1: /* $Id: imach.c,v 1.171 2014/12/23 13:26:59 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.171 2014/12/23 13:26:59 brouard
5: Summary: Back from Visual C
6:
7: Still problem with utsname.h on Windows
8:
9: Revision 1.170 2014/12/23 11:17:12 brouard
10: Summary: Cleaning some \%% back to %%
11:
12: The escape was mandatory for a specific compiler (which one?), but too many warnings.
13:
14: Revision 1.169 2014/12/22 23:08:31 brouard
15: Summary: 0.98p
16:
17: Outputs some informations on compiler used, OS etc. Testing on different platforms.
18:
19: Revision 1.168 2014/12/22 15:17:42 brouard
20: Summary: update
21:
22: Revision 1.167 2014/12/22 13:50:56 brouard
23: Summary: Testing uname and compiler version and if compiled 32 or 64
24:
25: Testing on Linux 64
26:
27: Revision 1.166 2014/12/22 11:40:47 brouard
28: *** empty log message ***
29:
30: Revision 1.165 2014/12/16 11:20:36 brouard
31: Summary: After compiling on Visual C
32:
33: * imach.c (Module): Merging 1.61 to 1.162
34:
35: Revision 1.164 2014/12/16 10:52:11 brouard
36: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
37:
38: * imach.c (Module): Merging 1.61 to 1.162
39:
40: Revision 1.163 2014/12/16 10:30:11 brouard
41: * imach.c (Module): Merging 1.61 to 1.162
42:
43: Revision 1.162 2014/09/25 11:43:39 brouard
44: Summary: temporary backup 0.99!
45:
46: Revision 1.1 2014/09/16 11:06:58 brouard
47: Summary: With some code (wrong) for nlopt
48:
49: Author:
50:
51: Revision 1.161 2014/09/15 20:41:41 brouard
52: Summary: Problem with macro SQR on Intel compiler
53:
54: Revision 1.160 2014/09/02 09:24:05 brouard
55: *** empty log message ***
56:
57: Revision 1.159 2014/09/01 10:34:10 brouard
58: Summary: WIN32
59: Author: Brouard
60:
61: Revision 1.158 2014/08/27 17:11:51 brouard
62: *** empty log message ***
63:
64: Revision 1.157 2014/08/27 16:26:55 brouard
65: Summary: Preparing windows Visual studio version
66: Author: Brouard
67:
68: In order to compile on Visual studio, time.h is now correct and time_t
69: and tm struct should be used. difftime should be used but sometimes I
70: just make the differences in raw time format (time(&now).
71: Trying to suppress #ifdef LINUX
72: Add xdg-open for __linux in order to open default browser.
73:
74: Revision 1.156 2014/08/25 20:10:10 brouard
75: *** empty log message ***
76:
77: Revision 1.155 2014/08/25 18:32:34 brouard
78: Summary: New compile, minor changes
79: Author: Brouard
80:
81: Revision 1.154 2014/06/20 17:32:08 brouard
82: Summary: Outputs now all graphs of convergence to period prevalence
83:
84: Revision 1.153 2014/06/20 16:45:46 brouard
85: Summary: If 3 live state, convergence to period prevalence on same graph
86: Author: Brouard
87:
88: Revision 1.152 2014/06/18 17:54:09 brouard
89: Summary: open browser, use gnuplot on same dir than imach if not found in the path
90:
91: Revision 1.151 2014/06/18 16:43:30 brouard
92: *** empty log message ***
93:
94: Revision 1.150 2014/06/18 16:42:35 brouard
95: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
96: Author: brouard
97:
98: Revision 1.149 2014/06/18 15:51:14 brouard
99: Summary: Some fixes in parameter files errors
100: Author: Nicolas Brouard
101:
102: Revision 1.148 2014/06/17 17:38:48 brouard
103: Summary: Nothing new
104: Author: Brouard
105:
106: Just a new packaging for OS/X version 0.98nS
107:
108: Revision 1.147 2014/06/16 10:33:11 brouard
109: *** empty log message ***
110:
111: Revision 1.146 2014/06/16 10:20:28 brouard
112: Summary: Merge
113: Author: Brouard
114:
115: Merge, before building revised version.
116:
117: Revision 1.145 2014/06/10 21:23:15 brouard
118: Summary: Debugging with valgrind
119: Author: Nicolas Brouard
120:
121: Lot of changes in order to output the results with some covariates
122: After the Edimburgh REVES conference 2014, it seems mandatory to
123: improve the code.
124: No more memory valgrind error but a lot has to be done in order to
125: continue the work of splitting the code into subroutines.
126: Also, decodemodel has been improved. Tricode is still not
127: optimal. nbcode should be improved. Documentation has been added in
128: the source code.
129:
130: Revision 1.143 2014/01/26 09:45:38 brouard
131: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
132:
133: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
134: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
135:
136: Revision 1.142 2014/01/26 03:57:36 brouard
137: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
138:
139: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
140:
141: Revision 1.141 2014/01/26 02:42:01 brouard
142: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
143:
144: Revision 1.140 2011/09/02 10:37:54 brouard
145: Summary: times.h is ok with mingw32 now.
146:
147: Revision 1.139 2010/06/14 07:50:17 brouard
148: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
149: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
150:
151: Revision 1.138 2010/04/30 18:19:40 brouard
152: *** empty log message ***
153:
154: Revision 1.137 2010/04/29 18:11:38 brouard
155: (Module): Checking covariates for more complex models
156: than V1+V2. A lot of change to be done. Unstable.
157:
158: Revision 1.136 2010/04/26 20:30:53 brouard
159: (Module): merging some libgsl code. Fixing computation
160: of likelione (using inter/intrapolation if mle = 0) in order to
161: get same likelihood as if mle=1.
162: Some cleaning of code and comments added.
163:
164: Revision 1.135 2009/10/29 15:33:14 brouard
165: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
166:
167: Revision 1.134 2009/10/29 13:18:53 brouard
168: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
169:
170: Revision 1.133 2009/07/06 10:21:25 brouard
171: just nforces
172:
173: Revision 1.132 2009/07/06 08:22:05 brouard
174: Many tings
175:
176: Revision 1.131 2009/06/20 16:22:47 brouard
177: Some dimensions resccaled
178:
179: Revision 1.130 2009/05/26 06:44:34 brouard
180: (Module): Max Covariate is now set to 20 instead of 8. A
181: lot of cleaning with variables initialized to 0. Trying to make
182: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
183:
184: Revision 1.129 2007/08/31 13:49:27 lievre
185: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
186:
187: Revision 1.128 2006/06/30 13:02:05 brouard
188: (Module): Clarifications on computing e.j
189:
190: Revision 1.127 2006/04/28 18:11:50 brouard
191: (Module): Yes the sum of survivors was wrong since
192: imach-114 because nhstepm was no more computed in the age
193: loop. Now we define nhstepma in the age loop.
194: (Module): In order to speed up (in case of numerous covariates) we
195: compute health expectancies (without variances) in a first step
196: and then all the health expectancies with variances or standard
197: deviation (needs data from the Hessian matrices) which slows the
198: computation.
199: In the future we should be able to stop the program is only health
200: expectancies and graph are needed without standard deviations.
201:
202: Revision 1.126 2006/04/28 17:23:28 brouard
203: (Module): Yes the sum of survivors was wrong since
204: imach-114 because nhstepm was no more computed in the age
205: loop. Now we define nhstepma in the age loop.
206: Version 0.98h
207:
208: Revision 1.125 2006/04/04 15:20:31 lievre
209: Errors in calculation of health expectancies. Age was not initialized.
210: Forecasting file added.
211:
212: Revision 1.124 2006/03/22 17:13:53 lievre
213: Parameters are printed with %lf instead of %f (more numbers after the comma).
214: The log-likelihood is printed in the log file
215:
216: Revision 1.123 2006/03/20 10:52:43 brouard
217: * imach.c (Module): <title> changed, corresponds to .htm file
218: name. <head> headers where missing.
219:
220: * imach.c (Module): Weights can have a decimal point as for
221: English (a comma might work with a correct LC_NUMERIC environment,
222: otherwise the weight is truncated).
223: Modification of warning when the covariates values are not 0 or
224: 1.
225: Version 0.98g
226:
227: Revision 1.122 2006/03/20 09:45:41 brouard
228: (Module): Weights can have a decimal point as for
229: English (a comma might work with a correct LC_NUMERIC environment,
230: otherwise the weight is truncated).
231: Modification of warning when the covariates values are not 0 or
232: 1.
233: Version 0.98g
234:
235: Revision 1.121 2006/03/16 17:45:01 lievre
236: * imach.c (Module): Comments concerning covariates added
237:
238: * imach.c (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 1.120 2006/03/16 15:10:38 lievre
243: (Module): refinements in the computation of lli if
244: status=-2 in order to have more reliable computation if stepm is
245: not 1 month. Version 0.98f
246:
247: Revision 1.119 2006/03/15 17:42:26 brouard
248: (Module): Bug if status = -2, the loglikelihood was
249: computed as likelihood omitting the logarithm. Version O.98e
250:
251: Revision 1.118 2006/03/14 18:20:07 brouard
252: (Module): varevsij Comments added explaining the second
253: table of variances if popbased=1 .
254: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
255: (Module): Function pstamp added
256: (Module): Version 0.98d
257:
258: Revision 1.117 2006/03/14 17:16:22 brouard
259: (Module): varevsij Comments added explaining the second
260: table of variances if popbased=1 .
261: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
262: (Module): Function pstamp added
263: (Module): Version 0.98d
264:
265: Revision 1.116 2006/03/06 10:29:27 brouard
266: (Module): Variance-covariance wrong links and
267: varian-covariance of ej. is needed (Saito).
268:
269: Revision 1.115 2006/02/27 12:17:45 brouard
270: (Module): One freematrix added in mlikeli! 0.98c
271:
272: Revision 1.114 2006/02/26 12:57:58 brouard
273: (Module): Some improvements in processing parameter
274: filename with strsep.
275:
276: Revision 1.113 2006/02/24 14:20:24 brouard
277: (Module): Memory leaks checks with valgrind and:
278: datafile was not closed, some imatrix were not freed and on matrix
279: allocation too.
280:
281: Revision 1.112 2006/01/30 09:55:26 brouard
282: (Module): Back to gnuplot.exe instead of wgnuplot.exe
283:
284: Revision 1.111 2006/01/25 20:38:18 brouard
285: (Module): Lots of cleaning and bugs added (Gompertz)
286: (Module): Comments can be added in data file. Missing date values
287: can be a simple dot '.'.
288:
289: Revision 1.110 2006/01/25 00:51:50 brouard
290: (Module): Lots of cleaning and bugs added (Gompertz)
291:
292: Revision 1.109 2006/01/24 19:37:15 brouard
293: (Module): Comments (lines starting with a #) are allowed in data.
294:
295: Revision 1.108 2006/01/19 18:05:42 lievre
296: Gnuplot problem appeared...
297: To be fixed
298:
299: Revision 1.107 2006/01/19 16:20:37 brouard
300: Test existence of gnuplot in imach path
301:
302: Revision 1.106 2006/01/19 13:24:36 brouard
303: Some cleaning and links added in html output
304:
305: Revision 1.105 2006/01/05 20:23:19 lievre
306: *** empty log message ***
307:
308: Revision 1.104 2005/09/30 16:11:43 lievre
309: (Module): sump fixed, loop imx fixed, and simplifications.
310: (Module): If the status is missing at the last wave but we know
311: that the person is alive, then we can code his/her status as -2
312: (instead of missing=-1 in earlier versions) and his/her
313: contributions to the likelihood is 1 - Prob of dying from last
314: health status (= 1-p13= p11+p12 in the easiest case of somebody in
315: the healthy state at last known wave). Version is 0.98
316:
317: Revision 1.103 2005/09/30 15:54:49 lievre
318: (Module): sump fixed, loop imx fixed, and simplifications.
319:
320: Revision 1.102 2004/09/15 17:31:30 brouard
321: Add the possibility to read data file including tab characters.
322:
323: Revision 1.101 2004/09/15 10:38:38 brouard
324: Fix on curr_time
325:
326: Revision 1.100 2004/07/12 18:29:06 brouard
327: Add version for Mac OS X. Just define UNIX in Makefile
328:
329: Revision 1.99 2004/06/05 08:57:40 brouard
330: *** empty log message ***
331:
332: Revision 1.98 2004/05/16 15:05:56 brouard
333: New version 0.97 . First attempt to estimate force of mortality
334: directly from the data i.e. without the need of knowing the health
335: state at each age, but using a Gompertz model: log u =a + b*age .
336: This is the basic analysis of mortality and should be done before any
337: other analysis, in order to test if the mortality estimated from the
338: cross-longitudinal survey is different from the mortality estimated
339: from other sources like vital statistic data.
340:
341: The same imach parameter file can be used but the option for mle should be -3.
342:
343: Agnès, who wrote this part of the code, tried to keep most of the
344: former routines in order to include the new code within the former code.
345:
346: The output is very simple: only an estimate of the intercept and of
347: the slope with 95% confident intervals.
348:
349: Current limitations:
350: A) Even if you enter covariates, i.e. with the
351: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
352: B) There is no computation of Life Expectancy nor Life Table.
353:
354: Revision 1.97 2004/02/20 13:25:42 lievre
355: Version 0.96d. Population forecasting command line is (temporarily)
356: suppressed.
357:
358: Revision 1.96 2003/07/15 15:38:55 brouard
359: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
360: rewritten within the same printf. Workaround: many printfs.
361:
362: Revision 1.95 2003/07/08 07:54:34 brouard
363: * imach.c (Repository):
364: (Repository): Using imachwizard code to output a more meaningful covariance
365: matrix (cov(a12,c31) instead of numbers.
366:
367: Revision 1.94 2003/06/27 13:00:02 brouard
368: Just cleaning
369:
370: Revision 1.93 2003/06/25 16:33:55 brouard
371: (Module): On windows (cygwin) function asctime_r doesn't
372: exist so I changed back to asctime which exists.
373: (Module): Version 0.96b
374:
375: Revision 1.92 2003/06/25 16:30:45 brouard
376: (Module): On windows (cygwin) function asctime_r doesn't
377: exist so I changed back to asctime which exists.
378:
379: Revision 1.91 2003/06/25 15:30:29 brouard
380: * imach.c (Repository): Duplicated warning errors corrected.
381: (Repository): Elapsed time after each iteration is now output. It
382: helps to forecast when convergence will be reached. Elapsed time
383: is stamped in powell. We created a new html file for the graphs
384: concerning matrix of covariance. It has extension -cov.htm.
385:
386: Revision 1.90 2003/06/24 12:34:15 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 1.89 2003/06/24 12:30:52 brouard
392: (Module): Some bugs corrected for windows. Also, when
393: mle=-1 a template is output in file "or"mypar.txt with the design
394: of the covariance matrix to be input.
395:
396: Revision 1.88 2003/06/23 17:54:56 brouard
397: * 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.
398:
399: Revision 1.87 2003/06/18 12:26:01 brouard
400: Version 0.96
401:
402: Revision 1.86 2003/06/17 20:04:08 brouard
403: (Module): Change position of html and gnuplot routines and added
404: routine fileappend.
405:
406: Revision 1.85 2003/06/17 13:12:43 brouard
407: * imach.c (Repository): Check when date of death was earlier that
408: current date of interview. It may happen when the death was just
409: prior to the death. In this case, dh was negative and likelihood
410: was wrong (infinity). We still send an "Error" but patch by
411: assuming that the date of death was just one stepm after the
412: interview.
413: (Repository): Because some people have very long ID (first column)
414: we changed int to long in num[] and we added a new lvector for
415: memory allocation. But we also truncated to 8 characters (left
416: truncation)
417: (Repository): No more line truncation errors.
418:
419: Revision 1.84 2003/06/13 21:44:43 brouard
420: * imach.c (Repository): Replace "freqsummary" at a correct
421: place. It differs from routine "prevalence" which may be called
422: many times. Probs is memory consuming and must be used with
423: parcimony.
424: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
425:
426: Revision 1.83 2003/06/10 13:39:11 lievre
427: *** empty log message ***
428:
429: Revision 1.82 2003/06/05 15:57:20 brouard
430: Add log in imach.c and fullversion number is now printed.
431:
432: */
433: /*
434: Interpolated Markov Chain
435:
436: Short summary of the programme:
437:
438: This program computes Healthy Life Expectancies from
439: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
440: first survey ("cross") where individuals from different ages are
441: interviewed on their health status or degree of disability (in the
442: case of a health survey which is our main interest) -2- at least a
443: second wave of interviews ("longitudinal") which measure each change
444: (if any) in individual health status. Health expectancies are
445: computed from the time spent in each health state according to a
446: model. More health states you consider, more time is necessary to reach the
447: Maximum Likelihood of the parameters involved in the model. The
448: simplest model is the multinomial logistic model where pij is the
449: probability to be observed in state j at the second wave
450: conditional to be observed in state i at the first wave. Therefore
451: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
452: 'age' is age and 'sex' is a covariate. If you want to have a more
453: complex model than "constant and age", you should modify the program
454: where the markup *Covariates have to be included here again* invites
455: you to do it. More covariates you add, slower the
456: convergence.
457:
458: The advantage of this computer programme, compared to a simple
459: multinomial logistic model, is clear when the delay between waves is not
460: identical for each individual. Also, if a individual missed an
461: intermediate interview, the information is lost, but taken into
462: account using an interpolation or extrapolation.
463:
464: hPijx is the probability to be observed in state i at age x+h
465: conditional to the observed state i at age x. The delay 'h' can be
466: split into an exact number (nh*stepm) of unobserved intermediate
467: states. This elementary transition (by month, quarter,
468: semester or year) is modelled as a multinomial logistic. The hPx
469: matrix is simply the matrix product of nh*stepm elementary matrices
470: and the contribution of each individual to the likelihood is simply
471: hPijx.
472:
473: Also this programme outputs the covariance matrix of the parameters but also
474: of the life expectancies. It also computes the period (stable) prevalence.
475:
476: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
477: Institut national d'études démographiques, Paris.
478: This software have been partly granted by Euro-REVES, a concerted action
479: from the European Union.
480: It is copyrighted identically to a GNU software product, ie programme and
481: software can be distributed freely for non commercial use. Latest version
482: can be accessed at http://euroreves.ined.fr/imach .
483:
484: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
485: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
486:
487: **********************************************************************/
488: /*
489: main
490: read parameterfile
491: read datafile
492: concatwav
493: freqsummary
494: if (mle >= 1)
495: mlikeli
496: print results files
497: if mle==1
498: computes hessian
499: read end of parameter file: agemin, agemax, bage, fage, estepm
500: begin-prev-date,...
501: open gnuplot file
502: open html file
503: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
504: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
505: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
506: freexexit2 possible for memory heap.
507:
508: h Pij x | pij_nom ficrestpij
509: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
510: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
511: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
512:
513: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
514: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
515: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
516: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
517: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
518:
519: forecasting if prevfcast==1 prevforecast call prevalence()
520: health expectancies
521: Variance-covariance of DFLE
522: prevalence()
523: movingaverage()
524: varevsij()
525: if popbased==1 varevsij(,popbased)
526: total life expectancies
527: Variance of period (stable) prevalence
528: end
529: */
530:
531: #define POWELL /* Instead of NLOPT */
532:
533: #include <math.h>
534: #include <stdio.h>
535: #include <stdlib.h>
536: #include <string.h>
537:
538: #ifdef _WIN32
539: #include <io.h>
540: #else
541: #include <unistd.h>
542: #endif
543:
544: #include <limits.h>
545: #include <sys/types.h>
546:
547: #if defined(__GNUC__)
548: #include <sys/utsname.h> /* Doesn't work on Windows */
549: #endif
550:
551: #include <sys/stat.h>
552: #include <errno.h>
553: /* extern int errno; */
554:
555: /* #ifdef LINUX */
556: /* #include <time.h> */
557: /* #include "timeval.h" */
558: /* #else */
559: /* #include <sys/time.h> */
560: /* #endif */
561:
562: #include <time.h>
563:
564: #ifdef GSL
565: #include <gsl/gsl_errno.h>
566: #include <gsl/gsl_multimin.h>
567: #endif
568:
569:
570: #ifdef NLOPT
571: #include <nlopt.h>
572: typedef struct {
573: double (* function)(double [] );
574: } myfunc_data ;
575: #endif
576:
577: /* #include <libintl.h> */
578: /* #define _(String) gettext (String) */
579:
580: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
581:
582: #define GNUPLOTPROGRAM "gnuplot"
583: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
584: #define FILENAMELENGTH 132
585:
586: #define GLOCK_ERROR_NOPATH -1 /* empty path */
587: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
588:
589: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
590: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
591:
592: #define NINTERVMAX 8
593: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
594: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
595: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
596: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
597: #define MAXN 20000
598: #define YEARM 12. /**< Number of months per year */
599: #define AGESUP 130
600: #define AGEBASE 40
601: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
602: #ifdef _WIN32
603: #define DIRSEPARATOR '\\'
604: #define CHARSEPARATOR "\\"
605: #define ODIRSEPARATOR '/'
606: #else
607: #define DIRSEPARATOR '/'
608: #define CHARSEPARATOR "/"
609: #define ODIRSEPARATOR '\\'
610: #endif
611:
612: /* $Id: imach.c,v 1.171 2014/12/23 13:26:59 brouard Exp $ */
613: /* $State: Exp $ */
614:
615: 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";
616: char fullversion[]="$Revision: 1.171 $ $Date: 2014/12/23 13:26:59 $";
617: char strstart[80];
618: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
619: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
620: int nvar=0, nforce=0; /* Number of variables, number of forces */
621: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
622: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
623: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
624: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
625: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
626: int cptcovprodnoage=0; /**< Number of covariate products without age */
627: int cptcoveff=0; /* Total number of covariates to vary for printing results */
628: int cptcov=0; /* Working variable */
629: int npar=NPARMAX;
630: int nlstate=2; /* Number of live states */
631: int ndeath=1; /* Number of dead states */
632: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
633: int popbased=0;
634:
635: int *wav; /* Number of waves for this individuual 0 is possible */
636: int maxwav=0; /* Maxim number of waves */
637: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
638: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
639: int gipmx=0, gsw=0; /* Global variables on the number of contributions
640: to the likelihood and the sum of weights (done by funcone)*/
641: int mle=1, weightopt=0;
642: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
643: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
644: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
645: * wave mi and wave mi+1 is not an exact multiple of stepm. */
646: int countcallfunc=0; /* Count the number of calls to func */
647: double jmean=1; /* Mean space between 2 waves */
648: double **matprod2(); /* test */
649: double **oldm, **newm, **savm; /* Working pointers to matrices */
650: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
651: /*FILE *fic ; */ /* Used in readdata only */
652: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
653: FILE *ficlog, *ficrespow;
654: int globpr=0; /* Global variable for printing or not */
655: double fretone; /* Only one call to likelihood */
656: long ipmx=0; /* Number of contributions */
657: double sw; /* Sum of weights */
658: char filerespow[FILENAMELENGTH];
659: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
660: FILE *ficresilk;
661: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
662: FILE *ficresprobmorprev;
663: FILE *fichtm, *fichtmcov; /* Html File */
664: FILE *ficreseij;
665: char filerese[FILENAMELENGTH];
666: FILE *ficresstdeij;
667: char fileresstde[FILENAMELENGTH];
668: FILE *ficrescveij;
669: char filerescve[FILENAMELENGTH];
670: FILE *ficresvij;
671: char fileresv[FILENAMELENGTH];
672: FILE *ficresvpl;
673: char fileresvpl[FILENAMELENGTH];
674: char title[MAXLINE];
675: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
676: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
677: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
678: char command[FILENAMELENGTH];
679: int outcmd=0;
680:
681: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
682:
683: char filelog[FILENAMELENGTH]; /* Log file */
684: char filerest[FILENAMELENGTH];
685: char fileregp[FILENAMELENGTH];
686: char popfile[FILENAMELENGTH];
687:
688: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
689:
690: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
691: /* struct timezone tzp; */
692: /* extern int gettimeofday(); */
693: struct tm tml, *gmtime(), *localtime();
694:
695: extern time_t time();
696:
697: struct tm start_time, end_time, curr_time, last_time, forecast_time;
698: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
699: struct tm tm;
700:
701: char strcurr[80], strfor[80];
702:
703: char *endptr;
704: long lval;
705: double dval;
706:
707: #define NR_END 1
708: #define FREE_ARG char*
709: #define FTOL 1.0e-10
710:
711: #define NRANSI
712: #define ITMAX 200
713:
714: #define TOL 2.0e-4
715:
716: #define CGOLD 0.3819660
717: #define ZEPS 1.0e-10
718: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
719:
720: #define GOLD 1.618034
721: #define GLIMIT 100.0
722: #define TINY 1.0e-20
723:
724: static double maxarg1,maxarg2;
725: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
726: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
727:
728: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
729: #define rint(a) floor(a+0.5)
730: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
731: /* #define mytinydouble 1.0e-16 */
732: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
733: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
734: /* static double dsqrarg; */
735: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
736: static double sqrarg;
737: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
738: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
739: int agegomp= AGEGOMP;
740:
741: int imx;
742: int stepm=1;
743: /* Stepm, step in month: minimum step interpolation*/
744:
745: int estepm;
746: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
747:
748: int m,nb;
749: long *num;
750: int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
751: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
752: double **pmmij, ***probs;
753: double *ageexmed,*agecens;
754: double dateintmean=0;
755:
756: double *weight;
757: int **s; /* Status */
758: double *agedc;
759: double **covar; /**< covar[j,i], value of jth covariate for individual i,
760: * covar=matrix(0,NCOVMAX,1,n);
761: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; */
762: double idx;
763: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
764: int *Ndum; /** Freq of modality (tricode */
765: int **codtab; /**< codtab=imatrix(1,100,1,10); */
766: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
767: double *lsurv, *lpop, *tpop;
768:
769: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
770: double ftolhess; /**< Tolerance for computing hessian */
771:
772: /**************** split *************************/
773: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
774: {
775: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
776: the name of the file (name), its extension only (ext) and its first part of the name (finame)
777: */
778: char *ss; /* pointer */
779: int l1, l2; /* length counters */
780:
781: l1 = strlen(path ); /* length of path */
782: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
783: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
784: if ( ss == NULL ) { /* no directory, so determine current directory */
785: strcpy( name, path ); /* we got the fullname name because no directory */
786: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
787: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
788: /* get current working directory */
789: /* extern char* getcwd ( char *buf , int len);*/
790: if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
791: return( GLOCK_ERROR_GETCWD );
792: }
793: /* got dirc from getcwd*/
794: printf(" DIRC = %s \n",dirc);
795: } else { /* strip direcotry from path */
796: ss++; /* after this, the filename */
797: l2 = strlen( ss ); /* length of filename */
798: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
799: strcpy( name, ss ); /* save file name */
800: strncpy( dirc, path, l1 - l2 ); /* now the directory */
801: dirc[l1-l2] = 0; /* add zero */
802: printf(" DIRC2 = %s \n",dirc);
803: }
804: /* We add a separator at the end of dirc if not exists */
805: l1 = strlen( dirc ); /* length of directory */
806: if( dirc[l1-1] != DIRSEPARATOR ){
807: dirc[l1] = DIRSEPARATOR;
808: dirc[l1+1] = 0;
809: printf(" DIRC3 = %s \n",dirc);
810: }
811: ss = strrchr( name, '.' ); /* find last / */
812: if (ss >0){
813: ss++;
814: strcpy(ext,ss); /* save extension */
815: l1= strlen( name);
816: l2= strlen(ss)+1;
817: strncpy( finame, name, l1-l2);
818: finame[l1-l2]= 0;
819: }
820:
821: return( 0 ); /* we're done */
822: }
823:
824:
825: /******************************************/
826:
827: void replace_back_to_slash(char *s, char*t)
828: {
829: int i;
830: int lg=0;
831: i=0;
832: lg=strlen(t);
833: for(i=0; i<= lg; i++) {
834: (s[i] = t[i]);
835: if (t[i]== '\\') s[i]='/';
836: }
837: }
838:
839: char *trimbb(char *out, char *in)
840: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
841: char *s;
842: s=out;
843: while (*in != '\0'){
844: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
845: in++;
846: }
847: *out++ = *in++;
848: }
849: *out='\0';
850: return s;
851: }
852:
853: char *cutl(char *blocc, char *alocc, char *in, char occ)
854: {
855: /* cuts string in into blocc and alocc where blocc ends before first occurence of char 'occ'
856: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
857: gives blocc="abcdef2ghi" and alocc="j".
