1: /* $Id: imach.c,v 1.170 2014/12/23 11:17:12 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.170 2014/12/23 11:17:12 brouard
5: Summary: Cleaning some \%% back to %%
6:
7: The escape was mandatory for a specific compiler (which one?), but too many warnings.
8:
9: Revision 1.169 2014/12/22 23:08:31 brouard
10: Summary: 0.98p
11:
12: Outputs some informations on compiler used, OS etc. Testing on different platforms.
13:
14: Revision 1.168 2014/12/22 15:17:42 brouard
15: Summary: update
16:
17: Revision 1.167 2014/12/22 13:50:56 brouard
18: Summary: Testing uname and compiler version and if compiled 32 or 64
19:
20: Testing on Linux 64
21:
22: Revision 1.166 2014/12/22 11:40:47 brouard
23: *** empty log message ***
24:
25: Revision 1.165 2014/12/16 11:20:36 brouard
26: Summary: After compiling on Visual C
27:
28: * imach.c (Module): Merging 1.61 to 1.162
29:
30: Revision 1.164 2014/12/16 10:52:11 brouard
31: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
32:
33: * imach.c (Module): Merging 1.61 to 1.162
34:
35: Revision 1.163 2014/12/16 10:30:11 brouard
36: * imach.c (Module): Merging 1.61 to 1.162
37:
38: Revision 1.162 2014/09/25 11:43:39 brouard
39: Summary: temporary backup 0.99!
40:
41: Revision 1.1 2014/09/16 11:06:58 brouard
42: Summary: With some code (wrong) for nlopt
43:
44: Author:
45:
46: Revision 1.161 2014/09/15 20:41:41 brouard
47: Summary: Problem with macro SQR on Intel compiler
48:
49: Revision 1.160 2014/09/02 09:24:05 brouard
50: *** empty log message ***
51:
52: Revision 1.159 2014/09/01 10:34:10 brouard
53: Summary: WIN32
54: Author: Brouard
55:
56: Revision 1.158 2014/08/27 17:11:51 brouard
57: *** empty log message ***
58:
59: Revision 1.157 2014/08/27 16:26:55 brouard
60: Summary: Preparing windows Visual studio version
61: Author: Brouard
62:
63: In order to compile on Visual studio, time.h is now correct and time_t
64: and tm struct should be used. difftime should be used but sometimes I
65: just make the differences in raw time format (time(&now).
66: Trying to suppress #ifdef LINUX
67: Add xdg-open for __linux in order to open default browser.
68:
69: Revision 1.156 2014/08/25 20:10:10 brouard
70: *** empty log message ***
71:
72: Revision 1.155 2014/08/25 18:32:34 brouard
73: Summary: New compile, minor changes
74: Author: Brouard
75:
76: Revision 1.154 2014/06/20 17:32:08 brouard
77: Summary: Outputs now all graphs of convergence to period prevalence
78:
79: Revision 1.153 2014/06/20 16:45:46 brouard
80: Summary: If 3 live state, convergence to period prevalence on same graph
81: Author: Brouard
82:
83: Revision 1.152 2014/06/18 17:54:09 brouard
84: Summary: open browser, use gnuplot on same dir than imach if not found in the path
85:
86: Revision 1.151 2014/06/18 16:43:30 brouard
87: *** empty log message ***
88:
89: Revision 1.150 2014/06/18 16:42:35 brouard
90: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
91: Author: brouard
92:
93: Revision 1.149 2014/06/18 15:51:14 brouard
94: Summary: Some fixes in parameter files errors
95: Author: Nicolas Brouard
96:
97: Revision 1.148 2014/06/17 17:38:48 brouard
98: Summary: Nothing new
99: Author: Brouard
100:
101: Just a new packaging for OS/X version 0.98nS
102:
103: Revision 1.147 2014/06/16 10:33:11 brouard
104: *** empty log message ***
105:
106: Revision 1.146 2014/06/16 10:20:28 brouard
107: Summary: Merge
108: Author: Brouard
109:
110: Merge, before building revised version.
111:
112: Revision 1.145 2014/06/10 21:23:15 brouard
113: Summary: Debugging with valgrind
114: Author: Nicolas Brouard
115:
116: Lot of changes in order to output the results with some covariates
117: After the Edimburgh REVES conference 2014, it seems mandatory to
118: improve the code.
119: No more memory valgrind error but a lot has to be done in order to
120: continue the work of splitting the code into subroutines.
121: Also, decodemodel has been improved. Tricode is still not
122: optimal. nbcode should be improved. Documentation has been added in
123: the source code.
124:
125: Revision 1.143 2014/01/26 09:45:38 brouard
126: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
127:
128: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
129: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
130:
131: Revision 1.142 2014/01/26 03:57:36 brouard
132: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
133:
134: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
135:
136: Revision 1.141 2014/01/26 02:42:01 brouard
137: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
138:
139: Revision 1.140 2011/09/02 10:37:54 brouard
140: Summary: times.h is ok with mingw32 now.
141:
142: Revision 1.139 2010/06/14 07:50:17 brouard
143: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
144: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
145:
146: Revision 1.138 2010/04/30 18:19:40 brouard
147: *** empty log message ***
148:
149: Revision 1.137 2010/04/29 18:11:38 brouard
150: (Module): Checking covariates for more complex models
151: than V1+V2. A lot of change to be done. Unstable.
152:
153: Revision 1.136 2010/04/26 20:30:53 brouard
154: (Module): merging some libgsl code. Fixing computation
155: of likelione (using inter/intrapolation if mle = 0) in order to
156: get same likelihood as if mle=1.
157: Some cleaning of code and comments added.
158:
159: Revision 1.135 2009/10/29 15:33:14 brouard
160: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
161:
162: Revision 1.134 2009/10/29 13:18:53 brouard
163: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
164:
165: Revision 1.133 2009/07/06 10:21:25 brouard
166: just nforces
167:
168: Revision 1.132 2009/07/06 08:22:05 brouard
169: Many tings
170:
171: Revision 1.131 2009/06/20 16:22:47 brouard
172: Some dimensions resccaled
173:
174: Revision 1.130 2009/05/26 06:44:34 brouard
175: (Module): Max Covariate is now set to 20 instead of 8. A
176: lot of cleaning with variables initialized to 0. Trying to make
177: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
178:
179: Revision 1.129 2007/08/31 13:49:27 lievre
180: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
181:
182: Revision 1.128 2006/06/30 13:02:05 brouard
183: (Module): Clarifications on computing e.j
184:
185: Revision 1.127 2006/04/28 18:11:50 brouard
186: (Module): Yes the sum of survivors was wrong since
187: imach-114 because nhstepm was no more computed in the age
188: loop. Now we define nhstepma in the age loop.
189: (Module): In order to speed up (in case of numerous covariates) we
190: compute health expectancies (without variances) in a first step
191: and then all the health expectancies with variances or standard
192: deviation (needs data from the Hessian matrices) which slows the
193: computation.
194: In the future we should be able to stop the program is only health
195: expectancies and graph are needed without standard deviations.
196:
197: Revision 1.126 2006/04/28 17:23:28 brouard
198: (Module): Yes the sum of survivors was wrong since
199: imach-114 because nhstepm was no more computed in the age
200: loop. Now we define nhstepma in the age loop.
201: Version 0.98h
202:
203: Revision 1.125 2006/04/04 15:20:31 lievre
204: Errors in calculation of health expectancies. Age was not initialized.
205: Forecasting file added.
206:
207: Revision 1.124 2006/03/22 17:13:53 lievre
208: Parameters are printed with %lf instead of %f (more numbers after the comma).
209: The log-likelihood is printed in the log file
210:
211: Revision 1.123 2006/03/20 10:52:43 brouard
212: * imach.c (Module): <title> changed, corresponds to .htm file
213: name. <head> headers where missing.
214:
215: * imach.c (Module): Weights can have a decimal point as for
216: English (a comma might work with a correct LC_NUMERIC environment,
217: otherwise the weight is truncated).
218: Modification of warning when the covariates values are not 0 or
219: 1.
220: Version 0.98g
221:
222: Revision 1.122 2006/03/20 09:45:41 brouard
223: (Module): Weights can have a decimal point as for
224: English (a comma might work with a correct LC_NUMERIC environment,
225: otherwise the weight is truncated).
226: Modification of warning when the covariates values are not 0 or
227: 1.
228: Version 0.98g
229:
230: Revision 1.121 2006/03/16 17:45:01 lievre
231: * imach.c (Module): Comments concerning covariates added
232:
233: * imach.c (Module): refinements in the computation of lli if
234: status=-2 in order to have more reliable computation if stepm is
235: not 1 month. Version 0.98f
236:
237: Revision 1.120 2006/03/16 15:10:38 lievre
238: (Module): refinements in the computation of lli if
239: status=-2 in order to have more reliable computation if stepm is
240: not 1 month. Version 0.98f
241:
242: Revision 1.119 2006/03/15 17:42:26 brouard
243: (Module): Bug if status = -2, the loglikelihood was
244: computed as likelihood omitting the logarithm. Version O.98e
245:
246: Revision 1.118 2006/03/14 18:20:07 brouard
247: (Module): varevsij Comments added explaining the second
248: table of variances if popbased=1 .
249: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
250: (Module): Function pstamp added
251: (Module): Version 0.98d
252:
253: Revision 1.117 2006/03/14 17:16:22 brouard
254: (Module): varevsij Comments added explaining the second
255: table of variances if popbased=1 .
256: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
257: (Module): Function pstamp added
258: (Module): Version 0.98d
259:
260: Revision 1.116 2006/03/06 10:29:27 brouard
261: (Module): Variance-covariance wrong links and
262: varian-covariance of ej. is needed (Saito).
263:
264: Revision 1.115 2006/02/27 12:17:45 brouard
265: (Module): One freematrix added in mlikeli! 0.98c
266:
267: Revision 1.114 2006/02/26 12:57:58 brouard
268: (Module): Some improvements in processing parameter
269: filename with strsep.
270:
271: Revision 1.113 2006/02/24 14:20:24 brouard
272: (Module): Memory leaks checks with valgrind and:
273: datafile was not closed, some imatrix were not freed and on matrix
274: allocation too.
275:
276: Revision 1.112 2006/01/30 09:55:26 brouard
277: (Module): Back to gnuplot.exe instead of wgnuplot.exe
278:
279: Revision 1.111 2006/01/25 20:38:18 brouard
280: (Module): Lots of cleaning and bugs added (Gompertz)
281: (Module): Comments can be added in data file. Missing date values
282: can be a simple dot '.'.
283:
284: Revision 1.110 2006/01/25 00:51:50 brouard
285: (Module): Lots of cleaning and bugs added (Gompertz)
286:
287: Revision 1.109 2006/01/24 19:37:15 brouard
288: (Module): Comments (lines starting with a #) are allowed in data.
289:
290: Revision 1.108 2006/01/19 18:05:42 lievre
291: Gnuplot problem appeared...
292: To be fixed
293:
294: Revision 1.107 2006/01/19 16:20:37 brouard
295: Test existence of gnuplot in imach path
296:
297: Revision 1.106 2006/01/19 13:24:36 brouard
298: Some cleaning and links added in html output
299:
300: Revision 1.105 2006/01/05 20:23:19 lievre
301: *** empty log message ***
302:
303: Revision 1.104 2005/09/30 16:11:43 lievre
304: (Module): sump fixed, loop imx fixed, and simplifications.
305: (Module): If the status is missing at the last wave but we know
306: that the person is alive, then we can code his/her status as -2
307: (instead of missing=-1 in earlier versions) and his/her
308: contributions to the likelihood is 1 - Prob of dying from last
309: health status (= 1-p13= p11+p12 in the easiest case of somebody in
310: the healthy state at last known wave). Version is 0.98
311:
312: Revision 1.103 2005/09/30 15:54:49 lievre
313: (Module): sump fixed, loop imx fixed, and simplifications.
314:
315: Revision 1.102 2004/09/15 17:31:30 brouard
316: Add the possibility to read data file including tab characters.
317:
318: Revision 1.101 2004/09/15 10:38:38 brouard
319: Fix on curr_time
320:
321: Revision 1.100 2004/07/12 18:29:06 brouard
322: Add version for Mac OS X. Just define UNIX in Makefile
323:
324: Revision 1.99 2004/06/05 08:57:40 brouard
325: *** empty log message ***
326:
327: Revision 1.98 2004/05/16 15:05:56 brouard
328: New version 0.97 . First attempt to estimate force of mortality
329: directly from the data i.e. without the need of knowing the health
330: state at each age, but using a Gompertz model: log u =a + b*age .
331: This is the basic analysis of mortality and should be done before any
332: other analysis, in order to test if the mortality estimated from the
333: cross-longitudinal survey is different from the mortality estimated
334: from other sources like vital statistic data.
335:
336: The same imach parameter file can be used but the option for mle should be -3.
337:
338: Agnès, who wrote this part of the code, tried to keep most of the
339: former routines in order to include the new code within the former code.
340:
341: The output is very simple: only an estimate of the intercept and of
342: the slope with 95% confident intervals.
343:
344: Current limitations:
345: A) Even if you enter covariates, i.e. with the
346: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
347: B) There is no computation of Life Expectancy nor Life Table.
348:
349: Revision 1.97 2004/02/20 13:25:42 lievre
350: Version 0.96d. Population forecasting command line is (temporarily)
351: suppressed.
352:
353: Revision 1.96 2003/07/15 15:38:55 brouard
354: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
355: rewritten within the same printf. Workaround: many printfs.
356:
357: Revision 1.95 2003/07/08 07:54:34 brouard
358: * imach.c (Repository):
359: (Repository): Using imachwizard code to output a more meaningful covariance
360: matrix (cov(a12,c31) instead of numbers.
361:
362: Revision 1.94 2003/06/27 13:00:02 brouard
363: Just cleaning
364:
365: Revision 1.93 2003/06/25 16:33:55 brouard
366: (Module): On windows (cygwin) function asctime_r doesn't
367: exist so I changed back to asctime which exists.
368: (Module): Version 0.96b
369:
370: Revision 1.92 2003/06/25 16:30:45 brouard
371: (Module): On windows (cygwin) function asctime_r doesn't
372: exist so I changed back to asctime which exists.
373:
374: Revision 1.91 2003/06/25 15:30:29 brouard
375: * imach.c (Repository): Duplicated warning errors corrected.
376: (Repository): Elapsed time after each iteration is now output. It
377: helps to forecast when convergence will be reached. Elapsed time
378: is stamped in powell. We created a new html file for the graphs
379: concerning matrix of covariance. It has extension -cov.htm.
380:
381: Revision 1.90 2003/06/24 12:34:15 brouard
382: (Module): Some bugs corrected for windows. Also, when
383: mle=-1 a template is output in file "or"mypar.txt with the design
384: of the covariance matrix to be input.
385:
386: Revision 1.89 2003/06/24 12:30:52 brouard
387: (Module): Some bugs corrected for windows. Also, when
388: mle=-1 a template is output in file "or"mypar.txt with the design
389: of the covariance matrix to be input.
390:
391: Revision 1.88 2003/06/23 17:54:56 brouard
392: * 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.
393:
394: Revision 1.87 2003/06/18 12:26:01 brouard
395: Version 0.96
396:
397: Revision 1.86 2003/06/17 20:04:08 brouard
398: (Module): Change position of html and gnuplot routines and added
399: routine fileappend.
400:
401: Revision 1.85 2003/06/17 13:12:43 brouard
402: * imach.c (Repository): Check when date of death was earlier that
403: current date of interview. It may happen when the death was just
404: prior to the death. In this case, dh was negative and likelihood
405: was wrong (infinity). We still send an "Error" but patch by
406: assuming that the date of death was just one stepm after the
407: interview.
408: (Repository): Because some people have very long ID (first column)
409: we changed int to long in num[] and we added a new lvector for
410: memory allocation. But we also truncated to 8 characters (left
411: truncation)
412: (Repository): No more line truncation errors.
413:
414: Revision 1.84 2003/06/13 21:44:43 brouard
415: * imach.c (Repository): Replace "freqsummary" at a correct
416: place. It differs from routine "prevalence" which may be called
417: many times. Probs is memory consuming and must be used with
418: parcimony.
419: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
420:
421: Revision 1.83 2003/06/10 13:39:11 lievre
422: *** empty log message ***
423:
424: Revision 1.82 2003/06/05 15:57:20 brouard
425: Add log in imach.c and fullversion number is now printed.
426:
427: */
428: /*
429: Interpolated Markov Chain
430:
431: Short summary of the programme:
432:
433: This program computes Healthy Life Expectancies from
434: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
435: first survey ("cross") where individuals from different ages are
436: interviewed on their health status or degree of disability (in the
437: case of a health survey which is our main interest) -2- at least a
438: second wave of interviews ("longitudinal") which measure each change
439: (if any) in individual health status. Health expectancies are
440: computed from the time spent in each health state according to a
441: model. More health states you consider, more time is necessary to reach the
442: Maximum Likelihood of the parameters involved in the model. The
443: simplest model is the multinomial logistic model where pij is the
444: probability to be observed in state j at the second wave
445: conditional to be observed in state i at the first wave. Therefore
446: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
447: 'age' is age and 'sex' is a covariate. If you want to have a more
448: complex model than "constant and age", you should modify the program
449: where the markup *Covariates have to be included here again* invites
450: you to do it. More covariates you add, slower the
451: convergence.
452:
453: The advantage of this computer programme, compared to a simple
454: multinomial logistic model, is clear when the delay between waves is not
455: identical for each individual. Also, if a individual missed an
456: intermediate interview, the information is lost, but taken into
457: account using an interpolation or extrapolation.
458:
459: hPijx is the probability to be observed in state i at age x+h
460: conditional to the observed state i at age x. The delay 'h' can be
461: split into an exact number (nh*stepm) of unobserved intermediate
462: states. This elementary transition (by month, quarter,
463: semester or year) is modelled as a multinomial logistic. The hPx
464: matrix is simply the matrix product of nh*stepm elementary matrices
465: and the contribution of each individual to the likelihood is simply
466: hPijx.
467:
468: Also this programme outputs the covariance matrix of the parameters but also
469: of the life expectancies. It also computes the period (stable) prevalence.
470:
471: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
472: Institut national d'études démographiques, Paris.
473: This software have been partly granted by Euro-REVES, a concerted action
474: from the European Union.
475: It is copyrighted identically to a GNU software product, ie programme and
476: software can be distributed freely for non commercial use. Latest version
477: can be accessed at http://euroreves.ined.fr/imach .
478:
479: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
480: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
481:
482: **********************************************************************/
483: /*
484: main
485: read parameterfile
486: read datafile
487: concatwav
488: freqsummary
489: if (mle >= 1)
490: mlikeli
491: print results files
492: if mle==1
493: computes hessian
494: read end of parameter file: agemin, agemax, bage, fage, estepm
495: begin-prev-date,...
496: open gnuplot file
497: open html file
498: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
499: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
500: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
501: freexexit2 possible for memory heap.
502:
503: h Pij x | pij_nom ficrestpij
504: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
505: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
506: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
507:
508: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
509: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
510: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
511: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
512: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
513:
514: forecasting if prevfcast==1 prevforecast call prevalence()
515: health expectancies
516: Variance-covariance of DFLE
517: prevalence()
518: movingaverage()
519: varevsij()
520: if popbased==1 varevsij(,popbased)
521: total life expectancies
522: Variance of period (stable) prevalence
523: end
524: */
525:
526: #define POWELL /* Instead of NLOPT */
527:
528: #include <math.h>
529: #include <stdio.h>
530: #include <stdlib.h>
531: #include <string.h>
532:
533: #ifdef _WIN32
534: #include <io.h>
535: #else
536: #include <unistd.h>
537: #endif
538:
539: #include <limits.h>
540: #include <sys/types.h>
541: #include <sys/utsname.h>
542: #include <sys/stat.h>
543: #include <errno.h>
544: /* extern int errno; */
545:
546: /* #ifdef LINUX */
547: /* #include <time.h> */
548: /* #include "timeval.h" */
549: /* #else */
550: /* #include <sys/time.h> */
551: /* #endif */
552:
553: #include <time.h>
554:
555: #ifdef GSL
556: #include <gsl/gsl_errno.h>
557: #include <gsl/gsl_multimin.h>
558: #endif
559:
560:
561: #ifdef NLOPT
562: #include <nlopt.h>
563: typedef struct {
564: double (* function)(double [] );
565: } myfunc_data ;
566: #endif
567:
568: /* #include <libintl.h> */
569: /* #define _(String) gettext (String) */
570:
571: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
572:
573: #define GNUPLOTPROGRAM "gnuplot"
574: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
575: #define FILENAMELENGTH 132
576:
577: #define GLOCK_ERROR_NOPATH -1 /* empty path */
578: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
579:
580: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
581: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
582:
583: #define NINTERVMAX 8
584: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
585: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
586: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
587: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
588: #define MAXN 20000
589: #define YEARM 12. /**< Number of months per year */
590: #define AGESUP 130
591: #define AGEBASE 40
592: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
593: #ifdef _WIN32
594: #define DIRSEPARATOR '\\'
595: #define CHARSEPARATOR "\\"
596: #define ODIRSEPARATOR '/'
597: #else
598: #define DIRSEPARATOR '/'
599: #define CHARSEPARATOR "/"
600: #define ODIRSEPARATOR '\\'
601: #endif
602:
603: /* $Id: imach.c,v 1.170 2014/12/23 11:17:12 brouard Exp $ */
604: /* $State: Exp $ */
605:
606: char version[]="Imach version 0.98p, December 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
607: char fullversion[]="$Revision: 1.170 $ $Date: 2014/12/23 11:17:12 $";
608: char strstart[80];
609: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
610: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
611: int nvar=0, nforce=0; /* Number of variables, number of forces */
612: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
613: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
614: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
615: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
616: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
617: int cptcovprodnoage=0; /**< Number of covariate products without age */
618: int cptcoveff=0; /* Total number of covariates to vary for printing results */
619: int cptcov=0; /* Working variable */
620: int npar=NPARMAX;
621: int nlstate=2; /* Number of live states */
622: int ndeath=1; /* Number of dead states */
623: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
624: int popbased=0;
625:
626: int *wav; /* Number of waves for this individuual 0 is possible */
627: int maxwav=0; /* Maxim number of waves */
628: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
629: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
630: int gipmx=0, gsw=0; /* Global variables on the number of contributions
631: to the likelihood and the sum of weights (done by funcone)*/
632: int mle=1, weightopt=0;
633: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
634: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
635: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
636: * wave mi and wave mi+1 is not an exact multiple of stepm. */
637: int countcallfunc=0; /* Count the number of calls to func */
638: double jmean=1; /* Mean space between 2 waves */
639: double **matprod2(); /* test */
640: double **oldm, **newm, **savm; /* Working pointers to matrices */
641: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
642: /*FILE *fic ; */ /* Used in readdata only */
643: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
644: FILE *ficlog, *ficrespow;
645: int globpr=0; /* Global variable for printing or not */
646: double fretone; /* Only one call to likelihood */
647: long ipmx=0; /* Number of contributions */
648: double sw; /* Sum of weights */
649: char filerespow[FILENAMELENGTH];
650: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
651: FILE *ficresilk;
652: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
653: FILE *ficresprobmorprev;
654: FILE *fichtm, *fichtmcov; /* Html File */
655: FILE *ficreseij;
656: char filerese[FILENAMELENGTH];
657: FILE *ficresstdeij;
658: char fileresstde[FILENAMELENGTH];
659: FILE *ficrescveij;
660: char filerescve[FILENAMELENGTH];
661: FILE *ficresvij;
662: char fileresv[FILENAMELENGTH];
663: FILE *ficresvpl;
664: char fileresvpl[FILENAMELENGTH];
665: char title[MAXLINE];
666: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
667: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
668: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
669: char command[FILENAMELENGTH];
670: int outcmd=0;
671:
672: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
673:
674: char filelog[FILENAMELENGTH]; /* Log file */
675: char filerest[FILENAMELENGTH];
676: char fileregp[FILENAMELENGTH];
677: char popfile[FILENAMELENGTH];
678:
679: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
680:
681: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
682: /* struct timezone tzp; */
683: /* extern int gettimeofday(); */
684: struct tm tml, *gmtime(), *localtime();
685:
686: extern time_t time();
687:
688: struct tm start_time, end_time, curr_time, last_time, forecast_time;
689: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
690: struct tm tm;
691:
692: char strcurr[80], strfor[80];
693:
694: char *endptr;
695: long lval;
696: double dval;
697:
698: #define NR_END 1
699: #define FREE_ARG char*
700: #define FTOL 1.0e-10
701:
702: #define NRANSI
703: #define ITMAX 200
704:
705: #define TOL 2.0e-4
706:
707: #define CGOLD 0.3819660
708: #define ZEPS 1.0e-10
709: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
710:
711: #define GOLD 1.618034
712: #define GLIMIT 100.0
713: #define TINY 1.0e-20
714:
715: static double maxarg1,maxarg2;
716: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
717: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
718:
719: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
720: #define rint(a) floor(a+0.5)
721: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
722: /* #define mytinydouble 1.0e-16 */
723: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
724: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
725: /* static double dsqrarg; */
726: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
727: static double sqrarg;
728: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
729: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
730: int agegomp= AGEGOMP;
731:
732: int imx;
733: int stepm=1;
734: /* Stepm, step in month: minimum step interpolation*/
735:
736: int estepm;
737: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
738:
739: int m,nb;
740: long *num;
741: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
742: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
743: double **pmmij, ***probs;
744: double *ageexmed,*agecens;
745: double dateintmean=0;
746:
747: double *weight;
748: int **s; /* Status */
749: double *agedc;
750: double **covar; /**< covar[j,i], value of jth covariate for individual i,
751: * covar=matrix(0,NCOVMAX,1,n);
752: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
753: double idx;
754: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
755: int *Ndum; /** Freq of modality (tricode */
756: int **codtab; /**< codtab=imatrix(1,100,1,10); */
757: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
758: double *lsurv, *lpop, *tpop;
759:
760: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
761: double ftolhess; /**< Tolerance for computing hessian */
762:
763: /**************** split *************************/
764: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
765: {
766: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
767: the name of the file (name), its extension only (ext) and its first part of the name (finame)
768: */
769: char *ss; /* pointer */
770: int l1, l2; /* length counters */
771:
772: l1 = strlen(path ); /* length of path */
773: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
774: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
775: if ( ss == NULL ) { /* no directory, so determine current directory */
776: strcpy( name, path ); /* we got the fullname name because no directory */
777: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
778: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
779: /* get current working directory */
780: /* extern char* getcwd ( char *buf , int len);*/
781: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
782: return( GLOCK_ERROR_GETCWD );
783: }
784: /* got dirc from getcwd*/
785: printf(" DIRC = %s \n",dirc);
786: } else { /* strip direcotry from path */
787: ss++; /* after this, the filename */
788: l2 = strlen( ss ); /* length of filename */
789: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
790: strcpy( name, ss ); /* save file name */
791: strncpy( dirc, path, l1 - l2 ); /* now the directory */
792: dirc[l1-l2] = 0; /* add zero */
793: printf(" DIRC2 = %s \n",dirc);
794: }
795: /* We add a separator at the end of dirc if not exists */
796: l1 = strlen( dirc ); /* length of directory */
797: if( dirc[l1-1] != DIRSEPARATOR ){
798: dirc[l1] = DIRSEPARATOR;
799: dirc[l1+1] = 0;
800: printf(" DIRC3 = %s \n",dirc);
801: }
802: ss = strrchr( name, '.' ); /* find last / */
803: if (ss >0){
804: ss++;
805: strcpy(ext,ss); /* save extension */
806: l1= strlen( name);
807: l2= strlen(ss)+1;
808: strncpy( finame, name, l1-l2);
809: finame[l1-l2]= 0;
810: }
811:
812: return( 0 ); /* we're done */
813: }
814:
815:
816: /******************************************/
817:
818: void replace_back_to_slash(char *s, char*t)
819: {
820: int i;
821: int lg=0;
822: i=0;
823: lg=strlen(t);
824: for(i=0; i<= lg; i++) {
825: (s[i] = t[i]);
826: if (t[i]== '\\') s[i]='/';
827: }
828: }
829:
830: char *trimbb(char *out, char *in)
831: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
832: char *s;
833: s=out;
834: while (*in != '\0'){
835: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
836: in++;
837: }
838: *out++ = *in++;
839: }
840: *out='\0';
841: return s;
842: }
843:
844: char *cutl(char *blocc, char *alocc, char *in, char occ)
845: {
846: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
847: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
848: gives blocc="abcdef2ghi" and alocc="j".
