1315: Minimization of a function func of n variables. Input consists of an initial starting point
1316: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1317: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1318: such that failure to decrease by more than this amount on one iteration signals doneness. On
1319: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1320: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1321: */
1.126 brouard 1322: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1323: double (*func)(double []))
1324: {
1325: void linmin(double p[], double xi[], int n, double *fret,
1326: double (*func)(double []));
1327: int i,ibig,j;
1328: double del,t,*pt,*ptt,*xit;
1329: double fp,fptt;
1330: double *xits;
1331: int niterf, itmp;
1332:
1333: pt=vector(1,n);
1334: ptt=vector(1,n);
1335: xit=vector(1,n);
1336: xits=vector(1,n);
1337: *fret=(*func)(p);
1338: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1339: rcurr_time = time(NULL);
1.126 brouard 1340: for (*iter=1;;++(*iter)) {
1341: fp=(*fret);
1342: ibig=0;
1343: del=0.0;
1.157 brouard 1344: rlast_time=rcurr_time;
1345: /* (void) gettimeofday(&curr_time,&tzp); */
1346: rcurr_time = time(NULL);
1347: curr_time = *localtime(&rcurr_time);
1348: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1349: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1350: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.126 brouard 1351: for (i=1;i<=n;i++) {
1352: printf(" %d %.12f",i, p[i]);
1353: fprintf(ficlog," %d %.12lf",i, p[i]);
1354: fprintf(ficrespow," %.12lf", p[i]);
1355: }
1356: printf("\n");
1357: fprintf(ficlog,"\n");
1358: fprintf(ficrespow,"\n");fflush(ficrespow);
1359: if(*iter <=3){
1.157 brouard 1360: tml = *localtime(&rcurr_time);
1361: strcpy(strcurr,asctime(&tml));
1362: rforecast_time=rcurr_time;
1.126 brouard 1363: itmp = strlen(strcurr);
1364: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1365: strcurr[itmp-1]='\0';
1.162 brouard 1366: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1367: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1368: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1369: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1370: forecast_time = *localtime(&rforecast_time);
1371: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1372: itmp = strlen(strfor);
1373: if(strfor[itmp-1]=='\n')
1374: strfor[itmp-1]='\0';
1.157 brouard 1375: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1376: 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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126 brouard 1377: }
1378: }
1379: for (i=1;i<=n;i++) {
1380: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1381: fptt=(*fret);
1382: #ifdef DEBUG
1383: printf("fret=%lf \n",*fret);
1384: fprintf(ficlog,"fret=%lf \n",*fret);
1385: #endif
1386: printf("%d",i);fflush(stdout);
1387: fprintf(ficlog,"%d",i);fflush(ficlog);
1388: linmin(p,xit,n,fret,func);
1389: if (fabs(fptt-(*fret)) > del) {
1390: del=fabs(fptt-(*fret));
1391: ibig=i;
1392: }
1393: #ifdef DEBUG
1394: printf("%d %.12e",i,(*fret));
1395: fprintf(ficlog,"%d %.12e",i,(*fret));
1396: for (j=1;j<=n;j++) {
1397: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1398: printf(" x(%d)=%.12e",j,xit[j]);
1399: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1400: }
1401: for(j=1;j<=n;j++) {
1.162 brouard 1402: printf(" p(%d)=%.12e",j,p[j]);
1403: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1404: }
1405: printf("\n");
1406: fprintf(ficlog,"\n");
1407: #endif
1.162 brouard 1408: } /* end i */
1.126 brouard 1409: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1410: #ifdef DEBUG
1411: int k[2],l;
1412: k[0]=1;
1413: k[1]=-1;
1414: printf("Max: %.12e",(*func)(p));
1415: fprintf(ficlog,"Max: %.12e",(*func)(p));
1416: for (j=1;j<=n;j++) {
1417: printf(" %.12e",p[j]);
1418: fprintf(ficlog," %.12e",p[j]);
1419: }
1420: printf("\n");
1421: fprintf(ficlog,"\n");
1422: for(l=0;l<=1;l++) {
1423: for (j=1;j<=n;j++) {
1424: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1425: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1426: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1427: }
1428: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1429: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1430: }
1431: #endif
1432:
1433:
1434: free_vector(xit,1,n);
1435: free_vector(xits,1,n);
1436: free_vector(ptt,1,n);
1437: free_vector(pt,1,n);
1438: return;
1439: }
1440: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.161 brouard 1441: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1.126 brouard 1442: ptt[j]=2.0*p[j]-pt[j];
1443: xit[j]=p[j]-pt[j];
1444: pt[j]=p[j];
1445: }
1446: fptt=(*func)(ptt);
1.161 brouard 1447: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.162 brouard 1448: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1449: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1450: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1451: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1452: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.161 brouard 1453: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1454: /* Thus we compare delta(2h) with observed f1-f3 */
1.162 brouard 1455: /* or best gain on one ancient line 'del' with total */
1456: /* gain f1-f2 = f1 - f2 - 'del' with del */
1.161 brouard 1457: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.162 brouard 1458:
1.161 brouard 1459: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1460: t= t- del*SQR(fp-fptt);
1461: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1462: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1463: #ifdef DEBUG
1464: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1465: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1466: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1467: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1468: printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1469: fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
1470: #endif
1471: if (t < 0.0) { /* Then we use it for last direction */
1472: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1.126 brouard 1473: for (j=1;j<=n;j++) {
1.161 brouard 1474: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1475: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1.126 brouard 1476: }
1.161 brouard 1477: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1478: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
1479:
1.126 brouard 1480: #ifdef DEBUG
1481: for(j=1;j<=n;j++){
1482: printf(" %.12e",xit[j]);
1483: fprintf(ficlog," %.12e",xit[j]);
1484: }
1485: printf("\n");
1486: fprintf(ficlog,"\n");
1487: #endif
1.162 brouard 1488: } /* end of t negative */
1489: } /* end if (fptt < fp) */
1.126 brouard 1490: }
1491: }
1492:
1493: /**** Prevalence limit (stable or period prevalence) ****************/
1494:
1495: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1496: {
1497: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1498: matrix by transitions matrix until convergence is reached */
1499:
1500: int i, ii,j,k;
1501: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1502: /* double **matprod2(); */ /* test */
1.131 brouard 1503: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1504: double **newm;
1505: double agefin, delaymax=50 ; /* Max number of years to converge */
1506:
1507: for (ii=1;ii<=nlstate+ndeath;ii++)
1508: for (j=1;j<=nlstate+ndeath;j++){
1509: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1510: }
1511:
1512: cov[1]=1.;
1513:
1514: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1515: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1516: newm=savm;
1517: /* Covariates have to be included here again */
1.138 brouard 1518: cov[2]=agefin;
1519:
1520: for (k=1; k<=cptcovn;k++) {
1521: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.145 brouard 1522: /*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 1523: }
1.145 brouard 1524: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1525: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1526: /* 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 1527:
1528: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1529: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1530: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1531: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1532: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1533: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1534:
1.126 brouard 1535: savm=oldm;
1536: oldm=newm;
1537: maxmax=0.;
1538: for(j=1;j<=nlstate;j++){
1539: min=1.;
1540: max=0.;
1541: for(i=1; i<=nlstate; i++) {
1542: sumnew=0;
1543: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1544: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1545: /*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 1546: max=FMAX(max,prlim[i][j]);
1547: min=FMIN(min,prlim[i][j]);
1548: }
1549: maxmin=max-min;
1550: maxmax=FMAX(maxmax,maxmin);
1551: }
1552: if(maxmax < ftolpl){
1553: return prlim;
1554: }
1555: }
1556: }
1557:
1558: /*************** transition probabilities ***************/
1559:
1560: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1561: {
1.138 brouard 1562: /* According to parameters values stored in x and the covariate's values stored in cov,
1563: computes the probability to be observed in state j being in state i by appying the
1564: model to the ncovmodel covariates (including constant and age).
1565: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1566: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1567: ncth covariate in the global vector x is given by the formula:
1568: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1569: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1570: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1571: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1572: Outputs ps[i][j] the probability to be observed in j being in j according to
1573: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1574: */
1575: double s1, lnpijopii;
1.126 brouard 1576: /*double t34;*/
1577: int i,j,j1, nc, ii, jj;
1578:
1579: for(i=1; i<= nlstate; i++){
1580: for(j=1; j<i;j++){
1.138 brouard 1581: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1582: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1583: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1584: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1585: }
1.138 brouard 1586: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1587: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1588: }
1589: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1590: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1591: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1592: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1593: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1594: }
1.138 brouard 1595: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1596: }
1597: }
1598:
1599: for(i=1; i<= nlstate; i++){
1600: s1=0;
1.131 brouard 1601: for(j=1; j<i; j++){
1.138 brouard 1602: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1603: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1604: }
1605: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1606: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1607: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1608: }
1.138 brouard 1609: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 1610: ps[i][i]=1./(s1+1.);
1.138 brouard 1611: /* Computing other pijs */
1.126 brouard 1612: for(j=1; j<i; j++)
1613: ps[i][j]= exp(ps[i][j])*ps[i][i];
1614: for(j=i+1; j<=nlstate+ndeath; j++)
1615: ps[i][j]= exp(ps[i][j])*ps[i][i];
1616: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1617: } /* end i */
1618:
1619: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1620: for(jj=1; jj<= nlstate+ndeath; jj++){
1621: ps[ii][jj]=0;
1622: ps[ii][ii]=1;
1623: }
1624: }
1625:
1.145 brouard 1626:
1627: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1628: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1629: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1630: /* } */
1631: /* printf("\n "); */
1632: /* } */
1633: /* printf("\n ");printf("%lf ",cov[2]);*/
1634: /*
1.126 brouard 1635: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1636: goto end;*/
1637: return ps;
1638: }
1639:
1640: /**************** Product of 2 matrices ******************/
1641:
1.145 brouard 1642: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 1643: {
1644: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1645: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1646: /* in, b, out are matrice of pointers which should have been initialized
1647: before: only the contents of out is modified. The function returns
1648: a pointer to pointers identical to out */
1.145 brouard 1649: int i, j, k;
1.126 brouard 1650: for(i=nrl; i<= nrh; i++)
1.145 brouard 1651: for(k=ncolol; k<=ncoloh; k++){
1652: out[i][k]=0.;
1653: for(j=ncl; j<=nch; j++)
1654: out[i][k] +=in[i][j]*b[j][k];
1655: }
1.126 brouard 1656: return out;
1657: }
1658:
1659:
1660: /************* Higher Matrix Product ***************/
1661:
1662: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1663: {
1664: /* Computes the transition matrix starting at age 'age' over
1665: 'nhstepm*hstepm*stepm' months (i.e. until
1666: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1667: nhstepm*hstepm matrices.
1668: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1669: (typically every 2 years instead of every month which is too big
1670: for the memory).
1671: Model is determined by parameters x and covariates have to be
1672: included manually here.
1673:
1674: */
1675:
1676: int i, j, d, h, k;
1.131 brouard 1677: double **out, cov[NCOVMAX+1];
1.126 brouard 1678: double **newm;
1679:
1680: /* Hstepm could be zero and should return the unit matrix */
1681: for (i=1;i<=nlstate+ndeath;i++)
1682: for (j=1;j<=nlstate+ndeath;j++){
1683: oldm[i][j]=(i==j ? 1.0 : 0.0);
1684: po[i][j][0]=(i==j ? 1.0 : 0.0);
1685: }
1686: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1687: for(h=1; h <=nhstepm; h++){
1688: for(d=1; d <=hstepm; d++){
1689: newm=savm;
1690: /* Covariates have to be included here again */
1691: cov[1]=1.;
1692: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1.131 brouard 1693: for (k=1; k<=cptcovn;k++)
1694: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.126 brouard 1695: for (k=1; k<=cptcovage;k++)
1696: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1.145 brouard 1697: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.126 brouard 1698: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1699:
1700:
1701: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1702: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1703: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1704: pmij(pmmij,cov,ncovmodel,x,nlstate));
1705: savm=oldm;
1706: oldm=newm;
1707: }
1708: for(i=1; i<=nlstate+ndeath; i++)
1709: for(j=1;j<=nlstate+ndeath;j++) {
1710: po[i][j][h]=newm[i][j];
1.128 brouard 1711: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 1712: }
1.128 brouard 1713: /*printf("h=%d ",h);*/
1.126 brouard 1714: } /* end h */
1.128 brouard 1715: /* printf("\n H=%d \n",h); */
1.126 brouard 1716: return po;
1717: }
1718:
1.162 brouard 1719: #ifdef NLOPT
1720: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1721: double fret;
1722: double *xt;
1723: int j;
1724: myfunc_data *d2 = (myfunc_data *) pd;
1725: /* xt = (p1-1); */
1726: xt=vector(1,n);
1727: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1728:
1729: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1730: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1731: printf("Function = %.12lf ",fret);
1732: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1733: printf("\n");
1734: free_vector(xt,1,n);
1735: return fret;
1736: }
1737: #endif
1.126 brouard 1738:
1739: /*************** log-likelihood *************/
1740: double func( double *x)
1741: {
1742: int i, ii, j, k, mi, d, kk;
1.131 brouard 1743: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 1744: double **out;
1745: double sw; /* Sum of weights */
1746: double lli; /* Individual log likelihood */
1747: int s1, s2;
1748: double bbh, survp;
1749: long ipmx;
1750: /*extern weight */
1751: /* We are differentiating ll according to initial status */
1752: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1753: /*for(i=1;i<imx;i++)
1754: printf(" %d\n",s[4][i]);
1755: */
1.162 brouard 1756:
1757: ++countcallfunc;
1758:
1.126 brouard 1759: cov[1]=1.;
1760:
1761: for(k=1; k<=nlstate; k++) ll[k]=0.;
1762:
1763: if(mle==1){
1764: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 1765: /* Computes the values of the ncovmodel covariates of the model
1766: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1767: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1768: to be observed in j being in i according to the model.
1769: */
1.145 brouard 1770: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1771: cov[2+k]=covar[Tvar[k]][i];
1772: }
1.137 brouard 1773: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 1774: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 1775: has been calculated etc */
1.126 brouard 1776: for(mi=1; mi<= wav[i]-1; mi++){
1777: for (ii=1;ii<=nlstate+ndeath;ii++)
1778: for (j=1;j<=nlstate+ndeath;j++){
1779: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1780: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1781: }
1782: for(d=0; d<dh[mi][i]; d++){
1783: newm=savm;
1784: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1785: for (kk=1; kk<=cptcovage;kk++) {
1.137 brouard 1786: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 1787: }
1788: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1789: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1790: savm=oldm;
1791: oldm=newm;
1792: } /* end mult */
1793:
1794: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1795: /* But now since version 0.9 we anticipate for bias at large stepm.
1796: * If stepm is larger than one month (smallest stepm) and if the exact delay
1797: * (in months) between two waves is not a multiple of stepm, we rounded to
1798: * the nearest (and in case of equal distance, to the lowest) interval but now
1799: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1800: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1801: * probability in order to take into account the bias as a fraction of the way
1802: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1803: * -stepm/2 to stepm/2 .
1804: * For stepm=1 the results are the same as for previous versions of Imach.
1805: * For stepm > 1 the results are less biased than in previous versions.
1806: */
1807: s1=s[mw[mi][i]][i];
1808: s2=s[mw[mi+1][i]][i];
1809: bbh=(double)bh[mi][i]/(double)stepm;
1810: /* bias bh is positive if real duration
1811: * is higher than the multiple of stepm and negative otherwise.
1812: */
1813: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1814: if( s2 > nlstate){
1815: /* i.e. if s2 is a death state and if the date of death is known
1816: then the contribution to the likelihood is the probability to
1817: die between last step unit time and current step unit time,
1818: which is also equal to probability to die before dh
1819: minus probability to die before dh-stepm .
1820: In version up to 0.92 likelihood was computed
1821: as if date of death was unknown. Death was treated as any other
1822: health state: the date of the interview describes the actual state
1823: and not the date of a change in health state. The former idea was
1824: to consider that at each interview the state was recorded
1825: (healthy, disable or death) and IMaCh was corrected; but when we
1826: introduced the exact date of death then we should have modified
1827: the contribution of an exact death to the likelihood. This new
1828: contribution is smaller and very dependent of the step unit
1829: stepm. It is no more the probability to die between last interview
1830: and month of death but the probability to survive from last
1831: interview up to one month before death multiplied by the
1832: probability to die within a month. Thanks to Chris
1833: Jackson for correcting this bug. Former versions increased
1834: mortality artificially. The bad side is that we add another loop
1835: which slows down the processing. The difference can be up to 10%
1836: lower mortality.
1837: */
1838: lli=log(out[s1][s2] - savm[s1][s2]);
1839:
1840:
1841: } else if (s2==-2) {
1842: for (j=1,survp=0. ; j<=nlstate; j++)
1843: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1844: /*survp += out[s1][j]; */
1845: lli= log(survp);
1846: }
1847:
1848: else if (s2==-4) {
1849: for (j=3,survp=0. ; j<=nlstate; j++)
1850: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1851: lli= log(survp);
1852: }
1853:
1854: else if (s2==-5) {
1855: for (j=1,survp=0. ; j<=2; j++)
1856: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1857: lli= log(survp);
1858: }
1859:
1860: else{
1861: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1862: /* 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 */
1863: }
1864: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1865: /*if(lli ==000.0)*/
1866: /*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); */
1867: ipmx +=1;
1868: sw += weight[i];
1869: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1870: } /* end of wave */
1871: } /* end of individual */
1872: } else if(mle==2){
1873: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1874: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1875: for(mi=1; mi<= wav[i]-1; mi++){
1876: for (ii=1;ii<=nlstate+ndeath;ii++)
1877: for (j=1;j<=nlstate+ndeath;j++){
1878: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1879: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1880: }
1881: for(d=0; d<=dh[mi][i]; d++){
1882: newm=savm;
1883: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1884: for (kk=1; kk<=cptcovage;kk++) {
1885: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1886: }
1887: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1888: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
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: 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 */
1897: ipmx +=1;
1898: sw += weight[i];
1899: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1900: } /* end of wave */
1901: } /* end of individual */
1902: } else if(mle==3){ /* exponential inter-extrapolation */
1903: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1904: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1905: for(mi=1; mi<= wav[i]-1; mi++){
1906: for (ii=1;ii<=nlstate+ndeath;ii++)
1907: for (j=1;j<=nlstate+ndeath;j++){
1908: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1909: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1910: }
1911: for(d=0; d<dh[mi][i]; d++){
1912: newm=savm;
1913: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1914: for (kk=1; kk<=cptcovage;kk++) {
1915: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1916: }
1917: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1918: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1919: savm=oldm;
1920: oldm=newm;
1921: } /* end mult */
1922:
1923: s1=s[mw[mi][i]][i];
1924: s2=s[mw[mi+1][i]][i];
1925: bbh=(double)bh[mi][i]/(double)stepm;
1926: 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 */
1927: ipmx +=1;
1928: sw += weight[i];
1929: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1930: } /* end of wave */
1931: } /* end of individual */
1932: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1933: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1934: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1935: for(mi=1; mi<= wav[i]-1; mi++){
1936: for (ii=1;ii<=nlstate+ndeath;ii++)
1937: for (j=1;j<=nlstate+ndeath;j++){
1938: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1939: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1940: }
1941: for(d=0; d<dh[mi][i]; d++){
1942: newm=savm;
1943: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1944: for (kk=1; kk<=cptcovage;kk++) {
1945: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1946: }
1947:
1948: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1949: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1950: savm=oldm;
1951: oldm=newm;
1952: } /* end mult */
1953:
1954: s1=s[mw[mi][i]][i];
1955: s2=s[mw[mi+1][i]][i];
1956: if( s2 > nlstate){
1957: lli=log(out[s1][s2] - savm[s1][s2]);
1958: }else{
1959: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1960: }
1961: ipmx +=1;
1962: sw += weight[i];
1963: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1964: /* 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]); */
1965: } /* end of wave */
1966: } /* end of individual */
1967: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
1968: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1969: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1970: for(mi=1; mi<= wav[i]-1; mi++){
1971: for (ii=1;ii<=nlstate+ndeath;ii++)
1972: for (j=1;j<=nlstate+ndeath;j++){
1973: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1974: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1975: }
1976: for(d=0; d<dh[mi][i]; d++){
1977: newm=savm;
1978: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1979: for (kk=1; kk<=cptcovage;kk++) {
1980: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1981: }
1982:
1983: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1984: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1985: savm=oldm;
1986: oldm=newm;
1987: } /* end mult */
1988:
1989: s1=s[mw[mi][i]][i];
1990: s2=s[mw[mi+1][i]][i];
1991: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
1992: ipmx +=1;
1993: sw += weight[i];
1994: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1995: /*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]);*/
1996: } /* end of wave */
1997: } /* end of individual */
1998: } /* End of if */
1999: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2000: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2001: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2002: return -l;
2003: }
2004:
2005: /*************** log-likelihood *************/
2006: double funcone( double *x)
2007: {
2008: /* Same as likeli but slower because of a lot of printf and if */
2009: int i, ii, j, k, mi, d, kk;
1.131 brouard 2010: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2011: double **out;
2012: double lli; /* Individual log likelihood */
2013: double llt;
2014: int s1, s2;
2015: double bbh, survp;
2016: /*extern weight */
2017: /* We are differentiating ll according to initial status */
2018: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2019: /*for(i=1;i<imx;i++)
2020: printf(" %d\n",s[4][i]);
2021: */
2022: cov[1]=1.;
2023:
2024: for(k=1; k<=nlstate; k++) ll[k]=0.;
2025:
2026: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2027: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2028: for(mi=1; mi<= wav[i]-1; mi++){
2029: for (ii=1;ii<=nlstate+ndeath;ii++)
2030: for (j=1;j<=nlstate+ndeath;j++){
2031: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2032: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2033: }
2034: for(d=0; d<dh[mi][i]; d++){
2035: newm=savm;
2036: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2037: for (kk=1; kk<=cptcovage;kk++) {
2038: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2039: }
1.145 brouard 2040: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2041: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2042: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2043: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2044: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2045: savm=oldm;
2046: oldm=newm;
2047: } /* end mult */
2048:
2049: s1=s[mw[mi][i]][i];
2050: s2=s[mw[mi+1][i]][i];
2051: bbh=(double)bh[mi][i]/(double)stepm;
2052: /* bias is positive if real duration
2053: * is higher than the multiple of stepm and negative otherwise.