858: If occ is not found blocc is null and alocc is equal to in. Returns blocc
859: */
860: char *s, *t;
861: t=in;s=in;
862: while ((*in != occ) && (*in != '\0')){
863: *alocc++ = *in++;
864: }
865: if( *in == occ){
866: *(alocc)='\0';
867: s=++in;
868: }
869:
870: if (s == t) {/* occ not found */
871: *(alocc-(in-s))='\0';
872: in=s;
873: }
874: while ( *in != '\0'){
875: *blocc++ = *in++;
876: }
877:
878: *blocc='\0';
879: return t;
880: }
881: char *cutv(char *blocc, char *alocc, char *in, char occ)
882: {
883: /* cuts string in into blocc and alocc where blocc ends before last occurence of char 'occ'
884: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
885: gives blocc="abcdef2ghi" and alocc="j".
886: If occ is not found blocc is null and alocc is equal to in. Returns alocc
887: */
888: char *s, *t;
889: t=in;s=in;
890: while (*in != '\0'){
891: while( *in == occ){
892: *blocc++ = *in++;
893: s=in;
894: }
895: *blocc++ = *in++;
896: }
897: if (s == t) /* occ not found */
898: *(blocc-(in-s))='\0';
899: else
900: *(blocc-(in-s)-1)='\0';
901: in=s;
902: while ( *in != '\0'){
903: *alocc++ = *in++;
904: }
905:
906: *alocc='\0';
907: return s;
908: }
909:
910: int nbocc(char *s, char occ)
911: {
912: int i,j=0;
913: int lg=20;
914: i=0;
915: lg=strlen(s);
916: for(i=0; i<= lg; i++) {
917: if (s[i] == occ ) j++;
918: }
919: return j;
920: }
921:
922: /* void cutv(char *u,char *v, char*t, char occ) */
923: /* { */
924: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
925: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
926: /* gives u="abcdef2ghi" and v="j" *\/ */
927: /* int i,lg,j,p=0; */
928: /* i=0; */
929: /* lg=strlen(t); */
930: /* for(j=0; j<=lg-1; j++) { */
931: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
932: /* } */
933:
934: /* for(j=0; j<p; j++) { */
935: /* (u[j] = t[j]); */
936: /* } */
937: /* u[p]='\0'; */
938:
939: /* for(j=0; j<= lg; j++) { */
940: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
941: /* } */
942: /* } */
943:
944: #ifdef _WIN32
945: char * strsep(char **pp, const char *delim)
946: {
947: char *p, *q;
948:
949: if ((p = *pp) == NULL)
950: return 0;
951: if ((q = strpbrk (p, delim)) != NULL)
952: {
953: *pp = q + 1;
954: *q = '\0';
955: }
956: else
957: *pp = 0;
958: return p;
959: }
960: #endif
961:
962: /********************** nrerror ********************/
963:
964: void nrerror(char error_text[])
965: {
966: fprintf(stderr,"ERREUR ...\n");
967: fprintf(stderr,"%s\n",error_text);
968: exit(EXIT_FAILURE);
969: }
970: /*********************** vector *******************/
971: double *vector(int nl, int nh)
972: {
973: double *v;
974: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
975: if (!v) nrerror("allocation failure in vector");
976: return v-nl+NR_END;
977: }
978:
979: /************************ free vector ******************/
980: void free_vector(double*v, int nl, int nh)
981: {
982: free((FREE_ARG)(v+nl-NR_END));
983: }
984:
985: /************************ivector *******************************/
986: int *ivector(long nl,long nh)
987: {
988: int *v;
989: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
990: if (!v) nrerror("allocation failure in ivector");
991: return v-nl+NR_END;
992: }
993:
994: /******************free ivector **************************/
995: void free_ivector(int *v, long nl, long nh)
996: {
997: free((FREE_ARG)(v+nl-NR_END));
998: }
999:
1000: /************************lvector *******************************/
1001: long *lvector(long nl,long nh)
1002: {
1003: long *v;
1004: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1005: if (!v) nrerror("allocation failure in ivector");
1006: return v-nl+NR_END;
1007: }
1008:
1009: /******************free lvector **************************/
1010: void free_lvector(long *v, long nl, long nh)
1011: {
1012: free((FREE_ARG)(v+nl-NR_END));
1013: }
1014:
1015: /******************* imatrix *******************************/
1016: int **imatrix(long nrl, long nrh, long ncl, long nch)
1017: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1018: {
1019: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1020: int **m;
1021:
1022: /* allocate pointers to rows */
1023: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1024: if (!m) nrerror("allocation failure 1 in matrix()");
1025: m += NR_END;
1026: m -= nrl;
1027:
1028:
1029: /* allocate rows and set pointers to them */
1030: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1031: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1032: m[nrl] += NR_END;
1033: m[nrl] -= ncl;
1034:
1035: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1036:
1037: /* return pointer to array of pointers to rows */
1038: return m;
1039: }
1040:
1041: /****************** free_imatrix *************************/
1042: void free_imatrix(m,nrl,nrh,ncl,nch)
1043: int **m;
1044: long nch,ncl,nrh,nrl;
1045: /* free an int matrix allocated by imatrix() */
1046: {
1047: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1048: free((FREE_ARG) (m+nrl-NR_END));
1049: }
1050:
1051: /******************* matrix *******************************/
1052: double **matrix(long nrl, long nrh, long ncl, long nch)
1053: {
1054: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1055: double **m;
1056:
1057: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1058: if (!m) nrerror("allocation failure 1 in matrix()");
1059: m += NR_END;
1060: m -= nrl;
1061:
1062: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1063: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1064: m[nrl] += NR_END;
1065: m[nrl] -= ncl;
1066:
1067: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1068: return m;
1069: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1070: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1071: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1072: */
1073: }
1074:
1075: /*************************free matrix ************************/
1076: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1077: {
1078: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1079: free((FREE_ARG)(m+nrl-NR_END));
1080: }
1081:
1082: /******************* ma3x *******************************/
1083: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1084: {
1085: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1086: double ***m;
1087:
1088: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1089: if (!m) nrerror("allocation failure 1 in matrix()");
1090: m += NR_END;
1091: m -= nrl;
1092:
1093: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1094: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1095: m[nrl] += NR_END;
1096: m[nrl] -= ncl;
1097:
1098: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1099:
1100: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1101: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1102: m[nrl][ncl] += NR_END;
1103: m[nrl][ncl] -= nll;
1104: for (j=ncl+1; j<=nch; j++)
1105: m[nrl][j]=m[nrl][j-1]+nlay;
1106:
1107: for (i=nrl+1; i<=nrh; i++) {
1108: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1109: for (j=ncl+1; j<=nch; j++)
1110: m[i][j]=m[i][j-1]+nlay;
1111: }
1112: return m;
1113: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1114: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1115: */
1116: }
1117:
1118: /*************************free ma3x ************************/
1119: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1120: {
1121: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1122: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1123: free((FREE_ARG)(m+nrl-NR_END));
1124: }
1125:
1126: /*************** function subdirf ***********/
1127: char *subdirf(char fileres[])
1128: {
1129: /* Caution optionfilefiname is hidden */
1130: strcpy(tmpout,optionfilefiname);
1131: strcat(tmpout,"/"); /* Add to the right */
1132: strcat(tmpout,fileres);
1133: return tmpout;
1134: }
1135:
1136: /*************** function subdirf2 ***********/
1137: char *subdirf2(char fileres[], char *preop)
1138: {
1139:
1140: /* Caution optionfilefiname is hidden */
1141: strcpy(tmpout,optionfilefiname);
1142: strcat(tmpout,"/");
1143: strcat(tmpout,preop);
1144: strcat(tmpout,fileres);
1145: return tmpout;
1146: }
1147:
1148: /*************** function subdirf3 ***********/
1149: char *subdirf3(char fileres[], char *preop, char *preop2)
1150: {
1151:
1152: /* Caution optionfilefiname is hidden */
1153: strcpy(tmpout,optionfilefiname);
1154: strcat(tmpout,"/");
1155: strcat(tmpout,preop);
1156: strcat(tmpout,preop2);
1157: strcat(tmpout,fileres);
1158: return tmpout;
1159: }
1160:
1161: char *asc_diff_time(long time_sec, char ascdiff[])
1162: {
1163: long sec_left, days, hours, minutes;
1164: days = (time_sec) / (60*60*24);
1165: sec_left = (time_sec) % (60*60*24);
1166: hours = (sec_left) / (60*60) ;
1167: sec_left = (sec_left) %(60*60);
1168: minutes = (sec_left) /60;
1169: sec_left = (sec_left) % (60);
1170: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1171: return ascdiff;
1172: }
1173:
1174: /***************** f1dim *************************/
1175: extern int ncom;
1176: extern double *pcom,*xicom;
1177: extern double (*nrfunc)(double []);
1178:
1179: double f1dim(double x)
1180: {
1181: int j;
1182: double f;
1183: double *xt;
1184:
1185: xt=vector(1,ncom);
1186: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1187: f=(*nrfunc)(xt);
1188: free_vector(xt,1,ncom);
1189: return f;
1190: }
1191:
1192: /*****************brent *************************/
1193: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1194: {
1195: int iter;
1196: double a,b,d,etemp;
1197: double fu=0,fv,fw,fx;
1198: double ftemp=0.;
1199: double p,q,r,tol1,tol2,u,v,w,x,xm;
1200: double e=0.0;
1201:
1202: a=(ax < cx ? ax : cx);
1203: b=(ax > cx ? ax : cx);
1204: x=w=v=bx;
1205: fw=fv=fx=(*f)(x);
1206: for (iter=1;iter<=ITMAX;iter++) {
1207: xm=0.5*(a+b);
1208: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1209: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1210: printf(".");fflush(stdout);
1211: fprintf(ficlog,".");fflush(ficlog);
1212: #ifdef DEBUGBRENT
1213: 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);
1214: 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);
1215: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1216: #endif
1217: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1218: *xmin=x;
1219: return fx;
1220: }
1221: ftemp=fu;
1222: if (fabs(e) > tol1) {
1223: r=(x-w)*(fx-fv);
1224: q=(x-v)*(fx-fw);
1225: p=(x-v)*q-(x-w)*r;
1226: q=2.0*(q-r);
1227: if (q > 0.0) p = -p;
1228: q=fabs(q);
1229: etemp=e;
1230: e=d;
1231: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1232: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1233: else {
1234: d=p/q;
1235: u=x+d;
1236: if (u-a < tol2 || b-u < tol2)
1237: d=SIGN(tol1,xm-x);
1238: }
1239: } else {
1240: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1241: }
1242: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1243: fu=(*f)(u);
1244: if (fu <= fx) {
1245: if (u >= x) a=x; else b=x;
1246: SHFT(v,w,x,u)
1247: SHFT(fv,fw,fx,fu)
1248: } else {
1249: if (u < x) a=u; else b=u;
1250: if (fu <= fw || w == x) {
1251: v=w;
1252: w=u;
1253: fv=fw;
1254: fw=fu;
1255: } else if (fu <= fv || v == x || v == w) {
1256: v=u;
1257: fv=fu;
1258: }
1259: }
1260: }
1261: nrerror("Too many iterations in brent");
1262: *xmin=x;
1263: return fx;
1264: }
1265:
1266: /****************** mnbrak ***********************/
1267:
1268: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1269: double (*func)(double))
1270: {
1271: double ulim,u,r,q, dum;
1272: double fu;
1273:
1274: *fa=(*func)(*ax);
1275: *fb=(*func)(*bx);
1276: if (*fb > *fa) {
1277: SHFT(dum,*ax,*bx,dum)
1278: SHFT(dum,*fb,*fa,dum)
1279: }
1280: *cx=(*bx)+GOLD*(*bx-*ax);
1281: *fc=(*func)(*cx);
1282: while (*fb > *fc) { /* Declining fa, fb, fc */
1283: r=(*bx-*ax)*(*fb-*fc);
1284: q=(*bx-*cx)*(*fb-*fa);
1285: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1286: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1287: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
1288: if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
1289: fu=(*func)(u);
1290: #ifdef DEBUG
1291: /* f(x)=A(x-u)**2+f(u) */
1292: double A, fparabu;
1293: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1294: fparabu= *fa - A*(*ax-u)*(*ax-u);
1295: 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);
1296: 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);
1297: #endif
1298: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1299: fu=(*func)(u);
1300: if (fu < *fc) {
1301: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1302: SHFT(*fb,*fc,fu,(*func)(u))
1303: }
1304: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1305: u=ulim;
1306: fu=(*func)(u);
1307: } else {
1308: u=(*cx)+GOLD*(*cx-*bx);
1309: fu=(*func)(u);
1310: }
1311: SHFT(*ax,*bx,*cx,u)
1312: SHFT(*fa,*fb,*fc,fu)
1313: }
1314: }
1315:
1316: /*************** linmin ************************/
1317: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1318: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1319: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1320: the value of func at the returned location p . This is actually all accomplished by calling the
1321: routines mnbrak and brent .*/
1322: int ncom;
1323: double *pcom,*xicom;
1324: double (*nrfunc)(double []);
1325:
1326: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1327: {
1328: double brent(double ax, double bx, double cx,
1329: double (*f)(double), double tol, double *xmin);
1330: double f1dim(double x);
1331: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1332: double *fc, double (*func)(double));
1333: int j;
1334: double xx,xmin,bx,ax;
1335: double fx,fb,fa;
1336:
1337: ncom=n;
1338: pcom=vector(1,n);
1339: xicom=vector(1,n);
1340: nrfunc=func;
1341: for (j=1;j<=n;j++) {
1342: pcom[j]=p[j];
1343: xicom[j]=xi[j];
1344: }
1345: ax=0.0;
1346: xx=1.0;
1347: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
1348: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
1349: #ifdef DEBUG
1350: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1351: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1352: #endif
1353: for (j=1;j<=n;j++) {
1354: xi[j] *= xmin;
1355: p[j] += xi[j];
1356: }
1357: free_vector(xicom,1,n);
1358: free_vector(pcom,1,n);
1359: }
1360:
1361:
1362: /*************** powell ************************/
1363: /*
1364: Minimization of a function func of n variables. Input consists of an initial starting point
1365: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1366: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1367: such that failure to decrease by more than this amount on one iteration signals doneness. On
1368: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1369: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1370: */
1371: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1372: double (*func)(double []))
1373: {
1374: void linmin(double p[], double xi[], int n, double *fret,
1375: double (*func)(double []));
1376: int i,ibig,j;
1377: double del,t,*pt,*ptt,*xit;
1378: double fp,fptt;
1379: double *xits;
1380: int niterf, itmp;
1381:
1382: pt=vector(1,n);
1383: ptt=vector(1,n);
1384: xit=vector(1,n);
1385: xits=vector(1,n);
1386: *fret=(*func)(p);
1387: for (j=1;j<=n;j++) pt[j]=p[j];
1388: rcurr_time = time(NULL);
1389: for (*iter=1;;++(*iter)) {
1390: fp=(*fret);
1391: ibig=0;
1392: del=0.0;
1393: rlast_time=rcurr_time;
1394: /* (void) gettimeofday(&curr_time,&tzp); */
1395: rcurr_time = time(NULL);
1396: curr_time = *localtime(&rcurr_time);
1397: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1398: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1399: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1400: for (i=1;i<=n;i++) {
1401: printf(" %d %.12f",i, p[i]);
1402: fprintf(ficlog," %d %.12lf",i, p[i]);
1403: fprintf(ficrespow," %.12lf", p[i]);
1404: }
1405: printf("\n");
1406: fprintf(ficlog,"\n");
1407: fprintf(ficrespow,"\n");fflush(ficrespow);
1408: if(*iter <=3){
1409: tml = *localtime(&rcurr_time);
1410: strcpy(strcurr,asctime(&tml));
1411: rforecast_time=rcurr_time;
1412: itmp = strlen(strcurr);
1413: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1414: strcurr[itmp-1]='\0';
1415: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1416: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1417: for(niterf=10;niterf<=30;niterf+=10){
1418: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1419: forecast_time = *localtime(&rforecast_time);
1420: strcpy(strfor,asctime(&forecast_time));
1421: itmp = strlen(strfor);
1422: if(strfor[itmp-1]=='\n')
1423: strfor[itmp-1]='\0';
1424: 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);
1425: 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);
1426: }
1427: }
1428: for (i=1;i<=n;i++) {
1429: for (j=1;j<=n;j++) xit[j]=xi[j][i];
1430: fptt=(*fret);
1431: #ifdef DEBUG
1432: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1433: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1434: #endif
1435: printf("%d",i);fflush(stdout);
1436: fprintf(ficlog,"%d",i);fflush(ficlog);
1437: linmin(p,xit,n,fret,func);
1438: if (fabs(fptt-(*fret)) > del) {
1439: del=fabs(fptt-(*fret));
1440: ibig=i;
1441: }
1442: #ifdef DEBUG
1443: printf("%d %.12e",i,(*fret));
1444: fprintf(ficlog,"%d %.12e",i,(*fret));
1445: for (j=1;j<=n;j++) {
1446: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1447: printf(" x(%d)=%.12e",j,xit[j]);
1448: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1449: }
1450: for(j=1;j<=n;j++) {
1451: printf(" p(%d)=%.12e",j,p[j]);
1452: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1453: }
1454: printf("\n");
1455: fprintf(ficlog,"\n");
1456: #endif
1457: } /* end i */
1458: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
1459: #ifdef DEBUG
1460: int k[2],l;
1461: k[0]=1;
1462: k[1]=-1;
1463: printf("Max: %.12e",(*func)(p));
1464: fprintf(ficlog,"Max: %.12e",(*func)(p));
1465: for (j=1;j<=n;j++) {
1466: printf(" %.12e",p[j]);
1467: fprintf(ficlog," %.12e",p[j]);
1468: }
1469: printf("\n");
1470: fprintf(ficlog,"\n");
1471: for(l=0;l<=1;l++) {
1472: for (j=1;j<=n;j++) {
1473: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1474: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1475: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1476: }
1477: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1478: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1479: }
1480: #endif
1481:
1482:
1483: free_vector(xit,1,n);
1484: free_vector(xits,1,n);
1485: free_vector(ptt,1,n);
1486: free_vector(pt,1,n);
1487: return;
1488: }
1489: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1490: for (j=1;j<=n;j++) { /* Computes an extrapolated point */
1491: ptt[j]=2.0*p[j]-pt[j];
1492: xit[j]=p[j]-pt[j];
1493: pt[j]=p[j];
1494: }
1495: fptt=(*func)(ptt);
1496: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1497: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1498: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1499: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1500: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1501: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1502: /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
1503: /* Thus we compare delta(2h) with observed f1-f3 */
1504: /* or best gain on one ancient line 'del' with total */
1505: /* gain f1-f2 = f1 - f2 - 'del' with del */
1506: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1507:
1508: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
1509: t= t- del*SQR(fp-fptt);
1510: printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
1511: 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);
1512: #ifdef DEBUG
1513: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1514: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1515: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1516: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1517: 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);
1518: 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);
1519: #endif
1520: if (t < 0.0) { /* Then we use it for last direction */
1521: linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
1522: for (j=1;j<=n;j++) {
1523: xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
1524: xi[j][n]=xit[j]; /* and nth direction by the extrapolated */
1525: }
1526: printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1527: fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1528:
1529: #ifdef DEBUG
1530: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1531: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1532: for(j=1;j<=n;j++){
1533: printf(" %.12e",xit[j]);
1534: fprintf(ficlog," %.12e",xit[j]);
1535: }
1536: printf("\n");
1537: fprintf(ficlog,"\n");
1538: #endif
1539: } /* end of t negative */
1540: } /* end if (fptt < fp) */
1541: }
1542: }
1543:
1544: /**** Prevalence limit (stable or period prevalence) ****************/
1545:
1546: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1547: {
1548: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1549: matrix by transitions matrix until convergence is reached */
1550:
1551: int i, ii,j,k;
1552: double min, max, maxmin, maxmax,sumnew=0.;
1553: /* double **matprod2(); */ /* test */
1554: double **out, cov[NCOVMAX+1], **pmij();
1555: double **newm;
1556: double agefin, delaymax=50 ; /* Max number of years to converge */
1557:
1558: for (ii=1;ii<=nlstate+ndeath;ii++)
1559: for (j=1;j<=nlstate+ndeath;j++){
1560: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1561: }
1562:
1563: cov[1]=1.;
1564:
1565: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1566: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1567: newm=savm;
1568: /* Covariates have to be included here again */
1569: cov[2]=agefin;
1570:
1571: for (k=1; k<=cptcovn;k++) {
1572: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1573: /*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]]);*/
1574: }
1575: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1576: /* for (k=1; k<=cptcovprod;k++) /\* Useless *\/ */
1577: /* cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]]; */
1578:
1579: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1580: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1581: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1582: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1583: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1584: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1585:
1586: savm=oldm;
1587: oldm=newm;
1588: maxmax=0.;
1589: for(j=1;j<=nlstate;j++){
1590: min=1.;
1591: max=0.;
1592: for(i=1; i<=nlstate; i++) {
1593: sumnew=0;
1594: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1595: prlim[i][j]= newm[i][j]/(1-sumnew);
1596: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1597: max=FMAX(max,prlim[i][j]);
1598: min=FMIN(min,prlim[i][j]);
1599: }
1600: maxmin=max-min;
1601: maxmax=FMAX(maxmax,maxmin);
1602: } /* j loop */
1603: if(maxmax < ftolpl){
1604: return prlim;
1605: }
1606: } /* age loop */
1607: return prlim; /* should not reach here */
1608: }
1609:
1610: /*************** transition probabilities ***************/
1611:
1612: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1613: {
1614: /* According to parameters values stored in x and the covariate's values stored in cov,
1615: computes the probability to be observed in state j being in state i by appying the
1616: model to the ncovmodel covariates (including constant and age).