849: If occ is not found blocc is null and alocc is equal to in. Returns blocc
850: */
851: char *s, *t;
852: t=in;s=in;
853: while ((*in != occ) && (*in != '\0')){
854: *alocc++ = *in++;
855: }
856: if( *in == occ){
857: *(alocc)='\0';
858: s=++in;
859: }
860:
861: if (s == t) {/* occ not found */
862: *(alocc-(in-s))='\0';
863: in=s;
864: }
865: while ( *in != '\0'){
866: *blocc++ = *in++;
867: }
868:
869: *blocc='\0';
870: return t;
871: }
872: char *cutv(char *blocc, char *alocc, char *in, char occ)
873: {
874: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
875: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
876: gives blocc="abcdef2ghi" and alocc="j".
877: If occ is not found blocc is null and alocc is equal to in. Returns alocc
878: */
879: char *s, *t;
880: t=in;s=in;
881: while (*in != '\0'){
882: while( *in == occ){
883: *blocc++ = *in++;
884: s=in;
885: }
886: *blocc++ = *in++;
887: }
888: if (s == t) /* occ not found */
889: *(blocc-(in-s))='\0';
890: else
891: *(blocc-(in-s)-1)='\0';
892: in=s;
893: while ( *in != '\0'){
894: *alocc++ = *in++;
895: }
896:
897: *alocc='\0';
898: return s;
899: }
900:
901: int nbocc(char *s, char occ)
902: {
903: int i,j=0;
904: int lg=20;
905: i=0;
906: lg=strlen(s);
907: for(i=0; i<= lg; i++) {
908: if (s[i] == occ ) j++;
909: }
910: return j;
911: }
912:
913: /* void cutv(char *u,char *v, char*t, char occ) */
914: /* { */
915: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
916: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
917: /* gives u="abcdef2ghi" and v="j" *\/ */
918: /* int i,lg,j,p=0; */
919: /* i=0; */
920: /* lg=strlen(t); */
921: /* for(j=0; j<=lg-1; j++) { */
922: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
923: /* } */
924:
925: /* for(j=0; j<p; j++) { */
926: /* (u[j] = t[j]); */
927: /* } */
928: /* u[p]='\0'; */
929:
930: /* for(j=0; j<= lg; j++) { */
931: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
932: /* } */
933: /* } */
934:
935: #ifdef _WIN32
936: char * strsep(char **pp, const char *delim)
937: {
938: char *p, *q;
939:
940: if ((p = *pp) == NULL)
941: return 0;
942: if ((q = strpbrk (p, delim)) != NULL)
943: {
944: *pp = q + 1;
945: *q = '\0';
946: }
947: else
948: *pp = 0;
949: return p;
950: }
951: #endif
952:
953: /********************** nrerror ********************/
954:
955: void nrerror(char error_text[])
956: {
957: fprintf(stderr,"ERREUR ...\n");
958: fprintf(stderr,"%s\n",error_text);
959: exit(EXIT_FAILURE);
960: }
961: /*********************** vector *******************/
962: double *vector(int nl, int nh)
963: {
964: double *v;
965: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
966: if (!v) nrerror("allocation failure in vector");
967: return v-nl+NR_END;
968: }
969:
970: /************************ free vector ******************/
971: void free_vector(double*v, int nl, int nh)
972: {
973: free((FREE_ARG)(v+nl-NR_END));
974: }
975:
976: /************************ivector *******************************/
977: int *ivector(long nl,long nh)
978: {
979: int *v;
980: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
981: if (!v) nrerror("allocation failure in ivector");
982: return v-nl+NR_END;
983: }
984:
985: /******************free ivector **************************/
986: void free_ivector(int *v, long nl, long nh)
987: {
988: free((FREE_ARG)(v+nl-NR_END));
989: }
990:
991: /************************lvector *******************************/
992: long *lvector(long nl,long nh)
993: {
994: long *v;
995: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
996: if (!v) nrerror("allocation failure in ivector");
997: return v-nl+NR_END;
998: }
999:
1000: /******************free lvector **************************/
1001: void free_lvector(long *v, long nl, long nh)
1002: {
1003: free((FREE_ARG)(v+nl-NR_END));
1004: }
1005:
1006: /******************* imatrix *******************************/
1007: int **imatrix(long nrl, long nrh, long ncl, long nch)
1008: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1009: {
1010: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1011: int **m;
1012:
1013: /* allocate pointers to rows */
1014: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1015: if (!m) nrerror("allocation failure 1 in matrix()");
1016: m += NR_END;
1017: m -= nrl;
1018:
1019:
1020: /* allocate rows and set pointers to them */
1021: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1022: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1023: m[nrl] += NR_END;
1024: m[nrl] -= ncl;
1025:
1026: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1027:
1028: /* return pointer to array of pointers to rows */
1029: return m;
1030: }
1031:
1032: /****************** free_imatrix *************************/
1033: void free_imatrix(m,nrl,nrh,ncl,nch)
1034: int **m;
1035: long nch,ncl,nrh,nrl;
1036: /* free an int matrix allocated by imatrix() */
1037: {
1038: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1039: free((FREE_ARG) (m+nrl-NR_END));
1040: }
1041:
1042: /******************* matrix *******************************/
1043: double **matrix(long nrl, long nrh, long ncl, long nch)
1044: {
1045: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1046: double **m;
1047:
1048: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1049: if (!m) nrerror("allocation failure 1 in matrix()");
1050: m += NR_END;
1051: m -= nrl;
1052:
1053: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1054: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1055: m[nrl] += NR_END;
1056: m[nrl] -= ncl;
1057:
1058: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1059: return m;
1060: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1061: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1062: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1063: */
1064: }
1065:
1066: /*************************free matrix ************************/
1067: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1068: {
1069: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1070: free((FREE_ARG)(m+nrl-NR_END));
1071: }
1072:
1073: /******************* ma3x *******************************/
1074: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1075: {
1076: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1077: double ***m;
1078:
1079: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1080: if (!m) nrerror("allocation failure 1 in matrix()");
1081: m += NR_END;
1082: m -= nrl;
1083:
1084: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1085: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1086: m[nrl] += NR_END;
1087: m[nrl] -= ncl;
1088:
1089: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1090:
1091: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1092: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1093: m[nrl][ncl] += NR_END;
1094: m[nrl][ncl] -= nll;
1095: for (j=ncl+1; j<=nch; j++)
1096: m[nrl][j]=m[nrl][j-1]+nlay;
1097:
1098: for (i=nrl+1; i<=nrh; i++) {
1099: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1100: for (j=ncl+1; j<=nch; j++)
1101: m[i][j]=m[i][j-1]+nlay;
1102: }
1103: return m;
1104: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1105: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1106: */
1107: }
1108:
1109: /*************************free ma3x ************************/
1110: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1111: {
1112: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1113: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1114: free((FREE_ARG)(m+nrl-NR_END));
1115: }
1116:
1117: /*************** function subdirf ***********/
1118: char *subdirf(char fileres[])
1119: {
1120: /* Caution optionfilefiname is hidden */
1121: strcpy(tmpout,optionfilefiname);
1122: strcat(tmpout,"/"); /* Add to the right */
1123: strcat(tmpout,fileres);
1124: return tmpout;
1125: }
1126:
1127: /*************** function subdirf2 ***********/
1128: char *subdirf2(char fileres[], char *preop)
1129: {
1130:
1131: /* Caution optionfilefiname is hidden */
1132: strcpy(tmpout,optionfilefiname);
1133: strcat(tmpout,"/");
1134: strcat(tmpout,preop);
1135: strcat(tmpout,fileres);
1136: return tmpout;
1137: }
1138:
1139: /*************** function subdirf3 ***********/
1140: char *subdirf3(char fileres[], char *preop, char *preop2)
1141: {
1142:
1143: /* Caution optionfilefiname is hidden */
1144: strcpy(tmpout,optionfilefiname);
1145: strcat(tmpout,"/");
1146: strcat(tmpout,preop);
1147: strcat(tmpout,preop2);
1148: strcat(tmpout,fileres);
1149: return tmpout;
1150: }
1151:
1152: char *asc_diff_time(long time_sec, char ascdiff[])
1153: {
1154: long sec_left, days, hours, minutes;
1155: days = (time_sec) / (60*60*24);
1156: sec_left = (time_sec) % (60*60*24);
1157: hours = (sec_left) / (60*60) ;
1158: sec_left = (sec_left) %(60*60);
1159: minutes = (sec_left) /60;
1160: sec_left = (sec_left) % (60);
1161: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1162: return ascdiff;
1163: }
1164:
1165: /***************** f1dim *************************/
1166: extern int ncom;
1167: extern double *pcom,*xicom;
1168: extern double (*nrfunc)(double []);
1169:
1170: double f1dim(double x)
1171: {
1172: int j;
1173: double f;
1174: double *xt;
1175:
1176: xt=vector(1,ncom);
1177: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1178: f=(*nrfunc)(xt);
1179: free_vector(xt,1,ncom);
1180: return f;
1181: }
1182:
1183: /*****************brent *************************/
1184: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1185: {
1186: int iter;
1187: double a,b,d,etemp;
1188: double fu=0,fv,fw,fx;
1189: double ftemp=0.;
1190: double p,q,r,tol1,tol2,u,v,w,x,xm;
1191: double e=0.0;
1192:
1193: a=(ax < cx ? ax : cx);
1194: b=(ax > cx ? ax : cx);
1195: x=w=v=bx;
1196: fw=fv=fx=(*f)(x);
1197: for (iter=1;iter<=ITMAX;iter++) {
1198: xm=0.5*(a+b);
1199: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1200: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1201: printf(".");fflush(stdout);
1202: fprintf(ficlog,".");fflush(ficlog);
1203: #ifdef DEBUGBRENT
1204: 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);
1205: 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);
1206: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1207: #endif
1208: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1209: *xmin=x;
1210: return fx;
1211: }
1212: ftemp=fu;
1213: if (fabs(e) > tol1) {
1214: r=(x-w)*(fx-fv);
1215: q=(x-v)*(fx-fw);
1216: p=(x-v)*q-(x-w)*r;
1217: q=2.0*(q-r);
1218: if (q > 0.0) p = -p;
1219: q=fabs(q);
1220: etemp=e;
1221: e=d;
1222: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1223: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1224: else {
1225: d=p/q;
1226: u=x+d;
1227: if (u-a < tol2 || b-u < tol2)
1228: d=SIGN(tol1,xm-x);
1229: }
1230: } else {
1231: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1232: }
1233: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1234: fu=(*f)(u);
1235: if (fu <= fx) {
1236: if (u >= x) a=x; else b=x;
1237: SHFT(v,w,x,u)
1238: SHFT(fv,fw,fx,fu)
1239: } else {
1240: if (u < x) a=u; else b=u;
1241: if (fu <= fw || w == x) {
1242: v=w;
1243: w=u;
1244: fv=fw;
1245: fw=fu;
1246: } else if (fu <= fv || v == x || v == w) {
1247: v=u;
1248: fv=fu;
1249: }
1250: }
1251: }
1252: nrerror("Too many iterations in brent");
1253: *xmin=x;
1254: return fx;
1255: }
1256:
1257: /****************** mnbrak ***********************/
1258:
1259: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1260: double (*func)(double))
1261: {
1262: double ulim,u,r,q, dum;
1263: double fu;
1264:
1265: *fa=(*func)(*ax);
1266: *fb=(*func)(*bx);
1267: if (*fb > *fa) {
1268: SHFT(dum,*ax,*bx,dum)
1269: SHFT(dum,*fb,*fa,dum)
1270: }
1271: *cx=(*bx)+GOLD*(*bx-*ax);
1272: *fc=(*func)(*cx);
1273: while (*fb > *fc) { /* Declining fa, fb, fc */
1274: r=(*bx-*ax)*(*fb-*fc);
1275: q=(*bx-*cx)*(*fb-*fa);
1276: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1277: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1278: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1279: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1280: fu=(*func)(u);
1281: #ifdef DEBUG
1282: /* f(x)=A(x-u)**2+f(u) */
1283: double A, fparabu;
1284: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1285: fparabu= *fa - A*(*ax-u)*(*ax-u);
1286: 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);
1287: 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);
1288: #endif
1289: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1290: fu=(*func)(u);
1291: if (fu < *fc) {
1292: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1293: SHFT(*fb,*fc,fu,(*func)(u))
1294: }
1295: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1296: u=ulim;
1297: fu=(*func)(u);
1298: } else {
1299: u=(*cx)+GOLD*(*cx-*bx);
1300: fu=(*func)(u);
1301: }
1302: SHFT(*ax,*bx,*cx,u)
1303: SHFT(*fa,*fb,*fc,fu)
1304: }
1305: }
1306:
1307: /*************** linmin ************************/
1308: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1309: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1310: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1311: the value of func at the returned location p . This is actually all accomplished by calling the
1312: routines mnbrak and brent .*/
1313: int ncom;
1314: double *pcom,*xicom;
1315: double (*nrfunc)(double []);
1316:
1317: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1318: {
1319: double brent(double ax, double bx, double cx,
1320: double (*f)(double), double tol, double *xmin);
1321: double f1dim(double x);
1322: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1323: double *fc, double (*func)(double));
1324: int j;
1325: double xx,xmin,bx,ax;
1326: double fx,fb,fa;
1327:
1328: ncom=n;
1329: pcom=vector(1,n);
1330: xicom=vector(1,n);
1331: nrfunc=func;
1332: for (j=1;j<=n;j++) {
1333: pcom[j]=p[j];
1334: xicom[j]=xi[j];
1335: }
1336: ax=0.0;
1337: xx=1.0;
1338: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1339: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1340: #ifdef DEBUG
1341: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1342: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1343: #endif
1344: for (j=1;j<=n;j++) {
1345: xi[j] *= xmin;
1346: p[j] += xi[j];
1347: }
1348: free_vector(xicom,1,n);
1349: free_vector(pcom,1,n);
1350: }
1351:
1352:
1353: /*************** powell ************************/
1354: /*
1355: Minimization of a function func of n variables. Input consists of an initial starting point
1356: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1357: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1358: such that failure to decrease by more than this amount on one iteration signals doneness. On
1359: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1360: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1361: */
1362: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1363: double (*func)(double []))
1364: {
1365: void linmin(double p[], double xi[], int n, double *fret,
1366: double (*func)(double []));
1367: int i,ibig,j;
1368: double del,t,*pt,*ptt,*xit;
1369: double fp,fptt;
1370: double *xits;
1371: int niterf, itmp;
1372:
1373: pt=vector(1,n);
1374: ptt=vector(1,n);
1375: xit=vector(1,n);
1376: xits=vector(1,n);
1377: *fret=(*func)(p);
1378: for (j=1;j<=n;j++) pt[j]=p[j];
1379: rcurr_time = time(NULL);
1380: for (*iter=1;;++(*iter)) {
1381: fp=(*fret);
1382: ibig=0;
1383: del=0.0;
1384: rlast_time=rcurr_time;
1385: /* (void) gettimeofday(&curr_time,&tzp); */
1386: rcurr_time = time(NULL);
1387: curr_time = *localtime(&rcurr_time);
1388: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1389: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1390: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1391: for (i=1;i<=n;i++) {
1392: printf(" %d %.12f",i, p[i]);
1393: fprintf(ficlog," %d %.12lf",i, p[i]);
1394: fprintf(ficrespow," %.12lf", p[i]);
1395: }
1396: printf("\n");
1397: fprintf(ficlog,"\n");
1398: fprintf(ficrespow,"\n");fflush(ficrespow);
1399: if(*iter <=3){
1400: tml = *localtime(&rcurr_time);
1401: strcpy(strcurr,asctime(&tml));
1402: rforecast_time=rcurr_time;
1403: itmp = strlen(strcurr);
1404: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1405: strcurr[itmp-1]='\0';
1406: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1407: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1408: for(niterf=10;niterf<=30;niterf+=10){
1409: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1410: forecast_time = *localtime(&rforecast_time);
1411: strcpy(strfor,asctime(&forecast_time));
1412: itmp = strlen(strfor);
1413: if(strfor[itmp-1]=='\n')
1414: strfor[itmp-1]='\0';
1415: 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);
1416: 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);
1417: }
1418: }
1419: for (i=1;i<=n;i++) {
1420: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1421: fptt=(*fret);
1422: #ifdef DEBUG
1423: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1424: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1425: #endif
1426: printf("%d",i);fflush(stdout);
1427: fprintf(ficlog,"%d",i);fflush(ficlog);
1428: linmin(p,xit,n,fret,func);
1429: if (fabs(fptt-(*fret)) > del) {
1430: del=fabs(fptt-(*fret));
1431: ibig=i;
1432: }
1433: #ifdef DEBUG
1434: printf("%d %.12e",i,(*fret));
1435: fprintf(ficlog,"%d %.12e",i,(*fret));
1436: for (j=1;j<=n;j++) {
1437: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1438: printf(" x(%d)=%.12e",j,xit[j]);
1439: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1440: }
1441: for(j=1;j<=n;j++) {
1442: printf(" p(%d)=%.12e",j,p[j]);
1443: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1444: }
1445: printf("\n");
1446: fprintf(ficlog,"\n");
1447: #endif
1448: } /* end i */
1449: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1450: #ifdef DEBUG
1451: int k[2],l;
1452: k[0]=1;
1453: k[1]=-1;
1454: printf("Max: %.12e",(*func)(p));
1455: fprintf(ficlog,"Max: %.12e",(*func)(p));
1456: for (j=1;j<=n;j++) {
1457: printf(" %.12e",p[j]);
1458: fprintf(ficlog," %.12e",p[j]);
1459: }
1460: printf("\n");
1461: fprintf(ficlog,"\n");
1462: for(l=0;l<=1;l++) {
1463: for (j=1;j<=n;j++) {
1464: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1465: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1466: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1467: }
1468: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1469: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1470: }
1471: #endif
1472:
1473:
1474: free_vector(xit,1,n);
1475: free_vector(xits,1,n);
1476: free_vector(ptt,1,n);
1477: free_vector(pt,1,n);
1478: return;
1479: }
1480: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1481: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1482: ptt[j]=2.0*p[j]-pt[j];
1483: xit[j]=p[j]-pt[j];
1484: pt[j]=p[j];
1485: }
1486: fptt=(*func)(ptt);
1487: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1488: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1489: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1490: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1491: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1492: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1493: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1494: /* Thus we compare delta(2h) with observed f1-f3 */
1495: /* or best gain on one ancient line 'del' with total */
1496: /* gain f1-f2 = f1 - f2 - 'del' with del */
1497: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1498:
1499: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1500: t= t- del*SQR(fp-fptt);
1501: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1502: 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);
1503: #ifdef DEBUG
1504: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1505: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1506: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1507: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1508: 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);
1509: 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);
1510: #endif
1511: if (t < 0.0) { /* Then we use it for last direction */
1512: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1513: for (j=1;j<=n;j++) {
1514: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1515: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1516: }
1517: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1518: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1519:
1520: #ifdef DEBUG
1521: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1522: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1523: for(j=1;j<=n;j++){
1524: printf(" %.12e",xit[j]);
1525: fprintf(ficlog," %.12e",xit[j]);
1526: }
1527: printf("\n");
1528: fprintf(ficlog,"\n");
1529: #endif
1530: } /* end of t negative */
1531: } /* end if (fptt < fp) */
1532: }
1533: }
1534:
1535: /**** Prevalence limit (stable or period prevalence) ****************/
1536:
1537: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1538: {
1539: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1540: matrix by transitions matrix until convergence is reached */
1541:
1542: int i, ii,j,k;
1543: double min, max, maxmin, maxmax,sumnew=0.;
1544: /* double **matprod2(); */ /* test */
1545: double **out, cov[NCOVMAX+1], **pmij();
1546: double **newm;
1547: double agefin, delaymax=50 ; /* Max number of years to converge */
1548:
1549: for (ii=1;ii<=nlstate+ndeath;ii++)
1550: for (j=1;j<=nlstate+ndeath;j++){
1551: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1552: }
1553:
1554: cov[1]=1.;
1555:
1556: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1557: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1558: newm=savm;
1559: /* Covariates have to be included here again */
1560: cov[2]=agefin;
1561:
1562: for (k=1; k<=cptcovn;k++) {
1563: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1564: /*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]]);*/
1565: }
1566: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1567: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1568: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1569:
1570: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1571: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1572: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1573: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1574: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1575: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1576:
1577: savm=oldm;
1578: oldm=newm;
1579: maxmax=0.;
1580: for(j=1;j<=nlstate;j++){
1581: min=1.;
1582: max=0.;
1583: for(i=1; i<=nlstate; i++) {
1584: sumnew=0;
1585: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1586: prlim[i][j]= newm[i][j]/(1-sumnew);
1587: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1588: max=FMAX(max,prlim[i][j]);
1589: min=FMIN(min,prlim[i][j]);
1590: }
1591: maxmin=max-min;
1592: maxmax=FMAX(maxmax,maxmin);
1593: } /* j loop */
1594: if(maxmax < ftolpl){
1595: return prlim;
1596: }
1597: } /* age loop */
1598: return prlim; /* should not reach here */
1599: }
1600:
1601: /*************** transition probabilities ***************/
1602:
1603: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1604: {
1605: /* According to parameters values stored in x and the covariate's values stored in cov,
1606: computes the probability to be observed in state j being in state i by appying the
1607: model to the ncovmodel covariates (including constant and age).