2054: */
2055: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2056: lli=log(out[s1][s2] - savm[s1][s2]);
2057: } else if (s2==-2) {
2058: for (j=1,survp=0. ; j<=nlstate; j++)
2059: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2060: lli= log(survp);
2061: }else if (mle==1){
2062: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2063: } else if(mle==2){
2064: 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 */
2065: } else if(mle==3){ /* exponential inter-extrapolation */
2066: 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 */
2067: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2068: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2069: } else{ /* mle=0 back to 1 */
2070: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2071: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2072: } /* End of if */
2073: ipmx +=1;
2074: sw += weight[i];
2075: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2076: /*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 2077: if(globpr){
1.141 brouard 2078: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2079: %11.6f %11.6f %11.6f ", \
2080: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2081: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2082: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2083: llt +=ll[k]*gipmx/gsw;
2084: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2085: }
2086: fprintf(ficresilk," %10.6f\n", -llt);
2087: }
2088: } /* end of wave */
2089: } /* end of individual */
2090: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2091: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2092: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2093: if(globpr==0){ /* First time we count the contributions and weights */
2094: gipmx=ipmx;
2095: gsw=sw;
2096: }
2097: return -l;
2098: }
2099:
2100:
2101: /*************** function likelione ***********/
2102: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2103: {
2104: /* This routine should help understanding what is done with
2105: the selection of individuals/waves and
2106: to check the exact contribution to the likelihood.
2107: Plotting could be done.
2108: */
2109: int k;
2110:
2111: if(*globpri !=0){ /* Just counts and sums, no printings */
2112: strcpy(fileresilk,"ilk");
2113: strcat(fileresilk,fileres);
2114: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2115: printf("Problem with resultfile: %s\n", fileresilk);
2116: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2117: }
2118: 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");
2119: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2120: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2121: for(k=1; k<=nlstate; k++)
2122: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2123: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2124: }
2125:
2126: *fretone=(*funcone)(p);
2127: if(*globpri !=0){
2128: fclose(ficresilk);
2129: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2130: fflush(fichtm);
2131: }
2132: return;
2133: }
2134:
2135:
2136: /*********** Maximum Likelihood Estimation ***************/
2137:
2138: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2139: {
2140: int i,j, iter;
2141: double **xi;
2142: double fret;
2143: double fretone; /* Only one call to likelihood */
2144: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2145:
2146: #ifdef NLOPT
2147: int creturn;
2148: nlopt_opt opt;
2149: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2150: double *lb;
2151: double minf; /* the minimum objective value, upon return */
2152: double * p1; /* Shifted parameters from 0 instead of 1 */
2153: myfunc_data dinst, *d = &dinst;
2154: #endif
2155:
2156:
1.126 brouard 2157: xi=matrix(1,npar,1,npar);
2158: for (i=1;i<=npar;i++)
2159: for (j=1;j<=npar;j++)
2160: xi[i][j]=(i==j ? 1.0 : 0.0);
2161: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2162: strcpy(filerespow,"pow");
2163: strcat(filerespow,fileres);
2164: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2165: printf("Problem with resultfile: %s\n", filerespow);
2166: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2167: }
2168: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2169: for (i=1;i<=nlstate;i++)
2170: for(j=1;j<=nlstate+ndeath;j++)
2171: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2172: fprintf(ficrespow,"\n");
1.162 brouard 2173: #ifdef POWELL
1.126 brouard 2174: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2175: #endif
1.126 brouard 2176:
1.162 brouard 2177: #ifdef NLOPT
2178: #ifdef NEWUOA
2179: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2180: #else
2181: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2182: #endif
2183: lb=vector(0,npar-1);
2184: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2185: nlopt_set_lower_bounds(opt, lb);
2186: nlopt_set_initial_step1(opt, 0.1);
2187:
2188: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2189: d->function = func;
2190: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2191: nlopt_set_min_objective(opt, myfunc, d);
2192: nlopt_set_xtol_rel(opt, ftol);
2193: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2194: printf("nlopt failed! %d\n",creturn);
2195: }
2196: else {
2197: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2198: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2199: iter=1; /* not equal */
2200: }
2201: nlopt_destroy(opt);
2202: #endif
1.126 brouard 2203: free_matrix(xi,1,npar,1,npar);
2204: fclose(ficrespow);
1.162 brouard 2205: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2206: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2207: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2208:
2209: }
2210:
2211: /**** Computes Hessian and covariance matrix ***/
2212: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2213: {
2214: double **a,**y,*x,pd;
2215: double **hess;
2216: int i, j,jk;
2217: int *indx;
2218:
2219: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2220: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2221: void lubksb(double **a, int npar, int *indx, double b[]) ;
2222: void ludcmp(double **a, int npar, int *indx, double *d) ;
2223: double gompertz(double p[]);
2224: hess=matrix(1,npar,1,npar);
2225:
2226: printf("\nCalculation of the hessian matrix. Wait...\n");
2227: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2228: for (i=1;i<=npar;i++){
2229: printf("%d",i);fflush(stdout);
2230: fprintf(ficlog,"%d",i);fflush(ficlog);
2231:
2232: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2233:
2234: /* printf(" %f ",p[i]);
2235: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2236: }
2237:
2238: for (i=1;i<=npar;i++) {
2239: for (j=1;j<=npar;j++) {
2240: if (j>i) {
2241: printf(".%d%d",i,j);fflush(stdout);
2242: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2243: hess[i][j]=hessij(p,delti,i,j,func,npar);
2244:
2245: hess[j][i]=hess[i][j];
2246: /*printf(" %lf ",hess[i][j]);*/
2247: }
2248: }
2249: }
2250: printf("\n");
2251: fprintf(ficlog,"\n");
2252:
2253: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2254: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2255:
2256: a=matrix(1,npar,1,npar);
2257: y=matrix(1,npar,1,npar);
2258: x=vector(1,npar);
2259: indx=ivector(1,npar);
2260: for (i=1;i<=npar;i++)
2261: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2262: ludcmp(a,npar,indx,&pd);
2263:
2264: for (j=1;j<=npar;j++) {
2265: for (i=1;i<=npar;i++) x[i]=0;
2266: x[j]=1;
2267: lubksb(a,npar,indx,x);
2268: for (i=1;i<=npar;i++){
2269: matcov[i][j]=x[i];
2270: }
2271: }
2272:
2273: printf("\n#Hessian matrix#\n");
2274: fprintf(ficlog,"\n#Hessian matrix#\n");
2275: for (i=1;i<=npar;i++) {
2276: for (j=1;j<=npar;j++) {
2277: printf("%.3e ",hess[i][j]);
2278: fprintf(ficlog,"%.3e ",hess[i][j]);
2279: }
2280: printf("\n");
2281: fprintf(ficlog,"\n");
2282: }
2283:
2284: /* Recompute Inverse */
2285: for (i=1;i<=npar;i++)
2286: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2287: ludcmp(a,npar,indx,&pd);
2288:
2289: /* printf("\n#Hessian matrix recomputed#\n");
2290:
2291: for (j=1;j<=npar;j++) {
2292: for (i=1;i<=npar;i++) x[i]=0;
2293: x[j]=1;
2294: lubksb(a,npar,indx,x);
2295: for (i=1;i<=npar;i++){
2296: y[i][j]=x[i];
2297: printf("%.3e ",y[i][j]);
2298: fprintf(ficlog,"%.3e ",y[i][j]);
2299: }
2300: printf("\n");
2301: fprintf(ficlog,"\n");
2302: }
2303: */
2304:
2305: free_matrix(a,1,npar,1,npar);
2306: free_matrix(y,1,npar,1,npar);
2307: free_vector(x,1,npar);
2308: free_ivector(indx,1,npar);
2309: free_matrix(hess,1,npar,1,npar);
2310:
2311:
2312: }
2313:
2314: /*************** hessian matrix ****************/
2315: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2316: {
2317: int i;
2318: int l=1, lmax=20;
2319: double k1,k2;
1.132 brouard 2320: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2321: double res;
2322: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2323: double fx;
2324: int k=0,kmax=10;
2325: double l1;
2326:
2327: fx=func(x);
2328: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2329: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2330: l1=pow(10,l);
2331: delts=delt;
2332: for(k=1 ; k <kmax; k=k+1){
2333: delt = delta*(l1*k);
2334: p2[theta]=x[theta] +delt;
1.145 brouard 2335: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2336: p2[theta]=x[theta]-delt;
2337: k2=func(p2)-fx;
2338: /*res= (k1-2.0*fx+k2)/delt/delt; */
2339: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2340:
1.132 brouard 2341: #ifdef DEBUGHESS
1.126 brouard 2342: 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);
2343: 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);
2344: #endif
2345: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2346: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2347: k=kmax;
2348: }
2349: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2350: k=kmax; l=lmax*10.;
2351: }
2352: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2353: delts=delt;
2354: }
2355: }
2356: }
2357: delti[theta]=delts;
2358: return res;
2359:
2360: }
2361:
2362: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2363: {
2364: int i;
2365: int l=1, l1, lmax=20;
2366: double k1,k2,k3,k4,res,fx;
1.132 brouard 2367: double p2[MAXPARM+1];
1.126 brouard 2368: int k;
2369:
2370: fx=func(x);
2371: for (k=1; k<=2; k++) {
2372: for (i=1;i<=npar;i++) p2[i]=x[i];
2373: p2[thetai]=x[thetai]+delti[thetai]/k;
2374: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2375: k1=func(p2)-fx;
2376:
2377: p2[thetai]=x[thetai]+delti[thetai]/k;
2378: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2379: k2=func(p2)-fx;
2380:
2381: p2[thetai]=x[thetai]-delti[thetai]/k;
2382: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2383: k3=func(p2)-fx;
2384:
2385: p2[thetai]=x[thetai]-delti[thetai]/k;
2386: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2387: k4=func(p2)-fx;
2388: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2389: #ifdef DEBUG
2390: 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);
2391: 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);
2392: #endif
2393: }
2394: return res;
2395: }
2396:
2397: /************** Inverse of matrix **************/
2398: void ludcmp(double **a, int n, int *indx, double *d)
2399: {
2400: int i,imax,j,k;
2401: double big,dum,sum,temp;
2402: double *vv;
2403:
2404: vv=vector(1,n);
2405: *d=1.0;
2406: for (i=1;i<=n;i++) {
2407: big=0.0;
2408: for (j=1;j<=n;j++)
2409: if ((temp=fabs(a[i][j])) > big) big=temp;
2410: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2411: vv[i]=1.0/big;
2412: }
2413: for (j=1;j<=n;j++) {
2414: for (i=1;i<j;i++) {
2415: sum=a[i][j];
2416: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2417: a[i][j]=sum;
2418: }
2419: big=0.0;
2420: for (i=j;i<=n;i++) {
2421: sum=a[i][j];
2422: for (k=1;k<j;k++)
2423: sum -= a[i][k]*a[k][j];
2424: a[i][j]=sum;
2425: if ( (dum=vv[i]*fabs(sum)) >= big) {
2426: big=dum;
2427: imax=i;
2428: }
2429: }
2430: if (j != imax) {
2431: for (k=1;k<=n;k++) {
2432: dum=a[imax][k];
2433: a[imax][k]=a[j][k];
2434: a[j][k]=dum;
2435: }
2436: *d = -(*d);
2437: vv[imax]=vv[j];
2438: }
2439: indx[j]=imax;
2440: if (a[j][j] == 0.0) a[j][j]=TINY;
2441: if (j != n) {
2442: dum=1.0/(a[j][j]);
2443: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2444: }
2445: }
2446: free_vector(vv,1,n); /* Doesn't work */
2447: ;
2448: }
2449:
2450: void lubksb(double **a, int n, int *indx, double b[])
2451: {
2452: int i,ii=0,ip,j;
2453: double sum;
2454:
2455: for (i=1;i<=n;i++) {
2456: ip=indx[i];
2457: sum=b[ip];
2458: b[ip]=b[i];
2459: if (ii)
2460: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2461: else if (sum) ii=i;
2462: b[i]=sum;
2463: }
2464: for (i=n;i>=1;i--) {
2465: sum=b[i];
2466: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2467: b[i]=sum/a[i][i];
2468: }
2469: }
2470:
2471: void pstamp(FILE *fichier)
2472: {
2473: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2474: }
2475:
2476: /************ Frequencies ********************/
2477: 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[])
2478: { /* Some frequencies */
2479:
1.130 brouard 2480: int i, m, jk, k1,i1, j1, bool, z1,j;
1.126 brouard 2481: int first;
2482: double ***freq; /* Frequencies */
2483: double *pp, **prop;
2484: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2485: char fileresp[FILENAMELENGTH];
2486:
2487: pp=vector(1,nlstate);
2488: prop=matrix(1,nlstate,iagemin,iagemax+3);
2489: strcpy(fileresp,"p");
2490: strcat(fileresp,fileres);
2491: if((ficresp=fopen(fileresp,"w"))==NULL) {
2492: printf("Problem with prevalence resultfile: %s\n", fileresp);
2493: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2494: exit(0);
2495: }
2496: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2497: j1=0;
2498:
2499: j=cptcoveff;
2500: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2501:
2502: first=1;
2503:
1.145 brouard 2504: /* for(k1=1; k1<=j ; k1++){ /* Loop on covariates */
2505: /* for(i1=1; i1<=ncodemax[k1];i1++){ /* Now it is 2 */
2506: /* j1++;
2507: */
2508: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2509: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2510: scanf("%d", i);*/
2511: for (i=-5; i<=nlstate+ndeath; i++)
2512: for (jk=-5; jk<=nlstate+ndeath; jk++)
2513: for(m=iagemin; m <= iagemax+3; m++)
2514: freq[i][jk][m]=0;
1.143 brouard 2515:
2516: for (i=1; i<=nlstate; i++)
2517: for(m=iagemin; m <= iagemax+3; m++)
2518: prop[i][m]=0;
1.126 brouard 2519:
2520: dateintsum=0;
2521: k2cpt=0;
2522: for (i=1; i<=imx; i++) {
2523: bool=1;
1.144 brouard 2524: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2525: for (z1=1; z1<=cptcoveff; z1++)
2526: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2527: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2528: bool=0;
1.145 brouard 2529: /* 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",
2530: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2531: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2532: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2533: }
1.126 brouard 2534: }
1.144 brouard 2535:
1.126 brouard 2536: if (bool==1){
2537: for(m=firstpass; m<=lastpass; m++){
2538: k2=anint[m][i]+(mint[m][i]/12.);
2539: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2540: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2541: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2542: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2543: if (m<lastpass) {
2544: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2545: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2546: }
2547:
2548: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2549: dateintsum=dateintsum+k2;
2550: k2cpt++;
2551: }
2552: /*}*/
2553: }
2554: }
1.145 brouard 2555: } /* end i */
1.126 brouard 2556:
2557: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2558: pstamp(ficresp);
2559: if (cptcovn>0) {
2560: fprintf(ficresp, "\n#********** Variable ");
2561: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2562: fprintf(ficresp, "**********\n#");
1.143 brouard 2563: fprintf(ficlog, "\n#********** Variable ");
2564: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2565: fprintf(ficlog, "**********\n#");
1.126 brouard 2566: }
2567: for(i=1; i<=nlstate;i++)
2568: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2569: fprintf(ficresp, "\n");
2570:
2571: for(i=iagemin; i <= iagemax+3; i++){
2572: if(i==iagemax+3){
2573: fprintf(ficlog,"Total");
2574: }else{
2575: if(first==1){
2576: first=0;
2577: printf("See log file for details...\n");
2578: }
2579: fprintf(ficlog,"Age %d", i);
2580: }
2581: for(jk=1; jk <=nlstate ; jk++){
2582: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2583: pp[jk] += freq[jk][m][i];
2584: }
2585: for(jk=1; jk <=nlstate ; jk++){
2586: for(m=-1, pos=0; m <=0 ; m++)
2587: pos += freq[jk][m][i];
2588: if(pp[jk]>=1.e-10){
2589: if(first==1){
1.132 brouard 2590: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 2591: }
2592: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2593: }else{
2594: if(first==1)
2595: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2596: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2597: }
2598: }
2599:
2600: for(jk=1; jk <=nlstate ; jk++){
2601: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2602: pp[jk] += freq[jk][m][i];
2603: }
2604: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2605: pos += pp[jk];
2606: posprop += prop[jk][i];
2607: }
2608: for(jk=1; jk <=nlstate ; jk++){
2609: if(pos>=1.e-5){
2610: if(first==1)
2611: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2612: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2613: }else{
2614: if(first==1)
2615: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2616: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2617: }
2618: if( i <= iagemax){
2619: if(pos>=1.e-5){
2620: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2621: /*probs[i][jk][j1]= pp[jk]/pos;*/
2622: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2623: }
2624: else
2625: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2626: }
2627: }
2628:
2629: for(jk=-1; jk <=nlstate+ndeath; jk++)
2630: for(m=-1; m <=nlstate+ndeath; m++)
2631: if(freq[jk][m][i] !=0 ) {
2632: if(first==1)
2633: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2634: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2635: }
2636: if(i <= iagemax)
2637: fprintf(ficresp,"\n");
2638: if(first==1)
2639: printf("Others in log...\n");
2640: fprintf(ficlog,"\n");
2641: }
1.145 brouard 2642: /*}*/
1.126 brouard 2643: }
2644: dateintmean=dateintsum/k2cpt;
2645:
2646: fclose(ficresp);
2647: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2648: free_vector(pp,1,nlstate);
2649: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2650: /* End of Freq */
2651: }
2652:
2653: /************ Prevalence ********************/
2654: 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)
2655: {
2656: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2657: in each health status at the date of interview (if between dateprev1 and dateprev2).
2658: We still use firstpass and lastpass as another selection.