1617: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1618: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1619: ncth covariate in the global vector x is given by the formula:
1620: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1621: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1622: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1623: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1624: Outputs ps[i][j] the probability to be observed in j being in j according to
1625: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1626: */
1627: double s1, lnpijopii;
1628: /*double t34;*/
1629: int i,j, nc, ii, jj;
1630:
1631: for(i=1; i<= nlstate; i++){
1632: for(j=1; j<i;j++){
1633: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1634: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1635: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1636: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1637: }
1638: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1639: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1640: }
1641: for(j=i+1; j<=nlstate+ndeath;j++){
1642: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1643: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1644: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1645: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1646: }
1647: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1648: }
1649: }
1650:
1651: for(i=1; i<= nlstate; i++){
1652: s1=0;
1653: for(j=1; j<i; j++){
1654: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1655: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1656: }
1657: for(j=i+1; j<=nlstate+ndeath; j++){
1658: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1659: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1660: }
1661: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1662: ps[i][i]=1./(s1+1.);
1663: /* Computing other pijs */
1664: for(j=1; j<i; j++)
1665: ps[i][j]= exp(ps[i][j])*ps[i][i];
1666: for(j=i+1; j<=nlstate+ndeath; j++)
1667: ps[i][j]= exp(ps[i][j])*ps[i][i];
1668: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
1669: } /* end i */
1670:
1671: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
1672: for(jj=1; jj<= nlstate+ndeath; jj++){
1673: ps[ii][jj]=0;
1674: ps[ii][ii]=1;
1675: }
1676: }
1677:
1678:
1679: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
1680: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
1681: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
1682: /* } */
1683: /* printf("\n "); */
1684: /* } */
1685: /* printf("\n ");printf("%lf ",cov[2]);*/
1686: /*
1687: for(i=1; i<= npar; i++) printf("%f ",x[i]);
1688: goto end;*/
1689: return ps;
1690: }
1691:
1692: /**************** Product of 2 matrices ******************/
1693:
1694: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1695: {
1696: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
1697: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
1698: /* in, b, out are matrice of pointers which should have been initialized
1699: before: only the contents of out is modified. The function returns
1700: a pointer to pointers identical to out */
1701: int i, j, k;
1702: for(i=nrl; i<= nrh; i++)
1703: for(k=ncolol; k<=ncoloh; k++){
1704: out[i][k]=0.;
1705: for(j=ncl; j<=nch; j++)
1706: out[i][k] +=in[i][j]*b[j][k];
1707: }
1708: return out;
1709: }
1710:
1711:
1712: /************* Higher Matrix Product ***************/
1713:
1714: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
1715: {
1716: /* Computes the transition matrix starting at age 'age' over
1717: 'nhstepm*hstepm*stepm' months (i.e. until
1718: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
1719: nhstepm*hstepm matrices.
1720: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
1721: (typically every 2 years instead of every month which is too big
1722: for the memory).
1723: Model is determined by parameters x and covariates have to be
1724: included manually here.
1725:
1726: */
1727:
1728: int i, j, d, h, k;
1729: double **out, cov[NCOVMAX+1];
1730: double **newm;
1731:
1732: /* Hstepm could be zero and should return the unit matrix */
1733: for (i=1;i<=nlstate+ndeath;i++)
1734: for (j=1;j<=nlstate+ndeath;j++){
1735: oldm[i][j]=(i==j ? 1.0 : 0.0);
1736: po[i][j][0]=(i==j ? 1.0 : 0.0);
1737: }
1738: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1739: for(h=1; h <=nhstepm; h++){
1740: for(d=1; d <=hstepm; d++){
1741: newm=savm;
1742: /* Covariates have to be included here again */
1743: cov[1]=1.;
1744: cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
1745: for (k=1; k<=cptcovn;k++)
1746: cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1747: for (k=1; k<=cptcovage;k++)
1748: cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
1749: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1750: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1751:
1752:
1753: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
1754: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
1755: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
1756: pmij(pmmij,cov,ncovmodel,x,nlstate));
1757: savm=oldm;
1758: oldm=newm;
1759: }
1760: for(i=1; i<=nlstate+ndeath; i++)
1761: for(j=1;j<=nlstate+ndeath;j++) {
1762: po[i][j][h]=newm[i][j];
1763: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1764: }
1765: /*printf("h=%d ",h);*/
1766: } /* end h */
1767: /* printf("\n H=%d \n",h); */
1768: return po;
1769: }
1770:
1771: #ifdef NLOPT
1772: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
1773: double fret;
1774: double *xt;
1775: int j;
1776: myfunc_data *d2 = (myfunc_data *) pd;
1777: /* xt = (p1-1); */
1778: xt=vector(1,n);
1779: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
1780:
1781: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
1782: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
1783: printf("Function = %.12lf ",fret);
1784: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
1785: printf("\n");
1786: free_vector(xt,1,n);
1787: return fret;
1788: }
1789: #endif
1790:
1791: /*************** log-likelihood *************/
1792: double func( double *x)
1793: {
1794: int i, ii, j, k, mi, d, kk;
1795: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1796: double **out;
1797: double sw; /* Sum of weights */
1798: double lli; /* Individual log likelihood */
1799: int s1, s2;
1800: double bbh, survp;
1801: long ipmx;
1802: /*extern weight */
1803: /* We are differentiating ll according to initial status */
1804: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
1805: /*for(i=1;i<imx;i++)
1806: printf(" %d\n",s[4][i]);
1807: */
1808:
1809: ++countcallfunc;
1810:
1811: cov[1]=1.;
1812:
1813: for(k=1; k<=nlstate; k++) ll[k]=0.;
1814:
1815: if(mle==1){
1816: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1817: /* Computes the values of the ncovmodel covariates of the model
1818: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
1819: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
1820: to be observed in j being in i according to the model.
1821: */
1822: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1823: cov[2+k]=covar[Tvar[k]][i];
1824: }
1825: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1826: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1827: has been calculated etc */
1828: for(mi=1; mi<= wav[i]-1; mi++){
1829: for (ii=1;ii<=nlstate+ndeath;ii++)
1830: for (j=1;j<=nlstate+ndeath;j++){
1831: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1832: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1833: }
1834: for(d=0; d<dh[mi][i]; d++){
1835: newm=savm;
1836: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1837: for (kk=1; kk<=cptcovage;kk++) {
1838: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2]; /* Tage[kk] gives the data-covariate associated with age */
1839: }
1840: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1841: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1842: savm=oldm;
1843: oldm=newm;
1844: } /* end mult */
1845:
1846: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
1847: /* But now since version 0.9 we anticipate for bias at large stepm.
1848: * If stepm is larger than one month (smallest stepm) and if the exact delay
1849: * (in months) between two waves is not a multiple of stepm, we rounded to
1850: * the nearest (and in case of equal distance, to the lowest) interval but now
1851: * we keep into memory the bias bh[mi][i] and also the previous matrix product
1852: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
1853: * probability in order to take into account the bias as a fraction of the way
1854: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
1855: * -stepm/2 to stepm/2 .
1856: * For stepm=1 the results are the same as for previous versions of Imach.
1857: * For stepm > 1 the results are less biased than in previous versions.
1858: */
1859: s1=s[mw[mi][i]][i];
1860: s2=s[mw[mi+1][i]][i];
1861: bbh=(double)bh[mi][i]/(double)stepm;
1862: /* bias bh is positive if real duration
1863: * is higher than the multiple of stepm and negative otherwise.
1864: */
1865: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
1866: if( s2 > nlstate){
1867: /* i.e. if s2 is a death state and if the date of death is known
1868: then the contribution to the likelihood is the probability to
1869: die between last step unit time and current step unit time,
1870: which is also equal to probability to die before dh
1871: minus probability to die before dh-stepm .
1872: In version up to 0.92 likelihood was computed
1873: as if date of death was unknown. Death was treated as any other
1874: health state: the date of the interview describes the actual state
1875: and not the date of a change in health state. The former idea was
1876: to consider that at each interview the state was recorded
1877: (healthy, disable or death) and IMaCh was corrected; but when we
1878: introduced the exact date of death then we should have modified
1879: the contribution of an exact death to the likelihood. This new
1880: contribution is smaller and very dependent of the step unit
1881: stepm. It is no more the probability to die between last interview
1882: and month of death but the probability to survive from last
1883: interview up to one month before death multiplied by the
1884: probability to die within a month. Thanks to Chris
1885: Jackson for correcting this bug. Former versions increased
1886: mortality artificially. The bad side is that we add another loop
1887: which slows down the processing. The difference can be up to 10%
1888: lower mortality.
1889: */
1890: lli=log(out[s1][s2] - savm[s1][s2]);
1891:
1892:
1893: } else if (s2==-2) {
1894: for (j=1,survp=0. ; j<=nlstate; j++)
1895: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1896: /*survp += out[s1][j]; */
1897: lli= log(survp);
1898: }
1899:
1900: else if (s2==-4) {
1901: for (j=3,survp=0. ; j<=nlstate; j++)
1902: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1903: lli= log(survp);
1904: }
1905:
1906: else if (s2==-5) {
1907: for (j=1,survp=0. ; j<=2; j++)
1908: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
1909: lli= log(survp);
1910: }
1911:
1912: else{
1913: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
1914: /* 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 */
1915: }
1916: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
1917: /*if(lli ==000.0)*/
1918: /*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); */
1919: ipmx +=1;
1920: sw += weight[i];
1921: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1922: } /* end of wave */
1923: } /* end of individual */
1924: } else if(mle==2){
1925: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1926: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1927: for(mi=1; mi<= wav[i]-1; mi++){
1928: for (ii=1;ii<=nlstate+ndeath;ii++)
1929: for (j=1;j<=nlstate+ndeath;j++){
1930: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1931: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1932: }
1933: for(d=0; d<=dh[mi][i]; d++){
1934: newm=savm;
1935: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1936: for (kk=1; kk<=cptcovage;kk++) {
1937: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1938: }
1939: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1940: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1941: savm=oldm;
1942: oldm=newm;
1943: } /* end mult */
1944:
1945: s1=s[mw[mi][i]][i];
1946: s2=s[mw[mi+1][i]][i];
1947: bbh=(double)bh[mi][i]/(double)stepm;
1948: 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 */
1949: ipmx +=1;
1950: sw += weight[i];
1951: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1952: } /* end of wave */
1953: } /* end of individual */
1954: } else if(mle==3){ /* exponential inter-extrapolation */
1955: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1956: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1957: for(mi=1; mi<= wav[i]-1; mi++){
1958: for (ii=1;ii<=nlstate+ndeath;ii++)
1959: for (j=1;j<=nlstate+ndeath;j++){
1960: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1961: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1962: }
1963: for(d=0; d<dh[mi][i]; d++){
1964: newm=savm;
1965: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1966: for (kk=1; kk<=cptcovage;kk++) {
1967: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1968: }
1969: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1970: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1971: savm=oldm;
1972: oldm=newm;
1973: } /* end mult */
1974:
1975: s1=s[mw[mi][i]][i];
1976: s2=s[mw[mi+1][i]][i];
1977: bbh=(double)bh[mi][i]/(double)stepm;
1978: 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 */
1979: ipmx +=1;
1980: sw += weight[i];
1981: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1982: } /* end of wave */
1983: } /* end of individual */
1984: }else if (mle==4){ /* ml=4 no inter-extrapolation */
1985: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1986: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
1987: for(mi=1; mi<= wav[i]-1; mi++){
1988: for (ii=1;ii<=nlstate+ndeath;ii++)
1989: for (j=1;j<=nlstate+ndeath;j++){
1990: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1991: savm[ii][j]=(ii==j ? 1.0 : 0.0);
1992: }
1993: for(d=0; d<dh[mi][i]; d++){
1994: newm=savm;
1995: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1996: for (kk=1; kk<=cptcovage;kk++) {
1997: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
1998: }
1999:
2000: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2001: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2002: savm=oldm;
2003: oldm=newm;
2004: } /* end mult */
2005:
2006: s1=s[mw[mi][i]][i];
2007: s2=s[mw[mi+1][i]][i];
2008: if( s2 > nlstate){
2009: lli=log(out[s1][s2] - savm[s1][s2]);
2010: }else{
2011: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2012: }
2013: ipmx +=1;
2014: sw += weight[i];
2015: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2016: /* 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]); */
2017: } /* end of wave */
2018: } /* end of individual */
2019: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2020: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2021: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2022: for(mi=1; mi<= wav[i]-1; mi++){
2023: for (ii=1;ii<=nlstate+ndeath;ii++)
2024: for (j=1;j<=nlstate+ndeath;j++){
2025: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2026: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2027: }
2028: for(d=0; d<dh[mi][i]; d++){
2029: newm=savm;
2030: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2031: for (kk=1; kk<=cptcovage;kk++) {
2032: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2033: }
2034:
2035: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2036: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2037: savm=oldm;
2038: oldm=newm;
2039: } /* end mult */
2040:
2041: s1=s[mw[mi][i]][i];
2042: s2=s[mw[mi+1][i]][i];
2043: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2044: ipmx +=1;
2045: sw += weight[i];
2046: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2047: /*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]);*/
2048: } /* end of wave */
2049: } /* end of individual */
2050: } /* End of if */
2051: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2052: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2053: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2054: return -l;
2055: }
2056:
2057: /*************** log-likelihood *************/
2058: double funcone( double *x)
2059: {
2060: /* Same as likeli but slower because of a lot of printf and if */
2061: int i, ii, j, k, mi, d, kk;
2062: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2063: double **out;
2064: double lli; /* Individual log likelihood */
2065: double llt;
2066: int s1, s2;
2067: double bbh, survp;
2068: /*extern weight */
2069: /* We are differentiating ll according to initial status */
2070: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2071: /*for(i=1;i<imx;i++)
2072: printf(" %d\n",s[4][i]);
2073: */
2074: cov[1]=1.;
2075:
2076: for(k=1; k<=nlstate; k++) ll[k]=0.;
2077:
2078: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2079: for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
2080: for(mi=1; mi<= wav[i]-1; mi++){
2081: for (ii=1;ii<=nlstate+ndeath;ii++)
2082: for (j=1;j<=nlstate+ndeath;j++){
2083: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2084: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2085: }
2086: for(d=0; d<dh[mi][i]; d++){
2087: newm=savm;
2088: cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
2089: for (kk=1; kk<=cptcovage;kk++) {
2090: cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
2091: }
2092: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2093: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2094: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2095: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2096: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2097: savm=oldm;
2098: oldm=newm;
2099: } /* end mult */
2100:
2101: s1=s[mw[mi][i]][i];
2102: s2=s[mw[mi+1][i]][i];
2103: bbh=(double)bh[mi][i]/(double)stepm;
2104: /* bias is positive if real duration
2105: * is higher than the multiple of stepm and negative otherwise.
2106: */
2107: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2108: lli=log(out[s1][s2] - savm[s1][s2]);
2109: } else if (s2==-2) {
2110: for (j=1,survp=0. ; j<=nlstate; j++)
2111: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2112: lli= log(survp);
2113: }else if (mle==1){
2114: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2115: } else if(mle==2){
2116: 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 */
2117: } else if(mle==3){ /* exponential inter-extrapolation */
2118: 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 */
2119: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2120: lli=log(out[s1][s2]); /* Original formula */
2121: } else{ /* mle=0 back to 1 */
2122: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2123: /*lli=log(out[s1][s2]); */ /* Original formula */
2124: } /* End of if */
2125: ipmx +=1;
2126: sw += weight[i];
2127: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2128: /*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]); */
2129: if(globpr){
2130: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2131: %11.6f %11.6f %11.6f ", \
2132: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2133: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2134: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2135: llt +=ll[k]*gipmx/gsw;
2136: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2137: }
2138: fprintf(ficresilk," %10.6f\n", -llt);
2139: }
2140: } /* end of wave */
2141: } /* end of individual */
2142: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2143: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2144: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2145: if(globpr==0){ /* First time we count the contributions and weights */
2146: gipmx=ipmx;
2147: gsw=sw;
2148: }
2149: return -l;
2150: }
2151:
2152:
2153: /*************** function likelione ***********/
2154: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2155: {
2156: /* This routine should help understanding what is done with
2157: the selection of individuals/waves and
2158: to check the exact contribution to the likelihood.
2159: Plotting could be done.
2160: */
2161: int k;
2162:
2163: if(*globpri !=0){ /* Just counts and sums, no printings */
2164: strcpy(fileresilk,"ilk");
2165: strcat(fileresilk,fileres);
2166: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2167: printf("Problem with resultfile: %s\n", fileresilk);
2168: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2169: }
2170: 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");
2171: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2172: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2173: for(k=1; k<=nlstate; k++)
2174: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2175: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2176: }
2177:
2178: *fretone=(*funcone)(p);
2179: if(*globpri !=0){
2180: fclose(ficresilk);
2181: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2182: fflush(fichtm);
2183: }
2184: return;
2185: }
2186:
2187:
2188: /*********** Maximum Likelihood Estimation ***************/
2189:
2190: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2191: {
2192: int i,j, iter=0;
2193: double **xi;
2194: double fret;
2195: double fretone; /* Only one call to likelihood */
2196: /* char filerespow[FILENAMELENGTH];*/
2197:
2198: #ifdef NLOPT
2199: int creturn;
2200: nlopt_opt opt;
2201: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2202: double *lb;
2203: double minf; /* the minimum objective value, upon return */
2204: double * p1; /* Shifted parameters from 0 instead of 1 */
2205: myfunc_data dinst, *d = &dinst;
2206: #endif
2207:
2208:
2209: xi=matrix(1,npar,1,npar);
2210: for (i=1;i<=npar;i++)
2211: for (j=1;j<=npar;j++)
2212: xi[i][j]=(i==j ? 1.0 : 0.0);
2213: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2214: strcpy(filerespow,"pow");
2215: strcat(filerespow,fileres);
2216: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2217: printf("Problem with resultfile: %s\n", filerespow);
2218: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2219: }
2220: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2221: for (i=1;i<=nlstate;i++)
2222: for(j=1;j<=nlstate+ndeath;j++)
2223: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2224: fprintf(ficrespow,"\n");
2225: #ifdef POWELL
2226: powell(p,xi,npar,ftol,&iter,&fret,func);
2227: #endif
2228:
2229: #ifdef NLOPT
2230: #ifdef NEWUOA
2231: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2232: #else
2233: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2234: #endif
2235: lb=vector(0,npar-1);
2236: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2237: nlopt_set_lower_bounds(opt, lb);
2238: nlopt_set_initial_step1(opt, 0.1);
2239:
2240: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2241: d->function = func;
2242: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2243: nlopt_set_min_objective(opt, myfunc, d);
2244: nlopt_set_xtol_rel(opt, ftol);
2245: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2246: printf("nlopt failed! %d\n",creturn);
2247: }
2248: else {
2249: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2250: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2251: iter=1; /* not equal */
2252: }
2253: nlopt_destroy(opt);
2254: #endif
2255: free_matrix(xi,1,npar,1,npar);
2256: fclose(ficrespow);
2257: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2258: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2259: fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2260:
2261: }
2262:
2263: /**** Computes Hessian and covariance matrix ***/
2264: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2265: {
2266: double **a,**y,*x,pd;
2267: double **hess;
2268: int i, j;
2269: int *indx;
2270:
2271: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2272: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2273: void lubksb(double **a, int npar, int *indx, double b[]) ;
2274: void ludcmp(double **a, int npar, int *indx, double *d) ;
2275: double gompertz(double p[]);
2276: hess=matrix(1,npar,1,npar);
2277:
2278: printf("\nCalculation of the hessian matrix. Wait...\n");
2279: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2280: for (i=1;i<=npar;i++){
2281: printf("%d",i);fflush(stdout);
2282: fprintf(ficlog,"%d",i);fflush(ficlog);
2283:
2284: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2285:
2286: /* printf(" %f ",p[i]);
2287: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2288: }
2289:
2290: for (i=1;i<=npar;i++) {
2291: for (j=1;j<=npar;j++) {
2292: if (j>i) {
2293: printf(".%d%d",i,j);fflush(stdout);
2294: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2295: hess[i][j]=hessij(p,delti,i,j,func,npar);
2296:
2297: hess[j][i]=hess[i][j];
2298: /*printf(" %lf ",hess[i][j]);*/
2299: }
2300: }
2301: }
2302: printf("\n");
2303: fprintf(ficlog,"\n");
2304:
2305: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2306: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2307:
2308: a=matrix(1,npar,1,npar);
2309: y=matrix(1,npar,1,npar);
2310: x=vector(1,npar);
2311: indx=ivector(1,npar);
2312: for (i=1;i<=npar;i++)
2313: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2314: ludcmp(a,npar,indx,&pd);
2315:
2316: for (j=1;j<=npar;j++) {
2317: for (i=1;i<=npar;i++) x[i]=0;
2318: x[j]=1;
2319: lubksb(a,npar,indx,x);
2320: for (i=1;i<=npar;i++){
2321: matcov[i][j]=x[i];
2322: }
2323: }
2324:
2325: printf("\n#Hessian matrix#\n");
2326: fprintf(ficlog,"\n#Hessian matrix#\n");
2327: for (i=1;i<=npar;i++) {
2328: for (j=1;j<=npar;j++) {
2329: printf("%.3e ",hess[i][j]);
2330: fprintf(ficlog,"%.3e ",hess[i][j]);
2331: }
2332: printf("\n");
2333: fprintf(ficlog,"\n");
2334: }
2335:
2336: /* Recompute Inverse */
2337: for (i=1;i<=npar;i++)
2338: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2339: ludcmp(a,npar,indx,&pd);
2340:
2341: /* printf("\n#Hessian matrix recomputed#\n");
2342:
2343: for (j=1;j<=npar;j++) {
2344: for (i=1;i<=npar;i++) x[i]=0;
2345: x[j]=1;
2346: lubksb(a,npar,indx,x);
2347: for (i=1;i<=npar;i++){
2348: y[i][j]=x[i];
2349: printf("%.3e ",y[i][j]);
2350: fprintf(ficlog,"%.3e ",y[i][j]);
2351: }
2352: printf("\n");
2353: fprintf(ficlog,"\n");
2354: }
2355: */
2356:
2357: free_matrix(a,1,npar,1,npar);
2358: free_matrix(y,1,npar,1,npar);
2359: free_vector(x,1,npar);
2360: free_ivector(indx,1,npar);
2361: free_matrix(hess,1,npar,1,npar);
2362:
2363:
2364: }
2365:
2366: /*************** hessian matrix ****************/
2367: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2368: {
2369: int i;
2370: int l=1, lmax=20;
2371: double k1,k2;
2372: double p2[MAXPARM+1]; /* identical to x */
2373: double res;
2374: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2375: double fx;
2376: int k=0,kmax=10;
2377: double l1;
2378:
2379: fx=func(x);
2380: for (i=1;i<=npar;i++) p2[i]=x[i];
2381: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2382: l1=pow(10,l);
2383: delts=delt;
2384: for(k=1 ; k <kmax; k=k+1){
2385: delt = delta*(l1*k);
2386: p2[theta]=x[theta] +delt;
2387: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2388: p2[theta]=x[theta]-delt;
2389: k2=func(p2)-fx;
2390: /*res= (k1-2.0*fx+k2)/delt/delt; */
2391: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2392:
2393: #ifdef DEBUGHESS
2394: 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);
2395: 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);
2396: #endif
2397: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2398: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2399: k=kmax;
2400: }
2401: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2402: k=kmax; l=lmax*10;
2403: }
2404: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2405: delts=delt;
2406: }
2407: }
2408: }
2409: delti[theta]=delts;
2410: return res;
2411:
2412: }
2413:
2414: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2415: {
2416: int i;
2417: int l=1, lmax=20;
2418: double k1,k2,k3,k4,res,fx;
2419: double p2[MAXPARM+1];
2420: int k;
2421:
2422: fx=func(x);
2423: for (k=1; k<=2; k++) {
2424: for (i=1;i<=npar;i++) p2[i]=x[i];
2425: p2[thetai]=x[thetai]+delti[thetai]/k;
2426: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2427: k1=func(p2)-fx;
2428:
2429: p2[thetai]=x[thetai]+delti[thetai]/k;
2430: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2431: k2=func(p2)-fx;
2432:
2433: p2[thetai]=x[thetai]-delti[thetai]/k;
2434: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2435: k3=func(p2)-fx;
2436:
2437: p2[thetai]=x[thetai]-delti[thetai]/k;
2438: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2439: k4=func(p2)-fx;
2440: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2441: #ifdef DEBUG
2442: 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);
2443: 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);
2444: #endif
2445: }
2446: return res;
2447: }
2448:
2449: /************** Inverse of matrix **************/
2450: void ludcmp(double **a, int n, int *indx, double *d)
2451: {
2452: int i,imax,j,k;
2453: double big,dum,sum,temp;
2454: double *vv;
2455:
2456: vv=vector(1,n);
2457: *d=1.0;
2458: for (i=1;i<=n;i++) {
2459: big=0.0;
2460: for (j=1;j<=n;j++)
2461: if ((temp=fabs(a[i][j])) > big) big=temp;
2462: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2463: vv[i]=1.0/big;
2464: }
2465: for (j=1;j<=n;j++) {
2466: for (i=1;i<j;i++) {
2467: sum=a[i][j];
2468: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2469: a[i][j]=sum;
2470: }
2471: big=0.0;
2472: for (i=j;i<=n;i++) {
2473: sum=a[i][j];
2474: for (k=1;k<j;k++)
2475: sum -= a[i][k]*a[k][j];
2476: a[i][j]=sum;
2477: if ( (dum=vv[i]*fabs(sum)) >= big) {
2478: big=dum;
2479: imax=i;
2480: }
2481: }
2482: if (j != imax) {
2483: for (k=1;k<=n;k++) {
2484: dum=a[imax][k];
2485: a[imax][k]=a[j][k];
2486: a[j][k]=dum;
2487: }
2488: *d = -(*d);
2489: vv[imax]=vv[j];
2490: }
2491: indx[j]=imax;
2492: if (a[j][j] == 0.0) a[j][j]=TINY;
2493: if (j != n) {
2494: dum=1.0/(a[j][j]);
2495: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2496: }
2497: }
2498: free_vector(vv,1,n); /* Doesn't work */
2499: ;
2500: }
2501:
2502: void lubksb(double **a, int n, int *indx, double b[])
2503: {
2504: int i,ii=0,ip,j;
2505: double sum;
2506:
2507: for (i=1;i<=n;i++) {
2508: ip=indx[i];
2509: sum=b[ip];
2510: b[ip]=b[i];
2511: if (ii)
2512: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2513: else if (sum) ii=i;
2514: b[i]=sum;
2515: }
2516: for (i=n;i>=1;i--) {
2517: sum=b[i];
2518: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2519: b[i]=sum/a[i][i];
2520: }
2521: }
2522:
2523: void pstamp(FILE *fichier)
2524: {
2525: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2526: }
2527:
2528: /************ Frequencies ********************/
2529: 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[])
2530: { /* Some frequencies */
2531:
2532: int i, m, jk, j1, bool, z1,j;
2533: int first;
2534: double ***freq; /* Frequencies */
2535: double *pp, **prop;
2536: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2537: char fileresp[FILENAMELENGTH];
2538:
2539: pp=vector(1,nlstate);
2540: prop=matrix(1,nlstate,iagemin,iagemax+3);
2541: strcpy(fileresp,"p");
2542: strcat(fileresp,fileres);
2543: if((ficresp=fopen(fileresp,"w"))==NULL) {
2544: printf("Problem with prevalence resultfile: %s\n", fileresp);
2545: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2546: exit(0);
2547: }
2548: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2549: j1=0;
2550:
2551: j=cptcoveff;
2552: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2553:
2554: first=1;
2555:
2556: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2557: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2558: /* j1++; */
2559: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2560: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2561: scanf("%d", i);*/
2562: for (i=-5; i<=nlstate+ndeath; i++)
2563: for (jk=-5; jk<=nlstate+ndeath; jk++)
2564: for(m=iagemin; m <= iagemax+3; m++)
2565: freq[i][jk][m]=0;
2566:
2567: for (i=1; i<=nlstate; i++)
2568: for(m=iagemin; m <= iagemax+3; m++)
2569: prop[i][m]=0;
2570:
2571: dateintsum=0;
2572: k2cpt=0;
2573: for (i=1; i<=imx; i++) {
2574: bool=1;
2575: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2576: for (z1=1; z1<=cptcoveff; z1++)
2577: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2578: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2579: bool=0;
2580: /* 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",
2581: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2582: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2583: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2584: }
2585: }
2586:
2587: if (bool==1){
2588: for(m=firstpass; m<=lastpass; m++){
2589: k2=anint[m][i]+(mint[m][i]/12.);
2590: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2591: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2592: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2593: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2594: if (m<lastpass) {
2595: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2596: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2597: }
2598:
2599: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2600: dateintsum=dateintsum+k2;
2601: k2cpt++;
2602: }
2603: /*}*/
2604: }
2605: }
2606: } /* end i */
2607:
2608: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2609: pstamp(ficresp);
2610: if (cptcovn>0) {
2611: fprintf(ficresp, "\n#********** Variable ");
2612: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2613: fprintf(ficresp, "**********\n#");
2614: fprintf(ficlog, "\n#********** Variable ");
2615: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2616: fprintf(ficlog, "**********\n#");
2617: }
2618: for(i=1; i<=nlstate;i++)
2619: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
2620: fprintf(ficresp, "\n");
2621:
2622: for(i=iagemin; i <= iagemax+3; i++){
2623: if(i==iagemax+3){
2624: fprintf(ficlog,"Total");
2625: }else{
2626: if(first==1){
2627: first=0;
2628: printf("See log file for details...\n");
2629: }
2630: fprintf(ficlog,"Age %d", i);
2631: }
2632: for(jk=1; jk <=nlstate ; jk++){
2633: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
2634: pp[jk] += freq[jk][m][i];
2635: }
2636: for(jk=1; jk <=nlstate ; jk++){
2637: for(m=-1, pos=0; m <=0 ; m++)
2638: pos += freq[jk][m][i];
2639: if(pp[jk]>=1.e-10){
2640: if(first==1){
2641: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2642: }
2643: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
2644: }else{
2645: if(first==1)
2646: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2647: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
2648: }
2649: }
2650:
2651: for(jk=1; jk <=nlstate ; jk++){
2652: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
2653: pp[jk] += freq[jk][m][i];
2654: }
2655: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
2656: pos += pp[jk];
2657: posprop += prop[jk][i];
2658: }
2659: for(jk=1; jk <=nlstate ; jk++){
2660: if(pos>=1.e-5){
2661: if(first==1)
2662: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2663: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
2664: }else{
2665: if(first==1)
2666: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2667: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
2668: }
2669: if( i <= iagemax){
2670: if(pos>=1.e-5){
2671: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
2672: /*probs[i][jk][j1]= pp[jk]/pos;*/
2673: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
2674: }
2675: else
2676: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
2677: }
2678: }
2679:
2680: for(jk=-1; jk <=nlstate+ndeath; jk++)
2681: for(m=-1; m <=nlstate+ndeath; m++)
2682: if(freq[jk][m][i] !=0 ) {
2683: if(first==1)
2684: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
2685: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
2686: }
2687: if(i <= iagemax)
2688: fprintf(ficresp,"\n");
2689: if(first==1)
2690: printf("Others in log...\n");
2691: fprintf(ficlog,"\n");
2692: }
2693: /*}*/
2694: }
2695: dateintmean=dateintsum/k2cpt;
2696:
2697: fclose(ficresp);
2698: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
2699: free_vector(pp,1,nlstate);
2700: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
2701: /* End of Freq */
2702: }
2703:
2704: /************ Prevalence ********************/
2705: 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)
2706: {
2707: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
2708: in each health status at the date of interview (if between dateprev1 and dateprev2).