1608: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1609: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1610: ncth covariate in the global vector x is given by the formula:
1611: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1612: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1613: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1614: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1615: Outputs ps[i][j] the probability to be observed in j being in j according to
1616: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1617: */
1618: double s1, lnpijopii;
1619: /*double t34;*/
1620: int i,j, nc, ii, jj;
1621:
1622: for(i=1; i<= nlstate; i++){
1623: for(j=1; j<i;j++){
1624: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1625: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1626: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1627: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1628: }
1629: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1630: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1631: }
1632: for(j=i+1; j<=nlstate+ndeath;j++){
1633: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1634: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1635: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1636: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1637: }
1638: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1639: }
1640: }
1641:
1642: for(i=1; i<= nlstate; i++){
1643: s1=0;
1644: for(j=1; j<i; j++){
1645: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1646: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1647: }
1648: for(j=i+1; j<=nlstate+ndeath; j++){
1649: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1650: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1651: }
1652: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1653: ps[i][i]=1./(s1+1.);
1654: /* Computing other pijs */
1655: for(j=1; j<i; j++)
1656: ps[i][j]= exp(ps[i][j])*ps[i][i];
1657: for(j=i+1; j<=nlstate+ndeath; j++)
1658: ps[i][j]= exp(ps[i][j])*ps[i][i];
1659: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1660: } /* end i */
1661:
1662: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1663: for(jj=1; jj<= nlstate+ndeath; jj++){
1664: ps[ii][jj]=0;
1665: ps[ii][ii]=1;
1666: }
1667: }
1668:
1669:
1670: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1671: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1672: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1673: /* } */
1674: /* printf("\n "); */
1675: /* } */
1676: /* printf("\n ");printf("%lf ",cov[2]);*/
1677: /*
1678: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1679: goto end;*/
1680: return ps;
1681: }
1682:
1683: /**************** Product of 2 matrices ******************/
1684:
1685: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1686: {
1687: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1688: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1689: /* in, b, out are matrice of pointers which should have been initialized
1690: before: only the contents of out is modified. The function returns
1691: a pointer to pointers identical to out */
1692: int i, j, k;
1693: for(i=nrl; i<= nrh; i++)
1694: for(k=ncolol; k<=ncoloh; k++){
1695: out[i][k]=0.;
1696: for(j=ncl; j<=nch; j++)
1697: out[i][k] +=in[i][j]*b[j][k];
1698: }
1699: return out;
1700: }
1701:
1702:
1703: /************* Higher Matrix Product ***************/
1704:
1705: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1706: {
1707: /* Computes the transition matrix starting at age 'age' over
1708: 'nhstepm*hstepm*stepm' months (i.e. until
1709: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1710: nhstepm*hstepm matrices.
1711: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1712: (typically every 2 years instead of every month which is too big
1713: for the memory).
1714: Model is determined by parameters x and covariates have to be
1715: included manually here.
1716:
1717: */
1718:
1719: int i, j, d, h, k;
1720: double **out, cov[NCOVMAX+1];
1721: double **newm;
1722:
1723: /* Hstepm could be zero and should return the unit matrix */
1724: for (i=1;i<=nlstate+ndeath;i++)
1725: for (j=1;j<=nlstate+ndeath;j++){
1726: oldm[i][j]=(i==j ? 1.0 : 0.0);
1727: po[i][j][0]=(i==j ? 1.0 : 0.0);
1728: }
1729: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1730: for(h=1; h <=nhstepm; h++){
1731: for(d=1; d <=hstepm; d++){
1732: newm=savm;
1733: /* Covariates have to be included here again */
1734: cov[1]=1.;
1735: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1736: for (k=1; k<=cptcovn;k++)
1737: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1738: for (k=1; k<=cptcovage;k++)
1739: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1740: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1741: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1742:
1743:
1744: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1745: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1746: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1747: pmij(pmmij,cov,ncovmodel,x,nlstate));
1748: savm=oldm;
1749: oldm=newm;
1750: }
1751: for(i=1; i<=nlstate+ndeath; i++)
1752: for(j=1;j<=nlstate+ndeath;j++) {
1753: po[i][j][h]=newm[i][j];
1754: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1755: }
1756: /*printf("h=%d ",h);*/
1757: } /* end h */
1758: /* printf("\n H=%d \n",h); */
1759: return po;
1760: }
1761:
1762: #ifdef NLOPT
1763: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1764: double fret;
1765: double *xt;
1766: int j;
1767: myfunc_data *d2 = (myfunc_data *) pd;
1768: /* xt = (p1-1); */
1769: xt=vector(1,n);
1770: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1771:
1772: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1773: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1774: printf("Function = %.12lf ",fret);
1775: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1776: printf("\n");
1777: free_vector(xt,1,n);
1778: return fret;
1779: }
1780: #endif
1781:
1782: /*************** log-likelihood *************/
1783: double func( double *x)
1784: {
1785: int i, ii, j, k, mi, d, kk;
1786: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1787: double **out;
1788: double sw; /* Sum of weights */
1789: double lli; /* Individual log likelihood */
1790: int s1, s2;
1791: double bbh, survp;
1792: long ipmx;
1793: /*extern weight */
1794: /* We are differentiating ll according to initial status */
1795: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1796: /*for(i=1;i<imx;i++)
1797: printf(" %d\n",s[4][i]);
1798: */
1799:
1800: ++countcallfunc;
1801:
1802: cov[1]=1.;
1803:
1804: for(k=1; k<=nlstate; k++) ll[k]=0.;
1805:
1806: if(mle==1){
1807: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1808: /* Computes the values of the ncovmodel covariates of the model
1809: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1810: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1811: to be observed in j being in i according to the model.
1812: */
1813: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1814: cov[2+k]=covar[Tvar[k]][i];
1815: }
1816: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1817: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1818: has been calculated etc */
1819: for(mi=1; mi<= wav[i]-1; mi++){
1820: for (ii=1;ii<=nlstate+ndeath;ii++)
1821: for (j=1;j<=nlstate+ndeath;j++){
1822: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1823: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1824: }
1825: for(d=0; d<dh[mi][i]; d++){
1826: newm=savm;
1827: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1828: for (kk=1; kk<=cptcovage;kk++) {
1829: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1830: }
1831: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1832: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1833: savm=oldm;
1834: oldm=newm;
1835: } /* end mult */
1836:
1837: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1838: /* But now since version 0.9 we anticipate for bias at large stepm.
1839: * If stepm is larger than one month (smallest stepm) and if the exact delay
1840: * (in months) between two waves is not a multiple of stepm, we rounded to
1841: * the nearest (and in case of equal distance, to the lowest) interval but now
1842: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1843: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1844: * probability in order to take into account the bias as a fraction of the way
1845: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1846: * -stepm/2 to stepm/2 .
1847: * For stepm=1 the results are the same as for previous versions of Imach.
1848: * For stepm > 1 the results are less biased than in previous versions.
1849: */
1850: s1=s[mw[mi][i]][i];
1851: s2=s[mw[mi+1][i]][i];
1852: bbh=(double)bh[mi][i]/(double)stepm;
1853: /* bias bh is positive if real duration
1854: * is higher than the multiple of stepm and negative otherwise.
1855: */
1856: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1857: if( s2 > nlstate){
1858: /* i.e. if s2 is a death state and if the date of death is known
1859: then the contribution to the likelihood is the probability to
1860: die between last step unit time and current step unit time,
1861: which is also equal to probability to die before dh
1862: minus probability to die before dh-stepm .
1863: In version up to 0.92 likelihood was computed
1864: as if date of death was unknown. Death was treated as any other
1865: health state: the date of the interview describes the actual state
1866: and not the date of a change in health state. The former idea was
1867: to consider that at each interview the state was recorded
1868: (healthy, disable or death) and IMaCh was corrected; but when we
1869: introduced the exact date of death then we should have modified
1870: the contribution of an exact death to the likelihood. This new
1871: contribution is smaller and very dependent of the step unit
1872: stepm. It is no more the probability to die between last interview
1873: and month of death but the probability to survive from last
1874: interview up to one month before death multiplied by the
1875: probability to die within a month. Thanks to Chris
1876: Jackson for correcting this bug. Former versions increased
1877: mortality artificially. The bad side is that we add another loop
1878: which slows down the processing. The difference can be up to 10%
1879: lower mortality.
1880: */
1881: lli=log(out[s1][s2] - savm[s1][s2]);
1882:
1883:
1884: } else if (s2==-2) {
1885: for (j=1,survp=0. ; j<=nlstate; j++)
1886: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1887: /*survp += out[s1][j]; */
1888: lli= log(survp);
1889: }
1890:
1891: else if (s2==-4) {
1892: for (j=3,survp=0. ; j<=nlstate; j++)
1893: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1894: lli= log(survp);
1895: }
1896:
1897: else if (s2==-5) {
1898: for (j=1,survp=0. ; j<=2; j++)
1899: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1900: lli= log(survp);
1901: }
1902:
1903: else{
1904: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1905: /* 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 */
1906: }
1907: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1908: /*if(lli ==000.0)*/
1909: /*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); */
1910: ipmx +=1;
1911: sw += weight[i];
1912: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1913: } /* end of wave */
1914: } /* end of individual */
1915: } else if(mle==2){
1916: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1917: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1918: for(mi=1; mi<= wav[i]-1; mi++){
1919: for (ii=1;ii<=nlstate+ndeath;ii++)
1920: for (j=1;j<=nlstate+ndeath;j++){
1921: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1922: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1923: }
1924: for(d=0; d<=dh[mi][i]; d++){
1925: newm=savm;
1926: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1927: for (kk=1; kk<=cptcovage;kk++) {
1928: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1929: }
1930: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1931: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1932: savm=oldm;
1933: oldm=newm;
1934: } /* end mult */
1935:
1936: s1=s[mw[mi][i]][i];
1937: s2=s[mw[mi+1][i]][i];
1938: bbh=(double)bh[mi][i]/(double)stepm;
1939: 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 */
1940: ipmx +=1;
1941: sw += weight[i];
1942: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1943: } /* end of wave */
1944: } /* end of individual */
1945: } else if(mle==3){ /* exponential inter-extrapolation */
1946: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1947: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1948: for(mi=1; mi<= wav[i]-1; mi++){
1949: for (ii=1;ii<=nlstate+ndeath;ii++)
1950: for (j=1;j<=nlstate+ndeath;j++){
1951: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1952: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1953: }
1954: for(d=0; d<dh[mi][i]; d++){
1955: newm=savm;
1956: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1957: for (kk=1; kk<=cptcovage;kk++) {
1958: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1959: }
1960: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1961: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1962: savm=oldm;
1963: oldm=newm;
1964: } /* end mult */
1965:
1966: s1=s[mw[mi][i]][i];
1967: s2=s[mw[mi+1][i]][i];
1968: bbh=(double)bh[mi][i]/(double)stepm;
1969: 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 */
1970: ipmx +=1;
1971: sw += weight[i];
1972: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1973: } /* end of wave */
1974: } /* end of individual */
1975: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1976: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1977: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1978: for(mi=1; mi<= wav[i]-1; mi++){
1979: for (ii=1;ii<=nlstate+ndeath;ii++)
1980: for (j=1;j<=nlstate+ndeath;j++){
1981: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1982: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1983: }
1984: for(d=0; d<dh[mi][i]; d++){
1985: newm=savm;
1986: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1987: for (kk=1; kk<=cptcovage;kk++) {
1988: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1989: }
1990:
1991: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1992: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1993: savm=oldm;
1994: oldm=newm;
1995: } /* end mult */
1996:
1997: s1=s[mw[mi][i]][i];
1998: s2=s[mw[mi+1][i]][i];
1999: if( s2 > nlstate){
2000: lli=log(out[s1][s2] - savm[s1][s2]);
2001: }else{
2002: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2003: }
2004: ipmx +=1;
2005: sw += weight[i];
2006: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2007: /* 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]); */
2008: } /* end of wave */
2009: } /* end of individual */
2010: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2011: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2012: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2013: for(mi=1; mi<= wav[i]-1; mi++){
2014: for (ii=1;ii<=nlstate+ndeath;ii++)
2015: for (j=1;j<=nlstate+ndeath;j++){
2016: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2017: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2018: }
2019: for(d=0; d<dh[mi][i]; d++){
2020: newm=savm;
2021: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2022: for (kk=1; kk<=cptcovage;kk++) {
2023: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2024: }
2025:
2026: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2027: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2028: savm=oldm;
2029: oldm=newm;
2030: } /* end mult */
2031:
2032: s1=s[mw[mi][i]][i];
2033: s2=s[mw[mi+1][i]][i];
2034: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2035: ipmx +=1;
2036: sw += weight[i];
2037: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2038: /*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]);*/
2039: } /* end of wave */
2040: } /* end of individual */
2041: } /* End of if */
2042: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2043: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2044: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2045: return -l;
2046: }
2047:
2048: /*************** log-likelihood *************/
2049: double funcone( double *x)
2050: {
2051: /* Same as likeli but slower because of a lot of printf and if */
2052: int i, ii, j, k, mi, d, kk;
2053: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2054: double **out;
2055: double lli; /* Individual log likelihood */
2056: double llt;
2057: int s1, s2;
2058: double bbh, survp;
2059: /*extern weight */
2060: /* We are differentiating ll according to initial status */
2061: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2062: /*for(i=1;i<imx;i++)
2063: printf(" %d\n",s[4][i]);
2064: */
2065: cov[1]=1.;
2066:
2067: for(k=1; k<=nlstate; k++) ll[k]=0.;
2068:
2069: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2070: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2071: for(mi=1; mi<= wav[i]-1; mi++){
2072: for (ii=1;ii<=nlstate+ndeath;ii++)
2073: for (j=1;j<=nlstate+ndeath;j++){
2074: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2075: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2076: }
2077: for(d=0; d<dh[mi][i]; d++){
2078: newm=savm;
2079: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2080: for (kk=1; kk<=cptcovage;kk++) {
2081: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2082: }
2083: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2084: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2085: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2086: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2087: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2088: savm=oldm;
2089: oldm=newm;
2090: } /* end mult */
2091:
2092: s1=s[mw[mi][i]][i];
2093: s2=s[mw[mi+1][i]][i];
2094: bbh=(double)bh[mi][i]/(double)stepm;
2095: /* bias is positive if real duration
2096: * is higher than the multiple of stepm and negative otherwise.
2097: */
2098: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2099: lli=log(out[s1][s2] - savm[s1][s2]);
2100: } else if (s2==-2) {
2101: for (j=1,survp=0. ; j<=nlstate; j++)
2102: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2103: lli= log(survp);
2104: }else if (mle==1){
2105: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2106: } else if(mle==2){
2107: 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 */
2108: } else if(mle==3){ /* exponential inter-extrapolation */
2109: 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 */
2110: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2111: lli=log(out[s1][s2]); /* Original formula */
2112: } else{ /* mle=0 back to 1 */
2113: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2114: /*lli=log(out[s1][s2]); */ /* Original formula */
2115: } /* End of if */
2116: ipmx +=1;
2117: sw += weight[i];
2118: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2119: /*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]); */
2120: if(globpr){
2121: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2122: %11.6f %11.6f %11.6f ", \
2123: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2124: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2125: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2126: llt +=ll[k]*gipmx/gsw;
2127: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2128: }
2129: fprintf(ficresilk," %10.6f\n", -llt);
2130: }
2131: } /* end of wave */
2132: } /* end of individual */
2133: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2134: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2135: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2136: if(globpr==0){ /* First time we count the contributions and weights */
2137: gipmx=ipmx;
2138: gsw=sw;
2139: }
2140: return -l;
2141: }
2142:
2143:
2144: /*************** function likelione ***********/
2145: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2146: {
2147: /* This routine should help understanding what is done with
2148: the selection of individuals/waves and
2149: to check the exact contribution to the likelihood.
2150: Plotting could be done.
2151: */
2152: int k;
2153:
2154: if(*globpri !=0){ /* Just counts and sums, no printings */
2155: strcpy(fileresilk,"ilk");
2156: strcat(fileresilk,fileres);
2157: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2158: printf("Problem with resultfile: %s\n", fileresilk);
2159: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2160: }
2161: 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");
2162: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2163: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2164: for(k=1; k<=nlstate; k++)
2165: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2166: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2167: }
2168:
2169: *fretone=(*funcone)(p);
2170: if(*globpri !=0){
2171: fclose(ficresilk);
2172: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2173: fflush(fichtm);
2174: }
2175: return;
2176: }
2177:
2178:
2179: /*********** Maximum Likelihood Estimation ***************/
2180:
2181: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2182: {
2183: int i,j, iter=0;
2184: double **xi;
2185: double fret;
2186: double fretone; /* Only one call to likelihood */
2187: /* char filerespow[FILENAMELENGTH];*/
2188:
2189: #ifdef NLOPT
2190: int creturn;
2191: nlopt_opt opt;
2192: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2193: double *lb;
2194: double minf; /* the minimum objective value, upon return */
2195: double * p1; /* Shifted parameters from 0 instead of 1 */
2196: myfunc_data dinst, *d = &dinst;
2197: #endif
2198:
2199:
2200: xi=matrix(1,npar,1,npar);
2201: for (i=1;i<=npar;i++)
2202: for (j=1;j<=npar;j++)
2203: xi[i][j]=(i==j ? 1.0 : 0.0);
2204: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2205: strcpy(filerespow,"pow");
2206: strcat(filerespow,fileres);
2207: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2208: printf("Problem with resultfile: %s\n", filerespow);
2209: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2210: }
2211: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2212: for (i=1;i<=nlstate;i++)
2213: for(j=1;j<=nlstate+ndeath;j++)
2214: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2215: fprintf(ficrespow,"\n");
2216: #ifdef POWELL
2217: powell(p,xi,npar,ftol,&iter,&fret,func);
2218: #endif
2219:
2220: #ifdef NLOPT
2221: #ifdef NEWUOA
2222: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2223: #else
2224: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2225: #endif
2226: lb=vector(0,npar-1);
2227: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2228: nlopt_set_lower_bounds(opt, lb);
2229: nlopt_set_initial_step1(opt, 0.1);
2230:
2231: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2232: d->function = func;
2233: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2234: nlopt_set_min_objective(opt, myfunc, d);
2235: nlopt_set_xtol_rel(opt, ftol);
2236: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2237: printf("nlopt failed! %d\n",creturn);
2238: }
2239: else {
2240: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2241: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2242: iter=1; /* not equal */
2243: }
2244: nlopt_destroy(opt);
2245: #endif
2246: free_matrix(xi,1,npar,1,npar);
2247: fclose(ficrespow);
2248: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2249: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2250: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2251:
2252: }
2253:
2254: /**** Computes Hessian and covariance matrix ***/
2255: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2256: {
2257: double **a,**y,*x,pd;
2258: double **hess;
2259: int i, j;
2260: int *indx;
2261:
2262: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2263: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2264: void lubksb(double **a, int npar, int *indx, double b[]) ;
2265: void ludcmp(double **a, int npar, int *indx, double *d) ;
2266: double gompertz(double p[]);
2267: hess=matrix(1,npar,1,npar);
2268:
2269: printf("\nCalculation of the hessian matrix. Wait...\n");
2270: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2271: for (i=1;i<=npar;i++){
2272: printf("%d",i);fflush(stdout);
2273: fprintf(ficlog,"%d",i);fflush(ficlog);
2274:
2275: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2276:
2277: /* printf(" %f ",p[i]);
2278: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2279: }
2280:
2281: for (i=1;i<=npar;i++) {
2282: for (j=1;j<=npar;j++) {
2283: if (j>i) {
2284: printf(".%d%d",i,j);fflush(stdout);
2285: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2286: hess[i][j]=hessij(p,delti,i,j,func,npar);
2287:
2288: hess[j][i]=hess[i][j];
2289: /*printf(" %lf ",hess[i][j]);*/
2290: }
2291: }
2292: }
2293: printf("\n");
2294: fprintf(ficlog,"\n");
2295:
2296: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2297: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2298:
2299: a=matrix(1,npar,1,npar);
2300: y=matrix(1,npar,1,npar);
2301: x=vector(1,npar);
2302: indx=ivector(1,npar);
2303: for (i=1;i<=npar;i++)
2304: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2305: ludcmp(a,npar,indx,&pd);
2306:
2307: for (j=1;j<=npar;j++) {
2308: for (i=1;i<=npar;i++) x[i]=0;
2309: x[j]=1;
2310: lubksb(a,npar,indx,x);
2311: for (i=1;i<=npar;i++){
2312: matcov[i][j]=x[i];
2313: }
2314: }
2315:
2316: printf("\n#Hessian matrix#\n");
2317: fprintf(ficlog,"\n#Hessian matrix#\n");
2318: for (i=1;i<=npar;i++) {
2319: for (j=1;j<=npar;j++) {
2320: printf("%.3e ",hess[i][j]);
2321: fprintf(ficlog,"%.3e ",hess[i][j]);
2322: }
2323: printf("\n");
2324: fprintf(ficlog,"\n");
2325: }
2326:
2327: /* Recompute Inverse */
2328: for (i=1;i<=npar;i++)
2329: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2330: ludcmp(a,npar,indx,&pd);
2331:
2332: /* printf("\n#Hessian matrix recomputed#\n");
2333:
2334: for (j=1;j<=npar;j++) {
2335: for (i=1;i<=npar;i++) x[i]=0;
2336: x[j]=1;
2337: lubksb(a,npar,indx,x);
2338: for (i=1;i<=npar;i++){
2339: y[i][j]=x[i];
2340: printf("%.3e ",y[i][j]);
2341: fprintf(ficlog,"%.3e ",y[i][j]);
2342: }
2343: printf("\n");
2344: fprintf(ficlog,"\n");
2345: }
2346: */
2347:
2348: free_matrix(a,1,npar,1,npar);
2349: free_matrix(y,1,npar,1,npar);
2350: free_vector(x,1,npar);
2351: free_ivector(indx,1,npar);
2352: free_matrix(hess,1,npar,1,npar);
2353:
2354:
2355: }
2356:
2357: /*************** hessian matrix ****************/
2358: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2359: {
2360: int i;
2361: int l=1, lmax=20;
2362: double k1,k2;
2363: double p2[MAXPARM+1]; /* identical to x */
2364: double res;
2365: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2366: double fx;
2367: int k=0,kmax=10;
2368: double l1;
2369:
2370: fx=func(x);
2371: for (i=1;i<=npar;i++) p2[i]=x[i];
2372: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2373: l1=pow(10,l);
2374: delts=delt;
2375: for(k=1 ; k <kmax; k=k+1){
2376: delt = delta*(l1*k);
2377: p2[theta]=x[theta] +delt;
2378: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2379: p2[theta]=x[theta]-delt;
2380: k2=func(p2)-fx;
2381: /*res= (k1-2.0*fx+k2)/delt/delt; */
2382: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2383:
2384: #ifdef DEBUGHESS
2385: 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);
2386: 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);
2387: #endif
2388: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2389: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2390: k=kmax;
2391: }
2392: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2393: k=kmax; l=lmax*10;
2394: }
2395: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2396: delts=delt;
2397: }
2398: }
2399: }
2400: delti[theta]=delts;
2401: return res;
2402:
2403: }
2404:
2405: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2406: {
2407: int i;
2408: int l=1, lmax=20;
2409: double k1,k2,k3,k4,res,fx;
2410: double p2[MAXPARM+1];
2411: int k;
2412:
2413: fx=func(x);
2414: for (k=1; k<=2; k++) {
2415: for (i=1;i<=npar;i++) p2[i]=x[i];
2416: p2[thetai]=x[thetai]+delti[thetai]/k;
2417: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2418: k1=func(p2)-fx;
2419:
2420: p2[thetai]=x[thetai]+delti[thetai]/k;
2421: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2422: k2=func(p2)-fx;
2423:
2424: p2[thetai]=x[thetai]-delti[thetai]/k;
2425: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2426: k3=func(p2)-fx;
2427:
2428: p2[thetai]=x[thetai]-delti[thetai]/k;
2429: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2430: k4=func(p2)-fx;
2431: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2432: #ifdef DEBUG
2433: 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);
2434: 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);
2435: #endif
2436: }
2437: return res;
2438: }
2439:
2440: /************** Inverse of matrix **************/
2441: void ludcmp(double **a, int n, int *indx, double *d)
2442: {
2443: int i,imax,j,k;
2444: double big,dum,sum,temp;
2445: double *vv;
2446:
2447: vv=vector(1,n);
2448: *d=1.0;
2449: for (i=1;i<=n;i++) {
2450: big=0.0;
2451: for (j=1;j<=n;j++)
2452: if ((temp=fabs(a[i][j])) > big) big=temp;
2453: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2454: vv[i]=1.0/big;
2455: }
2456: for (j=1;j<=n;j++) {
2457: for (i=1;i<j;i++) {
2458: sum=a[i][j];
2459: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2460: a[i][j]=sum;
2461: }
2462: big=0.0;
2463: for (i=j;i<=n;i++) {
2464: sum=a[i][j];
2465: for (k=1;k<j;k++)
2466: sum -= a[i][k]*a[k][j];
2467: a[i][j]=sum;
2468: if ( (dum=vv[i]*fabs(sum)) >= big) {
2469: big=dum;
2470: imax=i;
2471: }
2472: }
2473: if (j != imax) {
2474: for (k=1;k<=n;k++) {
2475: dum=a[imax][k];
2476: a[imax][k]=a[j][k];
2477: a[j][k]=dum;
2478: }
2479: *d = -(*d);
2480: vv[imax]=vv[j];
2481: }
2482: indx[j]=imax;
2483: if (a[j][j] == 0.0) a[j][j]=TINY;
2484: if (j != n) {
2485: dum=1.0/(a[j][j]);
2486: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2487: }
2488: }
2489: free_vector(vv,1,n); /* Doesn't work */
2490: ;
2491: }
2492:
2493: void lubksb(double **a, int n, int *indx, double b[])
2494: {
2495: int i,ii=0,ip,j;
2496: double sum;
2497:
2498: for (i=1;i<=n;i++) {
2499: ip=indx[i];
2500: sum=b[ip];
2501: b[ip]=b[i];
2502: if (ii)
2503: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2504: else if (sum) ii=i;
2505: b[i]=sum;
2506: }
2507: for (i=n;i>=1;i--) {
2508: sum=b[i];
2509: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2510: b[i]=sum/a[i][i];
2511: }
2512: }
2513:
2514: void pstamp(FILE *fichier)
2515: {
2516: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2517: }
2518:
2519: /************ Frequencies ********************/
2520: 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[])
2521: { /* Some frequencies */
2522:
2523: int i, m, jk, j1, bool, z1,j;
2524: int first;
2525: double ***freq; /* Frequencies */
2526: double *pp, **prop;
2527: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2528: char fileresp[FILENAMELENGTH];
2529:
2530: pp=vector(1,nlstate);
2531: prop=matrix(1,nlstate,iagemin,iagemax+3);
2532: strcpy(fileresp,"p");
2533: strcat(fileresp,fileres);
2534: if((ficresp=fopen(fileresp,"w"))==NULL) {
2535: printf("Problem with prevalence resultfile: %s\n", fileresp);
2536: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2537: exit(0);
2538: }
2539: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2540: j1=0;
2541:
2542: j=cptcoveff;
2543: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2544:
2545: first=1;
2546:
2547: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2548: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2549: /* j1++; */
2550: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2551: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2552: scanf("%d", i);*/
2553: for (i=-5; i<=nlstate+ndeath; i++)
2554: for (jk=-5; jk<=nlstate+ndeath; jk++)
2555: for(m=iagemin; m <= iagemax+3; m++)
2556: freq[i][jk][m]=0;
2557:
2558: for (i=1; i<=nlstate; i++)
2559: for(m=iagemin; m <= iagemax+3; m++)
2560: prop[i][m]=0;
2561:
2562: dateintsum=0;
2563: k2cpt=0;
2564: for (i=1; i<=imx; i++) {
2565: bool=1;
2566: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2567: for (z1=1; z1<=cptcoveff; z1++)
2568: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2569: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2570: bool=0;
2571: /* 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",
2572: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2573: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2574: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2575: }
2576: }
2577:
2578: if (bool==1){
2579: for(m=firstpass; m<=lastpass; m++){
2580: k2=anint[m][i]+(mint[m][i]/12.);
2581: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2582: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2583: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2584: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2585: if (m<lastpass) {
2586: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2587: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2588: }
2589:
2590: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2591: dateintsum=dateintsum+k2;
2592: k2cpt++;
2593: }
2594: /*}*/
2595: }
2596: }
2597: } /* end i */
2598:
2599: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2600: pstamp(ficresp);
2601: if (cptcovn>0) {
2602: fprintf(ficresp, "\n#********** Variable ");
2603: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2604: fprintf(ficresp, "**********\n#");
2605: fprintf(ficlog, "\n#********** Variable ");
2606: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2607: fprintf(ficlog, "**********\n#");
2608: }
2609: for(i=1; i<=nlstate;i++)
2610: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2611: fprintf(ficresp, "\n");
2612:
2613: for(i=iagemin; i <= iagemax+3; i++){
2614: if(i==iagemax+3){
2615: fprintf(ficlog,"Total");
2616: }else{
2617: if(first==1){
2618: first=0;
2619: printf("See log file for details...\n");
2620: }
2621: fprintf(ficlog,"Age %d", i);
2622: }
2623: for(jk=1; jk <=nlstate ; jk++){
2624: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2625: pp[jk] += freq[jk][m][i];
2626: }
2627: for(jk=1; jk <=nlstate ; jk++){
2628: for(m=-1, pos=0; m <=0 ; m++)
2629: pos += freq[jk][m][i];
2630: if(pp[jk]>=1.e-10){
2631: if(first==1){
2632: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2633: }
2634: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2635: }else{
2636: if(first==1)
2637: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2638: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2639: }
2640: }
2641:
2642: for(jk=1; jk <=nlstate ; jk++){
2643: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2644: pp[jk] += freq[jk][m][i];
2645: }
2646: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2647: pos += pp[jk];
2648: posprop += prop[jk][i];
2649: }
2650: for(jk=1; jk <=nlstate ; jk++){
2651: if(pos>=1.e-5){
2652: if(first==1)
2653: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2654: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2655: }else{
2656: if(first==1)
2657: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2658: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2659: }
2660: if( i <= iagemax){
2661: if(pos>=1.e-5){
2662: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2663: /*probs[i][jk][j1]= pp[jk]/pos;*/
2664: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2665: }
2666: else
2667: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2668: }
2669: }
2670:
2671: for(jk=-1; jk <=nlstate+ndeath; jk++)
2672: for(m=-1; m <=nlstate+ndeath; m++)
2673: if(freq[jk][m][i] !=0 ) {
2674: if(first==1)
2675: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2676: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2677: }
2678: if(i <= iagemax)
2679: fprintf(ficresp,"\n");
2680: if(first==1)
2681: printf("Others in log...\n");
2682: fprintf(ficlog,"\n");
2683: }
2684: /*}*/
2685: }
2686: dateintmean=dateintsum/k2cpt;
2687:
2688: fclose(ficresp);
2689: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2690: free_vector(pp,1,nlstate);
2691: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2692: /* End of Freq */
2693: }
2694:
2695: /************ Prevalence ********************/
2696: 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)
2697: {
2698: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2699: in each health status at the date of interview (if between dateprev1 and dateprev2).