2659: */
2660:
1.130 brouard 2661: int i, m, jk, k1, i1, j1, bool, z1,j;
1.126 brouard 2662: double ***freq; /* Frequencies */
2663: double *pp, **prop;
2664: double pos,posprop;
2665: double y2; /* in fractional years */
2666: int iagemin, iagemax;
1.145 brouard 2667: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 2668:
2669: iagemin= (int) agemin;
2670: iagemax= (int) agemax;
2671: /*pp=vector(1,nlstate);*/
2672: prop=matrix(1,nlstate,iagemin,iagemax+3);
2673: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2674: j1=0;
2675:
1.145 brouard 2676: /*j=cptcoveff;*/
1.126 brouard 2677: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2678:
1.145 brouard 2679: first=1;
2680: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2681: /*for(i1=1; i1<=ncodemax[k1];i1++){
2682: j1++;*/
1.126 brouard 2683:
2684: for (i=1; i<=nlstate; i++)
2685: for(m=iagemin; m <= iagemax+3; m++)
2686: prop[i][m]=0.0;
2687:
2688: for (i=1; i<=imx; i++) { /* Each individual */
2689: bool=1;
2690: if (cptcovn>0) {
2691: for (z1=1; z1<=cptcoveff; z1++)
2692: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2693: bool=0;
2694: }
2695: if (bool==1) {
2696: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2697: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2698: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2699: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2700: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2701: 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);
2702: if (s[m][i]>0 && s[m][i]<=nlstate) {
2703: /*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]]);*/
2704: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2705: prop[s[m][i]][iagemax+3] += weight[i];
2706: }
2707: }
2708: } /* end selection of waves */
2709: }
2710: }
2711: for(i=iagemin; i <= iagemax+3; i++){
2712: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2713: posprop += prop[jk][i];
2714: }
1.145 brouard 2715:
1.126 brouard 2716: for(jk=1; jk <=nlstate ; jk++){
2717: if( i <= iagemax){
2718: if(posprop>=1.e-5){
2719: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 2720: } else{
2721: if(first==1){
2722: first=0;
2723: 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]);
2724: }
2725: }
1.126 brouard 2726: }
2727: }/* end jk */
2728: }/* end i */
1.145 brouard 2729: /*} *//* end i1 */
2730: } /* end j1 */
1.126 brouard 2731:
2732: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2733: /*free_vector(pp,1,nlstate);*/
2734: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2735: } /* End of prevalence */
2736:
2737: /************* Waves Concatenation ***************/
2738:
2739: 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)
2740: {
2741: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2742: Death is a valid wave (if date is known).
2743: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2744: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2745: and mw[mi+1][i]. dh depends on stepm.
2746: */
2747:
2748: int i, mi, m;
2749: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2750: double sum=0., jmean=0.;*/
2751: int first;
2752: int j, k=0,jk, ju, jl;
2753: double sum=0.;
2754: first=0;
2755: jmin=1e+5;
2756: jmax=-1;
2757: jmean=0.;
2758: for(i=1; i<=imx; i++){
2759: mi=0;
2760: m=firstpass;
2761: while(s[m][i] <= nlstate){
2762: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2763: mw[++mi][i]=m;
2764: if(m >=lastpass)
2765: break;
2766: else
2767: m++;
2768: }/* end while */
2769: if (s[m][i] > nlstate){
2770: mi++; /* Death is another wave */
2771: /* if(mi==0) never been interviewed correctly before death */
2772: /* Only death is a correct wave */
2773: mw[mi][i]=m;
2774: }
2775:
2776: wav[i]=mi;
2777: if(mi==0){
2778: nbwarn++;
2779: if(first==0){
2780: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2781: first=1;
2782: }
2783: if(first==1){
2784: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2785: }
2786: } /* end mi==0 */
2787: } /* End individuals */
2788:
2789: for(i=1; i<=imx; i++){
2790: for(mi=1; mi<wav[i];mi++){
2791: if (stepm <=0)
2792: dh[mi][i]=1;
2793: else{
2794: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2795: if (agedc[i] < 2*AGESUP) {
2796: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2797: if(j==0) j=1; /* Survives at least one month after exam */
2798: else if(j<0){
2799: nberr++;
2800: 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]);
2801: j=1; /* Temporary Dangerous patch */
2802: 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);
2803: 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]);
2804: 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);
2805: }
2806: k=k+1;
2807: if (j >= jmax){
2808: jmax=j;
2809: ijmax=i;
2810: }
2811: if (j <= jmin){
2812: jmin=j;
2813: ijmin=i;
2814: }
2815: sum=sum+j;
2816: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2817: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2818: }
2819: }
2820: else{
2821: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2822: /* 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]); */
2823:
2824: k=k+1;
2825: if (j >= jmax) {
2826: jmax=j;
2827: ijmax=i;
2828: }
2829: else if (j <= jmin){
2830: jmin=j;
2831: ijmin=i;
2832: }
2833: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2834: /*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]);*/
2835: if(j<0){
2836: nberr++;
2837: 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]);
2838: 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]);
2839: }
2840: sum=sum+j;
2841: }
2842: jk= j/stepm;
2843: jl= j -jk*stepm;
2844: ju= j -(jk+1)*stepm;
2845: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2846: if(jl==0){
2847: dh[mi][i]=jk;
2848: bh[mi][i]=0;
2849: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 2850: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 2851: dh[mi][i]=jk+1;
2852: bh[mi][i]=ju;
2853: }
2854: }else{
2855: if(jl <= -ju){
2856: dh[mi][i]=jk;
2857: bh[mi][i]=jl; /* bias is positive if real duration
2858: * is higher than the multiple of stepm and negative otherwise.
2859: */
2860: }
2861: else{
2862: dh[mi][i]=jk+1;
2863: bh[mi][i]=ju;
2864: }
2865: if(dh[mi][i]==0){
2866: dh[mi][i]=1; /* At least one step */
2867: bh[mi][i]=ju; /* At least one step */
2868: /* 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);*/
2869: }
2870: } /* end if mle */
2871: }
2872: } /* end wave */
2873: }
2874: jmean=sum/k;
2875: 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 2876: 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 2877: }
2878:
2879: /*********** Tricode ****************************/
1.145 brouard 2880: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 2881: {
1.144 brouard 2882: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2883: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2884: /* Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 2885: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2886: /* nbcode[Tvar[j]][1]=
1.144 brouard 2887: */
1.130 brouard 2888:
1.145 brouard 2889: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 2890: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 2891: int cptcode=0; /* Modality max of covariates j */
2892: int modmincovj=0; /* Modality min of covariates j */
2893:
2894:
1.126 brouard 2895: cptcoveff=0;
2896:
1.145 brouard 2897: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.144 brouard 2898: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 2899:
1.145 brouard 2900: /* Loop on covariates without age and products */
2901: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2902: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
1.136 brouard 2903: modality of this covariate Vj*/
1.145 brouard 2904: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2905: * If product of Vn*Vm, still boolean *:
2906: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2907: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2908: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 2909: modality of the nth covariate of individual i. */
1.145 brouard 2910: if (ij > modmaxcovj)
2911: modmaxcovj=ij;
2912: else if (ij < modmincovj)
2913: modmincovj=ij;
2914: if ((ij < -1) && (ij > NCOVMAX)){
2915: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2916: exit(1);
2917: }else
1.136 brouard 2918: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 2919: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 2920: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 2921: /* getting the maximum value of the modality of the covariate
2922: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2923: female is 1, then modmaxcovj=1.*/
1.126 brouard 2924: }
1.145 brouard 2925: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2926: cptcode=modmaxcovj;
1.137 brouard 2927: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 2928: /*for (i=0; i<=cptcode; i++) {*/
2929: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2930: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2931: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2932: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2933: }
2934: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2935: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 2936: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 2937:
1.136 brouard 2938: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.145 brouard 2939: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2940: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2941: modmincovj=3; modmaxcovj = 7;
2942: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2943: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2944: variables V1_1 and V1_2.
2945: nbcode[Tvar[j]][ij]=k;
2946: nbcode[Tvar[j]][1]=0;
2947: nbcode[Tvar[j]][2]=1;
2948: nbcode[Tvar[j]][3]=2;
2949: */
2950: ij=1; /* ij is similar to i but can jumps over null modalities */
2951: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2952: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2953: /*recode from 0 */
1.131 brouard 2954: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2955: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2956: k is a modality. If we have model=V1+V1*sex
2957: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
1.126 brouard 2958: ij++;
2959: }
2960: if (ij > ncodemax[j]) break;
1.137 brouard 2961: } /* end of loop on */
2962: } /* end of loop on modality */
2963: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
2964:
1.145 brouard 2965: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 2966:
1.145 brouard 2967: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
2968: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
2969: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
2970: Ndum[ij]++;
2971: }
1.126 brouard 2972:
2973: ij=1;
1.145 brouard 2974: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
2975: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 2976: if((Ndum[i]!=0) && (i<=ncovcol)){
1.145 brouard 2977: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
2978: Tvaraff[ij]=i; /*For printing (unclear) */
1.126 brouard 2979: ij++;
1.145 brouard 2980: }else
2981: Tvaraff[ij]=0;
1.126 brouard 2982: }
1.131 brouard 2983: ij--;
1.144 brouard 2984: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 2985:
1.126 brouard 2986: }
2987:
1.145 brouard 2988:
1.126 brouard 2989: /*********** Health Expectancies ****************/
2990:
1.127 brouard 2991: 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 2992:
2993: {
2994: /* Health expectancies, no variances */
2995: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
2996: int nhstepma, nstepma; /* Decreasing with age */
2997: double age, agelim, hf;
2998: double ***p3mat;
2999: double eip;
3000:
3001: pstamp(ficreseij);
3002: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3003: fprintf(ficreseij,"# Age");
3004: for(i=1; i<=nlstate;i++){
3005: for(j=1; j<=nlstate;j++){
3006: fprintf(ficreseij," e%1d%1d ",i,j);
3007: }
3008: fprintf(ficreseij," e%1d. ",i);
3009: }
3010: fprintf(ficreseij,"\n");
3011:
3012:
3013: if(estepm < stepm){
3014: printf ("Problem %d lower than %d\n",estepm, stepm);
3015: }
3016: else hstepm=estepm;
3017: /* We compute the life expectancy from trapezoids spaced every estepm months
3018: * This is mainly to measure the difference between two models: for example
3019: * if stepm=24 months pijx are given only every 2 years and by summing them
3020: * we are calculating an estimate of the Life Expectancy assuming a linear
3021: * progression in between and thus overestimating or underestimating according
3022: * to the curvature of the survival function. If, for the same date, we
3023: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3024: * to compare the new estimate of Life expectancy with the same linear
3025: * hypothesis. A more precise result, taking into account a more precise
3026: * curvature will be obtained if estepm is as small as stepm. */
3027:
3028: /* For example we decided to compute the life expectancy with the smallest unit */
3029: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3030: nhstepm is the number of hstepm from age to agelim
3031: nstepm is the number of stepm from age to agelin.
3032: Look at hpijx to understand the reason of that which relies in memory size
3033: and note for a fixed period like estepm months */
3034: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3035: survival function given by stepm (the optimization length). Unfortunately it
3036: means that if the survival funtion is printed only each two years of age and if
3037: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3038: results. So we changed our mind and took the option of the best precision.
3039: */
3040: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3041:
3042: agelim=AGESUP;
3043: /* If stepm=6 months */
3044: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3045: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3046:
3047: /* nhstepm age range expressed in number of stepm */
3048: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3049: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3050: /* if (stepm >= YEARM) hstepm=1;*/
3051: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3052: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3053:
3054: for (age=bage; age<=fage; age ++){
3055: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3056: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3057: /* if (stepm >= YEARM) hstepm=1;*/
3058: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3059:
3060: /* If stepm=6 months */
3061: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3062: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3063:
3064: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3065:
3066: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3067:
3068: printf("%d|",(int)age);fflush(stdout);
3069: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3070:
3071: /* Computing expectancies */
3072: for(i=1; i<=nlstate;i++)
3073: for(j=1; j<=nlstate;j++)
3074: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3075: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3076:
3077: /* 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]);*/
3078:
3079: }
3080:
3081: fprintf(ficreseij,"%3.0f",age );
3082: for(i=1; i<=nlstate;i++){
3083: eip=0;
3084: for(j=1; j<=nlstate;j++){
3085: eip +=eij[i][j][(int)age];
3086: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3087: }
3088: fprintf(ficreseij,"%9.4f", eip );
3089: }
3090: fprintf(ficreseij,"\n");
3091:
3092: }
3093: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3094: printf("\n");
3095: fprintf(ficlog,"\n");
3096:
3097: }
3098:
1.127 brouard 3099: 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 3100:
3101: {
3102: /* Covariances of health expectancies eij and of total life expectancies according
3103: to initial status i, ei. .
3104: */
3105: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3106: int nhstepma, nstepma; /* Decreasing with age */
3107: double age, agelim, hf;
3108: double ***p3matp, ***p3matm, ***varhe;
3109: double **dnewm,**doldm;
3110: double *xp, *xm;
3111: double **gp, **gm;
3112: double ***gradg, ***trgradg;
3113: int theta;
3114:
3115: double eip, vip;
3116:
3117: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3118: xp=vector(1,npar);
3119: xm=vector(1,npar);
3120: dnewm=matrix(1,nlstate*nlstate,1,npar);
3121: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3122:
3123: pstamp(ficresstdeij);
3124: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3125: fprintf(ficresstdeij,"# Age");
3126: for(i=1; i<=nlstate;i++){
3127: for(j=1; j<=nlstate;j++)
3128: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3129: fprintf(ficresstdeij," e%1d. ",i);
3130: }
3131: fprintf(ficresstdeij,"\n");
3132:
3133: pstamp(ficrescveij);
3134: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3135: fprintf(ficrescveij,"# Age");
3136: for(i=1; i<=nlstate;i++)
3137: for(j=1; j<=nlstate;j++){
3138: cptj= (j-1)*nlstate+i;
3139: for(i2=1; i2<=nlstate;i2++)
3140: for(j2=1; j2<=nlstate;j2++){
3141: cptj2= (j2-1)*nlstate+i2;
3142: if(cptj2 <= cptj)
3143: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3144: }
3145: }
3146: fprintf(ficrescveij,"\n");
3147:
3148: if(estepm < stepm){
3149: printf ("Problem %d lower than %d\n",estepm, stepm);
3150: }
3151: else hstepm=estepm;
3152: /* We compute the life expectancy from trapezoids spaced every estepm months
3153: * This is mainly to measure the difference between two models: for example
3154: * if stepm=24 months pijx are given only every 2 years and by summing them
3155: * we are calculating an estimate of the Life Expectancy assuming a linear
3156: * progression in between and thus overestimating or underestimating according
3157: * to the curvature of the survival function. If, for the same date, we
3158: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3159: * to compare the new estimate of Life expectancy with the same linear
3160: * hypothesis. A more precise result, taking into account a more precise
3161: * curvature will be obtained if estepm is as small as stepm. */
3162:
3163: /* For example we decided to compute the life expectancy with the smallest unit */
3164: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3165: nhstepm is the number of hstepm from age to agelim
3166: nstepm is the number of stepm from age to agelin.
3167: Look at hpijx to understand the reason of that which relies in memory size
3168: and note for a fixed period like estepm months */
3169: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3170: survival function given by stepm (the optimization length). Unfortunately it
3171: means that if the survival funtion is printed only each two years of age and if
3172: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3173: results. So we changed our mind and took the option of the best precision.
3174: */
3175: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3176:
3177: /* If stepm=6 months */
3178: /* nhstepm age range expressed in number of stepm */
3179: agelim=AGESUP;
3180: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3181: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3182: /* if (stepm >= YEARM) hstepm=1;*/
3183: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3184:
3185: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3186: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3187: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3188: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3189: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3190: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3191:
3192: for (age=bage; age<=fage; age ++){
3193: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3194: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3195: /* if (stepm >= YEARM) hstepm=1;*/
3196: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3197:
3198: /* If stepm=6 months */
3199: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3200: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3201:
3202: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3203:
3204: /* Computing Variances of health expectancies */
3205: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3206: decrease memory allocation */
3207: for(theta=1; theta <=npar; theta++){
3208: for(i=1; i<=npar; i++){
3209: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3210: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3211: }
3212: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3213: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3214:
3215: for(j=1; j<= nlstate; j++){
3216: for(i=1; i<=nlstate; i++){
3217: for(h=0; h<=nhstepm-1; h++){
3218: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3219: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3220: }
3221: }
3222: }
3223:
3224: for(ij=1; ij<= nlstate*nlstate; ij++)
3225: for(h=0; h<=nhstepm-1; h++){
3226: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3227: }
3228: }/* End theta */
3229:
3230:
3231: for(h=0; h<=nhstepm-1; h++)
3232: for(j=1; j<=nlstate*nlstate;j++)
3233: for(theta=1; theta <=npar; theta++)
3234: trgradg[h][j][theta]=gradg[h][theta][j];
3235:
3236:
3237: for(ij=1;ij<=nlstate*nlstate;ij++)
3238: for(ji=1;ji<=nlstate*nlstate;ji++)
3239: varhe[ij][ji][(int)age] =0.;
3240:
3241: printf("%d|",(int)age);fflush(stdout);
3242: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3243: for(h=0;h<=nhstepm-1;h++){
3244: for(k=0;k<=nhstepm-1;k++){
3245: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3246: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3247: for(ij=1;ij<=nlstate*nlstate;ij++)
3248: for(ji=1;ji<=nlstate*nlstate;ji++)
3249: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3250: }
3251: }
3252:
3253: /* Computing expectancies */
3254: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3255: for(i=1; i<=nlstate;i++)
3256: for(j=1; j<=nlstate;j++)
3257: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3258: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3259:
3260: /* 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]);*/
3261:
3262: }
3263:
3264: fprintf(ficresstdeij,"%3.0f",age );
3265: for(i=1; i<=nlstate;i++){
3266: eip=0.;
3267: vip=0.;
3268: for(j=1; j<=nlstate;j++){
3269: eip += eij[i][j][(int)age];
3270: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3271: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3272: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3273: }
3274: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3275: }
3276: fprintf(ficresstdeij,"\n");
3277:
3278: fprintf(ficrescveij,"%3.0f",age );
3279: for(i=1; i<=nlstate;i++)
3280: for(j=1; j<=nlstate;j++){
3281: cptj= (j-1)*nlstate+i;
3282: for(i2=1; i2<=nlstate;i2++)
3283: for(j2=1; j2<=nlstate;j2++){
3284: cptj2= (j2-1)*nlstate+i2;
3285: if(cptj2 <= cptj)
3286: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3287: }
3288: }
3289: fprintf(ficrescveij,"\n");
3290:
3291: }
3292: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3293: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3294: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3295: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3296: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3297: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3298: printf("\n");
3299: fprintf(ficlog,"\n");
3300:
3301: free_vector(xm,1,npar);
3302: free_vector(xp,1,npar);
3303: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3304: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3305: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3306: }
3307:
3308: /************ Variance ******************/
3309: 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[])
3310: {
3311: /* Variance of health expectancies */
3312: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3313: /* double **newm;*/
3314: double **dnewm,**doldm;
3315: double **dnewmp,**doldmp;
3316: int i, j, nhstepm, hstepm, h, nstepm ;
3317: int k, cptcode;
3318: double *xp;
3319: double **gp, **gm; /* for var eij */
3320: double ***gradg, ***trgradg; /*for var eij */
3321: double **gradgp, **trgradgp; /* for var p point j */
3322: double *gpp, *gmp; /* for var p point j */
3323: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3324: double ***p3mat;
3325: double age,agelim, hf;
3326: double ***mobaverage;
3327: int theta;
3328: char digit[4];
3329: char digitp[25];
3330:
3331: char fileresprobmorprev[FILENAMELENGTH];
3332:
3333: if(popbased==1){
3334: if(mobilav!=0)
3335: strcpy(digitp,"-populbased-mobilav-");
3336: else strcpy(digitp,"-populbased-nomobil-");
3337: }
3338: else
3339: strcpy(digitp,"-stablbased-");
3340:
3341: if (mobilav!=0) {
3342: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3343: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3344: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3345: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3346: }
3347: }
3348:
3349: strcpy(fileresprobmorprev,"prmorprev");
3350: sprintf(digit,"%-d",ij);
3351: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3352: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3353: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3354: strcat(fileresprobmorprev,fileres);
3355: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3356: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3357: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3358: }
3359: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3360:
3361: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3362: pstamp(ficresprobmorprev);
3363: 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);
3364: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3365: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3366: fprintf(ficresprobmorprev," p.%-d SE",j);
3367: for(i=1; i<=nlstate;i++)
3368: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3369: }
3370: fprintf(ficresprobmorprev,"\n");
3371: fprintf(ficgp,"\n# Routine varevsij");
3372: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3373: 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");
3374: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3375: /* } */
3376: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3377: pstamp(ficresvij);
3378: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3379: if(popbased==1)
1.128 brouard 3380: 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 3381: else
3382: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3383: fprintf(ficresvij,"# Age");
3384: for(i=1; i<=nlstate;i++)
3385: for(j=1; j<=nlstate;j++)
3386: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3387: fprintf(ficresvij,"\n");
3388:
3389: xp=vector(1,npar);
3390: dnewm=matrix(1,nlstate,1,npar);
3391: doldm=matrix(1,nlstate,1,nlstate);
3392: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3393: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3394:
3395: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3396: gpp=vector(nlstate+1,nlstate+ndeath);
3397: gmp=vector(nlstate+1,nlstate+ndeath);
3398: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3399:
3400: if(estepm < stepm){
3401: printf ("Problem %d lower than %d\n",estepm, stepm);
3402: }
3403: else hstepm=estepm;
3404: /* For example we decided to compute the life expectancy with the smallest unit */
3405: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3406: nhstepm is the number of hstepm from age to agelim
3407: nstepm is the number of stepm from age to agelin.