2709: We still use firstpass and lastpass as another selection.
2710: */
2711:
2712: int i, m, jk, j1, bool, z1,j;
2713:
2714: double **prop;
2715: double posprop;
2716: double y2; /* in fractional years */
2717: int iagemin, iagemax;
2718: int first; /** to stop verbosity which is redirected to log file */
2719:
2720: iagemin= (int) agemin;
2721: iagemax= (int) agemax;
2722: /*pp=vector(1,nlstate);*/
2723: prop=matrix(1,nlstate,iagemin,iagemax+3);
2724: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
2725: j1=0;
2726:
2727: /*j=cptcoveff;*/
2728: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2729:
2730: first=1;
2731: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
2732: /*for(i1=1; i1<=ncodemax[k1];i1++){
2733: j1++;*/
2734:
2735: for (i=1; i<=nlstate; i++)
2736: for(m=iagemin; m <= iagemax+3; m++)
2737: prop[i][m]=0.0;
2738:
2739: for (i=1; i<=imx; i++) { /* Each individual */
2740: bool=1;
2741: if (cptcovn>0) {
2742: for (z1=1; z1<=cptcoveff; z1++)
2743: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
2744: bool=0;
2745: }
2746: if (bool==1) {
2747: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
2748: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
2749: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
2750: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2751: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2752: 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);
2753: if (s[m][i]>0 && s[m][i]<=nlstate) {
2754: /*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]]);*/
2755: prop[s[m][i]][(int)agev[m][i]] += weight[i];
2756: prop[s[m][i]][iagemax+3] += weight[i];
2757: }
2758: }
2759: } /* end selection of waves */
2760: }
2761: }
2762: for(i=iagemin; i <= iagemax+3; i++){
2763: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
2764: posprop += prop[jk][i];
2765: }
2766:
2767: for(jk=1; jk <=nlstate ; jk++){
2768: if( i <= iagemax){
2769: if(posprop>=1.e-5){
2770: probs[i][jk][j1]= prop[jk][i]/posprop;
2771: } else{
2772: if(first==1){
2773: first=0;
2774: 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]);
2775: }
2776: }
2777: }
2778: }/* end jk */
2779: }/* end i */
2780: /*} *//* end i1 */
2781: } /* end j1 */
2782:
2783: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
2784: /*free_vector(pp,1,nlstate);*/
2785: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
2786: } /* End of prevalence */
2787:
2788: /************* Waves Concatenation ***************/
2789:
2790: 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)
2791: {
2792: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
2793: Death is a valid wave (if date is known).
2794: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
2795: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2796: and mw[mi+1][i]. dh depends on stepm.
2797: */
2798:
2799: int i, mi, m;
2800: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
2801: double sum=0., jmean=0.;*/
2802: int first;
2803: int j, k=0,jk, ju, jl;
2804: double sum=0.;
2805: first=0;
2806: jmin=100000;
2807: jmax=-1;
2808: jmean=0.;
2809: for(i=1; i<=imx; i++){
2810: mi=0;
2811: m=firstpass;
2812: while(s[m][i] <= nlstate){
2813: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
2814: mw[++mi][i]=m;
2815: if(m >=lastpass)
2816: break;
2817: else
2818: m++;
2819: }/* end while */
2820: if (s[m][i] > nlstate){
2821: mi++; /* Death is another wave */
2822: /* if(mi==0) never been interviewed correctly before death */
2823: /* Only death is a correct wave */
2824: mw[mi][i]=m;
2825: }
2826:
2827: wav[i]=mi;
2828: if(mi==0){
2829: nbwarn++;
2830: if(first==0){
2831: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
2832: first=1;
2833: }
2834: if(first==1){
2835: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
2836: }
2837: } /* end mi==0 */
2838: } /* End individuals */
2839:
2840: for(i=1; i<=imx; i++){
2841: for(mi=1; mi<wav[i];mi++){
2842: if (stepm <=0)
2843: dh[mi][i]=1;
2844: else{
2845: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
2846: if (agedc[i] < 2*AGESUP) {
2847: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
2848: if(j==0) j=1; /* Survives at least one month after exam */
2849: else if(j<0){
2850: nberr++;
2851: 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]);
2852: j=1; /* Temporary Dangerous patch */
2853: 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);
2854: 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]);
2855: 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);
2856: }
2857: k=k+1;
2858: if (j >= jmax){
2859: jmax=j;
2860: ijmax=i;
2861: }
2862: if (j <= jmin){
2863: jmin=j;
2864: ijmin=i;
2865: }
2866: sum=sum+j;
2867: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
2868: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
2869: }
2870: }
2871: else{
2872: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
2873: /* 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]); */
2874:
2875: k=k+1;
2876: if (j >= jmax) {
2877: jmax=j;
2878: ijmax=i;
2879: }
2880: else if (j <= jmin){
2881: jmin=j;
2882: ijmin=i;
2883: }
2884: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
2885: /*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]);*/
2886: if(j<0){
2887: nberr++;
2888: 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]);
2889: 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]);
2890: }
2891: sum=sum+j;
2892: }
2893: jk= j/stepm;
2894: jl= j -jk*stepm;
2895: ju= j -(jk+1)*stepm;
2896: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
2897: if(jl==0){
2898: dh[mi][i]=jk;
2899: bh[mi][i]=0;
2900: }else{ /* We want a negative bias in order to only have interpolation ie
2901: * to avoid the price of an extra matrix product in likelihood */
2902: dh[mi][i]=jk+1;
2903: bh[mi][i]=ju;
2904: }
2905: }else{
2906: if(jl <= -ju){
2907: dh[mi][i]=jk;
2908: bh[mi][i]=jl; /* bias is positive if real duration
2909: * is higher than the multiple of stepm and negative otherwise.
2910: */
2911: }
2912: else{
2913: dh[mi][i]=jk+1;
2914: bh[mi][i]=ju;
2915: }
2916: if(dh[mi][i]==0){
2917: dh[mi][i]=1; /* At least one step */
2918: bh[mi][i]=ju; /* At least one step */
2919: /* 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);*/
2920: }
2921: } /* end if mle */
2922: }
2923: } /* end wave */
2924: }
2925: jmean=sum/k;
2926: 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);
2927: 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);
2928: }
2929:
2930: /*********** Tricode ****************************/
2931: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
2932: {
2933: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
2934: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
2935: * Boring subroutine which should only output nbcode[Tvar[j]][k]
2936: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
2937: * nbcode[Tvar[j]][1]=
2938: */
2939:
2940: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
2941: int modmaxcovj=0; /* Modality max of covariates j */
2942: int cptcode=0; /* Modality max of covariates j */
2943: int modmincovj=0; /* Modality min of covariates j */
2944:
2945:
2946: cptcoveff=0;
2947:
2948: for (k=-1; k < maxncov; k++) Ndum[k]=0;
2949: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
2950:
2951: /* Loop on covariates without age and products */
2952: for (j=1; j<=(cptcovs); j++) { /* model V1 + V2*age+ V3 + V3*V4 : V1 + V3 = 2 only */
2953: for (i=1; i<=imx; i++) { /* Lopp on individuals: reads the data file to get the maximum value of the
2954: modality of this covariate Vj*/
2955: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
2956: * If product of Vn*Vm, still boolean *:
2957: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
2958: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
2959: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
2960: modality of the nth covariate of individual i. */
2961: if (ij > modmaxcovj)
2962: modmaxcovj=ij;
2963: else if (ij < modmincovj)
2964: modmincovj=ij;
2965: if ((ij < -1) && (ij > NCOVMAX)){
2966: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
2967: exit(1);
2968: }else
2969: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
2970: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
2971: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
2972: /* getting the maximum value of the modality of the covariate
2973: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
2974: female is 1, then modmaxcovj=1.*/
2975: }
2976: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
2977: cptcode=modmaxcovj;
2978: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
2979: /*for (i=0; i<=cptcode; i++) {*/
2980: for (i=modmincovj; i<=modmaxcovj; i++) { /* i=-1 ? 0 and 1*//* For each value of the modality of model-cov j */
2981: printf("Frequencies of covariates %d V%d %d\n", j, Tvar[j], Ndum[i]);
2982: if( Ndum[i] != 0 ){ /* Counts if nobody answered, empty modality */
2983: ncodemax[j]++; /* ncodemax[j]= Number of non-null modalities of the j th covariate. */
2984: }
2985: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
2986: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
2987: } /* Ndum[-1] number of undefined modalities */
2988:
2989: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
2990: /* For covariate j, modalities could be 1, 2, 3, 4. If Ndum[2]=0 ncodemax[j] is not 4 but 3 */
2991: /* If Ndum[3}= 635; Ndum[4]=0; Ndum[5]=0; Ndum[6]=27; Ndum[7]=125;
2992: modmincovj=3; modmaxcovj = 7;
2993: There are only 3 modalities non empty (or 2 if 27 is too few) : ncodemax[j]=3;
2994: which will be coded 0, 1, 2 which in binary on 3-1 digits are 0=00 1=01, 2=10; defining two dummy
2995: variables V1_1 and V1_2.
2996: nbcode[Tvar[j]][ij]=k;
2997: nbcode[Tvar[j]][1]=0;
2998: nbcode[Tvar[j]][2]=1;
2999: nbcode[Tvar[j]][3]=2;
3000: */
3001: ij=1; /* ij is similar to i but can jumps over null modalities */
3002: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 */
3003: for (k=0; k<= cptcode; k++) { /* k=-1 ? k=0 to 1 *//* Could be 1 to 4 */
3004: /*recode from 0 */
3005: if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
3006: nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
3007: k is a modality. If we have model=V1+V1*sex
3008: then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3009: ij++;
3010: }
3011: if (ij > ncodemax[j]) break;
3012: } /* end of loop on */
3013: } /* end of loop on modality */
3014: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3015:
3016: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3017:
3018: for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
3019: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3020: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3021: Ndum[ij]++;
3022: }
3023:
3024: ij=1;
3025: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3026: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3027: if((Ndum[i]!=0) && (i<=ncovcol)){
3028: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3029: Tvaraff[ij]=i; /*For printing (unclear) */
3030: ij++;
3031: }else
3032: Tvaraff[ij]=0;
3033: }
3034: ij--;
3035: cptcoveff=ij; /*Number of total covariates*/
3036:
3037: }
3038:
3039:
3040: /*********** Health Expectancies ****************/
3041:
3042: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3043:
3044: {
3045: /* Health expectancies, no variances */
3046: int i, j, nhstepm, hstepm, h, nstepm;
3047: int nhstepma, nstepma; /* Decreasing with age */
3048: double age, agelim, hf;
3049: double ***p3mat;
3050: double eip;
3051:
3052: pstamp(ficreseij);
3053: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3054: fprintf(ficreseij,"# Age");
3055: for(i=1; i<=nlstate;i++){
3056: for(j=1; j<=nlstate;j++){
3057: fprintf(ficreseij," e%1d%1d ",i,j);
3058: }
3059: fprintf(ficreseij," e%1d. ",i);
3060: }
3061: fprintf(ficreseij,"\n");
3062:
3063:
3064: if(estepm < stepm){
3065: printf ("Problem %d lower than %d\n",estepm, stepm);
3066: }
3067: else hstepm=estepm;
3068: /* We compute the life expectancy from trapezoids spaced every estepm months
3069: * This is mainly to measure the difference between two models: for example
3070: * if stepm=24 months pijx are given only every 2 years and by summing them
3071: * we are calculating an estimate of the Life Expectancy assuming a linear
3072: * progression in between and thus overestimating or underestimating according
3073: * to the curvature of the survival function. If, for the same date, we
3074: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3075: * to compare the new estimate of Life expectancy with the same linear
3076: * hypothesis. A more precise result, taking into account a more precise
3077: * curvature will be obtained if estepm is as small as stepm. */
3078:
3079: /* For example we decided to compute the life expectancy with the smallest unit */
3080: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3081: nhstepm is the number of hstepm from age to agelim
3082: nstepm is the number of stepm from age to agelin.
3083: Look at hpijx to understand the reason of that which relies in memory size
3084: and note for a fixed period like estepm months */
3085: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3086: survival function given by stepm (the optimization length). Unfortunately it
3087: means that if the survival funtion is printed only each two years of age and if
3088: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3089: results. So we changed our mind and took the option of the best precision.
3090: */
3091: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3092:
3093: agelim=AGESUP;
3094: /* If stepm=6 months */
3095: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3096: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3097:
3098: /* nhstepm age range expressed in number of stepm */
3099: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3100: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3101: /* if (stepm >= YEARM) hstepm=1;*/
3102: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3103: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3104:
3105: for (age=bage; age<=fage; age ++){
3106: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3107: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3108: /* if (stepm >= YEARM) hstepm=1;*/
3109: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3110:
3111: /* If stepm=6 months */
3112: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3113: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3114:
3115: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3116:
3117: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3118:
3119: printf("%d|",(int)age);fflush(stdout);
3120: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3121:
3122: /* Computing expectancies */
3123: for(i=1; i<=nlstate;i++)
3124: for(j=1; j<=nlstate;j++)
3125: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3126: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3127:
3128: /* 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]);*/
3129:
3130: }
3131:
3132: fprintf(ficreseij,"%3.0f",age );
3133: for(i=1; i<=nlstate;i++){
3134: eip=0;
3135: for(j=1; j<=nlstate;j++){
3136: eip +=eij[i][j][(int)age];
3137: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3138: }
3139: fprintf(ficreseij,"%9.4f", eip );
3140: }
3141: fprintf(ficreseij,"\n");
3142:
3143: }
3144: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3145: printf("\n");
3146: fprintf(ficlog,"\n");
3147:
3148: }
3149:
3150: 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[] )
3151:
3152: {
3153: /* Covariances of health expectancies eij and of total life expectancies according
3154: to initial status i, ei. .
3155: */
3156: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3157: int nhstepma, nstepma; /* Decreasing with age */
3158: double age, agelim, hf;
3159: double ***p3matp, ***p3matm, ***varhe;
3160: double **dnewm,**doldm;
3161: double *xp, *xm;
3162: double **gp, **gm;
3163: double ***gradg, ***trgradg;
3164: int theta;
3165:
3166: double eip, vip;
3167:
3168: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3169: xp=vector(1,npar);
3170: xm=vector(1,npar);
3171: dnewm=matrix(1,nlstate*nlstate,1,npar);
3172: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3173:
3174: pstamp(ficresstdeij);
3175: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3176: fprintf(ficresstdeij,"# Age");
3177: for(i=1; i<=nlstate;i++){
3178: for(j=1; j<=nlstate;j++)
3179: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3180: fprintf(ficresstdeij," e%1d. ",i);
3181: }
3182: fprintf(ficresstdeij,"\n");
3183:
3184: pstamp(ficrescveij);
3185: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3186: fprintf(ficrescveij,"# Age");
3187: for(i=1; i<=nlstate;i++)
3188: for(j=1; j<=nlstate;j++){
3189: cptj= (j-1)*nlstate+i;
3190: for(i2=1; i2<=nlstate;i2++)
3191: for(j2=1; j2<=nlstate;j2++){
3192: cptj2= (j2-1)*nlstate+i2;
3193: if(cptj2 <= cptj)
3194: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3195: }
3196: }
3197: fprintf(ficrescveij,"\n");
3198:
3199: if(estepm < stepm){
3200: printf ("Problem %d lower than %d\n",estepm, stepm);
3201: }
3202: else hstepm=estepm;
3203: /* We compute the life expectancy from trapezoids spaced every estepm months
3204: * This is mainly to measure the difference between two models: for example
3205: * if stepm=24 months pijx are given only every 2 years and by summing them
3206: * we are calculating an estimate of the Life Expectancy assuming a linear
3207: * progression in between and thus overestimating or underestimating according
3208: * to the curvature of the survival function. If, for the same date, we
3209: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3210: * to compare the new estimate of Life expectancy with the same linear
3211: * hypothesis. A more precise result, taking into account a more precise
3212: * curvature will be obtained if estepm is as small as stepm. */
3213:
3214: /* For example we decided to compute the life expectancy with the smallest unit */
3215: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3216: nhstepm is the number of hstepm from age to agelim
3217: nstepm is the number of stepm from age to agelin.
3218: Look at hpijx to understand the reason of that which relies in memory size
3219: and note for a fixed period like estepm months */
3220: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3221: survival function given by stepm (the optimization length). Unfortunately it
3222: means that if the survival funtion is printed only each two years of age and if
3223: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3224: results. So we changed our mind and took the option of the best precision.
3225: */
3226: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3227:
3228: /* If stepm=6 months */
3229: /* nhstepm age range expressed in number of stepm */
3230: agelim=AGESUP;
3231: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3232: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3233: /* if (stepm >= YEARM) hstepm=1;*/
3234: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3235:
3236: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3237: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3238: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3239: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3240: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3241: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3242:
3243: for (age=bage; age<=fage; age ++){
3244: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3245: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3246: /* if (stepm >= YEARM) hstepm=1;*/
3247: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3248:
3249: /* If stepm=6 months */
3250: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3251: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3252:
3253: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3254:
3255: /* Computing Variances of health expectancies */
3256: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3257: decrease memory allocation */
3258: for(theta=1; theta <=npar; theta++){
3259: for(i=1; i<=npar; i++){
3260: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3261: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3262: }
3263: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3264: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3265:
3266: for(j=1; j<= nlstate; j++){
3267: for(i=1; i<=nlstate; i++){
3268: for(h=0; h<=nhstepm-1; h++){
3269: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3270: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3271: }
3272: }
3273: }
3274:
3275: for(ij=1; ij<= nlstate*nlstate; ij++)
3276: for(h=0; h<=nhstepm-1; h++){
3277: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3278: }
3279: }/* End theta */
3280:
3281:
3282: for(h=0; h<=nhstepm-1; h++)
3283: for(j=1; j<=nlstate*nlstate;j++)
3284: for(theta=1; theta <=npar; theta++)
3285: trgradg[h][j][theta]=gradg[h][theta][j];
3286:
3287:
3288: for(ij=1;ij<=nlstate*nlstate;ij++)
3289: for(ji=1;ji<=nlstate*nlstate;ji++)
3290: varhe[ij][ji][(int)age] =0.;
3291:
3292: printf("%d|",(int)age);fflush(stdout);
3293: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3294: for(h=0;h<=nhstepm-1;h++){
3295: for(k=0;k<=nhstepm-1;k++){
3296: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3297: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3298: for(ij=1;ij<=nlstate*nlstate;ij++)
3299: for(ji=1;ji<=nlstate*nlstate;ji++)
3300: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3301: }
3302: }
3303:
3304: /* Computing expectancies */
3305: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3306: for(i=1; i<=nlstate;i++)
3307: for(j=1; j<=nlstate;j++)
3308: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3309: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3310:
3311: /* 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]);*/
3312:
3313: }
3314:
3315: fprintf(ficresstdeij,"%3.0f",age );
3316: for(i=1; i<=nlstate;i++){
3317: eip=0.;
3318: vip=0.;
3319: for(j=1; j<=nlstate;j++){
3320: eip += eij[i][j][(int)age];
3321: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3322: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3323: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3324: }
3325: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3326: }
3327: fprintf(ficresstdeij,"\n");
3328:
3329: fprintf(ficrescveij,"%3.0f",age );
3330: for(i=1; i<=nlstate;i++)
3331: for(j=1; j<=nlstate;j++){
3332: cptj= (j-1)*nlstate+i;
3333: for(i2=1; i2<=nlstate;i2++)
3334: for(j2=1; j2<=nlstate;j2++){
3335: cptj2= (j2-1)*nlstate+i2;
3336: if(cptj2 <= cptj)
3337: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3338: }
3339: }
3340: fprintf(ficrescveij,"\n");
3341:
3342: }
3343: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3344: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3345: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3346: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3347: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3348: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3349: printf("\n");
3350: fprintf(ficlog,"\n");
3351:
3352: free_vector(xm,1,npar);
3353: free_vector(xp,1,npar);
3354: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3355: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3356: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3357: }
3358:
3359: /************ Variance ******************/
3360: 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[])
3361: {
3362: /* Variance of health expectancies */
3363: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3364: /* double **newm;*/
3365: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3366:
3367: int movingaverage();
3368: double **dnewm,**doldm;
3369: double **dnewmp,**doldmp;
3370: int i, j, nhstepm, hstepm, h, nstepm ;
3371: int k;
3372: double *xp;
3373: double **gp, **gm; /* for var eij */
3374: double ***gradg, ***trgradg; /*for var eij */
3375: double **gradgp, **trgradgp; /* for var p point j */
3376: double *gpp, *gmp; /* for var p point j */
3377: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3378: double ***p3mat;
3379: double age,agelim, hf;
3380: double ***mobaverage;
3381: int theta;
3382: char digit[4];
3383: char digitp[25];
3384:
3385: char fileresprobmorprev[FILENAMELENGTH];
3386:
3387: if(popbased==1){
3388: if(mobilav!=0)
3389: strcpy(digitp,"-populbased-mobilav-");
3390: else strcpy(digitp,"-populbased-nomobil-");
3391: }
3392: else
3393: strcpy(digitp,"-stablbased-");
3394:
3395: if (mobilav!=0) {
3396: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3397: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3398: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3399: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3400: }
3401: }
3402:
3403: strcpy(fileresprobmorprev,"prmorprev");
3404: sprintf(digit,"%-d",ij);
3405: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3406: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3407: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3408: strcat(fileresprobmorprev,fileres);
3409: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3410: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3411: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3412: }
3413: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3414:
3415: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3416: pstamp(ficresprobmorprev);
3417: 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);
3418: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3419: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3420: fprintf(ficresprobmorprev," p.%-d SE",j);
3421: for(i=1; i<=nlstate;i++)
3422: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3423: }
3424: fprintf(ficresprobmorprev,"\n");
3425: fprintf(ficgp,"\n# Routine varevsij");
3426: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3427: 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");
3428: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3429: /* } */
3430: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3431: pstamp(ficresvij);
3432: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3433: if(popbased==1)
3434: 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);
3435: else
3436: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3437: fprintf(ficresvij,"# Age");
3438: for(i=1; i<=nlstate;i++)
3439: for(j=1; j<=nlstate;j++)
3440: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3441: fprintf(ficresvij,"\n");
3442:
3443: xp=vector(1,npar);
3444: dnewm=matrix(1,nlstate,1,npar);
3445: doldm=matrix(1,nlstate,1,nlstate);
3446: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3447: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3448:
3449: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3450: gpp=vector(nlstate+1,nlstate+ndeath);
3451: gmp=vector(nlstate+1,nlstate+ndeath);
3452: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3453:
3454: if(estepm < stepm){
3455: printf ("Problem %d lower than %d\n",estepm, stepm);
3456: }
3457: else hstepm=estepm;
3458: /* For example we decided to compute the life expectancy with the smallest unit */
3459: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3460: nhstepm is the number of hstepm from age to agelim
3461: nstepm is the number of stepm from age to agelin.