2700: We still use firstpass and lastpass as another selection.
2701: */
2702:
2703: int i, m, jk, j1, bool, z1,j;
2704:
2705: double **prop;
2706: double posprop;
2707: double y2; /* in fractional years */
2708: int iagemin, iagemax;
2709: int first; /** to stop verbosity which is redirected to log file */
2710:
2711: iagemin= (int) agemin;
2712: iagemax= (int) agemax;
2713: /*pp=vector(1,nlstate);*/
2714: prop=matrix(1,nlstate,iagemin,iagemax+3);
2715: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2716: j1=0;
2717:
2718: /*j=cptcoveff;*/
2719: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2720:
2721: first=1;
2722: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2723: /*for(i1=1; i1<=ncodemax[k1];i1++){
2724: j1++;*/
2725:
2726: for (i=1; i<=nlstate; i++)
2727: for(m=iagemin; m <= iagemax+3; m++)
2728: prop[i][m]=0.0;
2729:
2730: for (i=1; i<=imx; i++) { /* Each individual */
2731: bool=1;
2732: if (cptcovn>0) {
2733: for (z1=1; z1<=cptcoveff; z1++)
2734: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2735: bool=0;
2736: }
2737: if (bool==1) {
2738: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2739: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2740: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2741: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2742: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2743: 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);
2744: if (s[m][i]>0 && s[m][i]<=nlstate) {
2745: /*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]]);*/
2746: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2747: prop[s[m][i]][iagemax+3] += weight[i];
2748: }
2749: }
2750: } /* end selection of waves */
2751: }
2752: }
2753: for(i=iagemin; i <= iagemax+3; i++){
2754: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2755: posprop += prop[jk][i];
2756: }
2757:
2758: for(jk=1; jk <=nlstate ; jk++){
2759: if( i <= iagemax){
2760: if(posprop>=1.e-5){
2761: probs[i][jk][j1]= prop[jk][i]/posprop;
2762: } else{
2763: if(first==1){
2764: first=0;
2765: 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]);
2766: }
2767: }
2768: }
2769: }/* end jk */
2770: }/* end i */
2771: /*} *//* end i1 */
2772: } /* end j1 */
2773:
2774: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2775: /*free_vector(pp,1,nlstate);*/
2776: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2777: } /* End of prevalence */
2778:
2779: /************* Waves Concatenation ***************/
2780:
2781: 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)
2782: {
2783: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2784: Death is a valid wave (if date is known).
2785: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2786: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2787: and mw[mi+1][i]. dh depends on stepm.
2788: */
2789:
2790: int i, mi, m;
2791: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2792: double sum=0., jmean=0.;*/
2793: int first;
2794: int j, k=0,jk, ju, jl;
2795: double sum=0.;
2796: first=0;
2797: jmin=100000;
2798: jmax=-1;
2799: jmean=0.;
2800: for(i=1; i<=imx; i++){
2801: mi=0;
2802: m=firstpass;
2803: while(s[m][i] <= nlstate){
2804: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2805: mw[++mi][i]=m;
2806: if(m >=lastpass)
2807: break;
2808: else
2809: m++;
2810: }/* end while */
2811: if (s[m][i] > nlstate){
2812: mi++; /* Death is another wave */
2813: /* if(mi==0) never been interviewed correctly before death */
2814: /* Only death is a correct wave */
2815: mw[mi][i]=m;
2816: }
2817:
2818: wav[i]=mi;
2819: if(mi==0){
2820: nbwarn++;
2821: if(first==0){
2822: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2823: first=1;
2824: }
2825: if(first==1){
2826: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2827: }
2828: } /* end mi==0 */
2829: } /* End individuals */
2830:
2831: for(i=1; i<=imx; i++){
2832: for(mi=1; mi<wav[i];mi++){
2833: if (stepm <=0)
2834: dh[mi][i]=1;
2835: else{
2836: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2837: if (agedc[i] < 2*AGESUP) {
2838: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2839: if(j==0) j=1; /* Survives at least one month after exam */
2840: else if(j<0){
2841: nberr++;
2842: 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]);
2843: j=1; /* Temporary Dangerous patch */
2844: 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);
2845: 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]);
2846: 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);
2847: }
2848: k=k+1;
2849: if (j >= jmax){
2850: jmax=j;
2851: ijmax=i;
2852: }
2853: if (j <= jmin){
2854: jmin=j;
2855: ijmin=i;
2856: }
2857: sum=sum+j;
2858: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2859: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2860: }
2861: }
2862: else{
2863: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2864: /* 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]); */
2865:
2866: k=k+1;
2867: if (j >= jmax) {
2868: jmax=j;
2869: ijmax=i;
2870: }
2871: else if (j <= jmin){
2872: jmin=j;
2873: ijmin=i;
2874: }
2875: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2876: /*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]);*/
2877: if(j<0){
2878: nberr++;
2879: 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]);
2880: 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]);
2881: }
2882: sum=sum+j;
2883: }
2884: jk= j/stepm;
2885: jl= j -jk*stepm;
2886: ju= j -(jk+1)*stepm;
2887: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2888: if(jl==0){
2889: dh[mi][i]=jk;
2890: bh[mi][i]=0;
2891: }else{ /* We want a negative bias in order to only have interpolation ie
2892: * to avoid the price of an extra matrix product in likelihood */
2893: dh[mi][i]=jk+1;
2894: bh[mi][i]=ju;
2895: }
2896: }else{
2897: if(jl <= -ju){
2898: dh[mi][i]=jk;
2899: bh[mi][i]=jl; /* bias is positive if real duration
2900: * is higher than the multiple of stepm and negative otherwise.
2901: */
2902: }
2903: else{
2904: dh[mi][i]=jk+1;
2905: bh[mi][i]=ju;
2906: }
2907: if(dh[mi][i]==0){
2908: dh[mi][i]=1; /* At least one step */
2909: bh[mi][i]=ju; /* At least one step */
2910: /* 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);*/
2911: }
2912: } /* end if mle */
2913: }
2914: } /* end wave */
2915: }
2916: jmean=sum/k;
2917: 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);
2918: 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);
2919: }
2920:
2921: /*********** Tricode ****************************/
2922: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2923: {
2924: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2925: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2926: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2927: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2928: * nbcode[Tvar[j]][1]=
2929: */
2930:
2931: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2932: int modmaxcovj=0; /* Modality max of covariates j */
2933: int cptcode=0; /* Modality max of covariates j */
2934: int modmincovj=0; /* Modality min of covariates j */
2935:
2936:
2937: cptcoveff=0;
2938:
2939: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2940: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2941:
2942: /* Loop on covariates without age and products */
2943: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2944: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2945: modality of this covariate Vj*/
2946: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2947: * If product of Vn*Vm, still boolean *:
2948: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2949: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2950: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2951: modality of the nth covariate of individual i. */
2952: if (ij > modmaxcovj)
2953: modmaxcovj=ij;
2954: else if (ij < modmincovj)
2955: modmincovj=ij;
2956: if ((ij < -1) && (ij > NCOVMAX)){
2957: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2958: exit(1);
2959: }else
2960: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2961: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2962: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2963: /* getting the maximum value of the modality of the covariate
2964: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2965: female is 1, then modmaxcovj=1.*/
2966: }
2967: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2968: cptcode=modmaxcovj;
2969: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2970: /*for (i=0; i<=cptcode; i++) {*/
2971: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2972: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2973: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2974: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2975: }
2976: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2977: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2978: } /* Ndum[-1] number of undefined modalities */
2979:
2980: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2981: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2982: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2983: modmincovj=3; modmaxcovj = 7;
2984: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2985: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2986: variables V1_1 and V1_2.
2987: nbcode[Tvar[j]][ij]=k;
2988: nbcode[Tvar[j]][1]=0;
2989: nbcode[Tvar[j]][2]=1;
2990: nbcode[Tvar[j]][3]=2;
2991: */
2992: ij=1; /* ij is similar to i but can jumps over null modalities */
2993: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
2994: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
2995: /*recode from 0 */
2996: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
2997: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
2998: k is a modality. If we have model=V1+V1*sex
2999: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3000: ij++;
3001: }
3002: if (ij > ncodemax[j]) break;
3003: } /* end of loop on */
3004: } /* end of loop on modality */
3005: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3006:
3007: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3008:
3009: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3010: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3011: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3012: Ndum[ij]++;
3013: }
3014:
3015: ij=1;
3016: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3017: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3018: if((Ndum[i]!=0) && (i<=ncovcol)){
3019: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3020: Tvaraff[ij]=i; /*For printing (unclear) */
3021: ij++;
3022: }else
3023: Tvaraff[ij]=0;
3024: }
3025: ij--;
3026: cptcoveff=ij; /*Number of total covariates*/
3027:
3028: }
3029:
3030:
3031: /*********** Health Expectancies ****************/
3032:
3033: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3034:
3035: {
3036: /* Health expectancies, no variances */
3037: int i, j, nhstepm, hstepm, h, nstepm;
3038: int nhstepma, nstepma; /* Decreasing with age */
3039: double age, agelim, hf;
3040: double ***p3mat;
3041: double eip;
3042:
3043: pstamp(ficreseij);
3044: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3045: fprintf(ficreseij,"# Age");
3046: for(i=1; i<=nlstate;i++){
3047: for(j=1; j<=nlstate;j++){
3048: fprintf(ficreseij," e%1d%1d ",i,j);
3049: }
3050: fprintf(ficreseij," e%1d. ",i);
3051: }
3052: fprintf(ficreseij,"\n");
3053:
3054:
3055: if(estepm < stepm){
3056: printf ("Problem %d lower than %d\n",estepm, stepm);
3057: }
3058: else hstepm=estepm;
3059: /* We compute the life expectancy from trapezoids spaced every estepm months
3060: * This is mainly to measure the difference between two models: for example
3061: * if stepm=24 months pijx are given only every 2 years and by summing them
3062: * we are calculating an estimate of the Life Expectancy assuming a linear
3063: * progression in between and thus overestimating or underestimating according
3064: * to the curvature of the survival function. If, for the same date, we
3065: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3066: * to compare the new estimate of Life expectancy with the same linear
3067: * hypothesis. A more precise result, taking into account a more precise
3068: * curvature will be obtained if estepm is as small as stepm. */
3069:
3070: /* For example we decided to compute the life expectancy with the smallest unit */
3071: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3072: nhstepm is the number of hstepm from age to agelim
3073: nstepm is the number of stepm from age to agelin.
3074: Look at hpijx to understand the reason of that which relies in memory size
3075: and note for a fixed period like estepm months */
3076: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3077: survival function given by stepm (the optimization length). Unfortunately it
3078: means that if the survival funtion is printed only each two years of age and if
3079: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3080: results. So we changed our mind and took the option of the best precision.
3081: */
3082: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3083:
3084: agelim=AGESUP;
3085: /* If stepm=6 months */
3086: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3087: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3088:
3089: /* nhstepm age range expressed in number of stepm */
3090: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3091: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3092: /* if (stepm >= YEARM) hstepm=1;*/
3093: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3094: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3095:
3096: for (age=bage; age<=fage; age ++){
3097: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3098: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3099: /* if (stepm >= YEARM) hstepm=1;*/
3100: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3101:
3102: /* If stepm=6 months */
3103: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3104: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3105:
3106: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3107:
3108: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3109:
3110: printf("%d|",(int)age);fflush(stdout);
3111: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3112:
3113: /* Computing expectancies */
3114: for(i=1; i<=nlstate;i++)
3115: for(j=1; j<=nlstate;j++)
3116: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3117: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3118:
3119: /* 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]);*/
3120:
3121: }
3122:
3123: fprintf(ficreseij,"%3.0f",age );
3124: for(i=1; i<=nlstate;i++){
3125: eip=0;
3126: for(j=1; j<=nlstate;j++){
3127: eip +=eij[i][j][(int)age];
3128: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3129: }
3130: fprintf(ficreseij,"%9.4f", eip );
3131: }
3132: fprintf(ficreseij,"\n");
3133:
3134: }
3135: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3136: printf("\n");
3137: fprintf(ficlog,"\n");
3138:
3139: }
3140:
3141: 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[] )
3142:
3143: {
3144: /* Covariances of health expectancies eij and of total life expectancies according
3145: to initial status i, ei. .
3146: */
3147: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3148: int nhstepma, nstepma; /* Decreasing with age */
3149: double age, agelim, hf;
3150: double ***p3matp, ***p3matm, ***varhe;
3151: double **dnewm,**doldm;
3152: double *xp, *xm;
3153: double **gp, **gm;
3154: double ***gradg, ***trgradg;
3155: int theta;
3156:
3157: double eip, vip;
3158:
3159: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3160: xp=vector(1,npar);
3161: xm=vector(1,npar);
3162: dnewm=matrix(1,nlstate*nlstate,1,npar);
3163: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3164:
3165: pstamp(ficresstdeij);
3166: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3167: fprintf(ficresstdeij,"# Age");
3168: for(i=1; i<=nlstate;i++){
3169: for(j=1; j<=nlstate;j++)
3170: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3171: fprintf(ficresstdeij," e%1d. ",i);
3172: }
3173: fprintf(ficresstdeij,"\n");
3174:
3175: pstamp(ficrescveij);
3176: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3177: fprintf(ficrescveij,"# Age");
3178: for(i=1; i<=nlstate;i++)
3179: for(j=1; j<=nlstate;j++){
3180: cptj= (j-1)*nlstate+i;
3181: for(i2=1; i2<=nlstate;i2++)
3182: for(j2=1; j2<=nlstate;j2++){
3183: cptj2= (j2-1)*nlstate+i2;
3184: if(cptj2 <= cptj)
3185: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3186: }
3187: }
3188: fprintf(ficrescveij,"\n");
3189:
3190: if(estepm < stepm){
3191: printf ("Problem %d lower than %d\n",estepm, stepm);
3192: }
3193: else hstepm=estepm;
3194: /* We compute the life expectancy from trapezoids spaced every estepm months
3195: * This is mainly to measure the difference between two models: for example
3196: * if stepm=24 months pijx are given only every 2 years and by summing them
3197: * we are calculating an estimate of the Life Expectancy assuming a linear
3198: * progression in between and thus overestimating or underestimating according
3199: * to the curvature of the survival function. If, for the same date, we
3200: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3201: * to compare the new estimate of Life expectancy with the same linear
3202: * hypothesis. A more precise result, taking into account a more precise
3203: * curvature will be obtained if estepm is as small as stepm. */
3204:
3205: /* For example we decided to compute the life expectancy with the smallest unit */
3206: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3207: nhstepm is the number of hstepm from age to agelim
3208: nstepm is the number of stepm from age to agelin.
3209: Look at hpijx to understand the reason of that which relies in memory size
3210: and note for a fixed period like estepm months */
3211: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3212: survival function given by stepm (the optimization length). Unfortunately it
3213: means that if the survival funtion is printed only each two years of age and if
3214: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3215: results. So we changed our mind and took the option of the best precision.
3216: */
3217: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3218:
3219: /* If stepm=6 months */
3220: /* nhstepm age range expressed in number of stepm */
3221: agelim=AGESUP;
3222: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3223: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3224: /* if (stepm >= YEARM) hstepm=1;*/
3225: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3226:
3227: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3228: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3229: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3230: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3231: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3232: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3233:
3234: for (age=bage; age<=fage; age ++){
3235: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3236: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3237: /* if (stepm >= YEARM) hstepm=1;*/
3238: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3239:
3240: /* If stepm=6 months */
3241: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3242: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3243:
3244: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3245:
3246: /* Computing Variances of health expectancies */
3247: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3248: decrease memory allocation */
3249: for(theta=1; theta <=npar; theta++){
3250: for(i=1; i<=npar; i++){
3251: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3252: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3253: }
3254: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3255: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3256:
3257: for(j=1; j<= nlstate; j++){
3258: for(i=1; i<=nlstate; i++){
3259: for(h=0; h<=nhstepm-1; h++){
3260: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3261: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3262: }
3263: }
3264: }
3265:
3266: for(ij=1; ij<= nlstate*nlstate; ij++)
3267: for(h=0; h<=nhstepm-1; h++){
3268: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3269: }
3270: }/* End theta */
3271:
3272:
3273: for(h=0; h<=nhstepm-1; h++)
3274: for(j=1; j<=nlstate*nlstate;j++)
3275: for(theta=1; theta <=npar; theta++)
3276: trgradg[h][j][theta]=gradg[h][theta][j];
3277:
3278:
3279: for(ij=1;ij<=nlstate*nlstate;ij++)
3280: for(ji=1;ji<=nlstate*nlstate;ji++)
3281: varhe[ij][ji][(int)age] =0.;
3282:
3283: printf("%d|",(int)age);fflush(stdout);
3284: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3285: for(h=0;h<=nhstepm-1;h++){
3286: for(k=0;k<=nhstepm-1;k++){
3287: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3288: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3289: for(ij=1;ij<=nlstate*nlstate;ij++)
3290: for(ji=1;ji<=nlstate*nlstate;ji++)
3291: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3292: }
3293: }
3294:
3295: /* Computing expectancies */
3296: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3297: for(i=1; i<=nlstate;i++)
3298: for(j=1; j<=nlstate;j++)
3299: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3300: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3301:
3302: /* 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]);*/
3303:
3304: }
3305:
3306: fprintf(ficresstdeij,"%3.0f",age );
3307: for(i=1; i<=nlstate;i++){
3308: eip=0.;
3309: vip=0.;
3310: for(j=1; j<=nlstate;j++){
3311: eip += eij[i][j][(int)age];
3312: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3313: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3314: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3315: }
3316: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3317: }
3318: fprintf(ficresstdeij,"\n");
3319:
3320: fprintf(ficrescveij,"%3.0f",age );
3321: for(i=1; i<=nlstate;i++)
3322: for(j=1; j<=nlstate;j++){
3323: cptj= (j-1)*nlstate+i;
3324: for(i2=1; i2<=nlstate;i2++)
3325: for(j2=1; j2<=nlstate;j2++){
3326: cptj2= (j2-1)*nlstate+i2;
3327: if(cptj2 <= cptj)
3328: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3329: }
3330: }
3331: fprintf(ficrescveij,"\n");
3332:
3333: }
3334: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3335: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3336: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3337: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3338: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3339: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3340: printf("\n");
3341: fprintf(ficlog,"\n");
3342:
3343: free_vector(xm,1,npar);
3344: free_vector(xp,1,npar);
3345: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3346: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3347: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3348: }
3349:
3350: /************ Variance ******************/
3351: 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[])
3352: {
3353: /* Variance of health expectancies */
3354: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3355: /* double **newm;*/
3356: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3357:
3358: int movingaverage();
3359: double **dnewm,**doldm;
3360: double **dnewmp,**doldmp;
3361: int i, j, nhstepm, hstepm, h, nstepm ;
3362: int k;
3363: double *xp;
3364: double **gp, **gm; /* for var eij */
3365: double ***gradg, ***trgradg; /*for var eij */
3366: double **gradgp, **trgradgp; /* for var p point j */
3367: double *gpp, *gmp; /* for var p point j */
3368: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3369: double ***p3mat;
3370: double age,agelim, hf;
3371: double ***mobaverage;
3372: int theta;
3373: char digit[4];
3374: char digitp[25];
3375:
3376: char fileresprobmorprev[FILENAMELENGTH];
3377:
3378: if(popbased==1){
3379: if(mobilav!=0)
3380: strcpy(digitp,"-populbased-mobilav-");
3381: else strcpy(digitp,"-populbased-nomobil-");
3382: }
3383: else
3384: strcpy(digitp,"-stablbased-");
3385:
3386: if (mobilav!=0) {
3387: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3388: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3389: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3390: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3391: }
3392: }
3393:
3394: strcpy(fileresprobmorprev,"prmorprev");
3395: sprintf(digit,"%-d",ij);
3396: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3397: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3398: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3399: strcat(fileresprobmorprev,fileres);
3400: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3401: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3402: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3403: }
3404: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3405:
3406: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3407: pstamp(ficresprobmorprev);
3408: 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);
3409: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3410: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3411: fprintf(ficresprobmorprev," p.%-d SE",j);
3412: for(i=1; i<=nlstate;i++)
3413: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3414: }
3415: fprintf(ficresprobmorprev,"\n");
3416: fprintf(ficgp,"\n# Routine varevsij");
3417: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3418: 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");
3419: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3420: /* } */
3421: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3422: pstamp(ficresvij);
3423: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3424: if(popbased==1)
3425: 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);
3426: else
3427: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3428: fprintf(ficresvij,"# Age");
3429: for(i=1; i<=nlstate;i++)
3430: for(j=1; j<=nlstate;j++)
3431: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3432: fprintf(ficresvij,"\n");
3433:
3434: xp=vector(1,npar);
3435: dnewm=matrix(1,nlstate,1,npar);
3436: doldm=matrix(1,nlstate,1,nlstate);
3437: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3438: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3439:
3440: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3441: gpp=vector(nlstate+1,nlstate+ndeath);
3442: gmp=vector(nlstate+1,nlstate+ndeath);
3443: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3444:
3445: if(estepm < stepm){
3446: printf ("Problem %d lower than %d\n",estepm, stepm);
3447: }
3448: else hstepm=estepm;
3449: /* For example we decided to compute the life expectancy with the smallest unit */
3450: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3451: nhstepm is the number of hstepm from age to agelim
3452: nstepm is the number of stepm from age to agelin.