1.128 brouard 3408: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3409: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3410: survival function given by stepm (the optimization length). Unfortunately it
3411: means that if the survival funtion is printed every two years of age and if
3412: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3413: results. So we changed our mind and took the option of the best precision.
3414: */
3415: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3416: agelim = AGESUP;
3417: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3418: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3419: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3420: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3421: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3422: gp=matrix(0,nhstepm,1,nlstate);
3423: gm=matrix(0,nhstepm,1,nlstate);
3424:
3425:
3426: for(theta=1; theta <=npar; theta++){
3427: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3428: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3429: }
3430: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3431: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3432:
3433: if (popbased==1) {
3434: if(mobilav ==0){
3435: for(i=1; i<=nlstate;i++)
3436: prlim[i][i]=probs[(int)age][i][ij];
3437: }else{ /* mobilav */
3438: for(i=1; i<=nlstate;i++)
3439: prlim[i][i]=mobaverage[(int)age][i][ij];
3440: }
3441: }
3442:
3443: for(j=1; j<= nlstate; j++){
3444: for(h=0; h<=nhstepm; h++){
3445: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3446: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3447: }
3448: }
3449: /* This for computing probability of death (h=1 means
3450: computed over hstepm matrices product = hstepm*stepm months)
3451: as a weighted average of prlim.
3452: */
3453: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3454: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3455: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3456: }
3457: /* end probability of death */
3458:
3459: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3460: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3461: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3462: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3463:
3464: if (popbased==1) {
3465: if(mobilav ==0){
3466: for(i=1; i<=nlstate;i++)
3467: prlim[i][i]=probs[(int)age][i][ij];
3468: }else{ /* mobilav */
3469: for(i=1; i<=nlstate;i++)
3470: prlim[i][i]=mobaverage[(int)age][i][ij];
3471: }
3472: }
3473:
1.128 brouard 3474: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3475: for(h=0; h<=nhstepm; h++){
3476: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3477: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3478: }
3479: }
3480: /* This for computing probability of death (h=1 means
3481: computed over hstepm matrices product = hstepm*stepm months)
3482: as a weighted average of prlim.
3483: */
3484: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3485: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3486: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3487: }
3488: /* end probability of death */
3489:
3490: for(j=1; j<= nlstate; j++) /* vareij */
3491: for(h=0; h<=nhstepm; h++){
3492: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3493: }
3494:
3495: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3496: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3497: }
3498:
3499: } /* End theta */
3500:
3501: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3502:
3503: for(h=0; h<=nhstepm; h++) /* veij */
3504: for(j=1; j<=nlstate;j++)
3505: for(theta=1; theta <=npar; theta++)
3506: trgradg[h][j][theta]=gradg[h][theta][j];
3507:
3508: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3509: for(theta=1; theta <=npar; theta++)
3510: trgradgp[j][theta]=gradgp[theta][j];
3511:
3512:
3513: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3514: for(i=1;i<=nlstate;i++)
3515: for(j=1;j<=nlstate;j++)
3516: vareij[i][j][(int)age] =0.;
3517:
3518: for(h=0;h<=nhstepm;h++){
3519: for(k=0;k<=nhstepm;k++){
3520: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3521: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3522: for(i=1;i<=nlstate;i++)
3523: for(j=1;j<=nlstate;j++)
3524: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3525: }
3526: }
3527:
3528: /* pptj */
3529: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3530: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3531: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3532: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3533: varppt[j][i]=doldmp[j][i];
3534: /* end ppptj */
3535: /* x centered again */
3536: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3537: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3538:
3539: if (popbased==1) {
3540: if(mobilav ==0){
3541: for(i=1; i<=nlstate;i++)
3542: prlim[i][i]=probs[(int)age][i][ij];
3543: }else{ /* mobilav */
3544: for(i=1; i<=nlstate;i++)
3545: prlim[i][i]=mobaverage[(int)age][i][ij];
3546: }
3547: }
3548:
3549: /* This for computing probability of death (h=1 means
3550: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3551: as a weighted average of prlim.
3552: */
3553: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3554: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3555: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3556: }
3557: /* end probability of death */
3558:
3559: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3560: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3561: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3562: for(i=1; i<=nlstate;i++){
3563: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3564: }
3565: }
3566: fprintf(ficresprobmorprev,"\n");
3567:
3568: fprintf(ficresvij,"%.0f ",age );
3569: for(i=1; i<=nlstate;i++)
3570: for(j=1; j<=nlstate;j++){
3571: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3572: }
3573: fprintf(ficresvij,"\n");
3574: free_matrix(gp,0,nhstepm,1,nlstate);
3575: free_matrix(gm,0,nhstepm,1,nlstate);
3576: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3577: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3578: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3579: } /* End age */
3580: free_vector(gpp,nlstate+1,nlstate+ndeath);
3581: free_vector(gmp,nlstate+1,nlstate+ndeath);
3582: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3583: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 3584: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 3585: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 3586: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 3587: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3588: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3589: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 3590: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3591: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3592: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 3593: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3594: 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);
3595: /* 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);
3596: */
3597: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3598: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3599:
3600: free_vector(xp,1,npar);
3601: free_matrix(doldm,1,nlstate,1,nlstate);
3602: free_matrix(dnewm,1,nlstate,1,npar);
3603: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3604: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3605: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3606: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3607: fclose(ficresprobmorprev);
3608: fflush(ficgp);
3609: fflush(fichtm);
3610: } /* end varevsij */
3611:
3612: /************ Variance of prevlim ******************/
3613: 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[])
3614: {
3615: /* Variance of prevalence limit */
3616: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3617: double **newm;
3618: double **dnewm,**doldm;
3619: int i, j, nhstepm, hstepm;
3620: int k, cptcode;
3621: double *xp;
3622: double *gp, *gm;
3623: double **gradg, **trgradg;
3624: double age,agelim;
3625: int theta;
3626:
3627: pstamp(ficresvpl);
3628: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3629: fprintf(ficresvpl,"# Age");
3630: for(i=1; i<=nlstate;i++)
3631: fprintf(ficresvpl," %1d-%1d",i,i);
3632: fprintf(ficresvpl,"\n");
3633:
3634: xp=vector(1,npar);
3635: dnewm=matrix(1,nlstate,1,npar);
3636: doldm=matrix(1,nlstate,1,nlstate);
3637:
3638: hstepm=1*YEARM; /* Every year of age */
3639: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3640: agelim = AGESUP;
3641: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3642: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3643: if (stepm >= YEARM) hstepm=1;
3644: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3645: gradg=matrix(1,npar,1,nlstate);
3646: gp=vector(1,nlstate);
3647: gm=vector(1,nlstate);
3648:
3649: for(theta=1; theta <=npar; theta++){
3650: for(i=1; i<=npar; i++){ /* Computes gradient */
3651: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3652: }
3653: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3654: for(i=1;i<=nlstate;i++)
3655: gp[i] = prlim[i][i];
3656:
3657: for(i=1; i<=npar; i++) /* Computes gradient */
3658: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3659: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3660: for(i=1;i<=nlstate;i++)
3661: gm[i] = prlim[i][i];
3662:
3663: for(i=1;i<=nlstate;i++)
3664: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3665: } /* End theta */
3666:
3667: trgradg =matrix(1,nlstate,1,npar);
3668:
3669: for(j=1; j<=nlstate;j++)
3670: for(theta=1; theta <=npar; theta++)
3671: trgradg[j][theta]=gradg[theta][j];
3672:
3673: for(i=1;i<=nlstate;i++)
3674: varpl[i][(int)age] =0.;
3675: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3676: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3677: for(i=1;i<=nlstate;i++)
3678: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3679:
3680: fprintf(ficresvpl,"%.0f ",age );
3681: for(i=1; i<=nlstate;i++)
3682: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3683: fprintf(ficresvpl,"\n");
3684: free_vector(gp,1,nlstate);
3685: free_vector(gm,1,nlstate);
3686: free_matrix(gradg,1,npar,1,nlstate);
3687: free_matrix(trgradg,1,nlstate,1,npar);
3688: } /* End age */
3689:
3690: free_vector(xp,1,npar);
3691: free_matrix(doldm,1,nlstate,1,npar);
3692: free_matrix(dnewm,1,nlstate,1,nlstate);
3693:
3694: }
3695:
3696: /************ Variance of one-step probabilities ******************/
3697: 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[])
3698: {
3699: int i, j=0, i1, k1, l1, t, tj;
3700: int k2, l2, j1, z1;
3701: int k=0,l, cptcode;
1.145 brouard 3702: int first=1, first1, first2;
1.126 brouard 3703: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3704: double **dnewm,**doldm;
3705: double *xp;
3706: double *gp, *gm;
3707: double **gradg, **trgradg;
3708: double **mu;
1.145 brouard 3709: double age,agelim, cov[NCOVMAX+1];
1.126 brouard 3710: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3711: int theta;
3712: char fileresprob[FILENAMELENGTH];
3713: char fileresprobcov[FILENAMELENGTH];
3714: char fileresprobcor[FILENAMELENGTH];
3715: double ***varpij;
3716:
3717: strcpy(fileresprob,"prob");
3718: strcat(fileresprob,fileres);
3719: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3720: printf("Problem with resultfile: %s\n", fileresprob);
3721: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3722: }
3723: strcpy(fileresprobcov,"probcov");
3724: strcat(fileresprobcov,fileres);
3725: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3726: printf("Problem with resultfile: %s\n", fileresprobcov);
3727: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3728: }
3729: strcpy(fileresprobcor,"probcor");
3730: strcat(fileresprobcor,fileres);
3731: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3732: printf("Problem with resultfile: %s\n", fileresprobcor);
3733: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3734: }
3735: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3736: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3737: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3738: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3739: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3740: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3741: pstamp(ficresprob);
3742: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3743: fprintf(ficresprob,"# Age");
3744: pstamp(ficresprobcov);
3745: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3746: fprintf(ficresprobcov,"# Age");
3747: pstamp(ficresprobcor);
3748: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3749: fprintf(ficresprobcor,"# Age");
3750:
3751:
3752: for(i=1; i<=nlstate;i++)
3753: for(j=1; j<=(nlstate+ndeath);j++){
3754: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3755: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3756: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3757: }
3758: /* fprintf(ficresprob,"\n");
3759: fprintf(ficresprobcov,"\n");
3760: fprintf(ficresprobcor,"\n");
3761: */
1.131 brouard 3762: xp=vector(1,npar);
1.126 brouard 3763: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3764: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3765: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3766: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3767: first=1;
3768: fprintf(ficgp,"\n# Routine varprob");
3769: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3770: fprintf(fichtm,"\n");
3771:
3772: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3773: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3774: file %s<br>\n",optionfilehtmcov);
3775: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3776: and drawn. It helps understanding how is the covariance between two incidences.\
3777: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3778: 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. \
3779: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3780: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3781: standard deviations wide on each axis. <br>\
3782: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3783: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3784: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3785:
3786: cov[1]=1;
1.145 brouard 3787: /* tj=cptcoveff; */
3788: tj = (int) pow(2,cptcoveff);
1.126 brouard 3789: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3790: j1=0;
1.145 brouard 3791: for(j1=1; j1<=tj;j1++){
3792: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3793: /*j1++;*/
1.126 brouard 3794: if (cptcovn>0) {
3795: fprintf(ficresprob, "\n#********** Variable ");
3796: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3797: fprintf(ficresprob, "**********\n#\n");
3798: fprintf(ficresprobcov, "\n#********** Variable ");
3799: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3800: fprintf(ficresprobcov, "**********\n#\n");
3801:
3802: fprintf(ficgp, "\n#********** Variable ");
3803: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3804: fprintf(ficgp, "**********\n#\n");
3805:
3806:
3807: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3808: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3809: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3810:
3811: fprintf(ficresprobcor, "\n#********** Variable ");
3812: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3813: fprintf(ficresprobcor, "**********\n#");
3814: }
3815:
1.145 brouard 3816: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3817: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3818: gp=vector(1,(nlstate)*(nlstate+ndeath));
3819: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 3820: for (age=bage; age<=fage; age ++){
3821: cov[2]=age;
3822: for (k=1; k<=cptcovn;k++) {
1.145 brouard 3823: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3824: * 1 1 1 1 1
3825: * 2 2 1 1 1
3826: * 3 1 2 1 1
3827: */
3828: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 3829: }
3830: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3831: for (k=1; k<=cptcovprod;k++)
3832: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3833:
3834:
3835: for(theta=1; theta <=npar; theta++){
3836: for(i=1; i<=npar; i++)
3837: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3838:
3839: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3840:
3841: k=0;
3842: for(i=1; i<= (nlstate); i++){
3843: for(j=1; j<=(nlstate+ndeath);j++){
3844: k=k+1;
3845: gp[k]=pmmij[i][j];
3846: }
3847: }
3848:
3849: for(i=1; i<=npar; i++)
3850: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3851:
3852: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3853: k=0;
3854: for(i=1; i<=(nlstate); i++){
3855: for(j=1; j<=(nlstate+ndeath);j++){
3856: k=k+1;
3857: gm[k]=pmmij[i][j];
3858: }
3859: }
3860:
3861: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3862: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3863: }
3864:
3865: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3866: for(theta=1; theta <=npar; theta++)
3867: trgradg[j][theta]=gradg[theta][j];
3868:
3869: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3870: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3871:
3872: pmij(pmmij,cov,ncovmodel,x,nlstate);
3873:
3874: k=0;
3875: for(i=1; i<=(nlstate); i++){
3876: for(j=1; j<=(nlstate+ndeath);j++){
3877: k=k+1;
3878: mu[k][(int) age]=pmmij[i][j];
3879: }
3880: }
3881: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3882: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3883: varpij[i][j][(int)age] = doldm[i][j];
3884:
3885: /*printf("\n%d ",(int)age);
3886: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3887: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3888: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3889: }*/
3890:
3891: fprintf(ficresprob,"\n%d ",(int)age);
3892: fprintf(ficresprobcov,"\n%d ",(int)age);
3893: fprintf(ficresprobcor,"\n%d ",(int)age);
3894:
3895: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3896: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3897: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3898: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3899: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3900: }
3901: i=0;
3902: for (k=1; k<=(nlstate);k++){
3903: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 3904: i++;
1.126 brouard 3905: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3906: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3907: for (j=1; j<=i;j++){
1.145 brouard 3908: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 3909: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3910: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3911: }
3912: }
3913: }/* end of loop for state */
3914: } /* end of loop for age */
1.145 brouard 3915: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3916: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3917: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3918: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3919:
1.126 brouard 3920: /* Confidence intervalle of pij */
3921: /*
1.131 brouard 3922: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 3923: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3924: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3925: 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);
3926: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3927: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3928: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3929: */
3930:
3931: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 3932: first1=1;first2=2;
1.126 brouard 3933: for (k2=1; k2<=(nlstate);k2++){
3934: for (l2=1; l2<=(nlstate+ndeath);l2++){
3935: if(l2==k2) continue;
3936: j=(k2-1)*(nlstate+ndeath)+l2;
3937: for (k1=1; k1<=(nlstate);k1++){
3938: for (l1=1; l1<=(nlstate+ndeath);l1++){
3939: if(l1==k1) continue;
3940: i=(k1-1)*(nlstate+ndeath)+l1;
3941: if(i<=j) continue;
3942: for (age=bage; age<=fage; age ++){
3943: if ((int)age %5==0){
3944: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3945: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3946: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3947: mu1=mu[i][(int) age]/stepm*YEARM ;
3948: mu2=mu[j][(int) age]/stepm*YEARM;
3949: c12=cv12/sqrt(v1*v2);
3950: /* Computing eigen value of matrix of covariance */
3951: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3952: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 3953: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 3954: if(first2==1){
3955: first1=0;
3956: 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);
3957: }
3958: 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);
3959: /* lc1=fabs(lc1); */ /* If we want to have them positive */
3960: /* lc2=fabs(lc2); */
1.135 brouard 3961: }
3962:
1.126 brouard 3963: /* Eigen vectors */
3964: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
3965: /*v21=sqrt(1.-v11*v11); *//* error */
3966: v21=(lc1-v1)/cv12*v11;
3967: v12=-v21;
3968: v22=v11;
3969: tnalp=v21/v11;
3970: if(first1==1){
3971: first1=0;
3972: 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);
3973: }
3974: 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);
3975: /*printf(fignu*/
3976: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
3977: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
3978: if(first==1){
3979: first=0;
3980: fprintf(ficgp,"\nset parametric;unset label");
3981: 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 3982: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 3983: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
3984: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
3985: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
3986: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
3987: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3988: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3989: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
3990: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
3991: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
3992: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
3993: 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",\
3994: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
3995: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
3996: }else{
3997: first=0;
3998: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
3999: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4000: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4001: 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",\
4002: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4003: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4004: }/* if first */
4005: } /* age mod 5 */
4006: } /* end loop age */
4007: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4008: first=1;
4009: } /*l12 */
4010: } /* k12 */
4011: } /*l1 */
4012: }/* k1 */
1.145 brouard 4013: /* } /* loop covariates */
1.126 brouard 4014: }
4015: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4016: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4017: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4018: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4019: free_vector(xp,1,npar);
4020: fclose(ficresprob);
4021: fclose(ficresprobcov);
4022: fclose(ficresprobcor);
4023: fflush(ficgp);
4024: fflush(fichtmcov);
4025: }
4026:
4027:
4028: /******************* Printing html file ***********/
4029: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4030: int lastpass, int stepm, int weightopt, char model[],\
4031: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4032: int popforecast, int estepm ,\
4033: double jprev1, double mprev1,double anprev1, \
4034: double jprev2, double mprev2,double anprev2){
4035: int jj1, k1, i1, cpt;
4036:
4037: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4038: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4039: </ul>");
4040: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4041: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4042: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4043: fprintf(fichtm,"\
4044: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4045: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4046: fprintf(fichtm,"\
4047: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4048: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4049: fprintf(fichtm,"\
1.128 brouard 4050: - (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 4051: <a href=\"%s\">%s</a> <br>\n",
4052: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4053: fprintf(fichtm,"\
4054: - Population projections by age and states: \
4055: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4056:
4057: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4058:
1.145 brouard 4059: m=pow(2,cptcoveff);
1.126 brouard 4060: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4061:
4062: jj1=0;
4063: for(k1=1; k1<=m;k1++){
4064: for(i1=1; i1<=ncodemax[k1];i1++){
4065: jj1++;
4066: if (cptcovn > 0) {
4067: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4068: for (cpt=1; cpt<=cptcoveff;cpt++)
4069: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4070: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4071: }
4072: /* Pij */
1.145 brouard 4073: 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> \
4074: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4075: /* Quasi-incidences */
4076: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4077: 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> \
4078: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4079: /* Period (stable) prevalence in each health state */
1.154 brouard 4080: for(cpt=1; cpt<=nlstate;cpt++){
4081: fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4082: <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4083: }
4084: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4085: fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
4086: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4087: }
4088: } /* end i1 */
4089: }/* End k1 */
4090: fprintf(fichtm,"</ul>");
4091:
4092:
4093: fprintf(fichtm,"\
4094: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4095: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4096:
4097: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4098: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4099: fprintf(fichtm,"\
4100: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4101: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4102:
4103: fprintf(fichtm,"\
4104: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4105: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4106: fprintf(fichtm,"\
4107: - 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): \
4108: <a href=\"%s\">%s</a> <br>\n</li>",
4109: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4110: fprintf(fichtm,"\
4111: - (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): \
4112: <a href=\"%s\">%s</a> <br>\n</li>",
4113: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4114: fprintf(fichtm,"\
1.128 brouard 4115: - 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 4116: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4117: fprintf(fichtm,"\
1.128 brouard 4118: - 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",
4119: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4120: fprintf(fichtm,"\
4121: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4122: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4123:
4124: /* if(popforecast==1) fprintf(fichtm,"\n */
4125: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4126: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4127: /* <br>",fileres,fileres,fileres,fileres); */
4128: /* else */
4129: /* 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); */
4130: fflush(fichtm);
4131: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4132:
1.145 brouard 4133: m=pow(2,cptcoveff);
1.126 brouard 4134: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4135:
4136: jj1=0;
4137: for(k1=1; k1<=m;k1++){
4138: for(i1=1; i1<=ncodemax[k1];i1++){
4139: jj1++;
4140: if (cptcovn > 0) {
4141: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4142: for (cpt=1; cpt<=cptcoveff;cpt++)
4143: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4144: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4145: }
4146: for(cpt=1; cpt<=nlstate;cpt++) {
4147: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4148: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4149: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4150: }
4151: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4152: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4153: true period expectancies (those weighted with period prevalences are also\
4154: drawn in addition to the population based expectancies computed using\
4155: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4156: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4157: } /* end i1 */
4158: }/* End k1 */
4159: fprintf(fichtm,"</ul>");
4160: fflush(fichtm);
4161: }
4162:
4163: /******************* Gnuplot file **************/
4164: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4165:
4166: char dirfileres[132],optfileres[132];
1.130 brouard 4167: int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4168: int ng=0;
1.126 brouard 4169: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4170: /* printf("Problem with file %s",optionfilegnuplot); */
4171: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4172: /* } */
4173:
4174: /*#ifdef windows */
4175: fprintf(ficgp,"cd \"%s\" \n",pathc);
4176: /*#endif */
4177: m=pow(2,cptcoveff);
4178:
4179: strcpy(dirfileres,optionfilefiname);
4180: strcpy(optfileres,"vpl");
4181: /* 1eme*/
1.153 brouard 4182: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4183: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4184: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4185: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4186: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4187: fprintf(ficgp,"set xlabel \"Age\" \n\
4188: set ylabel \"Probability\" \n\
1.145 brouard 4189: set ter png small size 320, 240\n\
1.126 brouard 4190: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4191:
4192: for (i=1; i<= nlstate ; i ++) {
4193: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
1.131 brouard 4194: else fprintf(ficgp," \%%*lf (\%%*lf)");
1.126 brouard 4195: }
1.145 brouard 4196: 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 4197: for (i=1; i<= nlstate ; i ++) {
4198: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4199: else fprintf(ficgp," \%%*lf (\%%*lf)");
4200: }
1.145 brouard 4201: fprintf(ficgp,"\" t\"95\%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4202: for (i=1; i<= nlstate ; i ++) {
4203: if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
4204: else fprintf(ficgp," \%%*lf (\%%*lf)");
4205: }
1.145 brouard 4206: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4207: }
4208: }
4209: /*2 eme*/
1.153 brouard 4210: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4211: for (k1=1; k1<= m ; k1 ++) {
4212: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4213: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4214:
4215: for (i=1; i<= nlstate+1 ; i ++) {
4216: k=2*i;
4217: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4218: for (j=1; j<= nlstate+1 ; j ++) {
4219: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4220: else fprintf(ficgp," \%%*lf (\%%*lf)");
4221: }
4222: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4223: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4224: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4225: for (j=1; j<= nlstate+1 ; j ++) {
4226: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4227: else fprintf(ficgp," \%%*lf (\%%*lf)");
4228: }
1.145 brouard 4229: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4230: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4231: for (j=1; j<= nlstate+1 ; j ++) {
4232: if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
4233: else fprintf(ficgp," \%%*lf (\%%*lf)");
4234: }
1.145 brouard 4235: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4236: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4237: }
4238: }
4239:
4240: /*3eme*/
4241:
4242: for (k1=1; k1<= m ; k1 ++) {
4243: for (cpt=1; cpt<= nlstate ; cpt ++) {
4244: /* k=2+nlstate*(2*cpt-2); */
4245: k=2+(nlstate+1)*(cpt-1);
4246: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4247: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4248: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4249: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4250: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4251: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4252: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4253: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4254: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4255:
4256: */
4257: for (i=1; i< nlstate ; i ++) {
4258: 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);
4259: /* 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);*/
4260:
4261: }
4262: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4263: }
4264: }
4265:
4266: /* CV preval stable (period) */
1.153 brouard 4267: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4268: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4269: k=3;
1.153 brouard 4270: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4271: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4272: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4273: set ter png small size 320, 240\n\
1.126 brouard 4274: unset log y\n\
1.153 brouard 4275: plot [%.f:%.f] ", ageminpar, agemaxpar);
4276: for (i=1; i<= nlstate ; i ++){
4277: if(i==1)
4278: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4279: else
4280: fprintf(ficgp,", '' ");
1.154 brouard 4281: l=(nlstate+ndeath)*(i-1)+1;
4282: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4283: for (j=1; j<= (nlstate-1) ; j ++)
4284: fprintf(ficgp,"+$%d",k+l+j);
4285: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4286: } /* nlstate */
4287: fprintf(ficgp,"\n");
4288: } /* end cpt state*/
4289: } /* end covariate */
1.126 brouard 4290:
4291: /* proba elementaires */
4292: for(i=1,jk=1; i <=nlstate; i++){
4293: for(k=1; k <=(nlstate+ndeath); k++){
4294: if (k != i) {
4295: for(j=1; j <=ncovmodel; j++){
4296: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4297: jk++;
4298: fprintf(ficgp,"\n");
4299: }
4300: }
4301: }
4302: }
1.145 brouard 4303: /*goto avoid;*/
1.126 brouard 4304: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4305: for(jk=1; jk <=m; jk++) {
1.145 brouard 4306: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4307: if (ng==2)
4308: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4309: else
4310: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4311: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4312: i=1;
4313: for(k2=1; k2<=nlstate; k2++) {
4314: k3=i;
4315: for(k=1; k<=(nlstate+ndeath); k++) {
4316: if (k != k2){
4317: if(ng==2)
4318: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4319: else
4320: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
1.141 brouard 4321: ij=1;/* To be checked else nbcode[0][0] wrong */
1.126 brouard 4322: for(j=3; j <=ncovmodel; j++) {
1.145 brouard 4323: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4324: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4325: /* ij++; */
4326: /* } */
4327: /* else */
1.126 brouard 4328: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4329: }
4330: fprintf(ficgp,")/(1");
4331:
4332: for(k1=1; k1 <=nlstate; k1++){
4333: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4334: ij=1;
4335: for(j=3; j <=ncovmodel; j++){
1.145 brouard 4336: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4337: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4338: /* ij++; */
4339: /* } */
4340: /* else */
1.126 brouard 4341: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4342: }
4343: fprintf(ficgp,")");
4344: }
4345: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4346: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4347: i=i+ncovmodel;
4348: }
4349: } /* end k */
4350: } /* end k2 */
4351: } /* end jk */
4352: } /* end ng */
1.145 brouard 4353: avoid:
1.126 brouard 4354: fflush(ficgp);
4355: } /* end gnuplot */
4356:
4357:
4358: /*************** Moving average **************/
4359: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4360:
4361: int i, cpt, cptcod;
4362: int modcovmax =1;
4363: int mobilavrange, mob;
4364: double age;
4365:
4366: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4367: a covariate has 2 modalities */
4368: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4369:
4370: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4371: if(mobilav==1) mobilavrange=5; /* default */
4372: else mobilavrange=mobilav;
4373: for (age=bage; age<=fage; age++)
4374: for (i=1; i<=nlstate;i++)
4375: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4376: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4377: /* We keep the original values on the extreme ages bage, fage and for
4378: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4379: we use a 5 terms etc. until the borders are no more concerned.
4380: */
4381: for (mob=3;mob <=mobilavrange;mob=mob+2){
4382: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4383: for (i=1; i<=nlstate;i++){
4384: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4385: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4386: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4387: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4388: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4389: }
4390: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4391: }
4392: }
4393: }/* end age */
4394: }/* end mob */
4395: }else return -1;
4396: return 0;
4397: }/* End movingaverage */
4398:
4399:
4400: /************** Forecasting ******************/
4401: 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){
4402: /* proj1, year, month, day of starting projection
4403: agemin, agemax range of age
4404: dateprev1 dateprev2 range of dates during which prevalence is computed
4405: anproj2 year of en of projection (same day and month as proj1).
4406: */
4407: int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
4408: int *popage;
4409: double agec; /* generic age */
4410: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4411: double *popeffectif,*popcount;
4412: double ***p3mat;
4413: double ***mobaverage;
4414: char fileresf[FILENAMELENGTH];
4415:
4416: agelim=AGESUP;
4417: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4418:
4419: strcpy(fileresf,"f");
4420: strcat(fileresf,fileres);
4421: if((ficresf=fopen(fileresf,"w"))==NULL) {
4422: printf("Problem with forecast resultfile: %s\n", fileresf);
4423: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4424: }
4425: printf("Computing forecasting: result on file '%s' \n", fileresf);
4426: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4427:
4428: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4429:
4430: if (mobilav!=0) {
4431: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4432: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4433: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4434: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4435: }
4436: }
4437:
4438: stepsize=(int) (stepm+YEARM-1)/YEARM;
4439: if (stepm<=12) stepsize=1;
4440: if(estepm < stepm){
4441: printf ("Problem %d lower than %d\n",estepm, stepm);
4442: }
4443: else hstepm=estepm;
4444:
4445: hstepm=hstepm/stepm;
4446: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4447: fractional in yp1 */
4448: anprojmean=yp;
4449: yp2=modf((yp1*12),&yp);
4450: mprojmean=yp;
4451: yp1=modf((yp2*30.5),&yp);
4452: jprojmean=yp;
4453: if(jprojmean==0) jprojmean=1;
4454: if(mprojmean==0) jprojmean=1;
4455:
4456: i1=cptcoveff;
4457: if (cptcovn < 1){i1=1;}
4458:
4459: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4460:
4461: fprintf(ficresf,"#****** Routine prevforecast **\n");
4462:
4463: /* if (h==(int)(YEARM*yearp)){ */
4464: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4465: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4466: k=k+1;
4467: fprintf(ficresf,"\n#******");
4468: for(j=1;j<=cptcoveff;j++) {
4469: 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]]);
4470: }
4471: fprintf(ficresf,"******\n");
4472: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4473: for(j=1; j<=nlstate+ndeath;j++){
4474: for(i=1; i<=nlstate;i++)
4475: fprintf(ficresf," p%d%d",i,j);
4476: fprintf(ficresf," p.%d",j);
4477: }
4478: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4479: fprintf(ficresf,"\n");
4480: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4481:
4482: for (agec=fage; agec>=(ageminpar-1); agec--){
4483: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4484: nhstepm = nhstepm/hstepm;
4485: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4486: oldm=oldms;savm=savms;
4487: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4488:
4489: for (h=0; h<=nhstepm; h++){
4490: if (h*hstepm/YEARM*stepm ==yearp) {
4491: fprintf(ficresf,"\n");
4492: for(j=1;j<=cptcoveff;j++)
4493: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4494: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4495: }
4496: for(j=1; j<=nlstate+ndeath;j++) {
4497: ppij=0.;
4498: for(i=1; i<=nlstate;i++) {
4499: if (mobilav==1)
4500: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4501: else {
4502: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4503: }
4504: if (h*hstepm/YEARM*stepm== yearp) {
4505: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4506: }
4507: } /* end i */
4508: if (h*hstepm/YEARM*stepm==yearp) {
4509: fprintf(ficresf," %.3f", ppij);
4510: }
4511: }/* end j */
4512: } /* end h */
4513: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4514: } /* end agec */
4515: } /* end yearp */
4516: } /* end cptcod */
4517: } /* end cptcov */
4518:
4519: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4520:
4521: fclose(ficresf);
4522: }
4523:
4524: /************** Forecasting *****not tested NB*************/
4525: 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){
4526:
4527: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4528: int *popage;
4529: double calagedatem, agelim, kk1, kk2;
4530: double *popeffectif,*popcount;
4531: double ***p3mat,***tabpop,***tabpopprev;
4532: double ***mobaverage;
4533: char filerespop[FILENAMELENGTH];
4534:
4535: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4536: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4537: agelim=AGESUP;
4538: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4539:
4540: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4541:
4542:
4543: strcpy(filerespop,"pop");
4544: strcat(filerespop,fileres);
4545: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4546: printf("Problem with forecast resultfile: %s\n", filerespop);
4547: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4548: }
4549: printf("Computing forecasting: result on file '%s' \n", filerespop);
4550: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4551:
4552: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4553:
4554: if (mobilav!=0) {
4555: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4556: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4557: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4558: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4559: }
4560: }
4561:
4562: stepsize=(int) (stepm+YEARM-1)/YEARM;
4563: if (stepm<=12) stepsize=1;
4564:
4565: agelim=AGESUP;
4566:
4567: hstepm=1;
4568: hstepm=hstepm/stepm;
4569:
4570: if (popforecast==1) {
4571: if((ficpop=fopen(popfile,"r"))==NULL) {
4572: printf("Problem with population file : %s\n",popfile);exit(0);
4573: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4574: }
4575: popage=ivector(0,AGESUP);
4576: popeffectif=vector(0,AGESUP);
4577: popcount=vector(0,AGESUP);
4578:
4579: i=1;
4580: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4581:
4582: imx=i;
4583: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4584: }
4585:
4586: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4587: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4588: k=k+1;
4589: fprintf(ficrespop,"\n#******");
4590: for(j=1;j<=cptcoveff;j++) {
4591: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4592: }
4593: fprintf(ficrespop,"******\n");
4594: fprintf(ficrespop,"# Age");
4595: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4596: if (popforecast==1) fprintf(ficrespop," [Population]");
4597:
4598: for (cpt=0; cpt<=0;cpt++) {
4599: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4600:
4601: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4602: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4603: nhstepm = nhstepm/hstepm;
4604:
4605: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4606: oldm=oldms;savm=savms;
4607: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4608:
4609: for (h=0; h<=nhstepm; h++){
4610: if (h==(int) (calagedatem+YEARM*cpt)) {
4611: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4612: }
4613: for(j=1; j<=nlstate+ndeath;j++) {
4614: kk1=0.;kk2=0;
4615: for(i=1; i<=nlstate;i++) {
4616: if (mobilav==1)
4617: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4618: else {
4619: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4620: }
4621: }
4622: if (h==(int)(calagedatem+12*cpt)){
4623: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4624: /*fprintf(ficrespop," %.3f", kk1);
4625: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4626: }
4627: }
4628: for(i=1; i<=nlstate;i++){
4629: kk1=0.;
4630: for(j=1; j<=nlstate;j++){
4631: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4632: }
4633: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4634: }
4635:
4636: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4637: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4638: }
4639: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4640: }
4641: }
4642:
4643: /******/
4644:
4645: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4646: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4647: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4648: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4649: nhstepm = nhstepm/hstepm;
4650:
4651: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4652: oldm=oldms;savm=savms;
4653: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4654: for (h=0; h<=nhstepm; h++){
4655: if (h==(int) (calagedatem+YEARM*cpt)) {
4656: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4657: }
4658: for(j=1; j<=nlstate+ndeath;j++) {
4659: kk1=0.;kk2=0;
4660: for(i=1; i<=nlstate;i++) {
4661: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4662: }
4663: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4664: }
4665: }
4666: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4667: }
4668: }
4669: }
4670: }
4671:
4672: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4673:
4674: if (popforecast==1) {
4675: free_ivector(popage,0,AGESUP);
4676: free_vector(popeffectif,0,AGESUP);
4677: free_vector(popcount,0,AGESUP);
4678: }
4679: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4680: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4681: fclose(ficrespop);
4682: } /* End of popforecast */
4683:
4684: int fileappend(FILE *fichier, char *optionfich)
4685: {
4686: if((fichier=fopen(optionfich,"a"))==NULL) {
4687: printf("Problem with file: %s\n", optionfich);
4688: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4689: return (0);
4690: }
4691: fflush(fichier);
4692: return (1);
4693: }
4694:
4695:
4696: /**************** function prwizard **********************/
4697: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4698: {
4699:
4700: /* Wizard to print covariance matrix template */
4701:
4702: char ca[32], cb[32], cc[32];
4703: int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
4704: int numlinepar;
4705:
4706: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4707: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4708: for(i=1; i <=nlstate; i++){
4709: jj=0;
4710: for(j=1; j <=nlstate+ndeath; j++){
4711: if(j==i) continue;
4712: jj++;
4713: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4714: printf("%1d%1d",i,j);
4715: fprintf(ficparo,"%1d%1d",i,j);
4716: for(k=1; k<=ncovmodel;k++){
4717: /* printf(" %lf",param[i][j][k]); */
4718: /* fprintf(ficparo," %lf",param[i][j][k]); */
4719: printf(" 0.");
4720: fprintf(ficparo," 0.");
4721: }
4722: printf("\n");
4723: fprintf(ficparo,"\n");
4724: }
4725: }
4726: printf("# Scales (for hessian or gradient estimation)\n");
4727: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4728: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4729: for(i=1; i <=nlstate; i++){
4730: jj=0;
4731: for(j=1; j <=nlstate+ndeath; j++){
4732: if(j==i) continue;
4733: jj++;
4734: fprintf(ficparo,"%1d%1d",i,j);
4735: printf("%1d%1d",i,j);
4736: fflush(stdout);
4737: for(k=1; k<=ncovmodel;k++){
4738: /* printf(" %le",delti3[i][j][k]); */
4739: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4740: printf(" 0.");
4741: fprintf(ficparo," 0.");
4742: }
4743: numlinepar++;
4744: printf("\n");
4745: fprintf(ficparo,"\n");
4746: }
4747: }
4748: printf("# Covariance matrix\n");
4749: /* # 121 Var(a12)\n\ */