3462: Look at function hpijx to understand why (it is linked to memory size questions) */
3463: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3464: survival function given by stepm (the optimization length). Unfortunately it
3465: means that if the survival funtion is printed every two years of age and if
3466: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3467: results. So we changed our mind and took the option of the best precision.
3468: */
3469: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3470: agelim = AGESUP;
3471: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3472: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3473: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3474: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3475: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3476: gp=matrix(0,nhstepm,1,nlstate);
3477: gm=matrix(0,nhstepm,1,nlstate);
3478:
3479:
3480: for(theta=1; theta <=npar; theta++){
3481: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3482: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3483: }
3484: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3485: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3486:
3487: if (popbased==1) {
3488: if(mobilav ==0){
3489: for(i=1; i<=nlstate;i++)
3490: prlim[i][i]=probs[(int)age][i][ij];
3491: }else{ /* mobilav */
3492: for(i=1; i<=nlstate;i++)
3493: prlim[i][i]=mobaverage[(int)age][i][ij];
3494: }
3495: }
3496:
3497: for(j=1; j<= nlstate; j++){
3498: for(h=0; h<=nhstepm; h++){
3499: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3500: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3501: }
3502: }
3503: /* This for computing probability of death (h=1 means
3504: computed over hstepm matrices product = hstepm*stepm months)
3505: as a weighted average of prlim.
3506: */
3507: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3508: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3509: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3510: }
3511: /* end probability of death */
3512:
3513: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3514: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3515: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3516: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3517:
3518: if (popbased==1) {
3519: if(mobilav ==0){
3520: for(i=1; i<=nlstate;i++)
3521: prlim[i][i]=probs[(int)age][i][ij];
3522: }else{ /* mobilav */
3523: for(i=1; i<=nlstate;i++)
3524: prlim[i][i]=mobaverage[(int)age][i][ij];
3525: }
3526: }
3527:
3528: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3529: for(h=0; h<=nhstepm; h++){
3530: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3531: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3532: }
3533: }
3534: /* This for computing probability of death (h=1 means
3535: computed over hstepm matrices product = hstepm*stepm months)
3536: as a weighted average of prlim.
3537: */
3538: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3539: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3540: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3541: }
3542: /* end probability of death */
3543:
3544: for(j=1; j<= nlstate; j++) /* vareij */
3545: for(h=0; h<=nhstepm; h++){
3546: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3547: }
3548:
3549: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3550: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3551: }
3552:
3553: } /* End theta */
3554:
3555: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3556:
3557: for(h=0; h<=nhstepm; h++) /* veij */
3558: for(j=1; j<=nlstate;j++)
3559: for(theta=1; theta <=npar; theta++)
3560: trgradg[h][j][theta]=gradg[h][theta][j];
3561:
3562: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3563: for(theta=1; theta <=npar; theta++)
3564: trgradgp[j][theta]=gradgp[theta][j];
3565:
3566:
3567: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3568: for(i=1;i<=nlstate;i++)
3569: for(j=1;j<=nlstate;j++)
3570: vareij[i][j][(int)age] =0.;
3571:
3572: for(h=0;h<=nhstepm;h++){
3573: for(k=0;k<=nhstepm;k++){
3574: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3575: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3576: for(i=1;i<=nlstate;i++)
3577: for(j=1;j<=nlstate;j++)
3578: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3579: }
3580: }
3581:
3582: /* pptj */
3583: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3584: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3585: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3586: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3587: varppt[j][i]=doldmp[j][i];
3588: /* end ppptj */
3589: /* x centered again */
3590: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3591: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3592:
3593: if (popbased==1) {
3594: if(mobilav ==0){
3595: for(i=1; i<=nlstate;i++)
3596: prlim[i][i]=probs[(int)age][i][ij];
3597: }else{ /* mobilav */
3598: for(i=1; i<=nlstate;i++)
3599: prlim[i][i]=mobaverage[(int)age][i][ij];
3600: }
3601: }
3602:
3603: /* This for computing probability of death (h=1 means
3604: computed over hstepm (estepm) matrices product = hstepm*stepm months)
3605: as a weighted average of prlim.
3606: */
3607: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3608: for(i=1,gmp[j]=0.;i<= nlstate; i++)
3609: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3610: }
3611: /* end probability of death */
3612:
3613: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
3614: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3615: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
3616: for(i=1; i<=nlstate;i++){
3617: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
3618: }
3619: }
3620: fprintf(ficresprobmorprev,"\n");
3621:
3622: fprintf(ficresvij,"%.0f ",age );
3623: for(i=1; i<=nlstate;i++)
3624: for(j=1; j<=nlstate;j++){
3625: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
3626: }
3627: fprintf(ficresvij,"\n");
3628: free_matrix(gp,0,nhstepm,1,nlstate);
3629: free_matrix(gm,0,nhstepm,1,nlstate);
3630: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
3631: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
3632: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3633: } /* End age */
3634: free_vector(gpp,nlstate+1,nlstate+ndeath);
3635: free_vector(gmp,nlstate+1,nlstate+ndeath);
3636: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
3637: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3638: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
3639: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
3640: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
3641: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
3642: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
3643: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
3644: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
3645: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
3646: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
3647: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
3648: 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);
3649: /* 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);
3650: */
3651: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
3652: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
3653:
3654: free_vector(xp,1,npar);
3655: free_matrix(doldm,1,nlstate,1,nlstate);
3656: free_matrix(dnewm,1,nlstate,1,npar);
3657: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3658: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
3659: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3660: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3661: fclose(ficresprobmorprev);
3662: fflush(ficgp);
3663: fflush(fichtm);
3664: } /* end varevsij */
3665:
3666: /************ Variance of prevlim ******************/
3667: 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[])
3668: {
3669: /* Variance of prevalence limit */
3670: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
3671:
3672: double **dnewm,**doldm;
3673: int i, j, nhstepm, hstepm;
3674: double *xp;
3675: double *gp, *gm;
3676: double **gradg, **trgradg;
3677: double age,agelim;
3678: int theta;
3679:
3680: pstamp(ficresvpl);
3681: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
3682: fprintf(ficresvpl,"# Age");
3683: for(i=1; i<=nlstate;i++)
3684: fprintf(ficresvpl," %1d-%1d",i,i);
3685: fprintf(ficresvpl,"\n");
3686:
3687: xp=vector(1,npar);
3688: dnewm=matrix(1,nlstate,1,npar);
3689: doldm=matrix(1,nlstate,1,nlstate);
3690:
3691: hstepm=1*YEARM; /* Every year of age */
3692: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
3693: agelim = AGESUP;
3694: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3695: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3696: if (stepm >= YEARM) hstepm=1;
3697: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
3698: gradg=matrix(1,npar,1,nlstate);
3699: gp=vector(1,nlstate);
3700: gm=vector(1,nlstate);
3701:
3702: for(theta=1; theta <=npar; theta++){
3703: for(i=1; i<=npar; i++){ /* Computes gradient */
3704: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3705: }
3706: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3707: for(i=1;i<=nlstate;i++)
3708: gp[i] = prlim[i][i];
3709:
3710: for(i=1; i<=npar; i++) /* Computes gradient */
3711: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3712: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3713: for(i=1;i<=nlstate;i++)
3714: gm[i] = prlim[i][i];
3715:
3716: for(i=1;i<=nlstate;i++)
3717: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
3718: } /* End theta */
3719:
3720: trgradg =matrix(1,nlstate,1,npar);
3721:
3722: for(j=1; j<=nlstate;j++)
3723: for(theta=1; theta <=npar; theta++)
3724: trgradg[j][theta]=gradg[theta][j];
3725:
3726: for(i=1;i<=nlstate;i++)
3727: varpl[i][(int)age] =0.;
3728: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
3729: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
3730: for(i=1;i<=nlstate;i++)
3731: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
3732:
3733: fprintf(ficresvpl,"%.0f ",age );
3734: for(i=1; i<=nlstate;i++)
3735: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
3736: fprintf(ficresvpl,"\n");
3737: free_vector(gp,1,nlstate);
3738: free_vector(gm,1,nlstate);
3739: free_matrix(gradg,1,npar,1,nlstate);
3740: free_matrix(trgradg,1,nlstate,1,npar);
3741: } /* End age */
3742:
3743: free_vector(xp,1,npar);
3744: free_matrix(doldm,1,nlstate,1,npar);
3745: free_matrix(dnewm,1,nlstate,1,nlstate);
3746:
3747: }
3748:
3749: /************ Variance of one-step probabilities ******************/
3750: 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[])
3751: {
3752: int i, j=0, k1, l1, tj;
3753: int k2, l2, j1, z1;
3754: int k=0, l;
3755: int first=1, first1, first2;
3756: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
3757: double **dnewm,**doldm;
3758: double *xp;
3759: double *gp, *gm;
3760: double **gradg, **trgradg;
3761: double **mu;
3762: double age, cov[NCOVMAX+1];
3763: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
3764: int theta;
3765: char fileresprob[FILENAMELENGTH];
3766: char fileresprobcov[FILENAMELENGTH];
3767: char fileresprobcor[FILENAMELENGTH];
3768: double ***varpij;
3769:
3770: strcpy(fileresprob,"prob");
3771: strcat(fileresprob,fileres);
3772: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
3773: printf("Problem with resultfile: %s\n", fileresprob);
3774: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
3775: }
3776: strcpy(fileresprobcov,"probcov");
3777: strcat(fileresprobcov,fileres);
3778: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
3779: printf("Problem with resultfile: %s\n", fileresprobcov);
3780: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
3781: }
3782: strcpy(fileresprobcor,"probcor");
3783: strcat(fileresprobcor,fileres);
3784: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
3785: printf("Problem with resultfile: %s\n", fileresprobcor);
3786: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
3787: }
3788: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3789: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
3790: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3791: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
3792: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3793: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
3794: pstamp(ficresprob);
3795: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
3796: fprintf(ficresprob,"# Age");
3797: pstamp(ficresprobcov);
3798: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
3799: fprintf(ficresprobcov,"# Age");
3800: pstamp(ficresprobcor);
3801: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
3802: fprintf(ficresprobcor,"# Age");
3803:
3804:
3805: for(i=1; i<=nlstate;i++)
3806: for(j=1; j<=(nlstate+ndeath);j++){
3807: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
3808: fprintf(ficresprobcov," p%1d-%1d ",i,j);
3809: fprintf(ficresprobcor," p%1d-%1d ",i,j);
3810: }
3811: /* fprintf(ficresprob,"\n");
3812: fprintf(ficresprobcov,"\n");
3813: fprintf(ficresprobcor,"\n");
3814: */
3815: xp=vector(1,npar);
3816: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3817: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
3818: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
3819: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
3820: first=1;
3821: fprintf(ficgp,"\n# Routine varprob");
3822: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
3823: fprintf(fichtm,"\n");
3824:
3825: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
3826: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
3827: file %s<br>\n",optionfilehtmcov);
3828: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
3829: and drawn. It helps understanding how is the covariance between two incidences.\
3830: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
3831: 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. \
3832: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
3833: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
3834: standard deviations wide on each axis. <br>\
3835: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
3836: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
3837: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
3838:
3839: cov[1]=1;
3840: /* tj=cptcoveff; */
3841: tj = (int) pow(2,cptcoveff);
3842: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
3843: j1=0;
3844: for(j1=1; j1<=tj;j1++){
3845: /*for(i1=1; i1<=ncodemax[t];i1++){ */
3846: /*j1++;*/
3847: if (cptcovn>0) {
3848: fprintf(ficresprob, "\n#********** Variable ");
3849: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3850: fprintf(ficresprob, "**********\n#\n");
3851: fprintf(ficresprobcov, "\n#********** Variable ");
3852: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3853: fprintf(ficresprobcov, "**********\n#\n");
3854:
3855: fprintf(ficgp, "\n#********** Variable ");
3856: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3857: fprintf(ficgp, "**********\n#\n");
3858:
3859:
3860: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
3861: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3862: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
3863:
3864: fprintf(ficresprobcor, "\n#********** Variable ");
3865: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3866: fprintf(ficresprobcor, "**********\n#");
3867: }
3868:
3869: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
3870: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
3871: gp=vector(1,(nlstate)*(nlstate+ndeath));
3872: gm=vector(1,(nlstate)*(nlstate+ndeath));
3873: for (age=bage; age<=fage; age ++){
3874: cov[2]=age;
3875: for (k=1; k<=cptcovn;k++) {
3876: cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
3877: * 1 1 1 1 1
3878: * 2 2 1 1 1
3879: * 3 1 2 1 1
3880: */
3881: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
3882: }
3883: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
3884: for (k=1; k<=cptcovprod;k++)
3885: cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
3886:
3887:
3888: for(theta=1; theta <=npar; theta++){
3889: for(i=1; i<=npar; i++)
3890: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
3891:
3892: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3893:
3894: k=0;
3895: for(i=1; i<= (nlstate); i++){
3896: for(j=1; j<=(nlstate+ndeath);j++){
3897: k=k+1;
3898: gp[k]=pmmij[i][j];
3899: }
3900: }
3901:
3902: for(i=1; i<=npar; i++)
3903: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
3904:
3905: pmij(pmmij,cov,ncovmodel,xp,nlstate);
3906: k=0;
3907: for(i=1; i<=(nlstate); i++){
3908: for(j=1; j<=(nlstate+ndeath);j++){
3909: k=k+1;
3910: gm[k]=pmmij[i][j];
3911: }
3912: }
3913:
3914: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
3915: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
3916: }
3917:
3918: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
3919: for(theta=1; theta <=npar; theta++)
3920: trgradg[j][theta]=gradg[theta][j];
3921:
3922: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
3923: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
3924:
3925: pmij(pmmij,cov,ncovmodel,x,nlstate);
3926:
3927: k=0;
3928: for(i=1; i<=(nlstate); i++){
3929: for(j=1; j<=(nlstate+ndeath);j++){
3930: k=k+1;
3931: mu[k][(int) age]=pmmij[i][j];
3932: }
3933: }
3934: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
3935: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
3936: varpij[i][j][(int)age] = doldm[i][j];
3937:
3938: /*printf("\n%d ",(int)age);
3939: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3940: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3941: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
3942: }*/
3943:
3944: fprintf(ficresprob,"\n%d ",(int)age);
3945: fprintf(ficresprobcov,"\n%d ",(int)age);
3946: fprintf(ficresprobcor,"\n%d ",(int)age);
3947:
3948: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
3949: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
3950: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
3951: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
3952: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
3953: }
3954: i=0;
3955: for (k=1; k<=(nlstate);k++){
3956: for (l=1; l<=(nlstate+ndeath);l++){
3957: i++;
3958: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
3959: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
3960: for (j=1; j<=i;j++){
3961: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
3962: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
3963: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
3964: }
3965: }
3966: }/* end of loop for state */
3967: } /* end of loop for age */
3968: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
3969: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
3970: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3971: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
3972:
3973: /* Confidence intervalle of pij */
3974: /*
3975: fprintf(ficgp,"\nunset parametric;unset label");
3976: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
3977: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
3978: 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);
3979: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
3980: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
3981: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
3982: */
3983:
3984: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
3985: first1=1;first2=2;
3986: for (k2=1; k2<=(nlstate);k2++){
3987: for (l2=1; l2<=(nlstate+ndeath);l2++){
3988: if(l2==k2) continue;
3989: j=(k2-1)*(nlstate+ndeath)+l2;
3990: for (k1=1; k1<=(nlstate);k1++){
3991: for (l1=1; l1<=(nlstate+ndeath);l1++){
3992: if(l1==k1) continue;
3993: i=(k1-1)*(nlstate+ndeath)+l1;
3994: if(i<=j) continue;
3995: for (age=bage; age<=fage; age ++){
3996: if ((int)age %5==0){
3997: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
3998: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
3999: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4000: mu1=mu[i][(int) age]/stepm*YEARM ;
4001: mu2=mu[j][(int) age]/stepm*YEARM;
4002: c12=cv12/sqrt(v1*v2);
4003: /* Computing eigen value of matrix of covariance */
4004: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4005: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4006: if ((lc2 <0) || (lc1 <0) ){
4007: if(first2==1){
4008: first1=0;
4009: 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);
4010: }
4011: 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);
4012: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4013: /* lc2=fabs(lc2); */
4014: }
4015:
4016: /* Eigen vectors */
4017: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4018: /*v21=sqrt(1.-v11*v11); *//* error */
4019: v21=(lc1-v1)/cv12*v11;
4020: v12=-v21;
4021: v22=v11;
4022: tnalp=v21/v11;
4023: if(first1==1){
4024: first1=0;
4025: 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);
4026: }
4027: 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);
4028: /*printf(fignu*/
4029: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4030: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4031: if(first==1){
4032: first=0;
4033: fprintf(ficgp,"\nset parametric;unset label");
4034: 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);
4035: fprintf(ficgp,"\nset ter png small size 320, 240");
4036: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4037: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4038: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4039: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4040: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4041: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4042: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4043: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4044: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4045: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4046: 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",\
4047: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4048: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4049: }else{
4050: first=0;
4051: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4052: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4053: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4054: 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",\
4055: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4056: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4057: }/* if first */
4058: } /* age mod 5 */
4059: } /* end loop age */
4060: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4061: first=1;
4062: } /*l12 */
4063: } /* k12 */
4064: } /*l1 */
4065: }/* k1 */
4066: /* } */ /* loop covariates */
4067: }
4068: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4069: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4070: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4071: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4072: free_vector(xp,1,npar);
4073: fclose(ficresprob);
4074: fclose(ficresprobcov);
4075: fclose(ficresprobcor);
4076: fflush(ficgp);
4077: fflush(fichtmcov);
4078: }
4079:
4080:
4081: /******************* Printing html file ***********/
4082: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4083: int lastpass, int stepm, int weightopt, char model[],\
4084: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4085: int popforecast, int estepm ,\
4086: double jprev1, double mprev1,double anprev1, \
4087: double jprev2, double mprev2,double anprev2){
4088: int jj1, k1, i1, cpt;
4089:
4090: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4091: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4092: </ul>");
4093: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4094: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4095: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4096: fprintf(fichtm,"\
4097: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4098: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4099: fprintf(fichtm,"\
4100: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4101: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4102: fprintf(fichtm,"\
4103: - (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): \
4104: <a href=\"%s\">%s</a> <br>\n",
4105: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4106: fprintf(fichtm,"\
4107: - Population projections by age and states: \
4108: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4109:
4110: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4111:
4112: m=pow(2,cptcoveff);
4113: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4114:
4115: jj1=0;
4116: for(k1=1; k1<=m;k1++){
4117: for(i1=1; i1<=ncodemax[k1];i1++){
4118: jj1++;
4119: if (cptcovn > 0) {
4120: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4121: for (cpt=1; cpt<=cptcoveff;cpt++)
4122: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4123: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4124: }
4125: /* Pij */
4126: 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> \
4127: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4128: /* Quasi-incidences */
4129: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4130: 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> \
4131: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4132: /* Period (stable) prevalence in each health state */
4133: for(cpt=1; cpt<=nlstate;cpt++){
4134: 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> \
4135: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4136: }
4137: for(cpt=1; cpt<=nlstate;cpt++) {
4138: 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> \
4139: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4140: }
4141: } /* end i1 */
4142: }/* End k1 */
4143: fprintf(fichtm,"</ul>");
4144:
4145:
4146: fprintf(fichtm,"\
4147: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4148: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
4149:
4150: fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4151: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4152: fprintf(fichtm,"\
4153: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4154: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4155:
4156: fprintf(fichtm,"\
4157: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4158: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4159: fprintf(fichtm,"\
4160: - 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): \
4161: <a href=\"%s\">%s</a> <br>\n</li>",
4162: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4163: fprintf(fichtm,"\
4164: - (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): \
4165: <a href=\"%s\">%s</a> <br>\n</li>",
4166: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4167: fprintf(fichtm,"\
4168: - 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",
4169: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4170: fprintf(fichtm,"\
4171: - 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",
4172: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4173: fprintf(fichtm,"\
4174: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4175: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4176:
4177: /* if(popforecast==1) fprintf(fichtm,"\n */
4178: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4179: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4180: /* <br>",fileres,fileres,fileres,fileres); */
4181: /* else */
4182: /* 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); */
4183: fflush(fichtm);
4184: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4185:
4186: m=pow(2,cptcoveff);
4187: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4188:
4189: jj1=0;
4190: for(k1=1; k1<=m;k1++){
4191: for(i1=1; i1<=ncodemax[k1];i1++){
4192: jj1++;
4193: if (cptcovn > 0) {
4194: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4195: for (cpt=1; cpt<=cptcoveff;cpt++)
4196: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4197: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4198: }
4199: for(cpt=1; cpt<=nlstate;cpt++) {
4200: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4201: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4202: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4203: }
4204: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4205: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4206: true period expectancies (those weighted with period prevalences are also\
4207: drawn in addition to the population based expectancies computed using\
4208: observed and cahotic prevalences: %s%d.png<br>\
4209: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4210: } /* end i1 */
4211: }/* End k1 */
4212: fprintf(fichtm,"</ul>");
4213: fflush(fichtm);
4214: }
4215:
4216: /******************* Gnuplot file **************/
4217: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4218:
4219: char dirfileres[132],optfileres[132];
4220: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4221: int ng=0;
4222: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4223: /* printf("Problem with file %s",optionfilegnuplot); */
4224: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4225: /* } */
4226:
4227: /*#ifdef windows */
4228: fprintf(ficgp,"cd \"%s\" \n",pathc);
4229: /*#endif */
4230: m=pow(2,cptcoveff);
4231:
4232: strcpy(dirfileres,optionfilefiname);
4233: strcpy(optfileres,"vpl");
4234: /* 1eme*/
4235: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4236: for (cpt=1; cpt<= nlstate ; cpt ++) {
4237: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4238: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4239: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4240: fprintf(ficgp,"set xlabel \"Age\" \n\
4241: set ylabel \"Probability\" \n\
4242: set ter png small size 320, 240\n\
4243: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4244:
4245: for (i=1; i<= nlstate ; i ++) {
4246: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4247: else fprintf(ficgp," %%*lf (%%*lf)");
4248: }
4249: 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);
4250: for (i=1; i<= nlstate ; i ++) {
4251: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4252: else fprintf(ficgp," %%*lf (%%*lf)");
4253: }
4254: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4255: for (i=1; i<= nlstate ; i ++) {
4256: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4257: else fprintf(ficgp," %%*lf (%%*lf)");
4258: }
4259: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4260: }
4261: }
4262: /*2 eme*/
4263: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4264: for (k1=1; k1<= m ; k1 ++) {
4265: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4266: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4267:
4268: for (i=1; i<= nlstate+1 ; i ++) {
4269: k=2*i;
4270: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4271: for (j=1; j<= nlstate+1 ; j ++) {
4272: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4273: else fprintf(ficgp," %%*lf (%%*lf)");
4274: }
4275: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4276: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4277: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4278: for (j=1; j<= nlstate+1 ; j ++) {
4279: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4280: else fprintf(ficgp," %%*lf (%%*lf)");
4281: }
4282: fprintf(ficgp,"\" t\"\" w l lt 0,");
4283: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4284: for (j=1; j<= nlstate+1 ; j ++) {
4285: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4286: else fprintf(ficgp," %%*lf (%%*lf)");
4287: }
4288: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4289: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4290: }
4291: }
4292:
4293: /*3eme*/
4294:
4295: for (k1=1; k1<= m ; k1 ++) {
4296: for (cpt=1; cpt<= nlstate ; cpt ++) {
4297: /* k=2+nlstate*(2*cpt-2); */
4298: k=2+(nlstate+1)*(cpt-1);
4299: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4300: fprintf(ficgp,"set ter png small size 320, 240\n\
4301: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4302: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4303: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4304: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4305: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4306: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4307: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4308:
4309: */
4310: for (i=1; i< nlstate ; i ++) {
4311: 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);
4312: /* 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);*/
4313:
4314: }
4315: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4316: }
4317: }
4318:
4319: /* CV preval stable (period) */
4320: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4321: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4322: k=3;
4323: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4324: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4325: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4326: set ter png small size 320, 240\n\
4327: unset log y\n\
4328: plot [%.f:%.f] ", ageminpar, agemaxpar);
4329: for (i=1; i<= nlstate ; i ++){
4330: if(i==1)
4331: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4332: else
4333: fprintf(ficgp,", '' ");
4334: l=(nlstate+ndeath)*(i-1)+1;
4335: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4336: for (j=1; j<= (nlstate-1) ; j ++)
4337: fprintf(ficgp,"+$%d",k+l+j);
4338: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4339: } /* nlstate */
4340: fprintf(ficgp,"\n");
4341: } /* end cpt state*/
4342: } /* end covariate */
4343:
4344: /* proba elementaires */
4345: for(i=1,jk=1; i <=nlstate; i++){
4346: for(k=1; k <=(nlstate+ndeath); k++){
4347: if (k != i) {
4348: for(j=1; j <=ncovmodel; j++){
4349: fprintf(ficgp,"p%d=%f ",jk,p[jk]);
4350: jk++;
4351: fprintf(ficgp,"\n");
4352: }
4353: }
4354: }
4355: }
4356: /*goto avoid;*/
4357: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4358: for(jk=1; jk <=m; jk++) {
4359: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4360: if (ng==2)
4361: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4362: else
4363: fprintf(ficgp,"\nset title \"Probability\"\n");
4364: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4365: i=1;
4366: for(k2=1; k2<=nlstate; k2++) {
4367: k3=i;
4368: for(k=1; k<=(nlstate+ndeath); k++) {
4369: if (k != k2){
4370: if(ng==2)
4371: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4372: else
4373: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4374: ij=1;/* To be checked else nbcode[0][0] wrong */
4375: for(j=3; j <=ncovmodel; j++) {
4376: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /\* Bug valgrind *\/ */
4377: /* /\*fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);*\/ */
4378: /* ij++; */
4379: /* } */
4380: /* else */
4381: fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4382: }
4383: fprintf(ficgp,")/(1");
4384:
4385: for(k1=1; k1 <=nlstate; k1++){
4386: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4387: ij=1;
4388: for(j=3; j <=ncovmodel; j++){
4389: /* if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { */
4390: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]); */
4391: /* ij++; */
4392: /* } */
4393: /* else */
4394: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4395: }
4396: fprintf(ficgp,")");
4397: }
4398: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4399: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4400: i=i+ncovmodel;
4401: }
4402: } /* end k */
4403: } /* end k2 */
4404: } /* end jk */
4405: } /* end ng */
4406: /* avoid: */
4407: fflush(ficgp);
4408: } /* end gnuplot */
4409:
4410:
4411: /*************** Moving average **************/
4412: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4413:
4414: int i, cpt, cptcod;
4415: int modcovmax =1;
4416: int mobilavrange, mob;
4417: double age;
4418:
4419: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4420: a covariate has 2 modalities */
4421: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4422:
4423: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4424: if(mobilav==1) mobilavrange=5; /* default */
4425: else mobilavrange=mobilav;
4426: for (age=bage; age<=fage; 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: /* We keep the original values on the extreme ages bage, fage and for
4431: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4432: we use a 5 terms etc. until the borders are no more concerned.