3453: Look at function hpijx to understand why (it is linked to memory size questions) */
3454: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3455: survival function given by stepm (the optimization length). Unfortunately it
3456: means that if the survival funtion is printed every two years of age and if
3457: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3458: results. So we changed our mind and took the option of the best precision.
3459: */
3460: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3461: agelim = AGESUP;
3462: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3463: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3464: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3465: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3466: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3467: gp=matrix(0,nhstepm,1,nlstate);
3468: gm=matrix(0,nhstepm,1,nlstate);
3469:
3470:
3471: for(theta=1; theta <=npar; theta++){
3472: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3473: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3474: }
3475: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3476: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3477:
3478: if (popbased==1) {
3479: if(mobilav ==0){
3480: for(i=1; i<=nlstate;i++)
3481: prlim[i][i]=probs[(int)age][i][ij];
3482: }else{ /* mobilav */
3483: for(i=1; i<=nlstate;i++)
3484: prlim[i][i]=mobaverage[(int)age][i][ij];
3485: }
3486: }
3487:
3488: for(j=1; j<= nlstate; j++){
3489: for(h=0; h<=nhstepm; h++){
3490: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3491: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3492: }
3493: }
3494: /* This for computing probability of death (h=1 means
3495: computed over hstepm matrices product = hstepm*stepm months)
3496: as a weighted average of prlim.
3497: */
3498: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3499: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3500: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3501: }
3502: /* end probability of death */
3503:
3504: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3505: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3506: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3507: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3508:
3509: if (popbased==1) {
3510: if(mobilav ==0){
3511: for(i=1; i<=nlstate;i++)
3512: prlim[i][i]=probs[(int)age][i][ij];
3513: }else{ /* mobilav */
3514: for(i=1; i<=nlstate;i++)
3515: prlim[i][i]=mobaverage[(int)age][i][ij];
3516: }
3517: }
3518:
3519: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3520: for(h=0; h<=nhstepm; h++){
3521: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3522: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3523: }
3524: }
3525: /* This for computing probability of death (h=1 means
3526: computed over hstepm matrices product = hstepm*stepm months)
3527: as a weighted average of prlim.
3528: */
3529: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3530: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3531: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3532: }
3533: /* end probability of death */
3534:
3535: for(j=1; j<= nlstate; j++) /* vareij */
3536: for(h=0; h<=nhstepm; h++){
3537: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3538: }
3539:
3540: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3541: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3542: }
3543:
3544: } /* End theta */
3545:
3546: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3547:
3548: for(h=0; h<=nhstepm; h++) /* veij */
3549: for(j=1; j<=nlstate;j++)
3550: for(theta=1; theta <=npar; theta++)
3551: trgradg[h][j][theta]=gradg[h][theta][j];
3552:
3553: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3554: for(theta=1; theta <=npar; theta++)
3555: trgradgp[j][theta]=gradgp[theta][j];
3556:
3557:
3558: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3559: for(i=1;i<=nlstate;i++)
3560: for(j=1;j<=nlstate;j++)
3561: vareij[i][j][(int)age] =0.;
3562:
3563: for(h=0;h<=nhstepm;h++){
3564: for(k=0;k<=nhstepm;k++){
3565: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3566: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3567: for(i=1;i<=nlstate;i++)
3568: for(j=1;j<=nlstate;j++)
3569: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3570: }
3571: }
3572:
3573: /* pptj */
3574: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3575: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3576: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3577: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3578: varppt[j][i]=doldmp[j][i];
3579: /* end ppptj */
3580: /* x centered again */
3581: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3582: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3583:
3584: if (popbased==1) {
3585: if(mobilav ==0){
3586: for(i=1; i<=nlstate;i++)
3587: prlim[i][i]=probs[(int)age][i][ij];
3588: }else{ /* mobilav */
3589: for(i=1; i<=nlstate;i++)
3590: prlim[i][i]=mobaverage[(int)age][i][ij];
3591: }
3592: }
3593:
3594: /* This for computing probability of death (h=1 means
3595: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3596: as a weighted average of prlim.
3597: */
3598: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3599: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3600: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3601: }
3602: /* end probability of death */
3603:
3604: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3605: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3606: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3607: for(i=1; i<=nlstate;i++){
3608: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3609: }
3610: }
3611: fprintf(ficresprobmorprev,"\n");
3612:
3613: fprintf(ficresvij,"%.0f ",age );
3614: for(i=1; i<=nlstate;i++)
3615: for(j=1; j<=nlstate;j++){
3616: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3617: }
3618: fprintf(ficresvij,"\n");
3619: free_matrix(gp,0,nhstepm,1,nlstate);
3620: free_matrix(gm,0,nhstepm,1,nlstate);
3621: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3622: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3623: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3624: } /* End age */
3625: free_vector(gpp,nlstate+1,nlstate+ndeath);
3626: free_vector(gmp,nlstate+1,nlstate+ndeath);
3627: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3628: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3629: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3630: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3631: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3632: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3633: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3634: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3635: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3636: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3637: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3638: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3639: 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);
3640: /* 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);
3641: */
3642: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3643: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3644:
3645: free_vector(xp,1,npar);
3646: free_matrix(doldm,1,nlstate,1,nlstate);
3647: free_matrix(dnewm,1,nlstate,1,npar);
3648: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3649: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3650: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3651: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3652: fclose(ficresprobmorprev);
3653: fflush(ficgp);
3654: fflush(fichtm);
3655: } /* end varevsij */
3656:
3657: /************ Variance of prevlim ******************/
3658: 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[])
3659: {
3660: /* Variance of prevalence limit */
3661: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3662:
3663: double **dnewm,**doldm;
3664: int i, j, nhstepm, hstepm;
3665: double *xp;
3666: double *gp, *gm;
3667: double **gradg, **trgradg;
3668: double age,agelim;
3669: int theta;
3670:
3671: pstamp(ficresvpl);
3672: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3673: fprintf(ficresvpl,"# Age");
3674: for(i=1; i<=nlstate;i++)
3675: fprintf(ficresvpl," %1d-%1d",i,i);
3676: fprintf(ficresvpl,"\n");
3677:
3678: xp=vector(1,npar);
3679: dnewm=matrix(1,nlstate,1,npar);
3680: doldm=matrix(1,nlstate,1,nlstate);
3681:
3682: hstepm=1*YEARM; /* Every year of age */
3683: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3684: agelim = AGESUP;
3685: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3686: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3687: if (stepm >= YEARM) hstepm=1;
3688: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3689: gradg=matrix(1,npar,1,nlstate);
3690: gp=vector(1,nlstate);
3691: gm=vector(1,nlstate);
3692:
3693: for(theta=1; theta <=npar; theta++){
3694: for(i=1; i<=npar; i++){ /* Computes gradient */
3695: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3696: }
3697: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3698: for(i=1;i<=nlstate;i++)
3699: gp[i] = prlim[i][i];
3700:
3701: for(i=1; i<=npar; i++) /* Computes gradient */
3702: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3703: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3704: for(i=1;i<=nlstate;i++)
3705: gm[i] = prlim[i][i];
3706:
3707: for(i=1;i<=nlstate;i++)
3708: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3709: } /* End theta */
3710:
3711: trgradg =matrix(1,nlstate,1,npar);
3712:
3713: for(j=1; j<=nlstate;j++)
3714: for(theta=1; theta <=npar; theta++)
3715: trgradg[j][theta]=gradg[theta][j];
3716:
3717: for(i=1;i<=nlstate;i++)
3718: varpl[i][(int)age] =0.;
3719: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3720: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3721: for(i=1;i<=nlstate;i++)
3722: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3723:
3724: fprintf(ficresvpl,"%.0f ",age );
3725: for(i=1; i<=nlstate;i++)
3726: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3727: fprintf(ficresvpl,"\n");
3728: free_vector(gp,1,nlstate);
3729: free_vector(gm,1,nlstate);
3730: free_matrix(gradg,1,npar,1,nlstate);
3731: free_matrix(trgradg,1,nlstate,1,npar);
3732: } /* End age */
3733:
3734: free_vector(xp,1,npar);
3735: free_matrix(doldm,1,nlstate,1,npar);
3736: free_matrix(dnewm,1,nlstate,1,nlstate);
3737:
3738: }
3739:
3740: /************ Variance of one-step probabilities ******************/
3741: 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[])
3742: {
3743: int i, j=0, k1, l1, tj;
3744: int k2, l2, j1, z1;
3745: int k=0, l;
3746: int first=1, first1, first2;
3747: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3748: double **dnewm,**doldm;
3749: double *xp;
3750: double *gp, *gm;
3751: double **gradg, **trgradg;
3752: double **mu;
3753: double age, cov[NCOVMAX+1];
3754: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3755: int theta;
3756: char fileresprob[FILENAMELENGTH];
3757: char fileresprobcov[FILENAMELENGTH];
3758: char fileresprobcor[FILENAMELENGTH];
3759: double ***varpij;
3760:
3761: strcpy(fileresprob,"prob");
3762: strcat(fileresprob,fileres);
3763: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3764: printf("Problem with resultfile: %s\n", fileresprob);
3765: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3766: }
3767: strcpy(fileresprobcov,"probcov");
3768: strcat(fileresprobcov,fileres);
3769: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3770: printf("Problem with resultfile: %s\n", fileresprobcov);
3771: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3772: }
3773: strcpy(fileresprobcor,"probcor");
3774: strcat(fileresprobcor,fileres);
3775: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3776: printf("Problem with resultfile: %s\n", fileresprobcor);
3777: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3778: }
3779: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3780: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3781: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3782: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3783: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3784: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3785: pstamp(ficresprob);
3786: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3787: fprintf(ficresprob,"# Age");
3788: pstamp(ficresprobcov);
3789: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3790: fprintf(ficresprobcov,"# Age");
3791: pstamp(ficresprobcor);
3792: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3793: fprintf(ficresprobcor,"# Age");
3794:
3795:
3796: for(i=1; i<=nlstate;i++)
3797: for(j=1; j<=(nlstate+ndeath);j++){
3798: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3799: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3800: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3801: }
3802: /* fprintf(ficresprob,"\n");
3803: fprintf(ficresprobcov,"\n");
3804: fprintf(ficresprobcor,"\n");
3805: */
3806: xp=vector(1,npar);
3807: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3808: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3809: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3810: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3811: first=1;
3812: fprintf(ficgp,"\n# Routine varprob");
3813: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3814: fprintf(fichtm,"\n");
3815:
3816: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3817: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3818: file %s<br>\n",optionfilehtmcov);
3819: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3820: and drawn. It helps understanding how is the covariance between two incidences.\
3821: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3822: 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. \
3823: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3824: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3825: standard deviations wide on each axis. <br>\
3826: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3827: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3828: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3829:
3830: cov[1]=1;
3831: /* tj=cptcoveff; */
3832: tj = (int) pow(2,cptcoveff);
3833: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3834: j1=0;
3835: for(j1=1; j1<=tj;j1++){
3836: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3837: /*j1++;*/
3838: if (cptcovn>0) {
3839: fprintf(ficresprob, "\n#********** Variable ");
3840: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3841: fprintf(ficresprob, "**********\n#\n");
3842: fprintf(ficresprobcov, "\n#********** Variable ");
3843: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3844: fprintf(ficresprobcov, "**********\n#\n");
3845:
3846: fprintf(ficgp, "\n#********** Variable ");
3847: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3848: fprintf(ficgp, "**********\n#\n");
3849:
3850:
3851: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3852: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3853: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3854:
3855: fprintf(ficresprobcor, "\n#********** Variable ");
3856: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3857: fprintf(ficresprobcor, "**********\n#");
3858: }
3859:
3860: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3861: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3862: gp=vector(1,(nlstate)*(nlstate+ndeath));
3863: gm=vector(1,(nlstate)*(nlstate+ndeath));
3864: for (age=bage; age<=fage; age ++){
3865: cov[2]=age;
3866: for (k=1; k<=cptcovn;k++) {
3867: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3868: * 1 1 1 1 1
3869: * 2 2 1 1 1
3870: * 3 1 2 1 1
3871: */
3872: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3873: }
3874: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3875: for (k=1; k<=cptcovprod;k++)
3876: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3877:
3878:
3879: for(theta=1; theta <=npar; theta++){
3880: for(i=1; i<=npar; i++)
3881: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3882:
3883: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3884:
3885: k=0;
3886: for(i=1; i<= (nlstate); i++){
3887: for(j=1; j<=(nlstate+ndeath);j++){
3888: k=k+1;
3889: gp[k]=pmmij[i][j];
3890: }
3891: }
3892:
3893: for(i=1; i<=npar; i++)
3894: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3895:
3896: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3897: k=0;
3898: for(i=1; i<=(nlstate); i++){
3899: for(j=1; j<=(nlstate+ndeath);j++){
3900: k=k+1;
3901: gm[k]=pmmij[i][j];
3902: }
3903: }
3904:
3905: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3906: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3907: }
3908:
3909: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3910: for(theta=1; theta <=npar; theta++)
3911: trgradg[j][theta]=gradg[theta][j];
3912:
3913: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3914: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3915:
3916: pmij(pmmij,cov,ncovmodel,x,nlstate);
3917:
3918: k=0;
3919: for(i=1; i<=(nlstate); i++){
3920: for(j=1; j<=(nlstate+ndeath);j++){
3921: k=k+1;
3922: mu[k][(int) age]=pmmij[i][j];
3923: }
3924: }
3925: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3926: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3927: varpij[i][j][(int)age] = doldm[i][j];
3928:
3929: /*printf("\n%d ",(int)age);
3930: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3931: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3932: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3933: }*/
3934:
3935: fprintf(ficresprob,"\n%d ",(int)age);
3936: fprintf(ficresprobcov,"\n%d ",(int)age);
3937: fprintf(ficresprobcor,"\n%d ",(int)age);
3938:
3939: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3940: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3941: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3942: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3943: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3944: }
3945: i=0;
3946: for (k=1; k<=(nlstate);k++){
3947: for (l=1; l<=(nlstate+ndeath);l++){
3948: i++;
3949: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3950: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3951: for (j=1; j<=i;j++){
3952: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3953: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3954: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3955: }
3956: }
3957: }/* end of loop for state */
3958: } /* end of loop for age */
3959: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3960: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3961: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3962: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3963:
3964: /* Confidence intervalle of pij */
3965: /*
3966: fprintf(ficgp,"\nunset parametric;unset label");
3967: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3968: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3969: 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);
3970: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3971: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3972: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3973: */
3974:
3975: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3976: first1=1;first2=2;
3977: for (k2=1; k2<=(nlstate);k2++){
3978: for (l2=1; l2<=(nlstate+ndeath);l2++){
3979: if(l2==k2) continue;
3980: j=(k2-1)*(nlstate+ndeath)+l2;
3981: for (k1=1; k1<=(nlstate);k1++){
3982: for (l1=1; l1<=(nlstate+ndeath);l1++){
3983: if(l1==k1) continue;
3984: i=(k1-1)*(nlstate+ndeath)+l1;
3985: if(i<=j) continue;
3986: for (age=bage; age<=fage; age ++){
3987: if ((int)age %5==0){
3988: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3989: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3990: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
3991: mu1=mu[i][(int) age]/stepm*YEARM ;
3992: mu2=mu[j][(int) age]/stepm*YEARM;
3993: c12=cv12/sqrt(v1*v2);
3994: /* Computing eigen value of matrix of covariance */
3995: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3996: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3997: if ((lc2 <0) || (lc1 <0) ){
3998: if(first2==1){
3999: first1=0;
4000: 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);
4001: }
4002: 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);
4003: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4004: /* lc2=fabs(lc2); */
4005: }
4006:
4007: /* Eigen vectors */
4008: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4009: /*v21=sqrt(1.-v11*v11); *//* error */
4010: v21=(lc1-v1)/cv12*v11;
4011: v12=-v21;
4012: v22=v11;
4013: tnalp=v21/v11;
4014: if(first1==1){
4015: first1=0;
4016: 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);
4017: }
4018: 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);
4019: /*printf(fignu*/
4020: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4021: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4022: if(first==1){
4023: first=0;
4024: fprintf(ficgp,"\nset parametric;unset label");
4025: 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);
4026: fprintf(ficgp,"\nset ter png small size 320, 240");
4027: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4028: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4029: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4030: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4031: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4032: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4033: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4034: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4035: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4036: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4037: 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",\
4038: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4039: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4040: }else{
4041: first=0;
4042: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4043: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4044: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4045: 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",\
4046: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4047: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4048: }/* if first */
4049: } /* age mod 5 */
4050: } /* end loop age */
4051: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4052: first=1;
4053: } /*l12 */
4054: } /* k12 */
4055: } /*l1 */
4056: }/* k1 */
4057: /* } */ /* loop covariates */
4058: }
4059: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4060: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4061: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4062: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4063: free_vector(xp,1,npar);
4064: fclose(ficresprob);
4065: fclose(ficresprobcov);
4066: fclose(ficresprobcor);
4067: fflush(ficgp);
4068: fflush(fichtmcov);
4069: }
4070:
4071:
4072: /******************* Printing html file ***********/
4073: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4074: int lastpass, int stepm, int weightopt, char model[],\
4075: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4076: int popforecast, int estepm ,\
4077: double jprev1, double mprev1,double anprev1, \
4078: double jprev2, double mprev2,double anprev2){
4079: int jj1, k1, i1, cpt;
4080:
4081: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4082: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4083: </ul>");
4084: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4085: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4086: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4087: fprintf(fichtm,"\
4088: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4089: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4090: fprintf(fichtm,"\
4091: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4092: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4093: fprintf(fichtm,"\
4094: - (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): \
4095: <a href=\"%s\">%s</a> <br>\n",
4096: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4097: fprintf(fichtm,"\
4098: - Population projections by age and states: \
4099: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4100:
4101: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4102:
4103: m=pow(2,cptcoveff);
4104: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4105:
4106: jj1=0;
4107: for(k1=1; k1<=m;k1++){
4108: for(i1=1; i1<=ncodemax[k1];i1++){
4109: jj1++;
4110: if (cptcovn > 0) {
4111: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4112: for (cpt=1; cpt<=cptcoveff;cpt++)
4113: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4114: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4115: }
4116: /* Pij */
4117: 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> \
4118: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4119: /* Quasi-incidences */
4120: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4121: 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> \
4122: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4123: /* Period (stable) prevalence in each health state */
4124: for(cpt=1; cpt<=nlstate;cpt++){
4125: fprintf(fichtm,"<br>- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
4126: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4127: }
4128: for(cpt=1; cpt<=nlstate;cpt++) {
4129: 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> \
4130: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4131: }
4132: } /* end i1 */
4133: }/* End k1 */
4134: fprintf(fichtm,"</ul>");
4135:
4136:
4137: fprintf(fichtm,"\
4138: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4139: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4140:
4141: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4142: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4143: fprintf(fichtm,"\
4144: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4145: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4146:
4147: fprintf(fichtm,"\
4148: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4149: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4150: fprintf(fichtm,"\
4151: - 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): \
4152: <a href=\"%s\">%s</a> <br>\n</li>",
4153: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4154: fprintf(fichtm,"\
4155: - (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): \
4156: <a href=\"%s\">%s</a> <br>\n</li>",
4157: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4158: fprintf(fichtm,"\
4159: - 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",
4160: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4161: fprintf(fichtm,"\
4162: - 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",
4163: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4164: fprintf(fichtm,"\
4165: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4166: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4167:
4168: /* if(popforecast==1) fprintf(fichtm,"\n */
4169: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4170: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4171: /* <br>",fileres,fileres,fileres,fileres); */
4172: /* else */
4173: /* 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); */
4174: fflush(fichtm);
4175: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4176:
4177: m=pow(2,cptcoveff);
4178: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4179:
4180: jj1=0;
4181: for(k1=1; k1<=m;k1++){
4182: for(i1=1; i1<=ncodemax[k1];i1++){
4183: jj1++;
4184: if (cptcovn > 0) {
4185: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4186: for (cpt=1; cpt<=cptcoveff;cpt++)
4187: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4188: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4189: }
4190: for(cpt=1; cpt<=nlstate;cpt++) {
4191: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4192: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4193: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4194: }
4195: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4196: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4197: true period expectancies (those weighted with period prevalences are also\
4198: drawn in addition to the population based expectancies computed using\
4199: observed and cahotic prevalences: %s%d.png<br>\
4200: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4201: } /* end i1 */
4202: }/* End k1 */
4203: fprintf(fichtm,"</ul>");
4204: fflush(fichtm);
4205: }
4206:
4207: /******************* Gnuplot file **************/
4208: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4209:
4210: char dirfileres[132],optfileres[132];
4211: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4212: int ng=0;
4213: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4214: /* printf("Problem with file %s",optionfilegnuplot); */
4215: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4216: /* } */
4217:
4218: /*#ifdef windows */
4219: fprintf(ficgp,"cd \"%s\" \n",pathc);
4220: /*#endif */
4221: m=pow(2,cptcoveff);
4222:
4223: strcpy(dirfileres,optionfilefiname);
4224: strcpy(optfileres,"vpl");
4225: /* 1eme*/
4226: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4227: for (cpt=1; cpt<= nlstate ; cpt ++) {
4228: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4229: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4230: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4231: fprintf(ficgp,"set xlabel \"Age\" \n\
4232: set ylabel \"Probability\" \n\
4233: set ter png small size 320, 240\n\
4234: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4235:
4236: for (i=1; i<= nlstate ; i ++) {
4237: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4238: else fprintf(ficgp," %%*lf (%%*lf)");
4239: }
4240: 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);
4241: for (i=1; i<= nlstate ; i ++) {
4242: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4243: else fprintf(ficgp," %%*lf (%%*lf)");
4244: }
4245: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4246: for (i=1; i<= nlstate ; i ++) {
4247: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4248: else fprintf(ficgp," %%*lf (%%*lf)");
4249: }
4250: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4251: }
4252: }
4253: /*2 eme*/
4254: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4255: for (k1=1; k1<= m ; k1 ++) {
4256: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4257: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4258:
4259: for (i=1; i<= nlstate+1 ; i ++) {
4260: k=2*i;
4261: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4262: for (j=1; j<= nlstate+1 ; j ++) {
4263: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4264: else fprintf(ficgp," %%*lf (%%*lf)");
4265: }
4266: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4267: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4268: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4269: for (j=1; j<= nlstate+1 ; j ++) {
4270: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4271: else fprintf(ficgp," %%*lf (%%*lf)");
4272: }
4273: fprintf(ficgp,"\" t\"\" w l lt 0,");
4274: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4275: for (j=1; j<= nlstate+1 ; j ++) {
4276: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4277: else fprintf(ficgp," %%*lf (%%*lf)");
4278: }
4279: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4280: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4281: }
4282: }
4283:
4284: /*3eme*/
4285:
4286: for (k1=1; k1<= m ; k1 ++) {
4287: for (cpt=1; cpt<= nlstate ; cpt ++) {
4288: /* k=2+nlstate*(2*cpt-2); */
4289: k=2+(nlstate+1)*(cpt-1);
4290: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4291: fprintf(ficgp,"set ter png small size 320, 240\n\
4292: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4293: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4294: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4295: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4296: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4297: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4298: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4299:
4300: */
4301: for (i=1; i< nlstate ; i ++) {
4302: 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);
4303: /* 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);*/
4304:
4305: }
4306: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4307: }
4308: }
4309:
4310: /* CV preval stable (period) */
4311: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4312: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4313: k=3;
4314: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4315: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4316: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4317: set ter png small size 320, 240\n\
4318: unset log y\n\
4319: plot [%.f:%.f] ", ageminpar, agemaxpar);
4320: for (i=1; i<= nlstate ; i ++){
4321: if(i==1)
4322: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4323: else
4324: fprintf(ficgp,", '' ");
4325: l=(nlstate+ndeath)*(i-1)+1;
4326: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4327: for (j=1; j<= (nlstate-1) ; j ++)
4328: fprintf(ficgp,"+$%d",k+l+j);
4329: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4330: } /* nlstate */
4331: fprintf(ficgp,"\n");
4332: } /* end cpt state*/
4333: } /* end covariate */
4334:
4335: /* proba elementaires */
4336: for(i=1,jk=1; i <=nlstate; i++){
4337: for(k=1; k <=(nlstate+ndeath); k++){
4338: if (k != i) {
4339: for(j=1; j <=ncovmodel; j++){
4340: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4341: jk++;
4342: fprintf(ficgp,"\n");
4343: }
4344: }
4345: }
4346: }
4347: /*goto avoid;*/
4348: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4349: for(jk=1; jk <=m; jk++) {
4350: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4351: if (ng==2)
4352: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4353: else
4354: fprintf(ficgp,"\nset title \"Probability\"\n");
4355: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4356: i=1;
4357: for(k2=1; k2<=nlstate; k2++) {
4358: k3=i;
4359: for(k=1; k<=(nlstate+ndeath); k++) {
4360: if (k != k2){
4361: if(ng==2)
4362: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4363: else
4364: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4365: ij=1;/* To be checked else nbcode[0][0] wrong */
4366: for(j=3; j <=ncovmodel; j++) {
4367: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4368: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4369: /* ij++; */
4370: /* } */
4371: /* else */
4372: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4373: }
4374: fprintf(ficgp,")/(1");
4375:
4376: for(k1=1; k1 <=nlstate; k1++){
4377: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4378: ij=1;
4379: for(j=3; j <=ncovmodel; j++){
4380: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4381: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4382: /* ij++; */
4383: /* } */
4384: /* else */
4385: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4386: }
4387: fprintf(ficgp,")");
4388: }
4389: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4390: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4391: i=i+ncovmodel;
4392: }
4393: } /* end k */
4394: } /* end k2 */
4395: } /* end jk */
4396: } /* end ng */
4397: /* avoid: */
4398: fflush(ficgp);
4399: } /* end gnuplot */
4400:
4401:
4402: /*************** Moving average **************/
4403: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4404:
4405: int i, cpt, cptcod;
4406: int modcovmax =1;
4407: int mobilavrange, mob;
4408: double age;
4409:
4410: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4411: a covariate has 2 modalities */
4412: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4413:
4414: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4415: if(mobilav==1) mobilavrange=5; /* default */
4416: else mobilavrange=mobilav;
4417: for (age=bage; age<=fage; age++)
4418: for (i=1; i<=nlstate;i++)
4419: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4420: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4421: /* We keep the original values on the extreme ages bage, fage and for
4422: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4423: we use a 5 terms etc. until the borders are no more concerned.