4750: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4751: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4752: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4753: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4754: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4755: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4756: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4757: fflush(stdout);
4758: fprintf(ficparo,"# Covariance matrix\n");
4759: /* # 121 Var(a12)\n\ */
4760: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4761: /* # ...\n\ */
4762: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4763:
4764: for(itimes=1;itimes<=2;itimes++){
4765: jj=0;
4766: for(i=1; i <=nlstate; i++){
4767: for(j=1; j <=nlstate+ndeath; j++){
4768: if(j==i) continue;
4769: for(k=1; k<=ncovmodel;k++){
4770: jj++;
4771: ca[0]= k+'a'-1;ca[1]='\0';
4772: if(itimes==1){
4773: printf("#%1d%1d%d",i,j,k);
4774: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4775: }else{
4776: printf("%1d%1d%d",i,j,k);
4777: fprintf(ficparo,"%1d%1d%d",i,j,k);
4778: /* printf(" %.5le",matcov[i][j]); */
4779: }
4780: ll=0;
4781: for(li=1;li <=nlstate; li++){
4782: for(lj=1;lj <=nlstate+ndeath; lj++){
4783: if(lj==li) continue;
4784: for(lk=1;lk<=ncovmodel;lk++){
4785: ll++;
4786: if(ll<=jj){
4787: cb[0]= lk +'a'-1;cb[1]='\0';
4788: if(ll<jj){
4789: if(itimes==1){
4790: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4791: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4792: }else{
4793: printf(" 0.");
4794: fprintf(ficparo," 0.");
4795: }
4796: }else{
4797: if(itimes==1){
4798: printf(" Var(%s%1d%1d)",ca,i,j);
4799: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4800: }else{
4801: printf(" 0.");
4802: fprintf(ficparo," 0.");
4803: }
4804: }
4805: }
4806: } /* end lk */
4807: } /* end lj */
4808: } /* end li */
4809: printf("\n");
4810: fprintf(ficparo,"\n");
4811: numlinepar++;
4812: } /* end k*/
4813: } /*end j */
4814: } /* end i */
4815: } /* end itimes */
4816:
4817: } /* end of prwizard */
4818: /******************* Gompertz Likelihood ******************************/
4819: double gompertz(double x[])
4820: {
4821: double A,B,L=0.0,sump=0.,num=0.;
4822: int i,n=0; /* n is the size of the sample */
4823:
4824: for (i=0;i<=imx-1 ; i++) {
4825: sump=sump+weight[i];
4826: /* sump=sump+1;*/
4827: num=num+1;
4828: }
4829:
4830:
4831: /* for (i=0; i<=imx; i++)
4832: 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]);*/
4833:
4834: for (i=1;i<=imx ; i++)
4835: {
4836: if (cens[i] == 1 && wav[i]>1)
4837: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4838:
4839: if (cens[i] == 0 && wav[i]>1)
4840: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4841: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4842:
4843: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4844: if (wav[i] > 1 ) { /* ??? */
4845: L=L+A*weight[i];
4846: /* 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]);*/
4847: }
4848: }
4849:
4850: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4851:
4852: return -2*L*num/sump;
4853: }
4854:
1.136 brouard 4855: #ifdef GSL
4856: /******************* Gompertz_f Likelihood ******************************/
4857: double gompertz_f(const gsl_vector *v, void *params)
4858: {
4859: double A,B,LL=0.0,sump=0.,num=0.;
4860: double *x= (double *) v->data;
4861: int i,n=0; /* n is the size of the sample */
4862:
4863: for (i=0;i<=imx-1 ; i++) {
4864: sump=sump+weight[i];
4865: /* sump=sump+1;*/
4866: num=num+1;
4867: }
4868:
4869:
4870: /* for (i=0; i<=imx; i++)
4871: 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]);*/
4872: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4873: for (i=1;i<=imx ; i++)
4874: {
4875: if (cens[i] == 1 && wav[i]>1)
4876: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4877:
4878: if (cens[i] == 0 && wav[i]>1)
4879: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4880: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4881:
4882: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4883: if (wav[i] > 1 ) { /* ??? */
4884: LL=LL+A*weight[i];
4885: /* 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]);*/
4886: }
4887: }
4888:
4889: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4890: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4891:
4892: return -2*LL*num/sump;
4893: }
4894: #endif
4895:
1.126 brouard 4896: /******************* Printing html file ***********/
4897: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4898: int lastpass, int stepm, int weightopt, char model[],\
4899: int imx, double p[],double **matcov,double agemortsup){
4900: int i,k;
4901:
4902: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4903: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4904: for (i=1;i<=2;i++)
4905: 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]));
4906: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4907: fprintf(fichtm,"</ul>");
4908:
4909: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4910:
4911: 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>");
4912:
4913: for (k=agegomp;k<(agemortsup-2);k++)
4914: 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]);
4915:
4916:
4917: fflush(fichtm);
4918: }
4919:
4920: /******************* Gnuplot file **************/
4921: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4922:
4923: char dirfileres[132],optfileres[132];
4924: int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
4925: int ng;
4926:
4927:
4928: /*#ifdef windows */
4929: fprintf(ficgp,"cd \"%s\" \n",pathc);
4930: /*#endif */
4931:
4932:
4933: strcpy(dirfileres,optionfilefiname);
4934: strcpy(optfileres,"vpl");
4935: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4936: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 4937: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4938: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 4939: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4940:
4941: }
4942:
1.136 brouard 4943: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4944: {
1.126 brouard 4945:
1.136 brouard 4946: /*-------- data file ----------*/
4947: FILE *fic;
4948: char dummy[]=" ";
4949: int i, j, n;
4950: int linei, month, year,iout;
4951: char line[MAXLINE], linetmp[MAXLINE];
4952: char stra[80], strb[80];
4953: char *stratrunc;
4954: int lstra;
1.126 brouard 4955:
4956:
1.136 brouard 4957: if((fic=fopen(datafile,"r"))==NULL) {
4958: printf("Problem while opening datafile: %s\n", datafile);return 1;
4959: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
4960: }
1.126 brouard 4961:
1.136 brouard 4962: i=1;
4963: linei=0;
4964: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
4965: linei=linei+1;
4966: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
4967: if(line[j] == '\t')
4968: line[j] = ' ';
4969: }
4970: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
4971: ;
4972: };
4973: line[j+1]=0; /* Trims blanks at end of line */
4974: if(line[0]=='#'){
4975: fprintf(ficlog,"Comment line\n%s\n",line);
4976: printf("Comment line\n%s\n",line);
4977: continue;
4978: }
4979: trimbb(linetmp,line); /* Trims multiple blanks in line */
4980: for (j=0; line[j]!='\0';j++){
4981: line[j]=linetmp[j];
4982: }
4983:
1.126 brouard 4984:
1.136 brouard 4985: for (j=maxwav;j>=1;j--){
1.137 brouard 4986: cutv(stra, strb, line, ' ');
1.136 brouard 4987: if(strb[0]=='.') { /* Missing status */
4988: lval=-1;
4989: }else{
4990: errno=0;
4991: lval=strtol(strb,&endptr,10);
4992: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
4993: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 4994: 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);
4995: 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 4996: return 1;
4997: }
4998: }
4999: s[j][i]=lval;
5000:
5001: strcpy(line,stra);
5002: cutv(stra, strb,line,' ');
5003: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5004: }
1.145 brouard 5005: else if(iout=sscanf(strb,"%s.",dummy) != 0){
1.136 brouard 5006: month=99;
5007: year=9999;
5008: }else{
1.141 brouard 5009: 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);
5010: 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 5011: return 1;
5012: }
5013: anint[j][i]= (double) year;
5014: mint[j][i]= (double)month;
5015: strcpy(line,stra);
5016: } /* ENd Waves */
5017:
5018: cutv(stra, strb,line,' ');
5019: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5020: }
5021: else if(iout=sscanf(strb,"%s.",dummy) != 0){
5022: month=99;
5023: year=9999;
5024: }else{
1.141 brouard 5025: 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);
5026: 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 5027: return 1;
5028: }
5029: andc[i]=(double) year;
5030: moisdc[i]=(double) month;
5031: strcpy(line,stra);
5032:
5033: cutv(stra, strb,line,' ');
5034: if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
5035: }
1.145 brouard 5036: else if(iout=sscanf(strb,"%s.", dummy) != 0){
1.136 brouard 5037: month=99;
5038: year=9999;
5039: }else{
1.141 brouard 5040: 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);
5041: 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 5042: return 1;
5043: }
5044: if (year==9999) {
1.141 brouard 5045: 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);
5046: 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 5047: return 1;
1.126 brouard 5048:
1.136 brouard 5049: }
5050: annais[i]=(double)(year);
5051: moisnais[i]=(double)(month);
5052: strcpy(line,stra);
5053:
5054: cutv(stra, strb,line,' ');
5055: errno=0;
5056: dval=strtod(strb,&endptr);
5057: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5058: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5059: 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 5060: fflush(ficlog);
5061: return 1;
5062: }
5063: weight[i]=dval;
5064: strcpy(line,stra);
5065:
5066: for (j=ncovcol;j>=1;j--){
5067: cutv(stra, strb,line,' ');
5068: if(strb[0]=='.') { /* Missing status */
5069: lval=-1;
5070: }else{
5071: errno=0;
5072: lval=strtol(strb,&endptr,10);
5073: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5074: 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);
5075: 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 5076: return 1;
5077: }
5078: }
5079: if(lval <-1 || lval >1){
1.141 brouard 5080: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5081: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5082: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5083: For example, for multinomial values like 1, 2 and 3,\n \
5084: build V1=0 V2=0 for the reference value (1),\n \
5085: V1=1 V2=0 for (2) \n \
5086: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5087: output of IMaCh is often meaningless.\n \
5088: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5089: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5090: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5091: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5092: For example, for multinomial values like 1, 2 and 3,\n \
5093: build V1=0 V2=0 for the reference value (1),\n \
5094: V1=1 V2=0 for (2) \n \
5095: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5096: output of IMaCh is often meaningless.\n \
5097: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5098: return 1;
5099: }
5100: covar[j][i]=(double)(lval);
5101: strcpy(line,stra);
5102: }
5103: lstra=strlen(stra);
5104:
5105: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5106: stratrunc = &(stra[lstra-9]);
5107: num[i]=atol(stratrunc);
5108: }
5109: else
5110: num[i]=atol(stra);
5111: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5112: 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;}*/
5113:
5114: i=i+1;
5115: } /* End loop reading data */
1.126 brouard 5116:
1.136 brouard 5117: *imax=i-1; /* Number of individuals */
5118: fclose(fic);
5119:
5120: return (0);
5121: endread:
5122: printf("Exiting readdata: ");
5123: fclose(fic);
5124: return (1);
1.126 brouard 5125:
5126:
5127:
1.136 brouard 5128: }
1.145 brouard 5129: void removespace(char *str) {
5130: char *p1 = str, *p2 = str;
5131: do
5132: while (*p2 == ' ')
5133: p2++;
5134: while (*p1++ = *p2++);
5135: }
5136:
5137: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5138: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5139: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5140: * - cptcovn or number of covariates k of the models excluding age*products =6
5141: * - cptcovage number of covariates with age*products =2
5142: * - cptcovs number of simple covariates
5143: * - 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
5144: * which is a new column after the 9 (ncovcol) variables.
5145: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5146: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5147: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5148: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5149: */
1.136 brouard 5150: {
1.145 brouard 5151: int i, j, k, ks;
1.136 brouard 5152: int i1, j1, k1, k2;
5153: char modelsav[80];
1.145 brouard 5154: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.136 brouard 5155:
1.145 brouard 5156: /*removespace(model);*/
1.136 brouard 5157: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5158: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5159: j=nbocc(model,'+'); /**< j=Number of '+' */
5160: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5161: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5162: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5163: /* including age products which are counted in cptcovage.
5164: /* but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5165: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5166: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
1.136 brouard 5167: strcpy(modelsav,model);
1.137 brouard 5168: if (strstr(model,"AGE") !=0){
5169: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5170: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
1.136 brouard 5171: return 1;
5172: }
1.141 brouard 5173: if (strstr(model,"v") !=0){
5174: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5175: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5176: return 1;
5177: }
1.136 brouard 5178:
1.145 brouard 5179: /* Design
5180: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5181: * < ncovcol=8 >
5182: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5183: * k= 1 2 3 4 5 6 7 8
5184: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5185: * covar[k,i], value of kth covariate if not including age for individual i:
5186: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5187: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5188: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5189: * Tage[++cptcovage]=k
5190: * if products, new covar are created after ncovcol with k1
5191: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5192: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5193: * 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
5194: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5195: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5196: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5197: * < ncovcol=8 >
5198: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5199: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5200: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5201: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5202: * p Tprod[1]@2={ 6, 5}
5203: *p Tvard[1][1]@4= {7, 8, 5, 6}
5204: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5205: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5206: *How to reorganize?
5207: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5208: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5209: * {2, 1, 4, 8, 5, 6, 3, 7}
5210: * Struct []
5211: */
5212:
1.136 brouard 5213: /* This loop fills the array Tvar from the string 'model'.*/
5214: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
1.137 brouard 5215: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5216: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5217: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5218: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5219: /* k=1 Tvar[1]=2 (from V2) */
5220: /* k=5 Tvar[5] */
5221: /* for (k=1; k<=cptcovn;k++) { */
5222: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5223: /* } */
5224: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.145 brouard 5225: /*
5226: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5227: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5228: Tvar[k]=0;
5229: cptcovage=0;
5230: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5231: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5232: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
1.137 brouard 5233: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
1.136 brouard 5234: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5235: /*scanf("%d",i);*/
1.145 brouard 5236: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5237: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5238: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5239: /* covar is not filled and then is empty */
1.136 brouard 5240: cptcovprod--;
1.145 brouard 5241: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5242: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
1.136 brouard 5243: cptcovage++; /* Sums the number of covariates which include age as a product */
1.137 brouard 5244: Tage[cptcovage]=k; /* Tage[1] = 4 */
1.136 brouard 5245: /*printf("stre=%s ", stre);*/
1.137 brouard 5246: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
1.136 brouard 5247: cptcovprod--;
1.145 brouard 5248: cutl(stre,strb,strc,'V');
1.136 brouard 5249: Tvar[k]=atoi(stre);
5250: cptcovage++;
5251: Tage[cptcovage]=k;
1.137 brouard 5252: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5253: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
1.145 brouard 5254: cptcovn++;
5255: cptcovprodnoage++;k1++;
5256: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5257: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
1.137 brouard 5258: because this model-covariate is a construction we invent a new column
5259: ncovcol + k1
5260: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5261: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
1.145 brouard 5262: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
1.137 brouard 5263: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
1.145 brouard 5264: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5265: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5266: k2=k2+2;
5267: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5268: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
1.137 brouard 5269: for (i=1; i<=lastobs;i++){
5270: /* Computes the new covariate which is a product of
1.145 brouard 5271: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
1.136 brouard 5272: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
1.137 brouard 5273: }
5274: } /* End age is not in the model */
5275: } /* End if model includes a product */
1.136 brouard 5276: else { /* no more sum */
5277: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5278: /* scanf("%d",i);*/
1.145 brouard 5279: cutl(strd,strc,strb,'V');
5280: ks++; /**< Number of simple covariates */
5281: cptcovn++;
5282: Tvar[k]=atoi(strd);
1.136 brouard 5283: }
1.137 brouard 5284: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
1.136 brouard 5285: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5286: scanf("%d",i);*/
5287: } /* end of loop + */
5288: } /* end model */
5289:
5290: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5291: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5292:
5293: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5294: printf("cptcovprod=%d ", cptcovprod);
5295: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5296:
5297: scanf("%d ",i);*/
5298:
5299:
1.137 brouard 5300: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.136 brouard 5301: endread:
5302: printf("Exiting decodemodel: ");
5303: return (1);
5304: }
5305:
5306: calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5307: {
5308: int i, m;
5309:
5310: for (i=1; i<=imx; i++) {
5311: for(m=2; (m<= maxwav); m++) {
5312: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5313: anint[m][i]=9999;
5314: s[m][i]=-1;
5315: }
5316: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5317: *nberr++;
5318: 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);
5319: 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);
5320: s[m][i]=-1;
5321: }
5322: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5323: *nberr++;
5324: 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]);
5325: 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]);
5326: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5327: }
5328: }
5329: }
5330:
5331: for (i=1; i<=imx; i++) {
5332: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5333: for(m=firstpass; (m<= lastpass); m++){
5334: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5335: if (s[m][i] >= nlstate+1) {
5336: if(agedc[i]>0)
5337: if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
5338: agev[m][i]=agedc[i];
5339: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5340: else {
5341: if ((int)andc[i]!=9999){
5342: nbwarn++;
5343: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5344: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5345: agev[m][i]=-1;
5346: }
5347: }
5348: }
5349: else if(s[m][i] !=9){ /* Standard case, age in fractional
5350: years but with the precision of a month */
5351: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5352: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5353: agev[m][i]=1;
5354: else if(agev[m][i] < *agemin){
5355: *agemin=agev[m][i];
5356: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5357: }
5358: else if(agev[m][i] >*agemax){
5359: *agemax=agev[m][i];
1.156 brouard 5360: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5361: }
5362: /*agev[m][i]=anint[m][i]-annais[i];*/
5363: /* agev[m][i] = age[i]+2*m;*/
5364: }
5365: else { /* =9 */
5366: agev[m][i]=1;
5367: s[m][i]=-1;
5368: }
5369: }
5370: else /*= 0 Unknown */
5371: agev[m][i]=1;
5372: }
5373:
5374: }
5375: for (i=1; i<=imx; i++) {
5376: for(m=firstpass; (m<=lastpass); m++){
5377: if (s[m][i] > (nlstate+ndeath)) {
5378: *nberr++;
5379: 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);
5380: 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);
5381: return 1;
5382: }
5383: }
5384: }
5385:
5386: /*for (i=1; i<=imx; i++){
5387: for (m=firstpass; (m<lastpass); m++){
5388: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5389: }
5390:
5391: }*/
5392:
5393:
1.139 brouard 5394: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5395: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5396:
5397: return (0);
5398: endread:
5399: printf("Exiting calandcheckages: ");
5400: return (1);
5401: }
5402:
5403:
5404: /***********************************************/
5405: /**************** Main Program *****************/
5406: /***********************************************/
5407:
5408: int main(int argc, char *argv[])
5409: {
5410: #ifdef GSL
5411: const gsl_multimin_fminimizer_type *T;
5412: size_t iteri = 0, it;
5413: int rval = GSL_CONTINUE;
5414: int status = GSL_SUCCESS;
5415: double ssval;
5416: #endif
5417: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5418: int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
5419: int linei, month, year,iout;
5420: int jj, ll, li, lj, lk, imk;
5421: int numlinepar=0; /* Current linenumber of parameter file */
5422: int itimes;
5423: int NDIM=2;
5424: int vpopbased=0;
5425:
5426: char ca[32], cb[32], cc[32];
5427: /* FILE *fichtm; *//* Html File */
5428: /* FILE *ficgp;*/ /*Gnuplot File */
5429: struct stat info;
5430: double agedeb, agefin,hf;
5431: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5432:
5433: double fret;
5434: double **xi,tmp,delta;
5435:
5436: double dum; /* Dummy variable */
5437: double ***p3mat;
5438: double ***mobaverage;
5439: int *indx;
5440: char line[MAXLINE], linepar[MAXLINE];
5441: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5442: char pathr[MAXLINE], pathimach[MAXLINE];
5443: char **bp, *tok, *val; /* pathtot */
5444: int firstobs=1, lastobs=10;
5445: int sdeb, sfin; /* Status at beginning and end */
5446: int c, h , cpt,l;
5447: int ju,jl, mi;
5448: int i1,j1, jk,aa,bb, stepsize, ij;
5449: int jnais,jdc,jint4,jint1,jint2,jint3,*tab;
5450: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5451: int mobilav=0,popforecast=0;
5452: int hstepm, nhstepm;
5453: int agemortsup;
5454: float sumlpop=0.;
5455: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5456: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5457:
5458: double bage, fage, age, agelim, agebase;
5459: double ftolpl=FTOL;
5460: double **prlim;
5461: double ***param; /* Matrix of parameters */
5462: double *p;
5463: double **matcov; /* Matrix of covariance */