4433: */
4434: for (mob=3;mob <=mobilavrange;mob=mob+2){
4435: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4436: for (i=1; i<=nlstate;i++){
4437: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4438: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4439: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4440: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4441: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4442: }
4443: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4444: }
4445: }
4446: }/* end age */
4447: }/* end mob */
4448: }else return -1;
4449: return 0;
4450: }/* End movingaverage */
4451:
4452:
4453: /************** Forecasting ******************/
4454: 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){
4455: /* proj1, year, month, day of starting projection
4456: agemin, agemax range of age
4457: dateprev1 dateprev2 range of dates during which prevalence is computed
4458: anproj2 year of en of projection (same day and month as proj1).
4459: */
4460: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4461: double agec; /* generic age */
4462: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4463: double *popeffectif,*popcount;
4464: double ***p3mat;
4465: double ***mobaverage;
4466: char fileresf[FILENAMELENGTH];
4467:
4468: agelim=AGESUP;
4469: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4470:
4471: strcpy(fileresf,"f");
4472: strcat(fileresf,fileres);
4473: if((ficresf=fopen(fileresf,"w"))==NULL) {
4474: printf("Problem with forecast resultfile: %s\n", fileresf);
4475: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4476: }
4477: printf("Computing forecasting: result on file '%s' \n", fileresf);
4478: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4479:
4480: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4481:
4482: if (mobilav!=0) {
4483: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4484: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4485: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4486: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4487: }
4488: }
4489:
4490: stepsize=(int) (stepm+YEARM-1)/YEARM;
4491: if (stepm<=12) stepsize=1;
4492: if(estepm < stepm){
4493: printf ("Problem %d lower than %d\n",estepm, stepm);
4494: }
4495: else hstepm=estepm;
4496:
4497: hstepm=hstepm/stepm;
4498: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4499: fractional in yp1 */
4500: anprojmean=yp;
4501: yp2=modf((yp1*12),&yp);
4502: mprojmean=yp;
4503: yp1=modf((yp2*30.5),&yp);
4504: jprojmean=yp;
4505: if(jprojmean==0) jprojmean=1;
4506: if(mprojmean==0) jprojmean=1;
4507:
4508: i1=cptcoveff;
4509: if (cptcovn < 1){i1=1;}
4510:
4511: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4512:
4513: fprintf(ficresf,"#****** Routine prevforecast **\n");
4514:
4515: /* if (h==(int)(YEARM*yearp)){ */
4516: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4517: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4518: k=k+1;
4519: fprintf(ficresf,"\n#******");
4520: for(j=1;j<=cptcoveff;j++) {
4521: 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]]);
4522: }
4523: fprintf(ficresf,"******\n");
4524: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4525: for(j=1; j<=nlstate+ndeath;j++){
4526: for(i=1; i<=nlstate;i++)
4527: fprintf(ficresf," p%d%d",i,j);
4528: fprintf(ficresf," p.%d",j);
4529: }
4530: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4531: fprintf(ficresf,"\n");
4532: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4533:
4534: for (agec=fage; agec>=(ageminpar-1); agec--){
4535: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4536: nhstepm = nhstepm/hstepm;
4537: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4538: oldm=oldms;savm=savms;
4539: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4540:
4541: for (h=0; h<=nhstepm; h++){
4542: if (h*hstepm/YEARM*stepm ==yearp) {
4543: fprintf(ficresf,"\n");
4544: for(j=1;j<=cptcoveff;j++)
4545: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4546: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4547: }
4548: for(j=1; j<=nlstate+ndeath;j++) {
4549: ppij=0.;
4550: for(i=1; i<=nlstate;i++) {
4551: if (mobilav==1)
4552: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4553: else {
4554: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4555: }
4556: if (h*hstepm/YEARM*stepm== yearp) {
4557: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4558: }
4559: } /* end i */
4560: if (h*hstepm/YEARM*stepm==yearp) {
4561: fprintf(ficresf," %.3f", ppij);
4562: }
4563: }/* end j */
4564: } /* end h */
4565: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4566: } /* end agec */
4567: } /* end yearp */
4568: } /* end cptcod */
4569: } /* end cptcov */
4570:
4571: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4572:
4573: fclose(ficresf);
4574: }
4575:
4576: /************** Forecasting *****not tested NB*************/
4577: 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){
4578:
4579: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
4580: int *popage;
4581: double calagedatem, agelim, kk1, kk2;
4582: double *popeffectif,*popcount;
4583: double ***p3mat,***tabpop,***tabpopprev;
4584: double ***mobaverage;
4585: char filerespop[FILENAMELENGTH];
4586:
4587: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4588: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4589: agelim=AGESUP;
4590: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
4591:
4592: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4593:
4594:
4595: strcpy(filerespop,"pop");
4596: strcat(filerespop,fileres);
4597: if((ficrespop=fopen(filerespop,"w"))==NULL) {
4598: printf("Problem with forecast resultfile: %s\n", filerespop);
4599: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
4600: }
4601: printf("Computing forecasting: result on file '%s' \n", filerespop);
4602: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
4603:
4604: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4605:
4606: if (mobilav!=0) {
4607: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4608: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4609: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4610: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4611: }
4612: }
4613:
4614: stepsize=(int) (stepm+YEARM-1)/YEARM;
4615: if (stepm<=12) stepsize=1;
4616:
4617: agelim=AGESUP;
4618:
4619: hstepm=1;
4620: hstepm=hstepm/stepm;
4621:
4622: if (popforecast==1) {
4623: if((ficpop=fopen(popfile,"r"))==NULL) {
4624: printf("Problem with population file : %s\n",popfile);exit(0);
4625: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
4626: }
4627: popage=ivector(0,AGESUP);
4628: popeffectif=vector(0,AGESUP);
4629: popcount=vector(0,AGESUP);
4630:
4631: i=1;
4632: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
4633:
4634: imx=i;
4635: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
4636: }
4637:
4638: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
4639: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4640: k=k+1;
4641: fprintf(ficrespop,"\n#******");
4642: for(j=1;j<=cptcoveff;j++) {
4643: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4644: }
4645: fprintf(ficrespop,"******\n");
4646: fprintf(ficrespop,"# Age");
4647: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
4648: if (popforecast==1) fprintf(ficrespop," [Population]");
4649:
4650: for (cpt=0; cpt<=0;cpt++) {
4651: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4652:
4653: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4654: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4655: nhstepm = nhstepm/hstepm;
4656:
4657: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4658: oldm=oldms;savm=savms;
4659: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4660:
4661: for (h=0; h<=nhstepm; h++){
4662: if (h==(int) (calagedatem+YEARM*cpt)) {
4663: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4664: }
4665: for(j=1; j<=nlstate+ndeath;j++) {
4666: kk1=0.;kk2=0;
4667: for(i=1; i<=nlstate;i++) {
4668: if (mobilav==1)
4669: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
4670: else {
4671: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
4672: }
4673: }
4674: if (h==(int)(calagedatem+12*cpt)){
4675: tabpop[(int)(agedeb)][j][cptcod]=kk1;
4676: /*fprintf(ficrespop," %.3f", kk1);
4677: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
4678: }
4679: }
4680: for(i=1; i<=nlstate;i++){
4681: kk1=0.;
4682: for(j=1; j<=nlstate;j++){
4683: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
4684: }
4685: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
4686: }
4687:
4688: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
4689: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
4690: }
4691: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4692: }
4693: }
4694:
4695: /******/
4696:
4697: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
4698: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
4699: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
4700: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
4701: nhstepm = nhstepm/hstepm;
4702:
4703: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4704: oldm=oldms;savm=savms;
4705: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
4706: for (h=0; h<=nhstepm; h++){
4707: if (h==(int) (calagedatem+YEARM*cpt)) {
4708: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
4709: }
4710: for(j=1; j<=nlstate+ndeath;j++) {
4711: kk1=0.;kk2=0;
4712: for(i=1; i<=nlstate;i++) {
4713: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
4714: }
4715: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
4716: }
4717: }
4718: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4719: }
4720: }
4721: }
4722: }
4723:
4724: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4725:
4726: if (popforecast==1) {
4727: free_ivector(popage,0,AGESUP);
4728: free_vector(popeffectif,0,AGESUP);
4729: free_vector(popcount,0,AGESUP);
4730: }
4731: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4732: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4733: fclose(ficrespop);
4734: } /* End of popforecast */
4735:
4736: int fileappend(FILE *fichier, char *optionfich)
4737: {
4738: if((fichier=fopen(optionfich,"a"))==NULL) {
4739: printf("Problem with file: %s\n", optionfich);
4740: fprintf(ficlog,"Problem with file: %s\n", optionfich);
4741: return (0);
4742: }
4743: fflush(fichier);
4744: return (1);
4745: }
4746:
4747:
4748: /**************** function prwizard **********************/
4749: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
4750: {
4751:
4752: /* Wizard to print covariance matrix template */
4753:
4754: char ca[32], cb[32];
4755: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
4756: int numlinepar;
4757:
4758: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4759: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
4760: for(i=1; i <=nlstate; i++){
4761: jj=0;
4762: for(j=1; j <=nlstate+ndeath; j++){
4763: if(j==i) continue;
4764: jj++;
4765: /*ca[0]= k+'a'-1;ca[1]='\0';*/
4766: printf("%1d%1d",i,j);
4767: fprintf(ficparo,"%1d%1d",i,j);
4768: for(k=1; k<=ncovmodel;k++){
4769: /* printf(" %lf",param[i][j][k]); */
4770: /* fprintf(ficparo," %lf",param[i][j][k]); */
4771: printf(" 0.");
4772: fprintf(ficparo," 0.");
4773: }
4774: printf("\n");
4775: fprintf(ficparo,"\n");
4776: }
4777: }
4778: printf("# Scales (for hessian or gradient estimation)\n");
4779: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
4780: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
4781: for(i=1; i <=nlstate; i++){
4782: jj=0;
4783: for(j=1; j <=nlstate+ndeath; j++){
4784: if(j==i) continue;
4785: jj++;
4786: fprintf(ficparo,"%1d%1d",i,j);
4787: printf("%1d%1d",i,j);
4788: fflush(stdout);
4789: for(k=1; k<=ncovmodel;k++){
4790: /* printf(" %le",delti3[i][j][k]); */
4791: /* fprintf(ficparo," %le",delti3[i][j][k]); */
4792: printf(" 0.");
4793: fprintf(ficparo," 0.");
4794: }
4795: numlinepar++;
4796: printf("\n");
4797: fprintf(ficparo,"\n");
4798: }
4799: }
4800: printf("# Covariance matrix\n");
4801: /* # 121 Var(a12)\n\ */
4802: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4803: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
4804: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
4805: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
4806: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
4807: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
4808: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4809: fflush(stdout);
4810: fprintf(ficparo,"# Covariance matrix\n");
4811: /* # 121 Var(a12)\n\ */
4812: /* # 122 Cov(b12,a12) Var(b12)\n\ */
4813: /* # ...\n\ */
4814: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
4815:
4816: for(itimes=1;itimes<=2;itimes++){
4817: jj=0;
4818: for(i=1; i <=nlstate; i++){
4819: for(j=1; j <=nlstate+ndeath; j++){
4820: if(j==i) continue;
4821: for(k=1; k<=ncovmodel;k++){
4822: jj++;
4823: ca[0]= k+'a'-1;ca[1]='\0';
4824: if(itimes==1){
4825: printf("#%1d%1d%d",i,j,k);
4826: fprintf(ficparo,"#%1d%1d%d",i,j,k);
4827: }else{
4828: printf("%1d%1d%d",i,j,k);
4829: fprintf(ficparo,"%1d%1d%d",i,j,k);
4830: /* printf(" %.5le",matcov[i][j]); */
4831: }
4832: ll=0;
4833: for(li=1;li <=nlstate; li++){
4834: for(lj=1;lj <=nlstate+ndeath; lj++){
4835: if(lj==li) continue;
4836: for(lk=1;lk<=ncovmodel;lk++){
4837: ll++;
4838: if(ll<=jj){
4839: cb[0]= lk +'a'-1;cb[1]='\0';
4840: if(ll<jj){
4841: if(itimes==1){
4842: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4843: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
4844: }else{
4845: printf(" 0.");
4846: fprintf(ficparo," 0.");
4847: }
4848: }else{
4849: if(itimes==1){
4850: printf(" Var(%s%1d%1d)",ca,i,j);
4851: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
4852: }else{
4853: printf(" 0.");
4854: fprintf(ficparo," 0.");
4855: }
4856: }
4857: }
4858: } /* end lk */
4859: } /* end lj */
4860: } /* end li */
4861: printf("\n");
4862: fprintf(ficparo,"\n");
4863: numlinepar++;
4864: } /* end k*/
4865: } /*end j */
4866: } /* end i */
4867: } /* end itimes */
4868:
4869: } /* end of prwizard */
4870: /******************* Gompertz Likelihood ******************************/
4871: double gompertz(double x[])
4872: {
4873: double A,B,L=0.0,sump=0.,num=0.;
4874: int i,n=0; /* n is the size of the sample */
4875:
4876: for (i=0;i<=imx-1 ; i++) {
4877: sump=sump+weight[i];
4878: /* sump=sump+1;*/
4879: num=num+1;
4880: }
4881:
4882:
4883: /* for (i=0; i<=imx; i++)
4884: 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]);*/
4885:
4886: for (i=1;i<=imx ; i++)
4887: {
4888: if (cens[i] == 1 && wav[i]>1)
4889: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
4890:
4891: if (cens[i] == 0 && wav[i]>1)
4892: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
4893: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
4894:
4895: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4896: if (wav[i] > 1 ) { /* ??? */
4897: L=L+A*weight[i];
4898: /* 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]);*/
4899: }
4900: }
4901:
4902: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4903:
4904: return -2*L*num/sump;
4905: }
4906:
4907: #ifdef GSL
4908: /******************* Gompertz_f Likelihood ******************************/
4909: double gompertz_f(const gsl_vector *v, void *params)
4910: {
4911: double A,B,LL=0.0,sump=0.,num=0.;
4912: double *x= (double *) v->data;
4913: int i,n=0; /* n is the size of the sample */
4914:
4915: for (i=0;i<=imx-1 ; i++) {
4916: sump=sump+weight[i];
4917: /* sump=sump+1;*/
4918: num=num+1;
4919: }
4920:
4921:
4922: /* for (i=0; i<=imx; i++)
4923: 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]);*/
4924: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
4925: for (i=1;i<=imx ; i++)
4926: {
4927: if (cens[i] == 1 && wav[i]>1)
4928: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
4929:
4930: if (cens[i] == 0 && wav[i]>1)
4931: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
4932: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
4933:
4934: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
4935: if (wav[i] > 1 ) { /* ??? */
4936: LL=LL+A*weight[i];
4937: /* 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]);*/
4938: }
4939: }
4940:
4941: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
4942: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
4943:
4944: return -2*LL*num/sump;
4945: }
4946: #endif
4947:
4948: /******************* Printing html file ***********/
4949: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
4950: int lastpass, int stepm, int weightopt, char model[],\
4951: int imx, double p[],double **matcov,double agemortsup){
4952: int i,k;
4953:
4954: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
4955: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
4956: for (i=1;i<=2;i++)
4957: 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]));
4958: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
4959: fprintf(fichtm,"</ul>");
4960:
4961: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
4962:
4963: 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>");
4964:
4965: for (k=agegomp;k<(agemortsup-2);k++)
4966: 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]);
4967:
4968:
4969: fflush(fichtm);
4970: }
4971:
4972: /******************* Gnuplot file **************/
4973: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4974:
4975: char dirfileres[132],optfileres[132];
4976:
4977: int ng;
4978:
4979:
4980: /*#ifdef windows */
4981: fprintf(ficgp,"cd \"%s\" \n",pathc);
4982: /*#endif */
4983:
4984:
4985: strcpy(dirfileres,optionfilefiname);
4986: strcpy(optfileres,"vpl");
4987: fprintf(ficgp,"set out \"graphmort.png\"\n ");
4988: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
4989: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
4990: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
4991: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
4992:
4993: }
4994:
4995: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
4996: {
4997:
4998: /*-------- data file ----------*/
4999: FILE *fic;
5000: char dummy[]=" ";
5001: int i=0, j=0, n=0;
5002: int linei, month, year,iout;
5003: char line[MAXLINE], linetmp[MAXLINE];
5004: char stra[MAXLINE], strb[MAXLINE];
5005: char *stratrunc;
5006: int lstra;
5007:
5008:
5009: if((fic=fopen(datafile,"r"))==NULL) {
5010: printf("Problem while opening datafile: %s\n", datafile);return 1;
5011: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);return 1;
5012: }
5013:
5014: i=1;
5015: linei=0;
5016: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5017: linei=linei+1;
5018: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5019: if(line[j] == '\t')
5020: line[j] = ' ';
5021: }
5022: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5023: ;
5024: };
5025: line[j+1]=0; /* Trims blanks at end of line */
5026: if(line[0]=='#'){
5027: fprintf(ficlog,"Comment line\n%s\n",line);
5028: printf("Comment line\n%s\n",line);
5029: continue;
5030: }
5031: trimbb(linetmp,line); /* Trims multiple blanks in line */
5032: strcpy(line, linetmp);
5033:
5034:
5035: for (j=maxwav;j>=1;j--){
5036: cutv(stra, strb, line, ' ');
5037: if(strb[0]=='.') { /* Missing status */
5038: lval=-1;
5039: }else{
5040: errno=0;
5041: lval=strtol(strb,&endptr,10);
5042: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5043: if( strb[0]=='\0' || (*endptr != '\0')){
5044: 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);
5045: 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);
5046: return 1;
5047: }
5048: }
5049: s[j][i]=lval;
5050:
5051: strcpy(line,stra);
5052: cutv(stra, strb,line,' ');
5053: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5054: }
5055: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5056: month=99;
5057: year=9999;
5058: }else{
5059: 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);
5060: 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);
5061: return 1;
5062: }
5063: anint[j][i]= (double) year;
5064: mint[j][i]= (double)month;
5065: strcpy(line,stra);
5066: } /* ENd Waves */
5067:
5068: cutv(stra, strb,line,' ');
5069: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5070: }
5071: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5072: month=99;
5073: year=9999;
5074: }else{
5075: 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);
5076: 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);
5077: return 1;
5078: }
5079: andc[i]=(double) year;
5080: moisdc[i]=(double) month;
5081: strcpy(line,stra);
5082:
5083: cutv(stra, strb,line,' ');
5084: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5085: }
5086: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5087: month=99;
5088: year=9999;
5089: }else{
5090: 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);
5091: 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);
5092: return 1;
5093: }
5094: if (year==9999) {
5095: 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);
5096: 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);
5097: return 1;
5098:
5099: }
5100: annais[i]=(double)(year);
5101: moisnais[i]=(double)(month);
5102: strcpy(line,stra);
5103:
5104: cutv(stra, strb,line,' ');
5105: errno=0;
5106: dval=strtod(strb,&endptr);
5107: if( strb[0]=='\0' || (*endptr != '\0')){
5108: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5109: 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);
5110: fflush(ficlog);
5111: return 1;
5112: }
5113: weight[i]=dval;
5114: strcpy(line,stra);
5115:
5116: for (j=ncovcol;j>=1;j--){
5117: cutv(stra, strb,line,' ');
5118: if(strb[0]=='.') { /* Missing status */
5119: lval=-1;
5120: }else{
5121: errno=0;
5122: lval=strtol(strb,&endptr,10);
5123: if( strb[0]=='\0' || (*endptr != '\0')){
5124: 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);
5125: 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);
5126: return 1;
5127: }
5128: }
5129: if(lval <-1 || lval >1){
5130: printf("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);
5139: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5140: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5141: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5142: For example, for multinomial values like 1, 2 and 3,\n \
5143: build V1=0 V2=0 for the reference value (1),\n \
5144: V1=1 V2=0 for (2) \n \
5145: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5146: output of IMaCh is often meaningless.\n \
5147: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5148: return 1;
5149: }
5150: covar[j][i]=(double)(lval);
5151: strcpy(line,stra);
5152: }
5153: lstra=strlen(stra);
5154:
5155: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5156: stratrunc = &(stra[lstra-9]);
5157: num[i]=atol(stratrunc);
5158: }
5159: else
5160: num[i]=atol(stra);
5161: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5162: 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;}*/
5163:
5164: i=i+1;
5165: } /* End loop reading data */
5166:
5167: *imax=i-1; /* Number of individuals */
5168: fclose(fic);
5169:
5170: return (0);
5171: /* endread: */
5172: printf("Exiting readdata: ");
5173: fclose(fic);
5174: return (1);
5175:
5176:
5177:
5178: }
5179: void removespace(char *str) {
5180: char *p1 = str, *p2 = str;
5181: do
5182: while (*p2 == ' ')
5183: p2++;
5184: while (*p1++ == *p2++);
5185: }
5186:
5187: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5188: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age
5189: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8
5190: * - cptcovn or number of covariates k of the models excluding age*products =6
5191: * - cptcovage number of covariates with age*products =2
5192: * - cptcovs number of simple covariates
5193: * - 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
5194: * which is a new column after the 9 (ncovcol) variables.