4424: */
4425: for (mob=3;mob <=mobilavrange;mob=mob+2){
4426: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4427: for (i=1; i<=nlstate;i++){
4428: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4429: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4430: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4431: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4432: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4433: }
4434: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4435: }
4436: }
4437: }/* end age */
4438: }/* end mob */
4439: }else return -1;
4440: return 0;
4441: }/* End movingaverage */
4442:
4443:
4444: /************** Forecasting ******************/
4445: void 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){
4446: /* proj1, year, month, day of starting projection
4447: agemin, agemax range of age
4448: dateprev1 dateprev2 range of dates during which prevalence is computed
4449: anproj2 year of en of projection (same day and month as proj1).
4450: */
4451: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4452: double agec; /* generic age */
4453: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4454: double *popeffectif,*popcount;
4455: double ***p3mat;
4456: double ***mobaverage;
4457: char fileresf[FILENAMELENGTH];
4458:
4459: agelim=AGESUP;
4460: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4461:
4462: strcpy(fileresf,"f");
4463: strcat(fileresf,fileres);
4464: if((ficresf=fopen(fileresf,"w"))==NULL) {
4465: printf("Problem with forecast resultfile: %s\n", fileresf);
4466: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4467: }
4468: printf("Computing forecasting: result on file '%s' \n", fileresf);
4469: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4470:
4471: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4472:
4473: if (mobilav!=0) {
4474: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4475: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4476: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4477: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4478: }
4479: }
4480:
4481: stepsize=(int) (stepm+YEARM-1)/YEARM;
4482: if (stepm<=12) stepsize=1;
4483: if(estepm < stepm){
4484: printf ("Problem %d lower than %d\n",estepm, stepm);
4485: }
4486: else hstepm=estepm;
4487:
4488: hstepm=hstepm/stepm;
4489: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4490: fractional in yp1 */
4491: anprojmean=yp;
4492: yp2=modf((yp1*12),&yp);
4493: mprojmean=yp;
4494: yp1=modf((yp2*30.5),&yp);
4495: jprojmean=yp;
4496: if(jprojmean==0) jprojmean=1;
4497: if(mprojmean==0) jprojmean=1;
4498:
4499: i1=cptcoveff;
4500: if (cptcovn < 1){i1=1;}
4501:
4502: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4503:
4504: fprintf(ficresf,"#****** Routine prevforecast **\n");
4505:
4506: /* if (h==(int)(YEARM*yearp)){ */
4507: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4508: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4509: k=k+1;
4510: fprintf(ficresf,"\n#******");
4511: for(j=1;j<=cptcoveff;j++) {
4512: 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]]);
4513: }
4514: fprintf(ficresf,"******\n");
4515: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4516: for(j=1; j<=nlstate+ndeath;j++){
4517: for(i=1; i<=nlstate;i++)
4518: fprintf(ficresf," p%d%d",i,j);
4519: fprintf(ficresf," p.%d",j);
4520: }
4521: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4522: fprintf(ficresf,"\n");
4523: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4524:
4525: for (agec=fage; agec>=(ageminpar-1); agec--){
4526: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4527: nhstepm = nhstepm/hstepm;
4528: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4529: oldm=oldms;savm=savms;
4530: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4531:
4532: for (h=0; h<=nhstepm; h++){
4533: if (h*hstepm/YEARM*stepm ==yearp) {
4534: fprintf(ficresf,"\n");
4535: for(j=1;j<=cptcoveff;j++)
4536: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4537: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4538: }
4539: for(j=1; j<=nlstate+ndeath;j++) {
4540: ppij=0.;
4541: for(i=1; i<=nlstate;i++) {
4542: if (mobilav==1)
4543: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4544: else {
4545: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4546: }
4547: if (h*hstepm/YEARM*stepm== yearp) {
4548: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4549: }
4550: } /* end i */
4551: if (h*hstepm/YEARM*stepm==yearp) {
4552: fprintf(ficresf," %.3f", ppij);
4553: }
4554: }/* end j */
4555: } /* end h */
4556: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4557: } /* end agec */
4558: } /* end yearp */
4559: } /* end cptcod */
4560: } /* end cptcov */
4561:
4562: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4563:
4564: fclose(ficresf);
4565: }
4566:
4567: /************** Forecasting *****not tested NB*************/
4568: void 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){
4569:
4570: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4571: int *popage;
4572: double calagedatem, agelim, kk1, kk2;
4573: double *popeffectif,*popcount;
4574: double ***p3mat,***tabpop,***tabpopprev;
4575: double ***mobaverage;
4576: char filerespop[FILENAMELENGTH];
4577:
4578: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4579: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4580: agelim=AGESUP;
4581: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4582:
4583: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4584:
4585:
4586: strcpy(filerespop,"pop");
4587: strcat(filerespop,fileres);
4588: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4589: printf("Problem with forecast resultfile: %s\n", filerespop);
4590: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4591: }
4592: printf("Computing forecasting: result on file '%s' \n", filerespop);
4593: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4594:
4595: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4596:
4597: if (mobilav!=0) {
4598: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4599: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4600: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4601: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4602: }
4603: }
4604:
4605: stepsize=(int) (stepm+YEARM-1)/YEARM;
4606: if (stepm<=12) stepsize=1;
4607:
4608: agelim=AGESUP;
4609:
4610: hstepm=1;
4611: hstepm=hstepm/stepm;
4612:
4613: if (popforecast==1) {
4614: if((ficpop=fopen(popfile,"r"))==NULL) {
4615: printf("Problem with population file : %s\n",popfile);exit(0);
4616: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4617: }
4618: popage=ivector(0,AGESUP);
4619: popeffectif=vector(0,AGESUP);
4620: popcount=vector(0,AGESUP);
4621:
4622: i=1;
4623: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4624:
4625: imx=i;
4626: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4627: }
4628:
4629: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4630: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4631: k=k+1;
4632: fprintf(ficrespop,"\n#******");
4633: for(j=1;j<=cptcoveff;j++) {
4634: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4635: }
4636: fprintf(ficrespop,"******\n");
4637: fprintf(ficrespop,"# Age");
4638: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4639: if (popforecast==1) fprintf(ficrespop," [Population]");
4640:
4641: for (cpt=0; cpt<=0;cpt++) {
4642: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4643:
4644: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4645: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4646: nhstepm = nhstepm/hstepm;
4647:
4648: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4649: oldm=oldms;savm=savms;
4650: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4651:
4652: for (h=0; h<=nhstepm; h++){
4653: if (h==(int) (calagedatem+YEARM*cpt)) {
4654: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4655: }
4656: for(j=1; j<=nlstate+ndeath;j++) {
4657: kk1=0.;kk2=0;
4658: for(i=1; i<=nlstate;i++) {
4659: if (mobilav==1)
4660: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4661: else {
4662: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4663: }
4664: }
4665: if (h==(int)(calagedatem+12*cpt)){
4666: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4667: /*fprintf(ficrespop," %.3f", kk1);
4668: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4669: }
4670: }
4671: for(i=1; i<=nlstate;i++){
4672: kk1=0.;
4673: for(j=1; j<=nlstate;j++){
4674: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4675: }
4676: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4677: }
4678:
4679: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4680: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4681: }
4682: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4683: }
4684: }
4685:
4686: /******/
4687:
4688: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4689: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4690: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4691: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4692: nhstepm = nhstepm/hstepm;
4693:
4694: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4695: oldm=oldms;savm=savms;
4696: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4697: for (h=0; h<=nhstepm; h++){
4698: if (h==(int) (calagedatem+YEARM*cpt)) {
4699: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4700: }
4701: for(j=1; j<=nlstate+ndeath;j++) {
4702: kk1=0.;kk2=0;
4703: for(i=1; i<=nlstate;i++) {
4704: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4705: }
4706: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4707: }
4708: }
4709: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4710: }
4711: }
4712: }
4713: }
4714:
4715: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4716:
4717: if (popforecast==1) {
4718: free_ivector(popage,0,AGESUP);
4719: free_vector(popeffectif,0,AGESUP);
4720: free_vector(popcount,0,AGESUP);
4721: }
4722: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4723: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4724: fclose(ficrespop);
4725: } /* End of popforecast */
4726:
4727: int fileappend(FILE *fichier, char *optionfich)
4728: {
4729: if((fichier=fopen(optionfich,"a"))==NULL) {
4730: printf("Problem with file: %s\n", optionfich);
4731: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4732: return (0);
4733: }
4734: fflush(fichier);
4735: return (1);
4736: }
4737:
4738:
4739: /**************** function prwizard **********************/
4740: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4741: {
4742:
4743: /* Wizard to print covariance matrix template */
4744:
4745: char ca[32], cb[32];
4746: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4747: int numlinepar;
4748:
4749: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4750: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4751: for(i=1; i <=nlstate; i++){
4752: jj=0;
4753: for(j=1; j <=nlstate+ndeath; j++){
4754: if(j==i) continue;
4755: jj++;
4756: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4757: printf("%1d%1d",i,j);
4758: fprintf(ficparo,"%1d%1d",i,j);
4759: for(k=1; k<=ncovmodel;k++){
4760: /* printf(" %lf",param[i][j][k]); */
4761: /* fprintf(ficparo," %lf",param[i][j][k]); */
4762: printf(" 0.");
4763: fprintf(ficparo," 0.");
4764: }
4765: printf("\n");
4766: fprintf(ficparo,"\n");
4767: }
4768: }
4769: printf("# Scales (for hessian or gradient estimation)\n");
4770: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4771: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4772: for(i=1; i <=nlstate; i++){
4773: jj=0;
4774: for(j=1; j <=nlstate+ndeath; j++){
4775: if(j==i) continue;
4776: jj++;
4777: fprintf(ficparo,"%1d%1d",i,j);
4778: printf("%1d%1d",i,j);
4779: fflush(stdout);
4780: for(k=1; k<=ncovmodel;k++){
4781: /* printf(" %le",delti3[i][j][k]); */
4782: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4783: printf(" 0.");
4784: fprintf(ficparo," 0.");
4785: }
4786: numlinepar++;
4787: printf("\n");
4788: fprintf(ficparo,"\n");
4789: }
4790: }
4791: printf("# Covariance matrix\n");
4792: /* # 121 Var(a12)\n\ */
4793: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4794: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4795: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4796: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4797: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4798: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4799: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4800: fflush(stdout);
4801: fprintf(ficparo,"# Covariance matrix\n");
4802: /* # 121 Var(a12)\n\ */
4803: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4804: /* # ...\n\ */
4805: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4806:
4807: for(itimes=1;itimes<=2;itimes++){
4808: jj=0;
4809: for(i=1; i <=nlstate; i++){
4810: for(j=1; j <=nlstate+ndeath; j++){
4811: if(j==i) continue;
4812: for(k=1; k<=ncovmodel;k++){
4813: jj++;
4814: ca[0]= k+'a'-1;ca[1]='\0';
4815: if(itimes==1){
4816: printf("#%1d%1d%d",i,j,k);
4817: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4818: }else{
4819: printf("%1d%1d%d",i,j,k);
4820: fprintf(ficparo,"%1d%1d%d",i,j,k);
4821: /* printf(" %.5le",matcov[i][j]); */
4822: }
4823: ll=0;
4824: for(li=1;li <=nlstate; li++){
4825: for(lj=1;lj <=nlstate+ndeath; lj++){
4826: if(lj==li) continue;
4827: for(lk=1;lk<=ncovmodel;lk++){
4828: ll++;
4829: if(ll<=jj){
4830: cb[0]= lk +'a'-1;cb[1]='\0';
4831: if(ll<jj){
4832: if(itimes==1){
4833: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4834: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4835: }else{
4836: printf(" 0.");
4837: fprintf(ficparo," 0.");
4838: }
4839: }else{
4840: if(itimes==1){
4841: printf(" Var(%s%1d%1d)",ca,i,j);
4842: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4843: }else{
4844: printf(" 0.");
4845: fprintf(ficparo," 0.");
4846: }
4847: }
4848: }
4849: } /* end lk */
4850: } /* end lj */
4851: } /* end li */
4852: printf("\n");
4853: fprintf(ficparo,"\n");
4854: numlinepar++;
4855: } /* end k*/
4856: } /*end j */
4857: } /* end i */
4858: } /* end itimes */
4859:
4860: } /* end of prwizard */
4861: /******************* Gompertz Likelihood ******************************/
4862: double gompertz(double x[])
4863: {
4864: double A,B,L=0.0,sump=0.,num=0.;
4865: int i,n=0; /* n is the size of the sample */
4866:
4867: for (i=0;i<=imx-1 ; i++) {
4868: sump=sump+weight[i];
4869: /* sump=sump+1;*/
4870: num=num+1;
4871: }
4872:
4873:
4874: /* for (i=0; i<=imx; i++)
4875: 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]);*/
4876:
4877: for (i=1;i<=imx ; i++)
4878: {
4879: if (cens[i] == 1 && wav[i]>1)
4880: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4881:
4882: if (cens[i] == 0 && wav[i]>1)
4883: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4884: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4885:
4886: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4887: if (wav[i] > 1 ) { /* ??? */
4888: L=L+A*weight[i];
4889: /* 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]);*/
4890: }
4891: }
4892:
4893: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4894:
4895: return -2*L*num/sump;
4896: }
4897:
4898: #ifdef GSL
4899: /******************* Gompertz_f Likelihood ******************************/
4900: double gompertz_f(const gsl_vector *v, void *params)
4901: {
4902: double A,B,LL=0.0,sump=0.,num=0.;
4903: double *x= (double *) v->data;
4904: int i,n=0; /* n is the size of the sample */
4905:
4906: for (i=0;i<=imx-1 ; i++) {
4907: sump=sump+weight[i];
4908: /* sump=sump+1;*/
4909: num=num+1;
4910: }
4911:
4912:
4913: /* for (i=0; i<=imx; i++)
4914: 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]);*/
4915: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4916: for (i=1;i<=imx ; i++)
4917: {
4918: if (cens[i] == 1 && wav[i]>1)
4919: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4920:
4921: if (cens[i] == 0 && wav[i]>1)
4922: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4923: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4924:
4925: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4926: if (wav[i] > 1 ) { /* ??? */
4927: LL=LL+A*weight[i];
4928: /* 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]);*/
4929: }
4930: }
4931:
4932: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4933: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4934:
4935: return -2*LL*num/sump;
4936: }
4937: #endif
4938:
4939: /******************* Printing html file ***********/
4940: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4941: int lastpass, int stepm, int weightopt, char model[],\
4942: int imx, double p[],double **matcov,double agemortsup){
4943: int i,k;
4944:
4945: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4946: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4947: for (i=1;i<=2;i++)
4948: 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]));
4949: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4950: fprintf(fichtm,"</ul>");
4951:
4952: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4953:
4954: 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>");
4955:
4956: for (k=agegomp;k<(agemortsup-2);k++)
4957: 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]);
4958:
4959:
4960: fflush(fichtm);
4961: }
4962:
4963: /******************* Gnuplot file **************/
4964: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4965:
4966: char dirfileres[132],optfileres[132];
4967:
4968: int ng;
4969:
4970:
4971: /*#ifdef windows */
4972: fprintf(ficgp,"cd \"%s\" \n",pathc);
4973: /*#endif */
4974:
4975:
4976: strcpy(dirfileres,optionfilefiname);
4977: strcpy(optfileres,"vpl");
4978: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4979: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4980: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4981: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4982: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4983:
4984: }
4985:
4986: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4987: {
4988:
4989: /*-------- data file ----------*/
4990: FILE *fic;
4991: char dummy[]=" ";
4992: int i=0, j=0, n=0;
4993: int linei, month, year,iout;
4994: char line[MAXLINE], linetmp[MAXLINE];
4995: char stra[MAXLINE], strb[MAXLINE];
4996: char *stratrunc;
4997: int lstra;
4998:
4999:
5000: if((fic=fopen(datafile,"r"))==NULL) {
5001: printf("Problem while opening datafile: %s\n", datafile);return 1;
5002: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5003: }
5004:
5005: i=1;
5006: linei=0;
5007: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5008: linei=linei+1;
5009: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5010: if(line[j] == '\t')
5011: line[j] = ' ';
5012: }
5013: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5014: ;
5015: };
5016: line[j+1]=0; /* Trims blanks at end of line */
5017: if(line[0]=='#'){
5018: fprintf(ficlog,"Comment line\n%s\n",line);
5019: printf("Comment line\n%s\n",line);
5020: continue;
5021: }
5022: trimbb(linetmp,line); /* Trims multiple blanks in line */
5023: strcpy(line, linetmp);
5024:
5025:
5026: for (j=maxwav;j>=1;j--){
5027: cutv(stra, strb, line, ' ');
5028: if(strb[0]=='.') { /* Missing status */
5029: lval=-1;
5030: }else{
5031: errno=0;
5032: lval=strtol(strb,&endptr,10);
5033: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5034: if( strb[0]=='\0' || (*endptr != '\0')){
5035: 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);
5036: 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);
5037: return 1;
5038: }
5039: }
5040: s[j][i]=lval;
5041:
5042: strcpy(line,stra);
5043: cutv(stra, strb,line,' ');
5044: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5045: }
5046: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5047: month=99;
5048: year=9999;
5049: }else{
5050: 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);
5051: 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);
5052: return 1;
5053: }
5054: anint[j][i]= (double) year;
5055: mint[j][i]= (double)month;
5056: strcpy(line,stra);
5057: } /* ENd Waves */
5058:
5059: cutv(stra, strb,line,' ');
5060: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5061: }
5062: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5063: month=99;
5064: year=9999;
5065: }else{
5066: 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);
5067: 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);
5068: return 1;
5069: }
5070: andc[i]=(double) year;
5071: moisdc[i]=(double) month;
5072: strcpy(line,stra);
5073:
5074: cutv(stra, strb,line,' ');
5075: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5076: }
5077: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5078: month=99;
5079: year=9999;
5080: }else{
5081: 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);
5082: 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);
5083: return 1;
5084: }
5085: if (year==9999) {
5086: 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);
5087: 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);
5088: return 1;
5089:
5090: }
5091: annais[i]=(double)(year);
5092: moisnais[i]=(double)(month);
5093: strcpy(line,stra);
5094:
5095: cutv(stra, strb,line,' ');
5096: errno=0;
5097: dval=strtod(strb,&endptr);
5098: if( strb[0]=='\0' || (*endptr != '\0')){
5099: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5100: 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);
5101: fflush(ficlog);
5102: return 1;
5103: }
5104: weight[i]=dval;
5105: strcpy(line,stra);
5106:
5107: for (j=ncovcol;j>=1;j--){
5108: cutv(stra, strb,line,' ');
5109: if(strb[0]=='.') { /* Missing status */
5110: lval=-1;
5111: }else{
5112: errno=0;
5113: lval=strtol(strb,&endptr,10);
5114: if( strb[0]=='\0' || (*endptr != '\0')){
5115: 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);
5116: 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);
5117: return 1;
5118: }
5119: }
5120: if(lval <-1 || lval >1){
5121: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5122: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5123: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5124: For example, for multinomial values like 1, 2 and 3,\n \
5125: build V1=0 V2=0 for the reference value (1),\n \
5126: V1=1 V2=0 for (2) \n \
5127: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5128: output of IMaCh is often meaningless.\n \
5129: Exiting.\n",lval,linei, i,line,j);
5130: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5131: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5132: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5133: For example, for multinomial values like 1, 2 and 3,\n \
5134: build V1=0 V2=0 for the reference value (1),\n \
5135: V1=1 V2=0 for (2) \n \
5136: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5137: output of IMaCh is often meaningless.\n \
5138: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5139: return 1;
5140: }
5141: covar[j][i]=(double)(lval);
5142: strcpy(line,stra);
5143: }
5144: lstra=strlen(stra);
5145:
5146: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5147: stratrunc = &(stra[lstra-9]);
5148: num[i]=atol(stratrunc);
5149: }
5150: else
5151: num[i]=atol(stra);
5152: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5153: 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;}*/
5154:
5155: i=i+1;
5156: } /* End loop reading data */
5157:
5158: *imax=i-1; /* Number of individuals */
5159: fclose(fic);
5160:
5161: return (0);
5162: /* endread: */
5163: printf("Exiting readdata: ");
5164: fclose(fic);
5165: return (1);
5166:
5167:
5168:
5169: }
5170: void removespace(char *str) {
5171: char *p1 = str, *p2 = str;
5172: do
5173: while (*p2 == ' ')
5174: p2++;
5175: while (*p1++ == *p2++);
5176: }
5177:
5178: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5179: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5180: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5181: * - cptcovn or number of covariates k of the models excluding age*products =6
5182: * - cptcovage number of covariates with age*products =2
5183: * - cptcovs number of simple covariates
5184: * - 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
5185: * which is a new column after the 9 (ncovcol) variables.
5186: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5187: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5188: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5189: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5190: */
5191: {
5192: int i, j, k, ks;
5193: int j1, k1, k2;
5194: char modelsav[80];
5195: char stra[80], strb[80], strc[80], strd[80],stre[80];
5196:
5197: /*removespace(model);*/
5198: if (strlen(model) >1){ /* If there is at least 1 covariate */
5199: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5200: j=nbocc(model,'+'); /**< j=Number of '+' */
5201: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5202: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5203: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5204: /* including age products which are counted in cptcovage.
5205: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5206: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5207: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5208: strcpy(modelsav,model);
5209: if (strstr(model,"AGE") !=0){
5210: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5211: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5212: return 1;
5213: }
5214: if (strstr(model,"v") !=0){
5215: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5216: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5217: return 1;
5218: }
5219:
5220: /* Design
5221: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5222: * < ncovcol=8 >
5223: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5224: * k= 1 2 3 4 5 6 7 8
5225: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5226: * covar[k,i], value of kth covariate if not including age for individual i:
5227: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5228: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5229: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5230: * Tage[++cptcovage]=k
5231: * if products, new covar are created after ncovcol with k1
5232: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5233: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5234: * 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
5235: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5236: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5237: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5238: * < ncovcol=8 >
5239: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5240: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5241: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5242: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5243: * p Tprod[1]@2={ 6, 5}
5244: *p Tvard[1][1]@4= {7, 8, 5, 6}
5245: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5246: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5247: *How to reorganize?