5464: double ***delti3; /* Scale */
5465: double *delti; /* Scale */
5466: double ***eij, ***vareij;
5467: double **varpl; /* Variances of prevalence limits by age */
5468: double *epj, vepp;
5469: double kk1, kk2;
5470: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5471: double **ximort;
1.145 brouard 5472: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 5473: int *dcwave;
5474:
5475: char z[1]="c", occ;
5476:
5477: /*char *strt;*/
5478: char strtend[80];
1.126 brouard 5479:
5480: long total_usecs;
5481:
5482: /* setlocale (LC_ALL, ""); */
5483: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5484: /* textdomain (PACKAGE); */
5485: /* setlocale (LC_CTYPE, ""); */
5486: /* setlocale (LC_MESSAGES, ""); */
5487:
5488: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 5489: rstart_time = time(NULL);
5490: /* (void) gettimeofday(&start_time,&tzp);*/
5491: start_time = *localtime(&rstart_time);
1.126 brouard 5492: curr_time=start_time;
1.157 brouard 5493: /*tml = *localtime(&start_time.tm_sec);*/
5494: /* strcpy(strstart,asctime(&tml)); */
5495: strcpy(strstart,asctime(&start_time));
1.126 brouard 5496:
5497: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 5498: /* tp.tm_sec = tp.tm_sec +86400; */
5499: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 5500: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5501: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5502: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 5503: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 5504: /* strt=asctime(&tmg); */
5505: /* printf("Time(after) =%s",strstart); */
5506: /* (void) time (&time_value);
5507: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5508: * tm = *localtime(&time_value);
5509: * strstart=asctime(&tm);
5510: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5511: */
5512:
5513: nberr=0; /* Number of errors and warnings */
5514: nbwarn=0;
5515: getcwd(pathcd, size);
5516:
5517: printf("\n%s\n%s",version,fullversion);
5518: if(argc <=1){
5519: printf("\nEnter the parameter file name: ");
5520: fgets(pathr,FILENAMELENGTH,stdin);
5521: i=strlen(pathr);
5522: if(pathr[i-1]=='\n')
5523: pathr[i-1]='\0';
1.156 brouard 5524: i=strlen(pathr);
5525: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5526: pathr[i-1]='\0';
1.126 brouard 5527: for (tok = pathr; tok != NULL; ){
5528: printf("Pathr |%s|\n",pathr);
5529: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5530: printf("val= |%s| pathr=%s\n",val,pathr);
5531: strcpy (pathtot, val);
5532: if(pathr[0] == '\0') break; /* Dirty */
5533: }
5534: }
5535: else{
5536: strcpy(pathtot,argv[1]);
5537: }
5538: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5539: /*cygwin_split_path(pathtot,path,optionfile);
5540: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5541: /* cutv(path,optionfile,pathtot,'\\');*/
5542:
5543: /* Split argv[0], imach program to get pathimach */
5544: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5545: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5546: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5547: /* strcpy(pathimach,argv[0]); */
5548: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5549: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5550: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5551: chdir(path); /* Can be a relative path */
5552: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5553: printf("Current directory %s!\n",pathcd);
5554: strcpy(command,"mkdir ");
5555: strcat(command,optionfilefiname);
5556: if((outcmd=system(command)) != 0){
5557: printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
5558: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5559: /* fclose(ficlog); */
5560: /* exit(1); */
5561: }
5562: /* if((imk=mkdir(optionfilefiname))<0){ */
5563: /* perror("mkdir"); */
5564: /* } */
5565:
5566: /*-------- arguments in the command line --------*/
5567:
5568: /* Log file */
5569: strcat(filelog, optionfilefiname);
5570: strcat(filelog,".log"); /* */
5571: if((ficlog=fopen(filelog,"w"))==NULL) {
5572: printf("Problem with logfile %s\n",filelog);
5573: goto end;
5574: }
5575: fprintf(ficlog,"Log filename:%s\n",filelog);
5576: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5577: fprintf(ficlog,"\nEnter the parameter file name: \n");
5578: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5579: path=%s \n\
5580: optionfile=%s\n\
5581: optionfilext=%s\n\
1.156 brouard 5582: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 5583:
5584: printf("Local time (at start):%s",strstart);
5585: fprintf(ficlog,"Local time (at start): %s",strstart);
5586: fflush(ficlog);
5587: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 5588: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 5589:
5590: /* */
5591: strcpy(fileres,"r");
5592: strcat(fileres, optionfilefiname);
5593: strcat(fileres,".txt"); /* Other files have txt extension */
5594:
5595: /*---------arguments file --------*/
5596:
5597: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 5598: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5599: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 5600: fflush(ficlog);
1.149 brouard 5601: /* goto end; */
5602: exit(70);
1.126 brouard 5603: }
5604:
5605:
5606:
5607: strcpy(filereso,"o");
5608: strcat(filereso,fileres);
5609: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5610: printf("Problem with Output resultfile: %s\n", filereso);
5611: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5612: fflush(ficlog);
5613: goto end;
5614: }
5615:
5616: /* Reads comments: lines beginning with '#' */
5617: numlinepar=0;
5618: while((c=getc(ficpar))=='#' && c!= EOF){
5619: ungetc(c,ficpar);
5620: fgets(line, MAXLINE, ficpar);
5621: numlinepar++;
1.141 brouard 5622: fputs(line,stdout);
1.126 brouard 5623: fputs(line,ficparo);
5624: fputs(line,ficlog);
5625: }
5626: ungetc(c,ficpar);
5627:
5628: 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);
5629: numlinepar++;
5630: 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);
5631: 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);
5632: 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);
5633: fflush(ficlog);
5634: while((c=getc(ficpar))=='#' && c!= EOF){
5635: ungetc(c,ficpar);
5636: fgets(line, MAXLINE, ficpar);
5637: numlinepar++;
1.141 brouard 5638: fputs(line, stdout);
5639: //puts(line);
1.126 brouard 5640: fputs(line,ficparo);
5641: fputs(line,ficlog);
5642: }
5643: ungetc(c,ficpar);
5644:
5645:
1.145 brouard 5646: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 5647: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5648: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5649: v1+v2*age+v2*v3 makes cptcovn = 3
5650: */
5651: if (strlen(model)>1)
1.145 brouard 5652: 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*/
5653: else
5654: ncovmodel=2;
1.126 brouard 5655: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
1.133 brouard 5656: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5657: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 5658: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5659: 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);
5660: 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);
5661: fflush(stdout);
5662: fclose (ficlog);
5663: goto end;
5664: }
1.126 brouard 5665: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5666: delti=delti3[1][1];
5667: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5668: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5669: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5670: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5671: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5672: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5673: fclose (ficparo);
5674: fclose (ficlog);
5675: goto end;
5676: exit(0);
5677: }
5678: else if(mle==-3) {
5679: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5680: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5681: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5682: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5683: matcov=matrix(1,npar,1,npar);
5684: }
5685: else{
1.145 brouard 5686: /* Read guessed parameters */
1.126 brouard 5687: /* Reads comments: lines beginning with '#' */
5688: while((c=getc(ficpar))=='#' && c!= EOF){
5689: ungetc(c,ficpar);
5690: fgets(line, MAXLINE, ficpar);
5691: numlinepar++;
1.141 brouard 5692: fputs(line,stdout);
1.126 brouard 5693: fputs(line,ficparo);
5694: fputs(line,ficlog);
5695: }
5696: ungetc(c,ficpar);
5697:
5698: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5699: for(i=1; i <=nlstate; i++){
5700: j=0;
5701: for(jj=1; jj <=nlstate+ndeath; jj++){
5702: if(jj==i) continue;
5703: j++;
5704: fscanf(ficpar,"%1d%1d",&i1,&j1);
5705: if ((i1 != i) && (j1 != j)){
5706: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5707: It might be a problem of design; if ncovcol and the model are correct\n \
5708: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5709: exit(1);
5710: }
5711: fprintf(ficparo,"%1d%1d",i1,j1);
5712: if(mle==1)
5713: printf("%1d%1d",i,j);
5714: fprintf(ficlog,"%1d%1d",i,j);
5715: for(k=1; k<=ncovmodel;k++){
5716: fscanf(ficpar," %lf",¶m[i][j][k]);
5717: if(mle==1){
5718: printf(" %lf",param[i][j][k]);
5719: fprintf(ficlog," %lf",param[i][j][k]);
5720: }
5721: else
5722: fprintf(ficlog," %lf",param[i][j][k]);
5723: fprintf(ficparo," %lf",param[i][j][k]);
5724: }
5725: fscanf(ficpar,"\n");
5726: numlinepar++;
5727: if(mle==1)
5728: printf("\n");
5729: fprintf(ficlog,"\n");
5730: fprintf(ficparo,"\n");
5731: }
5732: }
5733: fflush(ficlog);
5734:
1.145 brouard 5735: /* Reads scales values */
1.126 brouard 5736: p=param[1][1];
5737:
5738: /* Reads comments: lines beginning with '#' */
5739: while((c=getc(ficpar))=='#' && c!= EOF){
5740: ungetc(c,ficpar);
5741: fgets(line, MAXLINE, ficpar);
5742: numlinepar++;
1.141 brouard 5743: fputs(line,stdout);
1.126 brouard 5744: fputs(line,ficparo);
5745: fputs(line,ficlog);
5746: }
5747: ungetc(c,ficpar);
5748:
5749: for(i=1; i <=nlstate; i++){
5750: for(j=1; j <=nlstate+ndeath-1; j++){
5751: fscanf(ficpar,"%1d%1d",&i1,&j1);
5752: if ((i1-i)*(j1-j)!=0){
5753: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5754: exit(1);
5755: }
5756: printf("%1d%1d",i,j);
5757: fprintf(ficparo,"%1d%1d",i1,j1);
5758: fprintf(ficlog,"%1d%1d",i1,j1);
5759: for(k=1; k<=ncovmodel;k++){
5760: fscanf(ficpar,"%le",&delti3[i][j][k]);
5761: printf(" %le",delti3[i][j][k]);
5762: fprintf(ficparo," %le",delti3[i][j][k]);
5763: fprintf(ficlog," %le",delti3[i][j][k]);
5764: }
5765: fscanf(ficpar,"\n");
5766: numlinepar++;
5767: printf("\n");
5768: fprintf(ficparo,"\n");
5769: fprintf(ficlog,"\n");
5770: }
5771: }
5772: fflush(ficlog);
5773:
1.145 brouard 5774: /* Reads covariance matrix */
1.126 brouard 5775: delti=delti3[1][1];
5776:
5777:
5778: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5779:
5780: /* Reads comments: lines beginning with '#' */
5781: while((c=getc(ficpar))=='#' && c!= EOF){
5782: ungetc(c,ficpar);
5783: fgets(line, MAXLINE, ficpar);
5784: numlinepar++;
1.141 brouard 5785: fputs(line,stdout);
1.126 brouard 5786: fputs(line,ficparo);
5787: fputs(line,ficlog);
5788: }
5789: ungetc(c,ficpar);
5790:
5791: matcov=matrix(1,npar,1,npar);
1.131 brouard 5792: for(i=1; i <=npar; i++)
5793: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5794:
1.126 brouard 5795: for(i=1; i <=npar; i++){
1.145 brouard 5796: fscanf(ficpar,"%s",str);
1.126 brouard 5797: if(mle==1)
5798: printf("%s",str);
5799: fprintf(ficlog,"%s",str);
5800: fprintf(ficparo,"%s",str);
5801: for(j=1; j <=i; j++){
5802: fscanf(ficpar," %le",&matcov[i][j]);
5803: if(mle==1){
5804: printf(" %.5le",matcov[i][j]);
5805: }
5806: fprintf(ficlog," %.5le",matcov[i][j]);
5807: fprintf(ficparo," %.5le",matcov[i][j]);
5808: }
5809: fscanf(ficpar,"\n");
5810: numlinepar++;
5811: if(mle==1)
5812: printf("\n");
5813: fprintf(ficlog,"\n");
5814: fprintf(ficparo,"\n");
5815: }
5816: for(i=1; i <=npar; i++)
5817: for(j=i+1;j<=npar;j++)
5818: matcov[i][j]=matcov[j][i];
5819:
5820: if(mle==1)
5821: printf("\n");
5822: fprintf(ficlog,"\n");
5823:
5824: fflush(ficlog);
5825:
5826: /*-------- Rewriting parameter file ----------*/
5827: strcpy(rfileres,"r"); /* "Rparameterfile */
5828: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5829: strcat(rfileres,"."); /* */
5830: strcat(rfileres,optionfilext); /* Other files have txt extension */
5831: if((ficres =fopen(rfileres,"w"))==NULL) {
5832: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5833: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5834: }
5835: fprintf(ficres,"#%s\n",version);
5836: } /* End of mle != -3 */
5837:
5838:
5839: n= lastobs;
5840: num=lvector(1,n);
5841: moisnais=vector(1,n);
5842: annais=vector(1,n);
5843: moisdc=vector(1,n);
5844: andc=vector(1,n);
5845: agedc=vector(1,n);
5846: cod=ivector(1,n);
5847: weight=vector(1,n);
5848: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5849: mint=matrix(1,maxwav,1,n);
5850: anint=matrix(1,maxwav,1,n);
1.131 brouard 5851: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 5852: tab=ivector(1,NCOVMAX);
1.144 brouard 5853: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 5854:
1.136 brouard 5855: /* Reads data from file datafile */
5856: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5857: goto end;
5858:
5859: /* Calculation of the number of parameters from char model */
1.137 brouard 5860: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5861: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5862: k=3 V4 Tvar[k=3]= 4 (from V4)
5863: k=2 V1 Tvar[k=2]= 1 (from V1)
5864: k=1 Tvar[1]=2 (from V2)
5865: */
5866: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5867: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5868: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5869: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5870: */
5871: /* For model-covariate k tells which data-covariate to use but
5872: because this model-covariate is a construction we invent a new column
5873: ncovcol + k1
5874: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
5875: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 5876: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 5877: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
5878: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
5879: */
1.145 brouard 5880: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
5881: 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 5882: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
5883: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 5884: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 5885: 4 covariates (3 plus signs)
5886: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
5887: */
1.136 brouard 5888:
5889: if(decodemodel(model, lastobs) == 1)
5890: goto end;
5891:
1.137 brouard 5892: if((double)(lastobs-imx)/(double)imx > 1.10){
5893: nbwarn++;
5894: 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);
5895: 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);
5896: }
1.136 brouard 5897: /* if(mle==1){*/
1.137 brouard 5898: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
5899: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 5900: }
5901:
5902: /*-calculation of age at interview from date of interview and age at death -*/
5903: agev=matrix(1,maxwav,1,imx);
5904:
5905: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
5906: goto end;
5907:
1.126 brouard 5908:
1.136 brouard 5909: agegomp=(int)agemin;
5910: free_vector(moisnais,1,n);
5911: free_vector(annais,1,n);
1.126 brouard 5912: /* free_matrix(mint,1,maxwav,1,n);
5913: free_matrix(anint,1,maxwav,1,n);*/
5914: free_vector(moisdc,1,n);
5915: free_vector(andc,1,n);
1.145 brouard 5916: /* */
5917:
1.126 brouard 5918: wav=ivector(1,imx);
5919: dh=imatrix(1,lastpass-firstpass+1,1,imx);
5920: bh=imatrix(1,lastpass-firstpass+1,1,imx);
5921: mw=imatrix(1,lastpass-firstpass+1,1,imx);
5922:
5923: /* Concatenates waves */
5924: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 5925: /* */
5926:
1.126 brouard 5927: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
5928:
5929: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
5930: ncodemax[1]=1;
1.145 brouard 5931: Ndum =ivector(-1,NCOVMAX);
5932: if (ncovmodel > 2)
5933: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
5934:
5935: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
5936: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
5937: h=0;
5938:
5939:
5940: /*if (cptcovn > 0) */
1.126 brouard 5941:
1.145 brouard 5942:
1.126 brouard 5943: m=pow(2,cptcoveff);
5944:
1.131 brouard 5945: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
1.143 brouard 5946: 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 */
5947: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
5948: 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 5949: h++;
1.141 brouard 5950: if (h>m)
1.136 brouard 5951: h=1;
1.144 brouard 5952: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.143 brouard 5953: * h 1 2 3 4
5954: *______________________________
5955: * 1 i=1 1 i=1 1 i=1 1 i=1 1
5956: * 2 2 1 1 1
5957: * 3 i=2 1 2 1 1
5958: * 4 2 2 1 1
5959: * 5 i=3 1 i=2 1 2 1
5960: * 6 2 1 2 1
5961: * 7 i=4 1 2 2 1
5962: * 8 2 2 2 1
5963: * 9 i=5 1 i=3 1 i=2 1 1
5964: * 10 2 1 1 1
5965: * 11 i=6 1 2 1 1
5966: * 12 2 2 1 1
5967: * 13 i=7 1 i=4 1 2 1
5968: * 14 2 1 2 1
5969: * 15 i=8 1 2 2 1
5970: * 16 2 2 2 1
5971: */
1.141 brouard 5972: codtab[h][k]=j;
1.145 brouard 5973: /*codtab[h][Tvar[k]]=j;*/
1.130 brouard 5974: 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 5975: }
5976: }
5977: }
5978: }
5979: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
5980: codtab[1][2]=1;codtab[2][2]=2; */
5981: /* for(i=1; i <=m ;i++){
5982: for(k=1; k <=cptcovn; k++){
1.131 brouard 5983: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
1.126 brouard 5984: }
5985: printf("\n");
5986: }
5987: scanf("%d",i);*/
1.145 brouard 5988:
5989: free_ivector(Ndum,-1,NCOVMAX);
5990:
5991:
1.126 brouard 5992:
5993: /*------------ gnuplot -------------*/
5994: strcpy(optionfilegnuplot,optionfilefiname);
5995: if(mle==-3)
5996: strcat(optionfilegnuplot,"-mort");
5997: strcat(optionfilegnuplot,".gp");
5998:
5999: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6000: printf("Problem with file %s",optionfilegnuplot);
6001: }
6002: else{
6003: fprintf(ficgp,"\n# %s\n", version);
6004: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6005: //fprintf(ficgp,"set missing 'NaNq'\n");
6006: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6007: }
6008: /* fclose(ficgp);*/
6009: /*--------- index.htm --------*/
6010:
6011: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6012: if(mle==-3)
6013: strcat(optionfilehtm,"-mort");
6014: strcat(optionfilehtm,".htm");
6015: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 6016: printf("Problem with %s \n",optionfilehtm);
6017: exit(0);
1.126 brouard 6018: }
6019:
6020: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6021: strcat(optionfilehtmcov,"-cov.htm");
6022: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6023: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6024: }
6025: else{
6026: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6027: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6028: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6029: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6030: }
6031:
6032: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6033: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6034: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6035: \n\
6036: <hr size=\"2\" color=\"#EC5E5E\">\
6037: <ul><li><h4>Parameter files</h4>\n\
6038: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6039: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6040: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6041: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6042: - Date and time at start: %s</ul>\n",\
6043: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6044: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6045: fileres,fileres,\
6046: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6047: fflush(fichtm);
6048:
6049: strcpy(pathr,path);
6050: strcat(pathr,optionfilefiname);
6051: chdir(optionfilefiname); /* Move to directory named optionfile */
6052:
6053: /* Calculates basic frequencies. Computes observed prevalence at single age
6054: and prints on file fileres'p'. */
6055: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6056:
6057: fprintf(fichtm,"\n");
6058: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6059: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6060: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6061: imx,agemin,agemax,jmin,jmax,jmean);
6062: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6063: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6064: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6065: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6066: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6067:
6068:
6069: /* For Powell, parameters are in a vector p[] starting at p[1]
6070: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6071: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6072:
6073: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6074:
6075: if (mle==-3){
1.136 brouard 6076: ximort=matrix(1,NDIM,1,NDIM);
6077: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 6078: cens=ivector(1,n);
6079: ageexmed=vector(1,n);
6080: agecens=vector(1,n);
6081: dcwave=ivector(1,n);
6082:
6083: for (i=1; i<=imx; i++){
6084: dcwave[i]=-1;
6085: for (m=firstpass; m<=lastpass; m++)
6086: if (s[m][i]>nlstate) {
6087: dcwave[i]=m;
6088: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6089: break;
6090: }
6091: }
6092:
6093: for (i=1; i<=imx; i++) {
6094: if (wav[i]>0){
6095: ageexmed[i]=agev[mw[1][i]][i];
6096: j=wav[i];
6097: agecens[i]=1.;
6098:
6099: if (ageexmed[i]> 1 && wav[i] > 0){
6100: agecens[i]=agev[mw[j][i]][i];
6101: cens[i]= 1;
6102: }else if (ageexmed[i]< 1)
6103: cens[i]= -1;
6104: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6105: cens[i]=0 ;
6106: }
6107: else cens[i]=-1;
6108: }
6109:
6110: for (i=1;i<=NDIM;i++) {
6111: for (j=1;j<=NDIM;j++)
6112: ximort[i][j]=(i == j ? 1.0 : 0.0);
6113: }
6114:
1.145 brouard 6115: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 6116: /*printf("%lf %lf", p[1], p[2]);*/
6117:
6118:
1.136 brouard 6119: #ifdef GSL
6120: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 6121: #else
1.126 brouard 6122: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 6123: #endif
1.126 brouard 6124: strcpy(filerespow,"pow-mort");
6125: strcat(filerespow,fileres);
6126: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6127: printf("Problem with resultfile: %s\n", filerespow);
6128: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6129: }
1.136 brouard 6130: #ifdef GSL
6131: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 6132: #else
1.126 brouard 6133: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 6134: #endif
1.126 brouard 6135: /* for (i=1;i<=nlstate;i++)
6136: for(j=1;j<=nlstate+ndeath;j++)
6137: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6138: */
6139: fprintf(ficrespow,"\n");
1.136 brouard 6140: #ifdef GSL
6141: /* gsl starts here */
6142: T = gsl_multimin_fminimizer_nmsimplex;
6143: gsl_multimin_fminimizer *sfm = NULL;
6144: gsl_vector *ss, *x;
6145: gsl_multimin_function minex_func;
6146:
6147: /* Initial vertex size vector */
6148: ss = gsl_vector_alloc (NDIM);
6149:
6150: if (ss == NULL){
6151: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6152: }
6153: /* Set all step sizes to 1 */
6154: gsl_vector_set_all (ss, 0.001);
6155:
6156: /* Starting point */
1.126 brouard 6157:
1.136 brouard 6158: x = gsl_vector_alloc (NDIM);
6159:
6160: if (x == NULL){
6161: gsl_vector_free(ss);
6162: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6163: }
6164:
6165: /* Initialize method and iterate */
6166: /* p[1]=0.0268; p[NDIM]=0.083; */
6167: /* gsl_vector_set(x, 0, 0.0268); */
6168: /* gsl_vector_set(x, 1, 0.083); */
6169: gsl_vector_set(x, 0, p[1]);
6170: gsl_vector_set(x, 1, p[2]);
6171:
6172: minex_func.f = &gompertz_f;
6173: minex_func.n = NDIM;
6174: minex_func.params = (void *)&p; /* ??? */
6175:
6176: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6177: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6178:
6179: printf("Iterations beginning .....\n\n");
6180: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6181:
6182: iteri=0;
6183: while (rval == GSL_CONTINUE){
6184: iteri++;
6185: status = gsl_multimin_fminimizer_iterate(sfm);
6186:
6187: if (status) printf("error: %s\n", gsl_strerror (status));
6188: fflush(0);
6189:
6190: if (status)
6191: break;
6192:
6193: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6194: ssval = gsl_multimin_fminimizer_size (sfm);
6195:
6196: if (rval == GSL_SUCCESS)
6197: printf ("converged to a local maximum at\n");
6198:
6199: printf("%5d ", iteri);
6200: for (it = 0; it < NDIM; it++){
6201: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6202: }
6203: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6204: }
6205:
6206: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6207:
6208: gsl_vector_free(x); /* initial values */
6209: gsl_vector_free(ss); /* inital step size */
6210: for (it=0; it<NDIM; it++){
6211: p[it+1]=gsl_vector_get(sfm->x,it);
6212: fprintf(ficrespow," %.12lf", p[it]);
6213: }
6214: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6215: #endif
6216: #ifdef POWELL
6217: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6218: #endif
1.126 brouard 6219: fclose(ficrespow);
6220:
6221: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6222:
6223: for(i=1; i <=NDIM; i++)
6224: for(j=i+1;j<=NDIM;j++)
6225: matcov[i][j]=matcov[j][i];
6226:
6227: printf("\nCovariance matrix\n ");
6228: for(i=1; i <=NDIM; i++) {
6229: for(j=1;j<=NDIM;j++){
6230: printf("%f ",matcov[i][j]);
6231: }
6232: printf("\n ");
6233: }
6234:
6235: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6236: for (i=1;i<=NDIM;i++)
6237: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6238:
6239: lsurv=vector(1,AGESUP);
6240: lpop=vector(1,AGESUP);
6241: tpop=vector(1,AGESUP);
6242: lsurv[agegomp]=100000;
6243:
6244: for (k=agegomp;k<=AGESUP;k++) {
6245: agemortsup=k;
6246: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6247: }
6248:
6249: for (k=agegomp;k<agemortsup;k++)
6250: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6251:
6252: for (k=agegomp;k<agemortsup;k++){
6253: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6254: sumlpop=sumlpop+lpop[k];
6255: }
6256:
6257: tpop[agegomp]=sumlpop;
6258: for (k=agegomp;k<(agemortsup-3);k++){
6259: /* tpop[k+1]=2;*/
6260: tpop[k+1]=tpop[k]-lpop[k];
6261: }
6262:
6263:
6264: printf("\nAge lx qx dx Lx Tx e(x)\n");
6265: for (k=agegomp;k<(agemortsup-2);k++)
6266: 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]);
6267:
6268:
6269: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6270: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6271:
6272: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6273: stepm, weightopt,\
6274: model,imx,p,matcov,agemortsup);
6275:
6276: free_vector(lsurv,1,AGESUP);
6277: free_vector(lpop,1,AGESUP);
6278: free_vector(tpop,1,AGESUP);
1.136 brouard 6279: #ifdef GSL
6280: free_ivector(cens,1,n);
6281: free_vector(agecens,1,n);
6282: free_ivector(dcwave,1,n);
6283: free_matrix(ximort,1,NDIM,1,NDIM);
6284: #endif
1.126 brouard 6285: } /* Endof if mle==-3 */
6286:
6287: else{ /* For mle >=1 */
1.132 brouard 6288: globpr=0;/* debug */
6289: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 6290: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6291: for (k=1; k<=npar;k++)
6292: printf(" %d %8.5f",k,p[k]);
6293: printf("\n");
6294: globpr=1; /* to print the contributions */
6295: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6296: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6297: for (k=1; k<=npar;k++)
6298: printf(" %d %8.5f",k,p[k]);
6299: printf("\n");
6300: if(mle>=1){ /* Could be 1 or 2 */
6301: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6302: }
6303:
6304: /*--------- results files --------------*/
6305: 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);
6306:
6307:
6308: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6309: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6310: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6311: for(i=1,jk=1; i <=nlstate; i++){
6312: for(k=1; k <=(nlstate+ndeath); k++){
6313: if (k != i) {
6314: printf("%d%d ",i,k);
6315: fprintf(ficlog,"%d%d ",i,k);
6316: fprintf(ficres,"%1d%1d ",i,k);
6317: for(j=1; j <=ncovmodel; j++){
6318: printf("%lf ",p[jk]);
6319: fprintf(ficlog,"%lf ",p[jk]);
6320: fprintf(ficres,"%lf ",p[jk]);
6321: jk++;
6322: }
6323: printf("\n");
6324: fprintf(ficlog,"\n");
6325: fprintf(ficres,"\n");
6326: }
6327: }
6328: }
6329: if(mle!=0){
6330: /* Computing hessian and covariance matrix */
6331: ftolhess=ftol; /* Usually correct */
6332: hesscov(matcov, p, npar, delti, ftolhess, func);
6333: }
6334: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6335: printf("# Scales (for hessian or gradient estimation)\n");
6336: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6337: for(i=1,jk=1; i <=nlstate; i++){
6338: for(j=1; j <=nlstate+ndeath; j++){
6339: if (j!=i) {
6340: fprintf(ficres,"%1d%1d",i,j);
6341: printf("%1d%1d",i,j);
6342: fprintf(ficlog,"%1d%1d",i,j);
6343: for(k=1; k<=ncovmodel;k++){
6344: printf(" %.5e",delti[jk]);
6345: fprintf(ficlog," %.5e",delti[jk]);
6346: fprintf(ficres," %.5e",delti[jk]);
6347: jk++;
6348: }
6349: printf("\n");
6350: fprintf(ficlog,"\n");
6351: fprintf(ficres,"\n");
6352: }
6353: }
6354: }
6355:
6356: 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");
6357: if(mle>=1)
6358: 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");
6359: 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");
6360: /* # 121 Var(a12)\n\ */
6361: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6362: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6363: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6364: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6365: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6366: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6367: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6368:
6369:
6370: /* Just to have a covariance matrix which will be more understandable
6371: even is we still don't want to manage dictionary of variables
6372: */
6373: for(itimes=1;itimes<=2;itimes++){
6374: jj=0;
6375: for(i=1; i <=nlstate; i++){
6376: for(j=1; j <=nlstate+ndeath; j++){
6377: if(j==i) continue;
6378: for(k=1; k<=ncovmodel;k++){
6379: jj++;
6380: ca[0]= k+'a'-1;ca[1]='\0';
6381: if(itimes==1){
6382: if(mle>=1)
6383: printf("#%1d%1d%d",i,j,k);
6384: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6385: fprintf(ficres,"#%1d%1d%d",i,j,k);
6386: }else{
6387: if(mle>=1)
6388: printf("%1d%1d%d",i,j,k);
6389: fprintf(ficlog,"%1d%1d%d",i,j,k);
6390: fprintf(ficres,"%1d%1d%d",i,j,k);
6391: }
6392: ll=0;
6393: for(li=1;li <=nlstate; li++){
6394: for(lj=1;lj <=nlstate+ndeath; lj++){
6395: if(lj==li) continue;
6396: for(lk=1;lk<=ncovmodel;lk++){
6397: ll++;
6398: if(ll<=jj){
6399: cb[0]= lk +'a'-1;cb[1]='\0';
6400: if(ll<jj){
6401: if(itimes==1){
6402: if(mle>=1)
6403: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6404: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6405: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6406: }else{
6407: if(mle>=1)
6408: printf(" %.5e",matcov[jj][ll]);
6409: fprintf(ficlog," %.5e",matcov[jj][ll]);
6410: fprintf(ficres," %.5e",matcov[jj][ll]);
6411: }
6412: }else{
6413: if(itimes==1){
6414: if(mle>=1)
6415: printf(" Var(%s%1d%1d)",ca,i,j);
6416: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6417: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6418: }else{
6419: if(mle>=1)
6420: printf(" %.5e",matcov[jj][ll]);
6421: fprintf(ficlog," %.5e",matcov[jj][ll]);
6422: fprintf(ficres," %.5e",matcov[jj][ll]);
6423: }
6424: }
6425: }
6426: } /* end lk */
6427: } /* end lj */
6428: } /* end li */
6429: if(mle>=1)
6430: printf("\n");
6431: fprintf(ficlog,"\n");
6432: fprintf(ficres,"\n");
6433: numlinepar++;
6434: } /* end k*/
6435: } /*end j */
6436: } /* end i */
6437: } /* end itimes */
6438:
6439: fflush(ficlog);
6440: fflush(ficres);
6441:
6442: while((c=getc(ficpar))=='#' && c!= EOF){
6443: ungetc(c,ficpar);
6444: fgets(line, MAXLINE, ficpar);
1.141 brouard 6445: fputs(line,stdout);
1.126 brouard 6446: fputs(line,ficparo);
6447: }
6448: ungetc(c,ficpar);
6449:
6450: estepm=0;
6451: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6452: if (estepm==0 || estepm < stepm) estepm=stepm;
6453: if (fage <= 2) {
6454: bage = ageminpar;
6455: fage = agemaxpar;
6456: }
6457:
6458: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6459: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6460: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6461:
6462: while((c=getc(ficpar))=='#' && c!= EOF){
6463: ungetc(c,ficpar);
6464: fgets(line, MAXLINE, ficpar);
1.141 brouard 6465: fputs(line,stdout);
1.126 brouard 6466: fputs(line,ficparo);
6467: }
6468: ungetc(c,ficpar);
6469:
6470: 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);
6471: 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);
6472: 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);
6473: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6474: 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);
6475:
6476: while((c=getc(ficpar))=='#' && c!= EOF){
6477: ungetc(c,ficpar);
6478: fgets(line, MAXLINE, ficpar);
1.141 brouard 6479: fputs(line,stdout);
1.126 brouard 6480: fputs(line,ficparo);
6481: }
6482: ungetc(c,ficpar);
6483:
6484:
6485: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6486: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6487:
6488: fscanf(ficpar,"pop_based=%d\n",&popbased);
6489: fprintf(ficparo,"pop_based=%d\n",popbased);
6490: fprintf(ficres,"pop_based=%d\n",popbased);
6491:
6492: while((c=getc(ficpar))=='#' && c!= EOF){
6493: ungetc(c,ficpar);
6494: fgets(line, MAXLINE, ficpar);
1.141 brouard 6495: fputs(line,stdout);
1.126 brouard 6496: fputs(line,ficparo);
6497: }
6498: ungetc(c,ficpar);
6499:
6500: 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);
6501: 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);
6502: 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);
6503: 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);
6504: 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);
6505: /* day and month of proj2 are not used but only year anproj2.*/
6506:
6507:
6508:
1.145 brouard 6509: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6510: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 6511:
6512: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6513: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6514:
6515: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6516: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6517: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6518:
6519: /*------------ free_vector -------------*/
6520: /* chdir(path); */
6521:
6522: free_ivector(wav,1,imx);
6523: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6524: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6525: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6526: free_lvector(num,1,n);
6527: free_vector(agedc,1,n);
6528: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6529: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6530: fclose(ficparo);
6531: fclose(ficres);
6532:
6533:
6534: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.145 brouard 6535: #include "prevlim.h" /* Use ficrespl, ficlog */
1.126 brouard 6536: fclose(ficrespl);
6537:
1.145 brouard 6538: #ifdef FREEEXIT2
6539: #include "freeexit2.h"
6540: #endif
6541:
1.126 brouard 6542: /*------------- h Pij x at various ages ------------*/
1.145 brouard 6543: #include "hpijx.h"
6544: fclose(ficrespij);
1.126 brouard 6545:
1.145 brouard 6546: /*-------------- Variance of one-step probabilities---*/
6547: k=1;
1.126 brouard 6548: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6549:
6550:
6551: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6552: for(i=1;i<=AGESUP;i++)
6553: for(j=1;j<=NCOVMAX;j++)
6554: for(k=1;k<=NCOVMAX;k++)
6555: probs[i][j][k]=0.;
6556:
6557: /*---------- Forecasting ------------------*/
6558: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6559: if(prevfcast==1){
6560: /* if(stepm ==1){*/
6561: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6562: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6563: /* } */
6564: /* else{ */
6565: /* erreur=108; */
6566: /* 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); */
6567: /* 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); */
6568: /* } */
6569: }
6570:
6571:
1.127 brouard 6572: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6573:
6574: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6575: /* 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",\
6576: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6577: */
1.126 brouard 6578:
1.127 brouard 6579: if (mobilav!=0) {
6580: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6581: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6582: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6583: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6584: }
1.126 brouard 6585: }
6586:
6587:
1.127 brouard 6588: /*---------- Health expectancies, no variances ------------*/
6589:
1.126 brouard 6590: strcpy(filerese,"e");
6591: strcat(filerese,fileres);
6592: if((ficreseij=fopen(filerese,"w"))==NULL) {
6593: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6594: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6595: }
6596: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6597: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 6598: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6599: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6600:
6601: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 6602: fprintf(ficreseij,"\n#****** ");
6603: for(j=1;j<=cptcoveff;j++) {
6604: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6605: }
6606: fprintf(ficreseij,"******\n");
6607:
6608: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6609: oldm=oldms;savm=savms;
6610: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6611:
6612: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6613: /*}*/
1.127 brouard 6614: }
6615: fclose(ficreseij);
6616:
6617:
6618: /*---------- Health expectancies and variances ------------*/
6619:
6620:
6621: strcpy(filerest,"t");
6622: strcat(filerest,fileres);
6623: if((ficrest=fopen(filerest,"w"))==NULL) {
6624: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6625: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6626: }
6627: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6628: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6629:
1.126 brouard 6630:
6631: strcpy(fileresstde,"stde");
6632: strcat(fileresstde,fileres);
6633: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6634: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6635: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6636: }
6637: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6638: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6639:
6640: strcpy(filerescve,"cve");
6641: strcat(filerescve,fileres);
6642: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6643: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6644: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6645: }
6646: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6647: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6648:
6649: strcpy(fileresv,"v");
6650: strcat(fileresv,fileres);
6651: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6652: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6653: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6654: }
6655: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6656: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6657:
1.145 brouard 6658: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6659: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6660:
6661: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6662: fprintf(ficrest,"\n#****** ");
1.126 brouard 6663: for(j=1;j<=cptcoveff;j++)
6664: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6665: fprintf(ficrest,"******\n");
6666:
6667: fprintf(ficresstdeij,"\n#****** ");
6668: fprintf(ficrescveij,"\n#****** ");
6669: for(j=1;j<=cptcoveff;j++) {
6670: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6671: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6672: }
6673: fprintf(ficresstdeij,"******\n");
6674: fprintf(ficrescveij,"******\n");
6675:
6676: fprintf(ficresvij,"\n#****** ");
6677: for(j=1;j<=cptcoveff;j++)
6678: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6679: fprintf(ficresvij,"******\n");
6680:
6681: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6682: oldm=oldms;savm=savms;
1.127 brouard 6683: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 6684: /*
6685: */
6686: /* goto endfree; */
1.126 brouard 6687:
6688: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6689: pstamp(ficrest);
1.145 brouard 6690:
6691:
1.128 brouard 6692: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 6693: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 6694: cptcod= 0; /* To be deleted */
6695: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 6696: 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 6697: if(vpopbased==1)
6698: 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);
6699: else
6700: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6701: fprintf(ficrest,"# Age e.. (std) ");
6702: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6703: fprintf(ficrest,"\n");
1.126 brouard 6704:
1.128 brouard 6705: epj=vector(1,nlstate+1);
6706: for(age=bage; age <=fage ;age++){
6707: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6708: if (vpopbased==1) {
6709: if(mobilav ==0){
6710: for(i=1; i<=nlstate;i++)
6711: prlim[i][i]=probs[(int)age][i][k];
6712: }else{ /* mobilav */
6713: for(i=1; i<=nlstate;i++)
6714: prlim[i][i]=mobaverage[(int)age][i][k];
6715: }
1.126 brouard 6716: }
6717:
1.128 brouard 6718: fprintf(ficrest," %4.0f",age);
6719: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6720: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6721: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6722: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6723: }
6724: epj[nlstate+1] +=epj[j];
1.126 brouard 6725: }
6726:
1.128 brouard 6727: for(i=1, vepp=0.;i <=nlstate;i++)
6728: for(j=1;j <=nlstate;j++)
6729: vepp += vareij[i][j][(int)age];
6730: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6731: for(j=1;j <=nlstate;j++){
6732: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6733: }
6734: fprintf(ficrest,"\n");
1.126 brouard 6735: }
6736: }
6737: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6738: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6739: free_vector(epj,1,nlstate+1);
1.145 brouard 6740: /*}*/
1.126 brouard 6741: }
6742: free_vector(weight,1,n);
1.145 brouard 6743: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 6744: free_imatrix(s,1,maxwav+1,1,n);
6745: free_matrix(anint,1,maxwav,1,n);
6746: free_matrix(mint,1,maxwav,1,n);
6747: free_ivector(cod,1,n);
6748: free_ivector(tab,1,NCOVMAX);
6749: fclose(ficresstdeij);
6750: fclose(ficrescveij);
6751: fclose(ficresvij);
6752: fclose(ficrest);
6753: fclose(ficpar);
6754:
6755: /*------- Variance of period (stable) prevalence------*/
6756:
6757: strcpy(fileresvpl,"vpl");
6758: strcat(fileresvpl,fileres);
6759: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6760: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6761: exit(0);
6762: }
6763: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6764:
1.145 brouard 6765: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6766: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6767:
6768: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6769: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 6770: for(j=1;j<=cptcoveff;j++)
6771: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6772: fprintf(ficresvpl,"******\n");
6773:
6774: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6775: oldm=oldms;savm=savms;
6776: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6777: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 6778: /*}*/
1.126 brouard 6779: }
6780:
6781: fclose(ficresvpl);
6782:
6783: /*---------- End : free ----------------*/
6784: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6785: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6786: } /* mle==-3 arrives here for freeing */
1.131 brouard 6787: endfree:
1.141 brouard 6788: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 6789: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6790: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6791: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6792: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6793: free_matrix(covar,0,NCOVMAX,1,n);
6794: free_matrix(matcov,1,npar,1,npar);
6795: /*free_vector(delti,1,npar);*/
6796: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6797: free_matrix(agev,1,maxwav,1,imx);
6798: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6799:
1.145 brouard 6800: free_ivector(ncodemax,1,NCOVMAX);
6801: free_ivector(Tvar,1,NCOVMAX);
6802: free_ivector(Tprod,1,NCOVMAX);
6803: free_ivector(Tvaraff,1,NCOVMAX);
6804: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 6805:
6806: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6807: free_imatrix(codtab,1,100,1,10);
6808: fflush(fichtm);
6809: fflush(ficgp);
6810:
6811:
6812: if((nberr >0) || (nbwarn>0)){
6813: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6814: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6815: }else{
6816: printf("End of Imach\n");
6817: fprintf(ficlog,"End of Imach\n");
6818: }
6819: printf("See log file on %s\n",filelog);
6820: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 6821: /*(void) gettimeofday(&end_time,&tzp);*/
6822: rend_time = time(NULL);
6823: end_time = *localtime(&rend_time);
6824: /* tml = *localtime(&end_time.tm_sec); */
6825: strcpy(strtend,asctime(&end_time));
1.126 brouard 6826: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6827: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 6828: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 6829:
1.157 brouard 6830: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6831: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6832: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 6833: /* printf("Total time was %d uSec.\n", total_usecs);*/
6834: /* if(fileappend(fichtm,optionfilehtm)){ */
6835: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6836: fclose(fichtm);
6837: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6838: fclose(fichtmcov);
6839: fclose(ficgp);
6840: fclose(ficlog);
6841: /*------ End -----------*/
6842:
6843:
6844: printf("Before Current directory %s!\n",pathcd);
6845: if(chdir(pathcd) != 0)
6846: printf("Can't move to directory %s!\n",path);
6847: if(getcwd(pathcd,MAXLINE) > 0)
6848: printf("Current directory %s!\n",pathcd);
6849: /*strcat(plotcmd,CHARSEPARATOR);*/
6850: sprintf(plotcmd,"gnuplot");
1.157 brouard 6851: #ifdef _WIN32
1.126 brouard 6852: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6853: #endif
6854: if(!stat(plotcmd,&info)){
1.158 brouard 6855: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6856: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 6857: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 6858: }else
6859: strcpy(pplotcmd,plotcmd);
1.157 brouard 6860: #ifdef __unix
1.126 brouard 6861: strcpy(plotcmd,GNUPLOTPROGRAM);
6862: if(!stat(plotcmd,&info)){
1.158 brouard 6863: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6864: }else
6865: strcpy(pplotcmd,plotcmd);
6866: #endif
6867: }else
6868: strcpy(pplotcmd,plotcmd);
6869:
6870: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 6871: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 6872:
6873: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 6874: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 6875: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 6876: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 6877: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 6878: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 6879: }
1.158 brouard 6880: printf(" Successful, please wait...");
1.126 brouard 6881: while (z[0] != 'q') {
6882: /* chdir(path); */
1.154 brouard 6883: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 6884: scanf("%s",z);
6885: /* if (z[0] == 'c') system("./imach"); */
6886: if (z[0] == 'e') {
1.158 brouard 6887: #ifdef __APPLE__
1.152 brouard 6888: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 6889: #elif __linux
6890: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 6891: #else
1.152 brouard 6892: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 6893: #endif
6894: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
6895: system(pplotcmd);
1.126 brouard 6896: }
6897: else if (z[0] == 'g') system(plotcmd);
6898: else if (z[0] == 'q') exit(0);
6899: }
6900: end:
6901: while (z[0] != 'q') {
6902: printf("\nType q for exiting: ");
6903: scanf("%s",z);
6904: }
6905: }
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