5195: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5196: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5197: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5198: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5199: */
5200: {
5201: int i, j, k, ks;
5202: int j1, k1, k2;
5203: char modelsav[80];
5204: char stra[80], strb[80], strc[80], strd[80],stre[80];
5205:
5206: /*removespace(model);*/
5207: if (strlen(model) >1){ /* If there is at least 1 covariate */
5208: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5209: j=nbocc(model,'+'); /**< j=Number of '+' */
5210: j1=nbocc(model,'*'); /**< j1=Number of '*' */
5211: cptcovs=j+1-j1; /**< Number of simple covariates V1+V2*age+V3 +V3*V4=> V1 + V3 =2 */
5212: cptcovt= j+1; /* Number of total covariates in the model V1 + V2*age+ V3 + V3*V4=> 4*/
5213: /* including age products which are counted in cptcovage.
5214: * but the covariates which are products must be treated separately: ncovn=4- 2=2 (V1+V3). */
5215: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5216: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5217: strcpy(modelsav,model);
5218: if (strstr(model,"AGE") !=0){
5219: printf("Error. AGE must be in lower case 'age' model=%s ",model);
5220: fprintf(ficlog,"Error. AGE must be in lower case model=%s ",model);fflush(ficlog);
5221: return 1;
5222: }
5223: if (strstr(model,"v") !=0){
5224: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5225: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5226: return 1;
5227: }
5228:
5229: /* Design
5230: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5231: * < ncovcol=8 >
5232: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5233: * k= 1 2 3 4 5 6 7 8
5234: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5235: * covar[k,i], value of kth covariate if not including age for individual i:
5236: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5237: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5238: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5239: * Tage[++cptcovage]=k
5240: * if products, new covar are created after ncovcol with k1
5241: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5242: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5243: * 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
5244: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5245: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5246: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5247: * < ncovcol=8 >
5248: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5249: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5250: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5251: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5252: * p Tprod[1]@2={ 6, 5}
5253: *p Tvard[1][1]@4= {7, 8, 5, 6}
5254: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5255: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5256: *How to reorganize?
5257: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5258: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5259: * {2, 1, 4, 8, 5, 6, 3, 7}
5260: * Struct []
5261: */
5262:
5263: /* This loop fills the array Tvar from the string 'model'.*/
5264: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5265: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5266: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5267: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5268: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5269: /* k=1 Tvar[1]=2 (from V2) */
5270: /* k=5 Tvar[5] */
5271: /* for (k=1; k<=cptcovn;k++) { */
5272: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5273: /* } */
5274: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
5275: /*
5276: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5277: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5278: Tvar[k]=0;
5279: cptcovage=0;
5280: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5281: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5282: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5283: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5284: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5285: /*scanf("%d",i);*/
5286: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5287: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5288: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5289: /* covar is not filled and then is empty */
5290: cptcovprod--;
5291: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5292: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2 */
5293: cptcovage++; /* Sums the number of covariates which include age as a product */
5294: Tage[cptcovage]=k; /* Tage[1] = 4 */
5295: /*printf("stre=%s ", stre);*/
5296: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5297: cptcovprod--;
5298: cutl(stre,strb,strc,'V');
5299: Tvar[k]=atoi(stre);
5300: cptcovage++;
5301: Tage[cptcovage]=k;
5302: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5303: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5304: cptcovn++;
5305: cptcovprodnoage++;k1++;
5306: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5307: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5308: because this model-covariate is a construction we invent a new column
5309: ncovcol + k1
5310: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5311: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5312: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5313: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5314: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5315: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5316: k2=k2+2;
5317: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5318: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5319: for (i=1; i<=lastobs;i++){
5320: /* Computes the new covariate which is a product of
5321: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5322: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5323: }
5324: } /* End age is not in the model */
5325: } /* End if model includes a product */
5326: else { /* no more sum */
5327: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5328: /* scanf("%d",i);*/
5329: cutl(strd,strc,strb,'V');
5330: ks++; /**< Number of simple covariates */
5331: cptcovn++;
5332: Tvar[k]=atoi(strd);
5333: }
5334: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5335: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5336: scanf("%d",i);*/
5337: } /* end of loop + */
5338: } /* end model */
5339:
5340: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5341: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5342:
5343: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5344: printf("cptcovprod=%d ", cptcovprod);
5345: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5346:
5347: scanf("%d ",i);*/
5348:
5349:
5350: return (0); /* with covar[new additional covariate if product] and Tage if age */
5351: /*endread:*/
5352: printf("Exiting decodemodel: ");
5353: return (1);
5354: }
5355:
5356: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5357: {
5358: int i, m;
5359:
5360: for (i=1; i<=imx; i++) {
5361: for(m=2; (m<= maxwav); m++) {
5362: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5363: anint[m][i]=9999;
5364: s[m][i]=-1;
5365: }
5366: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5367: *nberr = *nberr + 1;
5368: 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);
5369: 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);
5370: s[m][i]=-1;
5371: }
5372: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5373: (*nberr)++;
5374: 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]);
5375: 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]);
5376: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5377: }
5378: }
5379: }
5380:
5381: for (i=1; i<=imx; i++) {
5382: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5383: for(m=firstpass; (m<= lastpass); m++){
5384: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5385: if (s[m][i] >= nlstate+1) {
5386: if(agedc[i]>0){
5387: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5388: agev[m][i]=agedc[i];
5389: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5390: }else {
5391: if ((int)andc[i]!=9999){
5392: nbwarn++;
5393: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5394: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5395: agev[m][i]=-1;
5396: }
5397: }
5398: } /* agedc > 0 */
5399: }
5400: else if(s[m][i] !=9){ /* Standard case, age in fractional
5401: years but with the precision of a month */
5402: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5403: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5404: agev[m][i]=1;
5405: else if(agev[m][i] < *agemin){
5406: *agemin=agev[m][i];
5407: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5408: }
5409: else if(agev[m][i] >*agemax){
5410: *agemax=agev[m][i];
5411: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5412: }
5413: /*agev[m][i]=anint[m][i]-annais[i];*/
5414: /* agev[m][i] = age[i]+2*m;*/
5415: }
5416: else { /* =9 */
5417: agev[m][i]=1;
5418: s[m][i]=-1;
5419: }
5420: }
5421: else /*= 0 Unknown */
5422: agev[m][i]=1;
5423: }
5424:
5425: }
5426: for (i=1; i<=imx; i++) {
5427: for(m=firstpass; (m<=lastpass); m++){
5428: if (s[m][i] > (nlstate+ndeath)) {
5429: (*nberr)++;
5430: 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);
5431: 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);
5432: return 1;
5433: }
5434: }
5435: }
5436:
5437: /*for (i=1; i<=imx; i++){
5438: for (m=firstpass; (m<lastpass); m++){
5439: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5440: }
5441:
5442: }*/
5443:
5444:
5445: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5446: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5447:
5448: return (0);
5449: /* endread:*/
5450: printf("Exiting calandcheckages: ");
5451: return (1);
5452: }
5453:
5454: void syscompilerinfo()
5455: {
5456: /* #include "syscompilerinfo.h"*/
5457: /* #include <gnu/libc-version.h> */ /* Only on gnu */
5458: #include <stdint.h>
5459: printf("Compiled with:");fprintf(ficlog,"Compiled with:");
5460: #if defined(__clang__)
5461: printf(" Clang/LLVM");fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
5462: #endif
5463: #if defined(__ICC) || defined(__INTEL_COMPILER)
5464: printf(" Intel ICC/ICPC");fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
5465: #endif
5466: #if defined(__GNUC__) || defined(__GNUG__)
5467: printf(" GNU GCC/G++");fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
5468: #endif
5469: #if defined(__HP_cc) || defined(__HP_aCC)
5470: printf(" Hewlett-Packard C/aC++");fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
5471: #endif
5472: #if defined(__IBMC__) || defined(__IBMCPP__)
5473: printf(" IBM XL C/C++"); fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
5474: #endif
5475: #if defined(_MSC_VER)
5476: printf(" Microsoft Visual Studio");fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
5477: #endif
5478: #if defined(__PGI)
5479: printf(" Portland Group PGCC/PGCPP");fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
5480: #endif
5481: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
5482: printf(" Oracle Solaris Studio");fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
5483: #endif
5484: printf(". ");fprintf(ficlog,". ");
5485:
5486: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
5487: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
5488: // Windows (x64 and x86)
5489: #elif __unix__ // all unices, not all compilers
5490: // Unix
5491: #elif __linux__
5492: // linux
5493: #elif __APPLE__
5494: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though...
5495: #endif
5496:
5497: /* __MINGW32__ */
5498: /* __CYGWIN__ */
5499: /* __MINGW64__ */
5500: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
5501: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
5502: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
5503: /* _WIN64 // Defined for applications for Win64. */
5504: /* _M_X64 // Defined for compilations that target x64 processors. */
5505: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
5506:
5507: #if UINTPTR_MAX == 0xffffffff
5508: printf(" 32-bit.\n"); fprintf(ficlog," 32-bit.\n");/* 32-bit */
5509: #elif UINTPTR_MAX == 0xffffffffffffffff
5510: printf(" 64-bit.\n"); fprintf(ficlog," 64-bit.\n");/* 64-bit */
5511: #else
5512: printf(" wtf-bit.\n"); fprintf(ficlog," wtf-bit.\n");/* wtf */
5513: #endif
5514:
5515: /* struct utsname sysInfo;
5516:
5517: if (uname(&sysInfo) != -1) {
5518: printf(" %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5519: fprintf(ficlog," %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
5520: }
5521: else
5522: perror("uname() error");
5523: */
5524: #if defined(__GNUC__)
5525: # if defined(__GNUC_PATCHLEVEL__)
5526: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5527: + __GNUC_MINOR__ * 100 \
5528: + __GNUC_PATCHLEVEL__)
5529: # else
5530: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
5531: + __GNUC_MINOR__ * 100)
5532: # endif
5533: printf("GNU C version %d.\n", __GNUC_VERSION__);
5534: fprintf(ficlog, "GNU C version %d.\n", __GNUC_VERSION__);
5535: #endif
5536: #if defined(_MSC_VER)
5537: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5538: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5539: #endif
5540:
5541: /* printf("GNU libc version: %s\n", gnu_get_libc_version()); */
5542:
5543: }
5544:
5545: /***********************************************/
5546: /**************** Main Program *****************/
5547: /***********************************************/
5548:
5549: int main(int argc, char *argv[])
5550: {
5551: #ifdef GSL
5552: const gsl_multimin_fminimizer_type *T;
5553: size_t iteri = 0, it;
5554: int rval = GSL_CONTINUE;
5555: int status = GSL_SUCCESS;
5556: double ssval;
5557: #endif
5558: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
5559: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
5560:
5561: int jj, ll, li, lj, lk;
5562: int numlinepar=0; /* Current linenumber of parameter file */
5563: int itimes;
5564: int NDIM=2;
5565: int vpopbased=0;
5566:
5567: char ca[32], cb[32];
5568: /* FILE *fichtm; *//* Html File */
5569: /* FILE *ficgp;*/ /*Gnuplot File */
5570: struct stat info;
5571: double agedeb;
5572: double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
5573:
5574: double fret;
5575: double dum; /* Dummy variable */
5576: double ***p3mat;
5577: double ***mobaverage;
5578:
5579: char line[MAXLINE];
5580: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
5581: char pathr[MAXLINE], pathimach[MAXLINE];
5582: char *tok, *val; /* pathtot */
5583: int firstobs=1, lastobs=10;
5584: int c, h , cpt;
5585: int jl;
5586: int i1, j1, jk, stepsize;
5587: int *tab;
5588: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
5589: int mobilav=0,popforecast=0;
5590: int hstepm, nhstepm;
5591: int agemortsup;
5592: float sumlpop=0.;
5593: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
5594: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
5595:
5596: double bage=0, fage=110, age, agelim, agebase;
5597: double ftolpl=FTOL;
5598: double **prlim;
5599: double ***param; /* Matrix of parameters */
5600: double *p;
5601: double **matcov; /* Matrix of covariance */
5602: double ***delti3; /* Scale */
5603: double *delti; /* Scale */
5604: double ***eij, ***vareij;
5605: double **varpl; /* Variances of prevalence limits by age */
5606: double *epj, vepp;
5607:
5608: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
5609: double **ximort;
5610: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
5611: int *dcwave;
5612:
5613: char z[1]="c";
5614:
5615: /*char *strt;*/
5616: char strtend[80];
5617:
5618:
5619: /* setlocale (LC_ALL, ""); */
5620: /* bindtextdomain (PACKAGE, LOCALEDIR); */
5621: /* textdomain (PACKAGE); */
5622: /* setlocale (LC_CTYPE, ""); */
5623: /* setlocale (LC_MESSAGES, ""); */
5624:
5625: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
5626: rstart_time = time(NULL);
5627: /* (void) gettimeofday(&start_time,&tzp);*/
5628: start_time = *localtime(&rstart_time);
5629: curr_time=start_time;
5630: /*tml = *localtime(&start_time.tm_sec);*/
5631: /* strcpy(strstart,asctime(&tml)); */
5632: strcpy(strstart,asctime(&start_time));
5633:
5634: /* printf("Localtime (at start)=%s",strstart); */
5635: /* tp.tm_sec = tp.tm_sec +86400; */
5636: /* tm = *localtime(&start_time.tm_sec); */
5637: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
5638: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
5639: /* tmg.tm_hour=tmg.tm_hour + 1; */
5640: /* tp.tm_sec = mktime(&tmg); */
5641: /* strt=asctime(&tmg); */
5642: /* printf("Time(after) =%s",strstart); */
5643: /* (void) time (&time_value);
5644: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
5645: * tm = *localtime(&time_value);
5646: * strstart=asctime(&tm);
5647: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
5648: */
5649:
5650: nberr=0; /* Number of errors and warnings */
5651: nbwarn=0;
5652: getcwd(pathcd, size);
5653:
5654: printf("\n%s\n%s",version,fullversion);
5655: if(argc <=1){
5656: printf("\nEnter the parameter file name: ");
5657: fgets(pathr,FILENAMELENGTH,stdin);
5658: i=strlen(pathr);
5659: if(pathr[i-1]=='\n')
5660: pathr[i-1]='\0';
5661: i=strlen(pathr);
5662: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
5663: pathr[i-1]='\0';
5664: for (tok = pathr; tok != NULL; ){
5665: printf("Pathr |%s|\n",pathr);
5666: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
5667: printf("val= |%s| pathr=%s\n",val,pathr);
5668: strcpy (pathtot, val);
5669: if(pathr[0] == '\0') break; /* Dirty */
5670: }
5671: }
5672: else{
5673: strcpy(pathtot,argv[1]);
5674: }
5675: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
5676: /*cygwin_split_path(pathtot,path,optionfile);
5677: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
5678: /* cutv(path,optionfile,pathtot,'\\');*/
5679:
5680: /* Split argv[0], imach program to get pathimach */
5681: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
5682: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5683: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
5684: /* strcpy(pathimach,argv[0]); */
5685: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
5686: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
5687: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
5688: chdir(path); /* Can be a relative path */
5689: if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
5690: printf("Current directory %s!\n",pathcd);
5691: strcpy(command,"mkdir ");
5692: strcat(command,optionfilefiname);
5693: if((outcmd=system(command)) != 0){
5694: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
5695: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
5696: /* fclose(ficlog); */
5697: /* exit(1); */
5698: }
5699: /* if((imk=mkdir(optionfilefiname))<0){ */
5700: /* perror("mkdir"); */
5701: /* } */
5702:
5703: /*-------- arguments in the command line --------*/
5704:
5705: /* Log file */
5706: strcat(filelog, optionfilefiname);
5707: strcat(filelog,".log"); /* */
5708: if((ficlog=fopen(filelog,"w"))==NULL) {
5709: printf("Problem with logfile %s\n",filelog);
5710: goto end;
5711: }
5712: fprintf(ficlog,"Log filename:%s\n",filelog);
5713: fprintf(ficlog,"\n%s\n%s",version,fullversion);
5714: fprintf(ficlog,"\nEnter the parameter file name: \n");
5715: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
5716: path=%s \n\
5717: optionfile=%s\n\
5718: optionfilext=%s\n\
5719: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
5720:
5721: syscompilerinfo();
5722:
5723: printf("Local time (at start):%s",strstart);
5724: fprintf(ficlog,"Local time (at start): %s",strstart);
5725: fflush(ficlog);
5726: /* (void) gettimeofday(&curr_time,&tzp); */
5727: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
5728:
5729: /* */
5730: strcpy(fileres,"r");
5731: strcat(fileres, optionfilefiname);
5732: strcat(fileres,".txt"); /* Other files have txt extension */
5733:
5734: /*---------arguments file --------*/
5735:
5736: if((ficpar=fopen(optionfile,"r"))==NULL) {
5737: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5738: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
5739: fflush(ficlog);
5740: /* goto end; */
5741: exit(70);
5742: }
5743:
5744:
5745:
5746: strcpy(filereso,"o");
5747: strcat(filereso,fileres);
5748: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
5749: printf("Problem with Output resultfile: %s\n", filereso);
5750: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
5751: fflush(ficlog);
5752: goto end;
5753: }
5754:
5755: /* Reads comments: lines beginning with '#' */
5756: numlinepar=0;
5757: while((c=getc(ficpar))=='#' && c!= EOF){
5758: ungetc(c,ficpar);
5759: fgets(line, MAXLINE, ficpar);
5760: numlinepar++;
5761: fputs(line,stdout);
5762: fputs(line,ficparo);
5763: fputs(line,ficlog);
5764: }
5765: ungetc(c,ficpar);
5766:
5767: 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);
5768: numlinepar++;
5769: 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);
5770: 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);
5771: 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);
5772: fflush(ficlog);
5773: while((c=getc(ficpar))=='#' && c!= EOF){
5774: ungetc(c,ficpar);
5775: fgets(line, MAXLINE, ficpar);
5776: numlinepar++;
5777: fputs(line, stdout);
5778: //puts(line);
5779: fputs(line,ficparo);
5780: fputs(line,ficlog);
5781: }
5782: ungetc(c,ficpar);
5783:
5784:
5785: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
5786: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
5787: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
5788: v1+v2*age+v2*v3 makes cptcovn = 3
5789: */
5790: if (strlen(model)>1)
5791: 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*/
5792: else
5793: ncovmodel=2;
5794: nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
5795: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
5796: npar= nforce*ncovmodel; /* Number of parameters like aij*/
5797: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
5798: 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);
5799: 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);
5800: fflush(stdout);
5801: fclose (ficlog);
5802: goto end;
5803: }
5804: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5805: delti=delti3[1][1];
5806: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
5807: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
5808: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5809: printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5810: fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
5811: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
5812: fclose (ficparo);
5813: fclose (ficlog);
5814: goto end;
5815: exit(0);
5816: }
5817: else if(mle==-3) {
5818: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
5819: printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5820: fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
5821: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5822: matcov=matrix(1,npar,1,npar);
5823: }
5824: else{
5825: /* Read guessed parameters */
5826: /* Reads comments: lines beginning with '#' */
5827: while((c=getc(ficpar))=='#' && c!= EOF){
5828: ungetc(c,ficpar);
5829: fgets(line, MAXLINE, ficpar);
5830: numlinepar++;
5831: fputs(line,stdout);
5832: fputs(line,ficparo);
5833: fputs(line,ficlog);
5834: }
5835: ungetc(c,ficpar);
5836:
5837: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
5838: for(i=1; i <=nlstate; i++){
5839: j=0;
5840: for(jj=1; jj <=nlstate+ndeath; jj++){
5841: if(jj==i) continue;
5842: j++;
5843: fscanf(ficpar,"%1d%1d",&i1,&j1);
5844: if ((i1 != i) && (j1 != j)){
5845: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
5846: It might be a problem of design; if ncovcol and the model are correct\n \
5847: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
5848: exit(1);
5849: }
5850: fprintf(ficparo,"%1d%1d",i1,j1);
5851: if(mle==1)
5852: printf("%1d%1d",i,j);
5853: fprintf(ficlog,"%1d%1d",i,j);
5854: for(k=1; k<=ncovmodel;k++){
5855: fscanf(ficpar," %lf",¶m[i][j][k]);
5856: if(mle==1){
5857: printf(" %lf",param[i][j][k]);
5858: fprintf(ficlog," %lf",param[i][j][k]);
5859: }
5860: else
5861: fprintf(ficlog," %lf",param[i][j][k]);
5862: fprintf(ficparo," %lf",param[i][j][k]);
5863: }
5864: fscanf(ficpar,"\n");
5865: numlinepar++;
5866: if(mle==1)
5867: printf("\n");
5868: fprintf(ficlog,"\n");
5869: fprintf(ficparo,"\n");
5870: }
5871: }
5872: fflush(ficlog);
5873:
5874: /* Reads scales values */
5875: p=param[1][1];
5876:
5877: /* Reads comments: lines beginning with '#' */
5878: while((c=getc(ficpar))=='#' && c!= EOF){
5879: ungetc(c,ficpar);
5880: fgets(line, MAXLINE, ficpar);
5881: numlinepar++;
5882: fputs(line,stdout);
5883: fputs(line,ficparo);
5884: fputs(line,ficlog);
5885: }
5886: ungetc(c,ficpar);
5887:
5888: for(i=1; i <=nlstate; i++){
5889: for(j=1; j <=nlstate+ndeath-1; j++){
5890: fscanf(ficpar,"%1d%1d",&i1,&j1);
5891: if ( (i1-i) * (j1-j) != 0){
5892: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
5893: exit(1);
5894: }
5895: printf("%1d%1d",i,j);
5896: fprintf(ficparo,"%1d%1d",i1,j1);
5897: fprintf(ficlog,"%1d%1d",i1,j1);
5898: for(k=1; k<=ncovmodel;k++){
5899: fscanf(ficpar,"%le",&delti3[i][j][k]);
5900: printf(" %le",delti3[i][j][k]);
5901: fprintf(ficparo," %le",delti3[i][j][k]);
5902: fprintf(ficlog," %le",delti3[i][j][k]);
5903: }
5904: fscanf(ficpar,"\n");
5905: numlinepar++;
5906: printf("\n");
5907: fprintf(ficparo,"\n");
5908: fprintf(ficlog,"\n");
5909: }
5910: }
5911: fflush(ficlog);
5912:
5913: /* Reads covariance matrix */
5914: delti=delti3[1][1];
5915:
5916:
5917: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
5918:
5919: /* Reads comments: lines beginning with '#' */
5920: while((c=getc(ficpar))=='#' && c!= EOF){
5921: ungetc(c,ficpar);
5922: fgets(line, MAXLINE, ficpar);
5923: numlinepar++;
5924: fputs(line,stdout);
5925: fputs(line,ficparo);
5926: fputs(line,ficlog);
5927: }
5928: ungetc(c,ficpar);
5929:
5930: matcov=matrix(1,npar,1,npar);
5931: for(i=1; i <=npar; i++)
5932: for(j=1; j <=npar; j++) matcov[i][j]=0.;
5933:
5934: for(i=1; i <=npar; i++){
5935: fscanf(ficpar,"%s",str);
5936: if(mle==1)
5937: printf("%s",str);
5938: fprintf(ficlog,"%s",str);
5939: fprintf(ficparo,"%s",str);
5940: for(j=1; j <=i; j++){
5941: fscanf(ficpar," %le",&matcov[i][j]);
5942: if(mle==1){
5943: printf(" %.5le",matcov[i][j]);
5944: }
5945: fprintf(ficlog," %.5le",matcov[i][j]);
5946: fprintf(ficparo," %.5le",matcov[i][j]);
5947: }
5948: fscanf(ficpar,"\n");
5949: numlinepar++;
5950: if(mle==1)
5951: printf("\n");
5952: fprintf(ficlog,"\n");
5953: fprintf(ficparo,"\n");
5954: }
5955: for(i=1; i <=npar; i++)
5956: for(j=i+1;j<=npar;j++)
5957: matcov[i][j]=matcov[j][i];
5958:
5959: if(mle==1)
5960: printf("\n");
5961: fprintf(ficlog,"\n");
5962:
5963: fflush(ficlog);
5964:
5965: /*-------- Rewriting parameter file ----------*/
5966: strcpy(rfileres,"r"); /* "Rparameterfile */
5967: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
5968: strcat(rfileres,"."); /* */
5969: strcat(rfileres,optionfilext); /* Other files have txt extension */
5970: if((ficres =fopen(rfileres,"w"))==NULL) {
5971: printf("Problem writing new parameter file: %s\n", fileres);goto end;
5972: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
5973: }
5974: fprintf(ficres,"#%s\n",version);
5975: } /* End of mle != -3 */
5976:
5977:
5978: n= lastobs;
5979: num=lvector(1,n);
5980: moisnais=vector(1,n);
5981: annais=vector(1,n);
5982: moisdc=vector(1,n);
5983: andc=vector(1,n);
5984: agedc=vector(1,n);
5985: cod=ivector(1,n);
5986: weight=vector(1,n);
5987: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
5988: mint=matrix(1,maxwav,1,n);
5989: anint=matrix(1,maxwav,1,n);
5990: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
5991: tab=ivector(1,NCOVMAX);
5992: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
5993:
5994: /* Reads data from file datafile */
5995: if (readdata(datafile, firstobs, lastobs, &imx)==1)
5996: goto end;
5997:
5998: /* Calculation of the number of parameters from char model */
5999: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6000: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6001: k=3 V4 Tvar[k=3]= 4 (from V4)