5248: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5249: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5250: * {2, 1, 4, 8, 5, 6, 3, 7}
5251: * Struct []
5252: */
5253:
5254: /* This loop fills the array Tvar from the string 'model'.*/
5255: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5256: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5257: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5258: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5259: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5260: /* k=1 Tvar[1]=2 (from V2) */
5261: /* k=5 Tvar[5] */
5262: /* for (k=1; k<=cptcovn;k++) { */
5263: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5264: /* } */
5265: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5266: /*
5267: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5268: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5269: Tvar[k]=0;
5270: cptcovage=0;
5271: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5272: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5273: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5274: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5275: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5276: /*scanf("%d",i);*/
5277: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5278: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5279: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5280: /* covar is not filled and then is empty */
5281: cptcovprod--;
5282: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5283: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5284: cptcovage++; /* Sums the number of covariates which include age as a product */
5285: Tage[cptcovage]=k; /* Tage[1] = 4 */
5286: /*printf("stre=%s ", stre);*/
5287: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5288: cptcovprod--;
5289: cutl(stre,strb,strc,'V');
5290: Tvar[k]=atoi(stre);
5291: cptcovage++;
5292: Tage[cptcovage]=k;
5293: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5294: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5295: cptcovn++;
5296: cptcovprodnoage++;k1++;
5297: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5298: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5299: because this model-covariate is a construction we invent a new column
5300: ncovcol + k1
5301: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5302: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5303: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5304: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5305: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5306: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5307: k2=k2+2;
5308: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5309: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5310: for (i=1; i<=lastobs;i++){
5311: /* Computes the new covariate which is a product of
5312: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5313: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5314: }
5315: } /* End age is not in the model */
5316: } /* End if model includes a product */
5317: else { /* no more sum */
5318: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5319: /* scanf("%d",i);*/
5320: cutl(strd,strc,strb,'V');
5321: ks++; /**< Number of simple covariates */
5322: cptcovn++;
5323: Tvar[k]=atoi(strd);
5324: }
5325: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5326: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5327: scanf("%d",i);*/
5328: } /* end of loop + */
5329: } /* end model */
5330:
5331: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5332: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5333:
5334: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5335: printf("cptcovprod=%d ", cptcovprod);
5336: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5337:
5338: scanf("%d ",i);*/
5339:
5340:
5341: return (0); /* with covar[new additional covariate if product] and Tage if age */
5342: /*endread:*/
5343: printf("Exiting decodemodel: ");
5344: return (1);
5345: }
5346:
5347: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5348: {
5349: int i, m;
5350:
5351: for (i=1; i<=imx; i++) {
5352: for(m=2; (m<= maxwav); m++) {
5353: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5354: anint[m][i]=9999;
5355: s[m][i]=-1;
5356: }
5357: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5358: *nberr = *nberr + 1;
5359: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5360: 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 (%d)\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr);
5361: s[m][i]=-1;
5362: }
5363: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5364: (*nberr)++;
5365: 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]);
5366: 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]);
5367: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5368: }
5369: }
5370: }
5371:
5372: for (i=1; i<=imx; i++) {
5373: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5374: for(m=firstpass; (m<= lastpass); m++){
5375: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5376: if (s[m][i] >= nlstate+1) {
5377: if(agedc[i]>0){
5378: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5379: agev[m][i]=agedc[i];
5380: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5381: }else {
5382: if ((int)andc[i]!=9999){
5383: nbwarn++;
5384: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5385: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5386: agev[m][i]=-1;
5387: }
5388: }
5389: } /* agedc > 0 */
5390: }
5391: else if(s[m][i] !=9){ /* Standard case, age in fractional
5392: years but with the precision of a month */
5393: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5394: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5395: agev[m][i]=1;
5396: else if(agev[m][i] < *agemin){
5397: *agemin=agev[m][i];
5398: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5399: }
5400: else if(agev[m][i] >*agemax){
5401: *agemax=agev[m][i];
5402: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5403: }
5404: /*agev[m][i]=anint[m][i]-annais[i];*/
5405: /* agev[m][i] = age[i]+2*m;*/
5406: }
5407: else { /* =9 */
5408: agev[m][i]=1;
5409: s[m][i]=-1;
5410: }
5411: }
5412: else /*= 0 Unknown */
5413: agev[m][i]=1;
5414: }
5415:
5416: }
5417: for (i=1; i<=imx; i++) {
5418: for(m=firstpass; (m<=lastpass); m++){
5419: if (s[m][i] > (nlstate+ndeath)) {
5420: (*nberr)++;
5421: 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);
5422: 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);
5423: return 1;
5424: }
5425: }
5426: }
5427:
5428: /*for (i=1; i<=imx; i++){
5429: for (m=firstpass; (m<lastpass); m++){
5430: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5431: }
5432:
5433: }*/
5434:
5435:
5436: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5437: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5438:
5439: return (0);
5440: /* endread:*/
5441: printf("Exiting calandcheckages: ");
5442: return (1);
5443: }
5444:
5445: void syscompilerinfo()
5446: {
5447: /* #include "syscompilerinfo.h"*/
5448: /* #include <gnu/libc-version.h> */ /* Only on gnu */
5449:
5450: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5451: #if defined(__clang__)
5452: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5453: #endif
5454: #if defined(__ICC) || defined(__INTEL_COMPILER)
5455: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5456: #endif
5457: #if defined(__GNUC__) || defined(__GNUG__)
5458: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5459: #endif
5460: #if defined(__HP_cc) || defined(__HP_aCC)
5461: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5462: #endif
5463: #if defined(__IBMC__) || defined(__IBMCPP__)
5464: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5465: #endif
5466: #if defined(_MSC_VER)
5467: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5468: #endif
5469: #if defined(__PGI)
5470: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5471: #endif
5472: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5473: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5474: #endif
5475: printf(". ");fprintf(ficlog,". ");
5476:
5477: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5478: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5479: // Windows (x64 and x86)
5480: #elif __unix__ // all unices, not all compilers
5481: // Unix
5482: #elif __linux__
5483: // linux
5484: #elif __APPLE__
5485: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5486: #endif
5487:
5488: /* __MINGW32__ */
5489: /* __CYGWIN__ */
5490: /* __MINGW64__ */
5491: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5492: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5493: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5494: /* _WIN64 // Defined for applications for Win64. */
5495: /* _M_X64 // Defined for compilations that target x64 processors. */
5496: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5497: #include <stdint.h>
5498: #if UINTPTR_MAX == 0xffffffff
5499: printf(" 32-bit."); /* 32-bit */
5500: #elif UINTPTR_MAX == 0xffffffffffffffff
5501: printf(" 64-bit.");/* 64-bit */
5502: #else
5503: printf(" wtf-bit."); /* wtf */
5504: #endif
5505:
5506: struct utsname sysInfo;
5507:
5508: if (uname(&sysInfo) != -1) {
5509: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5510: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5511: }
5512: else
5513: perror("uname() error");
5514: #if defined(__GNUC__)
5515: # if defined(__GNUC_PATCHLEVEL__)
5516: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5517: + __GNUC_MINOR__ * 100 \
5518: + __GNUC_PATCHLEVEL__)
5519: # else
5520: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5521: + __GNUC_MINOR__ * 100)
5522: # endif
5523: printf("GNU C version %d.\n", __GNUC_VERSION__);
5524: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
5525: #endif
5526: #if defined(_MSC_VER)
5527: printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);
5528: fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);
5529: #endif
5530:
5531: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
5532:
5533: }
5534:
5535: /***********************************************/
5536: /**************** Main Program *****************/
5537: /***********************************************/
5538:
5539: int main(int argc, char *argv[])
5540: {
5541: #ifdef GSL
5542: const gsl_multimin_fminimizer_type *T;
5543: size_t iteri = 0, it;
5544: int rval = GSL_CONTINUE;
5545: int status = GSL_SUCCESS;
5546: double ssval;
5547: #endif
5548: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5549: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5550:
5551: int jj, ll, li, lj, lk;
5552: int numlinepar=0; /* Current linenumber of parameter file */
5553: int itimes;
5554: int NDIM=2;
5555: int vpopbased=0;
5556:
5557: char ca[32], cb[32];
5558: /* FILE *fichtm; *//* Html File */
5559: /* FILE *ficgp;*/ /*Gnuplot File */
5560: struct stat info;
5561: double agedeb;
5562: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5563:
5564: double fret;
5565: double dum; /* Dummy variable */
5566: double ***p3mat;
5567: double ***mobaverage;
5568:
5569: char line[MAXLINE];
5570: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5571: char pathr[MAXLINE], pathimach[MAXLINE];
5572: char *tok, *val; /* pathtot */
5573: int firstobs=1, lastobs=10;
5574: int c, h , cpt;
5575: int jl;
5576: int i1, j1, jk, stepsize;
5577: int *tab;
5578: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5579: int mobilav=0,popforecast=0;
5580: int hstepm, nhstepm;
5581: int agemortsup;
5582: float sumlpop=0.;
5583: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5584: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5585:
5586: double bage=0, fage=110, age, agelim, agebase;
5587: double ftolpl=FTOL;
5588: double **prlim;
5589: double ***param; /* Matrix of parameters */
5590: double *p;
5591: double **matcov; /* Matrix of covariance */
5592: double ***delti3; /* Scale */
5593: double *delti; /* Scale */
5594: double ***eij, ***vareij;
5595: double **varpl; /* Variances of prevalence limits by age */
5596: double *epj, vepp;
5597:
5598: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5599: double **ximort;
5600: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5601: int *dcwave;
5602:
5603: char z[1]="c";
5604:
5605: /*char *strt;*/
5606: char strtend[80];
5607:
5608:
5609: /* setlocale (LC_ALL, ""); */
5610: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5611: /* textdomain (PACKAGE); */
5612: /* setlocale (LC_CTYPE, ""); */
5613: /* setlocale (LC_MESSAGES, ""); */
5614:
5615: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5616: rstart_time = time(NULL);
5617: /* (void) gettimeofday(&start_time,&tzp);*/
5618: start_time = *localtime(&rstart_time);
5619: curr_time=start_time;
5620: /*tml = *localtime(&start_time.tm_sec);*/
5621: /* strcpy(strstart,asctime(&tml)); */
5622: strcpy(strstart,asctime(&start_time));
5623:
5624: /* printf("Localtime (at start)=%s",strstart); */
5625: /* tp.tm_sec = tp.tm_sec +86400; */
5626: /* tm = *localtime(&start_time.tm_sec); */
5627: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5628: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5629: /* tmg.tm_hour=tmg.tm_hour + 1; */
5630: /* tp.tm_sec = mktime(&tmg); */
5631: /* strt=asctime(&tmg); */
5632: /* printf("Time(after) =%s",strstart); */
5633: /* (void) time (&time_value);
5634: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5635: * tm = *localtime(&time_value);
5636: * strstart=asctime(&tm);
5637: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5638: */
5639:
5640: nberr=0; /* Number of errors and warnings */
5641: nbwarn=0;
5642: getcwd(pathcd, size);
5643:
5644: printf("\n%s\n%s",version,fullversion);
5645: if(argc <=1){
5646: printf("\nEnter the parameter file name: ");
5647: fgets(pathr,FILENAMELENGTH,stdin);
5648: i=strlen(pathr);
5649: if(pathr[i-1]=='\n')
5650: pathr[i-1]='\0';
5651: i=strlen(pathr);
5652: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5653: pathr[i-1]='\0';
5654: for (tok = pathr; tok != NULL; ){
5655: printf("Pathr |%s|\n",pathr);
5656: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5657: printf("val= |%s| pathr=%s\n",val,pathr);
5658: strcpy (pathtot, val);
5659: if(pathr[0] == '\0') break; /* Dirty */
5660: }
5661: }
5662: else{
5663: strcpy(pathtot,argv[1]);
5664: }
5665: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5666: /*cygwin_split_path(pathtot,path,optionfile);
5667: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5668: /* cutv(path,optionfile,pathtot,'\\');*/
5669:
5670: /* Split argv[0], imach program to get pathimach */
5671: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5672: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5673: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5674: /* strcpy(pathimach,argv[0]); */
5675: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5676: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5677: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5678: chdir(path); /* Can be a relative path */
5679: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5680: printf("Current directory %s!\n",pathcd);
5681: strcpy(command,"mkdir ");
5682: strcat(command,optionfilefiname);
5683: if((outcmd=system(command)) != 0){
5684: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5685: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5686: /* fclose(ficlog); */
5687: /* exit(1); */
5688: }
5689: /* if((imk=mkdir(optionfilefiname))<0){ */
5690: /* perror("mkdir"); */
5691: /* } */
5692:
5693: /*-------- arguments in the command line --------*/
5694:
5695: /* Log file */
5696: strcat(filelog, optionfilefiname);
5697: strcat(filelog,".log"); /* */
5698: if((ficlog=fopen(filelog,"w"))==NULL) {
5699: printf("Problem with logfile %s\n",filelog);
5700: goto end;
5701: }
5702: fprintf(ficlog,"Log filename:%s\n",filelog);
5703: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5704: fprintf(ficlog,"\nEnter the parameter file name: \n");
5705: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5706: path=%s \n\
5707: optionfile=%s\n\
5708: optionfilext=%s\n\
5709: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5710:
5711: syscompilerinfo();
5712:
5713: printf("Local time (at start):%s",strstart);
5714: fprintf(ficlog,"Local time (at start): %s",strstart);
5715: fflush(ficlog);
5716: /* (void) gettimeofday(&curr_time,&tzp); */
5717: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5718:
5719: /* */
5720: strcpy(fileres,"r");
5721: strcat(fileres, optionfilefiname);
5722: strcat(fileres,".txt"); /* Other files have txt extension */
5723:
5724: /*---------arguments file --------*/
5725:
5726: if((ficpar=fopen(optionfile,"r"))==NULL) {
5727: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5728: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5729: fflush(ficlog);
5730: /* goto end; */
5731: exit(70);
5732: }
5733:
5734:
5735:
5736: strcpy(filereso,"o");
5737: strcat(filereso,fileres);
5738: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5739: printf("Problem with Output resultfile: %s\n", filereso);
5740: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5741: fflush(ficlog);
5742: goto end;
5743: }
5744:
5745: /* Reads comments: lines beginning with '#' */
5746: numlinepar=0;
5747: while((c=getc(ficpar))=='#' && c!= EOF){
5748: ungetc(c,ficpar);
5749: fgets(line, MAXLINE, ficpar);
5750: numlinepar++;
5751: fputs(line,stdout);
5752: fputs(line,ficparo);
5753: fputs(line,ficlog);
5754: }
5755: ungetc(c,ficpar);
5756:
5757: 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);
5758: numlinepar++;
5759: 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);
5760: 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);
5761: 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);
5762: fflush(ficlog);
5763: while((c=getc(ficpar))=='#' && c!= EOF){
5764: ungetc(c,ficpar);
5765: fgets(line, MAXLINE, ficpar);
5766: numlinepar++;
5767: fputs(line, stdout);
5768: //puts(line);
5769: fputs(line,ficparo);
5770: fputs(line,ficlog);
5771: }
5772: ungetc(c,ficpar);
5773:
5774:
5775: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5776: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5777: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5778: v1+v2*age+v2*v3 makes cptcovn = 3
5779: */
5780: if (strlen(model)>1)
5781: 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*/
5782: else
5783: ncovmodel=2;
5784: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5785: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5786: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5787: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5788: 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);
5789: 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);
5790: fflush(stdout);
5791: fclose (ficlog);
5792: goto end;
5793: }
5794: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5795: delti=delti3[1][1];
5796: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5797: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5798: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5799: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5800: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5801: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5802: fclose (ficparo);
5803: fclose (ficlog);
5804: goto end;
5805: exit(0);
5806: }
5807: else if(mle==-3) {
5808: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5809: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5810: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5811: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5812: matcov=matrix(1,npar,1,npar);
5813: }
5814: else{
5815: /* Read guessed parameters */
5816: /* Reads comments: lines beginning with '#' */
5817: while((c=getc(ficpar))=='#' && c!= EOF){
5818: ungetc(c,ficpar);
5819: fgets(line, MAXLINE, ficpar);
5820: numlinepar++;
5821: fputs(line,stdout);
5822: fputs(line,ficparo);
5823: fputs(line,ficlog);
5824: }
5825: ungetc(c,ficpar);
5826:
5827: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5828: for(i=1; i <=nlstate; i++){
5829: j=0;
5830: for(jj=1; jj <=nlstate+ndeath; jj++){
5831: if(jj==i) continue;
5832: j++;
5833: fscanf(ficpar,"%1d%1d",&i1,&j1);
5834: if ((i1 != i) && (j1 != j)){
5835: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5836: It might be a problem of design; if ncovcol and the model are correct\n \
5837: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5838: exit(1);
5839: }
5840: fprintf(ficparo,"%1d%1d",i1,j1);
5841: if(mle==1)
5842: printf("%1d%1d",i,j);
5843: fprintf(ficlog,"%1d%1d",i,j);
5844: for(k=1; k<=ncovmodel;k++){
5845: fscanf(ficpar," %lf",¶m[i][j][k]);
5846: if(mle==1){
5847: printf(" %lf",param[i][j][k]);
5848: fprintf(ficlog," %lf",param[i][j][k]);
5849: }
5850: else
5851: fprintf(ficlog," %lf",param[i][j][k]);
5852: fprintf(ficparo," %lf",param[i][j][k]);
5853: }
5854: fscanf(ficpar,"\n");
5855: numlinepar++;
5856: if(mle==1)
5857: printf("\n");
5858: fprintf(ficlog,"\n");
5859: fprintf(ficparo,"\n");
5860: }
5861: }
5862: fflush(ficlog);
5863:
5864: /* Reads scales values */
5865: p=param[1][1];
5866:
5867: /* Reads comments: lines beginning with '#' */
5868: while((c=getc(ficpar))=='#' && c!= EOF){
5869: ungetc(c,ficpar);
5870: fgets(line, MAXLINE, ficpar);
5871: numlinepar++;
5872: fputs(line,stdout);
5873: fputs(line,ficparo);
5874: fputs(line,ficlog);
5875: }
5876: ungetc(c,ficpar);
5877:
5878: for(i=1; i <=nlstate; i++){
5879: for(j=1; j <=nlstate+ndeath-1; j++){
5880: fscanf(ficpar,"%1d%1d",&i1,&j1);
5881: if ( (i1-i) * (j1-j) != 0){
5882: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5883: exit(1);
5884: }
5885: printf("%1d%1d",i,j);
5886: fprintf(ficparo,"%1d%1d",i1,j1);
5887: fprintf(ficlog,"%1d%1d",i1,j1);
5888: for(k=1; k<=ncovmodel;k++){
5889: fscanf(ficpar,"%le",&delti3[i][j][k]);
5890: printf(" %le",delti3[i][j][k]);
5891: fprintf(ficparo," %le",delti3[i][j][k]);
5892: fprintf(ficlog," %le",delti3[i][j][k]);
5893: }
5894: fscanf(ficpar,"\n");
5895: numlinepar++;
5896: printf("\n");
5897: fprintf(ficparo,"\n");
5898: fprintf(ficlog,"\n");
5899: }
5900: }
5901: fflush(ficlog);
5902:
5903: /* Reads covariance matrix */
5904: delti=delti3[1][1];
5905:
5906:
5907: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5908:
5909: /* Reads comments: lines beginning with '#' */
5910: while((c=getc(ficpar))=='#' && c!= EOF){
5911: ungetc(c,ficpar);
5912: fgets(line, MAXLINE, ficpar);
5913: numlinepar++;
5914: fputs(line,stdout);
5915: fputs(line,ficparo);
5916: fputs(line,ficlog);
5917: }
5918: ungetc(c,ficpar);
5919:
5920: matcov=matrix(1,npar,1,npar);
5921: for(i=1; i <=npar; i++)
5922: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5923:
5924: for(i=1; i <=npar; i++){
5925: fscanf(ficpar,"%s",str);
5926: if(mle==1)
5927: printf("%s",str);
5928: fprintf(ficlog,"%s",str);
5929: fprintf(ficparo,"%s",str);
5930: for(j=1; j <=i; j++){
5931: fscanf(ficpar," %le",&matcov[i][j]);
5932: if(mle==1){
5933: printf(" %.5le",matcov[i][j]);
5934: }
5935: fprintf(ficlog," %.5le",matcov[i][j]);
5936: fprintf(ficparo," %.5le",matcov[i][j]);
5937: }
5938: fscanf(ficpar,"\n");
5939: numlinepar++;
5940: if(mle==1)
5941: printf("\n");
5942: fprintf(ficlog,"\n");
5943: fprintf(ficparo,"\n");
5944: }
5945: for(i=1; i <=npar; i++)
5946: for(j=i+1;j<=npar;j++)
5947: matcov[i][j]=matcov[j][i];
5948:
5949: if(mle==1)
5950: printf("\n");
5951: fprintf(ficlog,"\n");
5952:
5953: fflush(ficlog);
5954:
5955: /*-------- Rewriting parameter file ----------*/
5956: strcpy(rfileres,"r"); /* "Rparameterfile */
5957: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5958: strcat(rfileres,"."); /* */
5959: strcat(rfileres,optionfilext); /* Other files have txt extension */
5960: if((ficres =fopen(rfileres,"w"))==NULL) {
5961: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5962: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5963: }
5964: fprintf(ficres,"#%s\n",version);
5965: } /* End of mle != -3 */
5966:
5967:
5968: n= lastobs;
5969: num=lvector(1,n);
5970: moisnais=vector(1,n);
5971: annais=vector(1,n);
5972: moisdc=vector(1,n);
5973: andc=vector(1,n);
5974: agedc=vector(1,n);
5975: cod=ivector(1,n);
5976: weight=vector(1,n);
5977: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5978: mint=matrix(1,maxwav,1,n);
5979: anint=matrix(1,maxwav,1,n);
5980: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5981: tab=ivector(1,NCOVMAX);
5982: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5983:
5984: /* Reads data from file datafile */
5985: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5986: goto end;
5987:
5988: /* Calculation of the number of parameters from char model */
5989: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
5990: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
5991: k=3 V4 Tvar[k=3]= 4 (from V4)
5992: k=2 V1 Tvar[k=2]= 1 (from V1)
5993: k=1 Tvar[1]=2 (from V2)
5994: */
5995: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
5996: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
5997: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
5998: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
5999: */
6000: /* For model-covariate k tells which data-covariate to use but
6001: because this model-covariate is a construction we invent a new column
6002: ncovcol + k1
6003: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6004: Tvar[3=V1*V4]=4+1 etc */
6005: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6006: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6007: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6008: */
6009: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6010: 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
6011: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6012: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6013: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6014: 4 covariates (3 plus signs)
6015: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6016: */
6017:
6018: if(decodemodel(model, lastobs) == 1)
6019: goto end;
6020:
6021: if((double)(lastobs-imx)/(double)imx > 1.10){
6022: nbwarn++;
6023: 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);
6024: 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);
6025: }
6026: /* if(mle==1){*/
6027: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6028: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6029: }
6030:
6031: /*-calculation of age at interview from date of interview and age at death -*/
6032: agev=matrix(1,maxwav,1,imx);
6033:
6034: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6035: goto end;
6036:
6037:
6038: agegomp=(int)agemin;
6039: free_vector(moisnais,1,n);
6040: free_vector(annais,1,n);
6041: /* free_matrix(mint,1,maxwav,1,n);
6042: free_matrix(anint,1,maxwav,1,n);*/
6043: free_vector(moisdc,1,n);
6044: free_vector(andc,1,n);
6045: /* */
6046:
6047: wav=ivector(1,imx);
6048: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6049: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6050: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6051:
6052: /* Concatenates waves */
6053: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6054: /* */
6055:
6056: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6057:
6058: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6059: ncodemax[1]=1;
6060: Ndum =ivector(-1,NCOVMAX);
6061: if (ncovmodel > 2)
6062: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6063:
6064: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6065: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6066: h=0;
6067:
6068:
6069: /*if (cptcovn > 0) */
6070:
6071:
6072: m=pow(2,cptcoveff);
6073:
6074: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6075: 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 */
6076: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6077: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6078: h++;
6079: if (h>m)
6080: h=1;
6081: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6082: * h 1 2 3 4
6083: *______________________________
6084: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6085: * 2 2 1 1 1
6086: * 3 i=2 1 2 1 1
6087: * 4 2 2 1 1
6088: * 5 i=3 1 i=2 1 2 1
6089: * 6 2 1 2 1
6090: * 7 i=4 1 2 2 1
6091: * 8 2 2 2 1
6092: * 9 i=5 1 i=3 1 i=2 1 1
6093: * 10 2 1 1 1
6094: * 11 i=6 1 2 1 1
6095: * 12 2 2 1 1
6096: * 13 i=7 1 i=4 1 2 1
6097: * 14 2 1 2 1
6098: * 15 i=8 1 2 2 1
6099: * 16 2 2 2 1
6100: */
6101: codtab[h][k]=j;
6102: /*codtab[h][Tvar[k]]=j;*/
6103: 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]]);
6104: }
6105: }
6106: }
6107: }
6108: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6109: codtab[1][2]=1;codtab[2][2]=2; */
6110: /* for(i=1; i <=m ;i++){
6111: for(k=1; k <=cptcovn; k++){
6112: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6113: }
6114: printf("\n");
6115: }
6116: scanf("%d",i);*/
6117:
6118: free_ivector(Ndum,-1,NCOVMAX);
6119:
6120:
6121:
6122: /*------------ gnuplot -------------*/
6123: strcpy(optionfilegnuplot,optionfilefiname);
6124: if(mle==-3)
6125: strcat(optionfilegnuplot,"-mort");
6126: strcat(optionfilegnuplot,".gp");
6127:
6128: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6129: printf("Problem with file %s",optionfilegnuplot);
6130: }
6131: else{
6132: fprintf(ficgp,"\n# %s\n", version);
6133: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6134: //fprintf(ficgp,"set missing 'NaNq'\n");
6135: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6136: }
6137: /* fclose(ficgp);*/
6138: /*--------- index.htm --------*/
6139:
6140: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6141: if(mle==-3)
6142: strcat(optionfilehtm,"-mort");
6143: strcat(optionfilehtm,".htm");
6144: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6145: printf("Problem with %s \n",optionfilehtm);
6146: exit(0);
6147: }
6148:
6149: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6150: strcat(optionfilehtmcov,"-cov.htm");
6151: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6152: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6153: }
6154: else{
6155: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6156: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6157: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6158: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6159: }
6160:
6161: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6162: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6163: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6164: \n\
6165: <hr size=\"2\" color=\"#EC5E5E\">\
6166: <ul><li><h4>Parameter files</h4>\n\
6167: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6168: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6169: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6170: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6171: - Date and time at start: %s</ul>\n",\
6172: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6173: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6174: fileres,fileres,\
6175: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6176: fflush(fichtm);
6177:
6178: strcpy(pathr,path);
6179: strcat(pathr,optionfilefiname);
6180: chdir(optionfilefiname); /* Move to directory named optionfile */
6181:
6182: /* Calculates basic frequencies. Computes observed prevalence at single age
6183: and prints on file fileres'p'. */
6184: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6185:
6186: fprintf(fichtm,"\n");
6187: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6188: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6189: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6190: imx,agemin,agemax,jmin,jmax,jmean);
6191: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6192: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6193: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6194: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6195: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6196:
6197:
6198: /* For Powell, parameters are in a vector p[] starting at p[1]
6199: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6200: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6201:
6202: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6203:
6204: if (mle==-3){
6205: ximort=matrix(1,NDIM,1,NDIM);
6206: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6207: cens=ivector(1,n);
6208: ageexmed=vector(1,n);
6209: agecens=vector(1,n);
6210: dcwave=ivector(1,n);
6211:
6212: for (i=1; i<=imx; i++){
6213: dcwave[i]=-1;
6214: for (m=firstpass; m<=lastpass; m++)
6215: if (s[m][i]>nlstate) {
6216: dcwave[i]=m;
6217: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6218: break;
6219: }
6220: }
6221:
6222: for (i=1; i<=imx; i++) {
6223: if (wav[i]>0){
6224: ageexmed[i]=agev[mw[1][i]][i];
6225: j=wav[i];
6226: agecens[i]=1.;
6227:
6228: if (ageexmed[i]> 1 && wav[i] > 0){
6229: agecens[i]=agev[mw[j][i]][i];
6230: cens[i]= 1;
6231: }else if (ageexmed[i]< 1)
6232: cens[i]= -1;
6233: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6234: cens[i]=0 ;
6235: }
6236: else cens[i]=-1;
6237: }
6238:
6239: for (i=1;i<=NDIM;i++) {
6240: for (j=1;j<=NDIM;j++)
6241: ximort[i][j]=(i == j ? 1.0 : 0.0);
6242: }
6243:
6244: /*p[1]=0.0268; p[NDIM]=0.083;*/
6245: /*printf("%lf %lf", p[1], p[2]);*/
6246:
6247:
6248: #ifdef GSL
6249: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6250: #else
6251: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6252: #endif
6253: strcpy(filerespow,"pow-mort");
6254: strcat(filerespow,fileres);
6255: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6256: printf("Problem with resultfile: %s\n", filerespow);
6257: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6258: }
6259: #ifdef GSL
6260: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6261: #else
6262: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6263: #endif
6264: /* for (i=1;i<=nlstate;i++)
6265: for(j=1;j<=nlstate+ndeath;j++)
6266: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6267: */
6268: fprintf(ficrespow,"\n");
6269: #ifdef GSL
6270: /* gsl starts here */
6271: T = gsl_multimin_fminimizer_nmsimplex;
6272: gsl_multimin_fminimizer *sfm = NULL;
6273: gsl_vector *ss, *x;
6274: gsl_multimin_function minex_func;
6275:
6276: /* Initial vertex size vector */
6277: ss = gsl_vector_alloc (NDIM);
6278:
6279: if (ss == NULL){
6280: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6281: }
6282: /* Set all step sizes to 1 */
6283: gsl_vector_set_all (ss, 0.001);
6284:
6285: /* Starting point */
6286:
6287: x = gsl_vector_alloc (NDIM);
6288:
6289: if (x == NULL){
6290: gsl_vector_free(ss);
6291: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6292: }
6293:
6294: /* Initialize method and iterate */
6295: /* p[1]=0.0268; p[NDIM]=0.083; */
6296: /* gsl_vector_set(x, 0, 0.0268); */
6297: /* gsl_vector_set(x, 1, 0.083); */
6298: gsl_vector_set(x, 0, p[1]);
6299: gsl_vector_set(x, 1, p[2]);
6300:
6301: minex_func.f = &gompertz_f;
6302: minex_func.n = NDIM;
6303: minex_func.params = (void *)&p; /* ??? */
6304:
6305: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6306: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6307:
6308: printf("Iterations beginning .....\n\n");
6309: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6310:
6311: iteri=0;
6312: while (rval == GSL_CONTINUE){
6313: iteri++;
6314: status = gsl_multimin_fminimizer_iterate(sfm);
6315:
6316: if (status) printf("error: %s\n", gsl_strerror (status));
6317: fflush(0);
6318:
6319: if (status)
6320: break;
6321:
6322: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6323: ssval = gsl_multimin_fminimizer_size (sfm);
6324:
6325: if (rval == GSL_SUCCESS)
6326: printf ("converged to a local maximum at\n");
6327:
6328: printf("%5d ", iteri);
6329: for (it = 0; it < NDIM; it++){
6330: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6331: }
6332: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6333: }
6334:
6335: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6336:
6337: gsl_vector_free(x); /* initial values */
6338: gsl_vector_free(ss); /* inital step size */
6339: for (it=0; it<NDIM; it++){
6340: p[it+1]=gsl_vector_get(sfm->x,it);
6341: fprintf(ficrespow," %.12lf", p[it]);
6342: }
6343: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6344: #endif
6345: #ifdef POWELL
6346: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6347: #endif
6348: fclose(ficrespow);
6349:
6350: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6351:
6352: for(i=1; i <=NDIM; i++)
6353: for(j=i+1;j<=NDIM;j++)
6354: matcov[i][j]=matcov[j][i];
6355:
6356: printf("\nCovariance matrix\n ");
6357: for(i=1; i <=NDIM; i++) {
6358: for(j=1;j<=NDIM;j++){
6359: printf("%f ",matcov[i][j]);
6360: }
6361: printf("\n ");
6362: }
6363:
6364: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6365: for (i=1;i<=NDIM;i++)
6366: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6367:
6368: lsurv=vector(1,AGESUP);
6369: lpop=vector(1,AGESUP);
6370: tpop=vector(1,AGESUP);
6371: lsurv[agegomp]=100000;
6372:
6373: for (k=agegomp;k<=AGESUP;k++) {
6374: agemortsup=k;
6375: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6376: }
6377:
6378: for (k=agegomp;k<agemortsup;k++)
6379: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6380:
6381: for (k=agegomp;k<agemortsup;k++){
6382: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6383: sumlpop=sumlpop+lpop[k];
6384: }
6385:
6386: tpop[agegomp]=sumlpop;
6387: for (k=agegomp;k<(agemortsup-3);k++){
6388: /* tpop[k+1]=2;*/
6389: tpop[k+1]=tpop[k]-lpop[k];
6390: }
6391:
6392:
6393: printf("\nAge lx qx dx Lx Tx e(x)\n");
6394: for (k=agegomp;k<(agemortsup-2);k++)
6395: 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]);
6396:
6397:
6398: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6399: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6400:
6401: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6402: stepm, weightopt,\
6403: model,imx,p,matcov,agemortsup);
6404:
6405: free_vector(lsurv,1,AGESUP);
6406: free_vector(lpop,1,AGESUP);
6407: free_vector(tpop,1,AGESUP);
6408: #ifdef GSL
6409: free_ivector(cens,1,n);
6410: free_vector(agecens,1,n);
6411: free_ivector(dcwave,1,n);
6412: free_matrix(ximort,1,NDIM,1,NDIM);
6413: #endif
6414: } /* Endof if mle==-3 */
6415:
6416: else{ /* For mle >=1 */
6417: globpr=0;/* debug */
6418: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6419: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6420: for (k=1; k<=npar;k++)
6421: printf(" %d %8.5f",k,p[k]);
6422: printf("\n");
6423: globpr=1; /* to print the contributions */
6424: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6425: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6426: for (k=1; k<=npar;k++)
6427: printf(" %d %8.5f",k,p[k]);
6428: printf("\n");
6429: if(mle>=1){ /* Could be 1 or 2 */
6430: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6431: }
6432:
6433: /*--------- results files --------------*/
6434: 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);
6435:
6436:
6437: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6438: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6439: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6440: for(i=1,jk=1; i <=nlstate; i++){
6441: for(k=1; k <=(nlstate+ndeath); k++){
6442: if (k != i) {
6443: printf("%d%d ",i,k);
6444: fprintf(ficlog,"%d%d ",i,k);
6445: fprintf(ficres,"%1d%1d ",i,k);
6446: for(j=1; j <=ncovmodel; j++){
6447: printf("%lf ",p[jk]);
6448: fprintf(ficlog,"%lf ",p[jk]);
6449: fprintf(ficres,"%lf ",p[jk]);
6450: jk++;
6451: }
6452: printf("\n");
6453: fprintf(ficlog,"\n");
6454: fprintf(ficres,"\n");
6455: }
6456: }
6457: }
6458: if(mle!=0){
6459: /* Computing hessian and covariance matrix */
6460: ftolhess=ftol; /* Usually correct */
6461: hesscov(matcov, p, npar, delti, ftolhess, func);
6462: }
6463: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6464: printf("# Scales (for hessian or gradient estimation)\n");
6465: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6466: for(i=1,jk=1; i <=nlstate; i++){
6467: for(j=1; j <=nlstate+ndeath; j++){
6468: if (j!=i) {
6469: fprintf(ficres,"%1d%1d",i,j);
6470: printf("%1d%1d",i,j);
6471: fprintf(ficlog,"%1d%1d",i,j);
6472: for(k=1; k<=ncovmodel;k++){
6473: printf(" %.5e",delti[jk]);
6474: fprintf(ficlog," %.5e",delti[jk]);
6475: fprintf(ficres," %.5e",delti[jk]);
6476: jk++;
6477: }
6478: printf("\n");
6479: fprintf(ficlog,"\n");
6480: fprintf(ficres,"\n");
6481: }
6482: }
6483: }
6484:
6485: 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");
6486: if(mle>=1)
6487: 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");
6488: 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");
6489: /* # 121 Var(a12)\n\ */
6490: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6491: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6492: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6493: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6494: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6495: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6496: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6497:
6498:
6499: /* Just to have a covariance matrix which will be more understandable
6500: even is we still don't want to manage dictionary of variables
6501: */
6502: for(itimes=1;itimes<=2;itimes++){
6503: jj=0;
6504: for(i=1; i <=nlstate; i++){
6505: for(j=1; j <=nlstate+ndeath; j++){
6506: if(j==i) continue;
6507: for(k=1; k<=ncovmodel;k++){
6508: jj++;
6509: ca[0]= k+'a'-1;ca[1]='\0';
6510: if(itimes==1){
6511: if(mle>=1)
6512: printf("#%1d%1d%d",i,j,k);
6513: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6514: fprintf(ficres,"#%1d%1d%d",i,j,k);
6515: }else{
6516: if(mle>=1)
6517: printf("%1d%1d%d",i,j,k);
6518: fprintf(ficlog,"%1d%1d%d",i,j,k);
6519: fprintf(ficres,"%1d%1d%d",i,j,k);
6520: }
6521: ll=0;
6522: for(li=1;li <=nlstate; li++){
6523: for(lj=1;lj <=nlstate+ndeath; lj++){
6524: if(lj==li) continue;
6525: for(lk=1;lk<=ncovmodel;lk++){
6526: ll++;
6527: if(ll<=jj){
6528: cb[0]= lk +'a'-1;cb[1]='\0';
6529: if(ll<jj){
6530: if(itimes==1){
6531: if(mle>=1)
6532: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6533: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6534: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6535: }else{
6536: if(mle>=1)
6537: printf(" %.5e",matcov[jj][ll]);
6538: fprintf(ficlog," %.5e",matcov[jj][ll]);
6539: fprintf(ficres," %.5e",matcov[jj][ll]);
6540: }
6541: }else{
6542: if(itimes==1){
6543: if(mle>=1)
6544: printf(" Var(%s%1d%1d)",ca,i,j);
6545: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6546: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6547: }else{
6548: if(mle>=1)
6549: printf(" %.5e",matcov[jj][ll]);
6550: fprintf(ficlog," %.5e",matcov[jj][ll]);
6551: fprintf(ficres," %.5e",matcov[jj][ll]);
6552: }
6553: }
6554: }
6555: } /* end lk */
6556: } /* end lj */
6557: } /* end li */
6558: if(mle>=1)
6559: printf("\n");
6560: fprintf(ficlog,"\n");
6561: fprintf(ficres,"\n");
6562: numlinepar++;
6563: } /* end k*/
6564: } /*end j */
6565: } /* end i */
6566: } /* end itimes */
6567:
6568: fflush(ficlog);
6569: fflush(ficres);
6570:
6571: while((c=getc(ficpar))=='#' && c!= EOF){
6572: ungetc(c,ficpar);
6573: fgets(line, MAXLINE, ficpar);
6574: fputs(line,stdout);
6575: fputs(line,ficparo);
6576: }
6577: ungetc(c,ficpar);
6578:
6579: estepm=0;
6580: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6581: if (estepm==0 || estepm < stepm) estepm=stepm;
6582: if (fage <= 2) {
6583: bage = ageminpar;
6584: fage = agemaxpar;
6585: }
6586:
6587: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6588: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6589: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6590:
6591: while((c=getc(ficpar))=='#' && c!= EOF){
6592: ungetc(c,ficpar);
6593: fgets(line, MAXLINE, ficpar);
6594: fputs(line,stdout);
6595: fputs(line,ficparo);
6596: }
6597: ungetc(c,ficpar);
6598:
6599: 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);
6600: 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);
6601: 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);
6602: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6603: 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);
6604:
6605: while((c=getc(ficpar))=='#' && c!= EOF){
6606: ungetc(c,ficpar);
6607: fgets(line, MAXLINE, ficpar);
6608: fputs(line,stdout);
6609: fputs(line,ficparo);
6610: }
6611: ungetc(c,ficpar);
6612:
6613:
6614: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6615: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6616:
6617: fscanf(ficpar,"pop_based=%d\n",&popbased);
6618: fprintf(ficparo,"pop_based=%d\n",popbased);
6619: fprintf(ficres,"pop_based=%d\n",popbased);
6620:
6621: while((c=getc(ficpar))=='#' && c!= EOF){
6622: ungetc(c,ficpar);
6623: fgets(line, MAXLINE, ficpar);
6624: fputs(line,stdout);
6625: fputs(line,ficparo);
6626: }
6627: ungetc(c,ficpar);
6628:
6629: 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);
6630: 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);
6631: 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);
6632: 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);
6633: 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);
6634: /* day and month of proj2 are not used but only year anproj2.*/
6635:
6636:
6637:
6638: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6639: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6640:
6641: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6642: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6643:
6644: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6645: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6646: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6647:
6648: /*------------ free_vector -------------*/
6649: /* chdir(path); */
6650:
6651: free_ivector(wav,1,imx);
6652: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6653: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6654: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6655: free_lvector(num,1,n);
6656: free_vector(agedc,1,n);
6657: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6658: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6659: fclose(ficparo);
6660: fclose(ficres);
6661:
6662:
6663: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6664: #include "prevlim.h" /* Use ficrespl, ficlog */
6665: fclose(ficrespl);
6666:
6667: #ifdef FREEEXIT2
6668: #include "freeexit2.h"
6669: #endif
6670:
6671: /*------------- h Pij x at various ages ------------*/
6672: #include "hpijx.h"
6673: fclose(ficrespij);
6674:
6675: /*-------------- Variance of one-step probabilities---*/
6676: k=1;
6677: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6678:
6679:
6680: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6681: for(i=1;i<=AGESUP;i++)
6682: for(j=1;j<=NCOVMAX;j++)
6683: for(k=1;k<=NCOVMAX;k++)
6684: probs[i][j][k]=0.;
6685:
6686: /*---------- Forecasting ------------------*/
6687: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6688: if(prevfcast==1){
6689: /* if(stepm ==1){*/
6690: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6691: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6692: /* } */
6693: /* else{ */
6694: /* erreur=108; */
6695: /* 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); */
6696: /* 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); */
6697: /* } */
6698: }
6699:
6700:
6701: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6702:
6703: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6704: /* 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",\
6705: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6706: */
6707:
6708: if (mobilav!=0) {
6709: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6710: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6711: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6712: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6713: }
6714: }
6715:
6716:
6717: /*---------- Health expectancies, no variances ------------*/
6718:
6719: strcpy(filerese,"e");
6720: strcat(filerese,fileres);
6721: if((ficreseij=fopen(filerese,"w"))==NULL) {
6722: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6723: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6724: }
6725: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6726: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6727: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6728: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6729:
6730: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6731: fprintf(ficreseij,"\n#****** ");
6732: for(j=1;j<=cptcoveff;j++) {
6733: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6734: }
6735: fprintf(ficreseij,"******\n");
6736:
6737: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6738: oldm=oldms;savm=savms;
6739: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6740:
6741: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6742: /*}*/
6743: }
6744: fclose(ficreseij);
6745:
6746:
6747: /*---------- Health expectancies and variances ------------*/
6748:
6749:
6750: strcpy(filerest,"t");
6751: strcat(filerest,fileres);
6752: if((ficrest=fopen(filerest,"w"))==NULL) {
6753: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6754: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6755: }
6756: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6757: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6758:
6759:
6760: strcpy(fileresstde,"stde");
6761: strcat(fileresstde,fileres);
6762: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6763: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6764: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6765: }
6766: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6767: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6768:
6769: strcpy(filerescve,"cve");
6770: strcat(filerescve,fileres);
6771: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6772: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6773: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6774: }
6775: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6776: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6777:
6778: strcpy(fileresv,"v");
6779: strcat(fileresv,fileres);
6780: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6781: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6782: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6783: }
6784: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6785: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6786:
6787: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6788: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6789:
6790: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6791: fprintf(ficrest,"\n#****** ");
6792: for(j=1;j<=cptcoveff;j++)
6793: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6794: fprintf(ficrest,"******\n");
6795:
6796: fprintf(ficresstdeij,"\n#****** ");
6797: fprintf(ficrescveij,"\n#****** ");
6798: for(j=1;j<=cptcoveff;j++) {
6799: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6800: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6801: }
6802: fprintf(ficresstdeij,"******\n");
6803: fprintf(ficrescveij,"******\n");
6804:
6805: fprintf(ficresvij,"\n#****** ");
6806: for(j=1;j<=cptcoveff;j++)
6807: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6808: fprintf(ficresvij,"******\n");
6809:
6810: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6811: oldm=oldms;savm=savms;
6812: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6813: /*
6814: */
6815: /* goto endfree; */
6816:
6817: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6818: pstamp(ficrest);
6819:
6820:
6821: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6822: oldm=oldms;savm=savms; /* Segmentation fault */
6823: cptcod= 0; /* To be deleted */
6824: 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 */
6825: 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 ");
6826: if(vpopbased==1)
6827: 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);
6828: else
6829: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6830: fprintf(ficrest,"# Age e.. (std) ");
6831: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6832: fprintf(ficrest,"\n");
6833:
6834: epj=vector(1,nlstate+1);
6835: for(age=bage; age <=fage ;age++){
6836: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6837: if (vpopbased==1) {
6838: if(mobilav ==0){
6839: for(i=1; i<=nlstate;i++)
6840: prlim[i][i]=probs[(int)age][i][k];
6841: }else{ /* mobilav */
6842: for(i=1; i<=nlstate;i++)
6843: prlim[i][i]=mobaverage[(int)age][i][k];
6844: }
6845: }
6846:
6847: fprintf(ficrest," %4.0f",age);
6848: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6849: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6850: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6851: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6852: }
6853: epj[nlstate+1] +=epj[j];
6854: }
6855:
6856: for(i=1, vepp=0.;i <=nlstate;i++)
6857: for(j=1;j <=nlstate;j++)
6858: vepp += vareij[i][j][(int)age];
6859: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6860: for(j=1;j <=nlstate;j++){
6861: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6862: }
6863: fprintf(ficrest,"\n");
6864: }
6865: }
6866: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6867: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6868: free_vector(epj,1,nlstate+1);
6869: /*}*/
6870: }
6871: free_vector(weight,1,n);
6872: free_imatrix(Tvard,1,NCOVMAX,1,2);
6873: free_imatrix(s,1,maxwav+1,1,n);
6874: free_matrix(anint,1,maxwav,1,n);
6875: free_matrix(mint,1,maxwav,1,n);
6876: free_ivector(cod,1,n);
6877: free_ivector(tab,1,NCOVMAX);
6878: fclose(ficresstdeij);
6879: fclose(ficrescveij);
6880: fclose(ficresvij);
6881: fclose(ficrest);
6882: fclose(ficpar);
6883:
6884: /*------- Variance of period (stable) prevalence------*/
6885:
6886: strcpy(fileresvpl,"vpl");
6887: strcat(fileresvpl,fileres);
6888: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6889: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6890: exit(0);
6891: }
6892: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6893:
6894: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6895: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6896:
6897: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6898: fprintf(ficresvpl,"\n#****** ");
6899: for(j=1;j<=cptcoveff;j++)
6900: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6901: fprintf(ficresvpl,"******\n");
6902:
6903: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6904: oldm=oldms;savm=savms;
6905: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6906: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6907: /*}*/
6908: }
6909:
6910: fclose(ficresvpl);
6911:
6912: /*---------- End : free ----------------*/
6913: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6914: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6915: } /* mle==-3 arrives here for freeing */
6916: /* endfree:*/
6917: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6918: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6919: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6920: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6921: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6922: free_matrix(covar,0,NCOVMAX,1,n);
6923: free_matrix(matcov,1,npar,1,npar);
6924: /*free_vector(delti,1,npar);*/
6925: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6926: free_matrix(agev,1,maxwav,1,imx);
6927: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6928:
6929: free_ivector(ncodemax,1,NCOVMAX);
6930: free_ivector(Tvar,1,NCOVMAX);
6931: free_ivector(Tprod,1,NCOVMAX);
6932: free_ivector(Tvaraff,1,NCOVMAX);
6933: free_ivector(Tage,1,NCOVMAX);
6934:
6935: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6936: free_imatrix(codtab,1,100,1,10);
6937: fflush(fichtm);
6938: fflush(ficgp);
6939:
6940:
6941: if((nberr >0) || (nbwarn>0)){
6942: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6943: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6944: }else{
6945: printf("End of Imach\n");
6946: fprintf(ficlog,"End of Imach\n");
6947: }
6948: printf("See log file on %s\n",filelog);
6949: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6950: /*(void) gettimeofday(&end_time,&tzp);*/
6951: rend_time = time(NULL);
6952: end_time = *localtime(&rend_time);
6953: /* tml = *localtime(&end_time.tm_sec); */
6954: strcpy(strtend,asctime(&end_time));
6955: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6956: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6957: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6958:
6959: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6960: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6961: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6962: /* printf("Total time was %d uSec.\n", total_usecs);*/
6963: /* if(fileappend(fichtm,optionfilehtm)){ */
6964: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6965: fclose(fichtm);
6966: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6967: fclose(fichtmcov);
6968: fclose(ficgp);
6969: fclose(ficlog);
6970: /*------ End -----------*/
6971:
6972:
6973: printf("Before Current directory %s!\n",pathcd);
6974: if(chdir(pathcd) != 0)
6975: printf("Can't move to directory %s!\n",path);
6976: if(getcwd(pathcd,MAXLINE) > 0)
6977: printf("Current directory %s!\n",pathcd);
6978: /*strcat(plotcmd,CHARSEPARATOR);*/
6979: sprintf(plotcmd,"gnuplot");
6980: #ifdef _WIN32
6981: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6982: #endif
6983: if(!stat(plotcmd,&info)){
6984: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6985: if(!stat(getenv("GNUPLOTBIN"),&info)){
6986: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6987: }else
6988: strcpy(pplotcmd,plotcmd);
6989: #ifdef __unix
6990: strcpy(plotcmd,GNUPLOTPROGRAM);
6991: if(!stat(plotcmd,&info)){
6992: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6993: }else
6994: strcpy(pplotcmd,plotcmd);
6995: #endif
6996: }else
6997: strcpy(pplotcmd,plotcmd);
6998:
6999: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7000: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7001:
7002: if((outcmd=system(plotcmd)) != 0){
7003: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7004: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7005: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7006: if((outcmd=system(plotcmd)) != 0)
7007: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7008: }
7009: printf(" Successful, please wait...");
7010: while (z[0] != 'q') {
7011: /* chdir(path); */
7012: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7013: scanf("%s",z);
7014: /* if (z[0] == 'c') system("./imach"); */
7015: if (z[0] == 'e') {
7016: #ifdef __APPLE__
7017: sprintf(pplotcmd, "open %s", optionfilehtm);
7018: #elif __linux
7019: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7020: #else
7021: sprintf(pplotcmd, "%s", optionfilehtm);
7022: #endif
7023: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7024: system(pplotcmd);
7025: }
7026: else if (z[0] == 'g') system(plotcmd);
7027: else if (z[0] == 'q') exit(0);
7028: }
7029: end:
7030: while (z[0] != 'q') {
7031: printf("\nType q for exiting: ");
7032: scanf("%s",z);
7033: }
7034: }
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