6002: k=2 V1 Tvar[k=2]= 1 (from V1)
6003: k=1 Tvar[1]=2 (from V2)
6004: */
6005: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6006: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6007: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6008: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6009: */
6010: /* For model-covariate k tells which data-covariate to use but
6011: because this model-covariate is a construction we invent a new column
6012: ncovcol + k1
6013: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6014: Tvar[3=V1*V4]=4+1 etc */
6015: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6016: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6017: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6018: */
6019: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6020: 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
6021: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6022: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6023: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6024: 4 covariates (3 plus signs)
6025: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6026: */
6027:
6028: if(decodemodel(model, lastobs) == 1)
6029: goto end;
6030:
6031: if((double)(lastobs-imx)/(double)imx > 1.10){
6032: nbwarn++;
6033: 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);
6034: 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);
6035: }
6036: /* if(mle==1){*/
6037: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6038: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6039: }
6040:
6041: /*-calculation of age at interview from date of interview and age at death -*/
6042: agev=matrix(1,maxwav,1,imx);
6043:
6044: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6045: goto end;
6046:
6047:
6048: agegomp=(int)agemin;
6049: free_vector(moisnais,1,n);
6050: free_vector(annais,1,n);
6051: /* free_matrix(mint,1,maxwav,1,n);
6052: free_matrix(anint,1,maxwav,1,n);*/
6053: free_vector(moisdc,1,n);
6054: free_vector(andc,1,n);
6055: /* */
6056:
6057: wav=ivector(1,imx);
6058: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6059: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6060: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6061:
6062: /* Concatenates waves */
6063: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6064: /* */
6065:
6066: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6067:
6068: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6069: ncodemax[1]=1;
6070: Ndum =ivector(-1,NCOVMAX);
6071: if (ncovmodel > 2)
6072: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6073:
6074: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6075: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6076: h=0;
6077:
6078:
6079: /*if (cptcovn > 0) */
6080:
6081:
6082: m=pow(2,cptcoveff);
6083:
6084: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6085: 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 */
6086: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6087: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6088: h++;
6089: if (h>m)
6090: h=1;
6091: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6092: * h 1 2 3 4
6093: *______________________________
6094: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6095: * 2 2 1 1 1
6096: * 3 i=2 1 2 1 1
6097: * 4 2 2 1 1
6098: * 5 i=3 1 i=2 1 2 1
6099: * 6 2 1 2 1
6100: * 7 i=4 1 2 2 1
6101: * 8 2 2 2 1
6102: * 9 i=5 1 i=3 1 i=2 1 1
6103: * 10 2 1 1 1
6104: * 11 i=6 1 2 1 1
6105: * 12 2 2 1 1
6106: * 13 i=7 1 i=4 1 2 1
6107: * 14 2 1 2 1
6108: * 15 i=8 1 2 2 1
6109: * 16 2 2 2 1
6110: */
6111: codtab[h][k]=j;
6112: /*codtab[h][Tvar[k]]=j;*/
6113: 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]]);
6114: }
6115: }
6116: }
6117: }
6118: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6119: codtab[1][2]=1;codtab[2][2]=2; */
6120: /* for(i=1; i <=m ;i++){
6121: for(k=1; k <=cptcovn; k++){
6122: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6123: }
6124: printf("\n");
6125: }
6126: scanf("%d",i);*/
6127:
6128: free_ivector(Ndum,-1,NCOVMAX);
6129:
6130:
6131:
6132: /*------------ gnuplot -------------*/
6133: strcpy(optionfilegnuplot,optionfilefiname);
6134: if(mle==-3)
6135: strcat(optionfilegnuplot,"-mort");
6136: strcat(optionfilegnuplot,".gp");
6137:
6138: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6139: printf("Problem with file %s",optionfilegnuplot);
6140: }
6141: else{
6142: fprintf(ficgp,"\n# %s\n", version);
6143: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6144: //fprintf(ficgp,"set missing 'NaNq'\n");
6145: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6146: }
6147: /* fclose(ficgp);*/
6148: /*--------- index.htm --------*/
6149:
6150: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6151: if(mle==-3)
6152: strcat(optionfilehtm,"-mort");
6153: strcat(optionfilehtm,".htm");
6154: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6155: printf("Problem with %s \n",optionfilehtm);
6156: exit(0);
6157: }
6158:
6159: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6160: strcat(optionfilehtmcov,"-cov.htm");
6161: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6162: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6163: }
6164: else{
6165: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6166: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6167: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6168: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6169: }
6170:
6171: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6172: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6173: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6174: \n\
6175: <hr size=\"2\" color=\"#EC5E5E\">\
6176: <ul><li><h4>Parameter files</h4>\n\
6177: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6178: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6179: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6180: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6181: - Date and time at start: %s</ul>\n",\
6182: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6183: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6184: fileres,fileres,\
6185: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6186: fflush(fichtm);
6187:
6188: strcpy(pathr,path);
6189: strcat(pathr,optionfilefiname);
6190: chdir(optionfilefiname); /* Move to directory named optionfile */
6191:
6192: /* Calculates basic frequencies. Computes observed prevalence at single age
6193: and prints on file fileres'p'. */
6194: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6195:
6196: fprintf(fichtm,"\n");
6197: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6198: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6199: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6200: imx,agemin,agemax,jmin,jmax,jmean);
6201: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6202: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6203: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6204: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6205: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6206:
6207:
6208: /* For Powell, parameters are in a vector p[] starting at p[1]
6209: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6210: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6211:
6212: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6213:
6214: if (mle==-3){
6215: ximort=matrix(1,NDIM,1,NDIM);
6216: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6217: cens=ivector(1,n);
6218: ageexmed=vector(1,n);
6219: agecens=vector(1,n);
6220: dcwave=ivector(1,n);
6221:
6222: for (i=1; i<=imx; i++){
6223: dcwave[i]=-1;
6224: for (m=firstpass; m<=lastpass; m++)
6225: if (s[m][i]>nlstate) {
6226: dcwave[i]=m;
6227: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
6228: break;
6229: }
6230: }
6231:
6232: for (i=1; i<=imx; i++) {
6233: if (wav[i]>0){
6234: ageexmed[i]=agev[mw[1][i]][i];
6235: j=wav[i];
6236: agecens[i]=1.;
6237:
6238: if (ageexmed[i]> 1 && wav[i] > 0){
6239: agecens[i]=agev[mw[j][i]][i];
6240: cens[i]= 1;
6241: }else if (ageexmed[i]< 1)
6242: cens[i]= -1;
6243: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
6244: cens[i]=0 ;
6245: }
6246: else cens[i]=-1;
6247: }
6248:
6249: for (i=1;i<=NDIM;i++) {
6250: for (j=1;j<=NDIM;j++)
6251: ximort[i][j]=(i == j ? 1.0 : 0.0);
6252: }
6253:
6254: /*p[1]=0.0268; p[NDIM]=0.083;*/
6255: /*printf("%lf %lf", p[1], p[2]);*/
6256:
6257:
6258: #ifdef GSL
6259: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
6260: #else
6261: printf("Powell\n"); fprintf(ficlog,"Powell\n");
6262: #endif
6263: strcpy(filerespow,"pow-mort");
6264: strcat(filerespow,fileres);
6265: if((ficrespow=fopen(filerespow,"w"))==NULL) {
6266: printf("Problem with resultfile: %s\n", filerespow);
6267: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
6268: }
6269: #ifdef GSL
6270: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
6271: #else
6272: fprintf(ficrespow,"# Powell\n# iter -2*LL");
6273: #endif
6274: /* for (i=1;i<=nlstate;i++)
6275: for(j=1;j<=nlstate+ndeath;j++)
6276: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
6277: */
6278: fprintf(ficrespow,"\n");
6279: #ifdef GSL
6280: /* gsl starts here */
6281: T = gsl_multimin_fminimizer_nmsimplex;
6282: gsl_multimin_fminimizer *sfm = NULL;
6283: gsl_vector *ss, *x;
6284: gsl_multimin_function minex_func;
6285:
6286: /* Initial vertex size vector */
6287: ss = gsl_vector_alloc (NDIM);
6288:
6289: if (ss == NULL){
6290: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
6291: }
6292: /* Set all step sizes to 1 */
6293: gsl_vector_set_all (ss, 0.001);
6294:
6295: /* Starting point */
6296:
6297: x = gsl_vector_alloc (NDIM);
6298:
6299: if (x == NULL){
6300: gsl_vector_free(ss);
6301: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
6302: }
6303:
6304: /* Initialize method and iterate */
6305: /* p[1]=0.0268; p[NDIM]=0.083; */
6306: /* gsl_vector_set(x, 0, 0.0268); */
6307: /* gsl_vector_set(x, 1, 0.083); */
6308: gsl_vector_set(x, 0, p[1]);
6309: gsl_vector_set(x, 1, p[2]);
6310:
6311: minex_func.f = &gompertz_f;
6312: minex_func.n = NDIM;
6313: minex_func.params = (void *)&p; /* ??? */
6314:
6315: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
6316: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
6317:
6318: printf("Iterations beginning .....\n\n");
6319: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
6320:
6321: iteri=0;
6322: while (rval == GSL_CONTINUE){
6323: iteri++;
6324: status = gsl_multimin_fminimizer_iterate(sfm);
6325:
6326: if (status) printf("error: %s\n", gsl_strerror (status));
6327: fflush(0);
6328:
6329: if (status)
6330: break;
6331:
6332: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
6333: ssval = gsl_multimin_fminimizer_size (sfm);
6334:
6335: if (rval == GSL_SUCCESS)
6336: printf ("converged to a local maximum at\n");
6337:
6338: printf("%5d ", iteri);
6339: for (it = 0; it < NDIM; it++){
6340: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
6341: }
6342: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
6343: }
6344:
6345: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
6346:
6347: gsl_vector_free(x); /* initial values */
6348: gsl_vector_free(ss); /* inital step size */
6349: for (it=0; it<NDIM; it++){
6350: p[it+1]=gsl_vector_get(sfm->x,it);
6351: fprintf(ficrespow," %.12lf", p[it]);
6352: }
6353: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
6354: #endif
6355: #ifdef POWELL
6356: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
6357: #endif
6358: fclose(ficrespow);
6359:
6360: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
6361:
6362: for(i=1; i <=NDIM; i++)
6363: for(j=i+1;j<=NDIM;j++)
6364: matcov[i][j]=matcov[j][i];
6365:
6366: printf("\nCovariance matrix\n ");
6367: for(i=1; i <=NDIM; i++) {
6368: for(j=1;j<=NDIM;j++){
6369: printf("%f ",matcov[i][j]);
6370: }
6371: printf("\n ");
6372: }
6373:
6374: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
6375: for (i=1;i<=NDIM;i++)
6376: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
6377:
6378: lsurv=vector(1,AGESUP);
6379: lpop=vector(1,AGESUP);
6380: tpop=vector(1,AGESUP);
6381: lsurv[agegomp]=100000;
6382:
6383: for (k=agegomp;k<=AGESUP;k++) {
6384: agemortsup=k;
6385: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
6386: }
6387:
6388: for (k=agegomp;k<agemortsup;k++)
6389: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
6390:
6391: for (k=agegomp;k<agemortsup;k++){
6392: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
6393: sumlpop=sumlpop+lpop[k];
6394: }
6395:
6396: tpop[agegomp]=sumlpop;
6397: for (k=agegomp;k<(agemortsup-3);k++){
6398: /* tpop[k+1]=2;*/
6399: tpop[k+1]=tpop[k]-lpop[k];
6400: }
6401:
6402:
6403: printf("\nAge lx qx dx Lx Tx e(x)\n");
6404: for (k=agegomp;k<(agemortsup-2);k++)
6405: 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]);
6406:
6407:
6408: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6409: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6410:
6411: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
6412: stepm, weightopt,\
6413: model,imx,p,matcov,agemortsup);
6414:
6415: free_vector(lsurv,1,AGESUP);
6416: free_vector(lpop,1,AGESUP);
6417: free_vector(tpop,1,AGESUP);
6418: #ifdef GSL
6419: free_ivector(cens,1,n);
6420: free_vector(agecens,1,n);
6421: free_ivector(dcwave,1,n);
6422: free_matrix(ximort,1,NDIM,1,NDIM);
6423: #endif
6424: } /* Endof if mle==-3 */
6425:
6426: else{ /* For mle >=1 */
6427: globpr=0;/* debug */
6428: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6429: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6430: for (k=1; k<=npar;k++)
6431: printf(" %d %8.5f",k,p[k]);
6432: printf("\n");
6433: globpr=1; /* to print the contributions */
6434: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
6435: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
6436: for (k=1; k<=npar;k++)
6437: printf(" %d %8.5f",k,p[k]);
6438: printf("\n");
6439: if(mle>=1){ /* Could be 1 or 2 */
6440: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
6441: }
6442:
6443: /*--------- results files --------------*/
6444: 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);
6445:
6446:
6447: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6448: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6449: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
6450: for(i=1,jk=1; i <=nlstate; i++){
6451: for(k=1; k <=(nlstate+ndeath); k++){
6452: if (k != i) {
6453: printf("%d%d ",i,k);
6454: fprintf(ficlog,"%d%d ",i,k);
6455: fprintf(ficres,"%1d%1d ",i,k);
6456: for(j=1; j <=ncovmodel; j++){
6457: printf("%lf ",p[jk]);
6458: fprintf(ficlog,"%lf ",p[jk]);
6459: fprintf(ficres,"%lf ",p[jk]);
6460: jk++;
6461: }
6462: printf("\n");
6463: fprintf(ficlog,"\n");
6464: fprintf(ficres,"\n");
6465: }
6466: }
6467: }
6468: if(mle!=0){
6469: /* Computing hessian and covariance matrix */
6470: ftolhess=ftol; /* Usually correct */
6471: hesscov(matcov, p, npar, delti, ftolhess, func);
6472: }
6473: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
6474: printf("# Scales (for hessian or gradient estimation)\n");
6475: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
6476: for(i=1,jk=1; i <=nlstate; i++){
6477: for(j=1; j <=nlstate+ndeath; j++){
6478: if (j!=i) {
6479: fprintf(ficres,"%1d%1d",i,j);
6480: printf("%1d%1d",i,j);
6481: fprintf(ficlog,"%1d%1d",i,j);
6482: for(k=1; k<=ncovmodel;k++){
6483: printf(" %.5e",delti[jk]);
6484: fprintf(ficlog," %.5e",delti[jk]);
6485: fprintf(ficres," %.5e",delti[jk]);
6486: jk++;
6487: }
6488: printf("\n");
6489: fprintf(ficlog,"\n");
6490: fprintf(ficres,"\n");
6491: }
6492: }
6493: }
6494:
6495: 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");
6496: if(mle>=1)
6497: 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");
6498: 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");
6499: /* # 121 Var(a12)\n\ */
6500: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6501: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6502: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6503: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6504: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6505: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6506: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6507:
6508:
6509: /* Just to have a covariance matrix which will be more understandable
6510: even is we still don't want to manage dictionary of variables
6511: */
6512: for(itimes=1;itimes<=2;itimes++){
6513: jj=0;
6514: for(i=1; i <=nlstate; i++){
6515: for(j=1; j <=nlstate+ndeath; j++){
6516: if(j==i) continue;
6517: for(k=1; k<=ncovmodel;k++){
6518: jj++;
6519: ca[0]= k+'a'-1;ca[1]='\0';
6520: if(itimes==1){
6521: if(mle>=1)
6522: printf("#%1d%1d%d",i,j,k);
6523: fprintf(ficlog,"#%1d%1d%d",i,j,k);
6524: fprintf(ficres,"#%1d%1d%d",i,j,k);
6525: }else{
6526: if(mle>=1)
6527: printf("%1d%1d%d",i,j,k);
6528: fprintf(ficlog,"%1d%1d%d",i,j,k);
6529: fprintf(ficres,"%1d%1d%d",i,j,k);
6530: }
6531: ll=0;
6532: for(li=1;li <=nlstate; li++){
6533: for(lj=1;lj <=nlstate+ndeath; lj++){
6534: if(lj==li) continue;
6535: for(lk=1;lk<=ncovmodel;lk++){
6536: ll++;
6537: if(ll<=jj){
6538: cb[0]= lk +'a'-1;cb[1]='\0';
6539: if(ll<jj){
6540: if(itimes==1){
6541: if(mle>=1)
6542: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6543: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6544: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6545: }else{
6546: if(mle>=1)
6547: printf(" %.5e",matcov[jj][ll]);
6548: fprintf(ficlog," %.5e",matcov[jj][ll]);
6549: fprintf(ficres," %.5e",matcov[jj][ll]);
6550: }
6551: }else{
6552: if(itimes==1){
6553: if(mle>=1)
6554: printf(" Var(%s%1d%1d)",ca,i,j);
6555: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
6556: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
6557: }else{
6558: if(mle>=1)
6559: printf(" %.5e",matcov[jj][ll]);
6560: fprintf(ficlog," %.5e",matcov[jj][ll]);
6561: fprintf(ficres," %.5e",matcov[jj][ll]);
6562: }
6563: }
6564: }
6565: } /* end lk */
6566: } /* end lj */
6567: } /* end li */
6568: if(mle>=1)
6569: printf("\n");
6570: fprintf(ficlog,"\n");
6571: fprintf(ficres,"\n");
6572: numlinepar++;
6573: } /* end k*/
6574: } /*end j */
6575: } /* end i */
6576: } /* end itimes */
6577:
6578: fflush(ficlog);
6579: fflush(ficres);
6580:
6581: while((c=getc(ficpar))=='#' && c!= EOF){
6582: ungetc(c,ficpar);
6583: fgets(line, MAXLINE, ficpar);
6584: fputs(line,stdout);
6585: fputs(line,ficparo);
6586: }
6587: ungetc(c,ficpar);
6588:
6589: estepm=0;
6590: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
6591: if (estepm==0 || estepm < stepm) estepm=stepm;
6592: if (fage <= 2) {
6593: bage = ageminpar;
6594: fage = agemaxpar;
6595: }
6596:
6597: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
6598: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6599: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
6600:
6601: while((c=getc(ficpar))=='#' && c!= EOF){
6602: ungetc(c,ficpar);
6603: fgets(line, MAXLINE, ficpar);
6604: fputs(line,stdout);
6605: fputs(line,ficparo);
6606: }
6607: ungetc(c,ficpar);
6608:
6609: 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);
6610: 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);
6611: 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);
6612: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
6613: 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);
6614:
6615: while((c=getc(ficpar))=='#' && c!= EOF){
6616: ungetc(c,ficpar);
6617: fgets(line, MAXLINE, ficpar);
6618: fputs(line,stdout);
6619: fputs(line,ficparo);
6620: }
6621: ungetc(c,ficpar);
6622:
6623:
6624: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
6625: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
6626:
6627: fscanf(ficpar,"pop_based=%d\n",&popbased);
6628: fprintf(ficparo,"pop_based=%d\n",popbased);
6629: fprintf(ficres,"pop_based=%d\n",popbased);
6630:
6631: while((c=getc(ficpar))=='#' && c!= EOF){
6632: ungetc(c,ficpar);
6633: fgets(line, MAXLINE, ficpar);
6634: fputs(line,stdout);
6635: fputs(line,ficparo);
6636: }
6637: ungetc(c,ficpar);
6638:
6639: 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);
6640: 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);
6641: 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);
6642: 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);
6643: 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);
6644: /* day and month of proj2 are not used but only year anproj2.*/
6645:
6646:
6647:
6648: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
6649: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
6650:
6651: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
6652: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
6653:
6654: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
6655: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
6656: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
6657:
6658: /*------------ free_vector -------------*/
6659: /* chdir(path); */
6660:
6661: free_ivector(wav,1,imx);
6662: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
6663: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
6664: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
6665: free_lvector(num,1,n);
6666: free_vector(agedc,1,n);
6667: /*free_matrix(covar,0,NCOVMAX,1,n);*/
6668: /*free_matrix(covar,1,NCOVMAX,1,n);*/
6669: fclose(ficparo);
6670: fclose(ficres);
6671:
6672:
6673: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6674: #include "prevlim.h" /* Use ficrespl, ficlog */
6675: fclose(ficrespl);
6676:
6677: #ifdef FREEEXIT2
6678: #include "freeexit2.h"
6679: #endif
6680:
6681: /*------------- h Pij x at various ages ------------*/
6682: #include "hpijx.h"
6683: fclose(ficrespij);
6684:
6685: /*-------------- Variance of one-step probabilities---*/
6686: k=1;
6687: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
6688:
6689:
6690: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6691: for(i=1;i<=AGESUP;i++)
6692: for(j=1;j<=NCOVMAX;j++)
6693: for(k=1;k<=NCOVMAX;k++)
6694: probs[i][j][k]=0.;
6695:
6696: /*---------- Forecasting ------------------*/
6697: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
6698: if(prevfcast==1){
6699: /* if(stepm ==1){*/
6700: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
6701: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
6702: /* } */
6703: /* else{ */
6704: /* erreur=108; */
6705: /* 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); */
6706: /* 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); */
6707: /* } */
6708: }
6709:
6710:
6711: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
6712:
6713: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
6714: /* 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",\
6715: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
6716: */
6717:
6718: if (mobilav!=0) {
6719: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6720: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
6721: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
6722: printf(" Error in movingaverage mobilav=%d\n",mobilav);
6723: }
6724: }
6725:
6726:
6727: /*---------- Health expectancies, no variances ------------*/
6728:
6729: strcpy(filerese,"e");
6730: strcat(filerese,fileres);
6731: if((ficreseij=fopen(filerese,"w"))==NULL) {
6732: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6733: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
6734: }
6735: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
6736: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
6737: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6738: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6739:
6740: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6741: fprintf(ficreseij,"\n#****** ");
6742: for(j=1;j<=cptcoveff;j++) {
6743: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6744: }
6745: fprintf(ficreseij,"******\n");
6746:
6747: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6748: oldm=oldms;savm=savms;
6749: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
6750:
6751: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6752: /*}*/
6753: }
6754: fclose(ficreseij);
6755:
6756:
6757: /*---------- Health expectancies and variances ------------*/
6758:
6759:
6760: strcpy(filerest,"t");
6761: strcat(filerest,fileres);
6762: if((ficrest=fopen(filerest,"w"))==NULL) {
6763: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
6764: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
6765: }
6766: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6767: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
6768:
6769:
6770: strcpy(fileresstde,"stde");
6771: strcat(fileresstde,fileres);
6772: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
6773: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6774: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
6775: }
6776: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6777: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
6778:
6779: strcpy(filerescve,"cve");
6780: strcat(filerescve,fileres);
6781: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
6782: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6783: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
6784: }
6785: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6786: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
6787:
6788: strcpy(fileresv,"v");
6789: strcat(fileresv,fileres);
6790: if((ficresvij=fopen(fileresv,"w"))==NULL) {
6791: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
6792: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
6793: }
6794: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6795: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
6796:
6797: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6798: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6799:
6800: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6801: fprintf(ficrest,"\n#****** ");
6802: for(j=1;j<=cptcoveff;j++)
6803: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6804: fprintf(ficrest,"******\n");
6805:
6806: fprintf(ficresstdeij,"\n#****** ");
6807: fprintf(ficrescveij,"\n#****** ");
6808: for(j=1;j<=cptcoveff;j++) {
6809: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6810: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6811: }
6812: fprintf(ficresstdeij,"******\n");
6813: fprintf(ficrescveij,"******\n");
6814:
6815: fprintf(ficresvij,"\n#****** ");
6816: for(j=1;j<=cptcoveff;j++)
6817: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6818: fprintf(ficresvij,"******\n");
6819:
6820: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6821: oldm=oldms;savm=savms;
6822: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
6823: /*
6824: */
6825: /* goto endfree; */
6826:
6827: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
6828: pstamp(ficrest);
6829:
6830:
6831: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
6832: oldm=oldms;savm=savms; /* Segmentation fault */
6833: cptcod= 0; /* To be deleted */
6834: 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 */
6835: 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 ");
6836: if(vpopbased==1)
6837: 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);
6838: else
6839: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
6840: fprintf(ficrest,"# Age e.. (std) ");
6841: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
6842: fprintf(ficrest,"\n");
6843:
6844: epj=vector(1,nlstate+1);
6845: for(age=bage; age <=fage ;age++){
6846: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6847: if (vpopbased==1) {
6848: if(mobilav ==0){
6849: for(i=1; i<=nlstate;i++)
6850: prlim[i][i]=probs[(int)age][i][k];
6851: }else{ /* mobilav */
6852: for(i=1; i<=nlstate;i++)
6853: prlim[i][i]=mobaverage[(int)age][i][k];
6854: }
6855: }
6856:
6857: fprintf(ficrest," %4.0f",age);
6858: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
6859: for(i=1, epj[j]=0.;i <=nlstate;i++) {
6860: epj[j] += prlim[i][i]*eij[i][j][(int)age];
6861: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
6862: }
6863: epj[nlstate+1] +=epj[j];
6864: }
6865:
6866: for(i=1, vepp=0.;i <=nlstate;i++)
6867: for(j=1;j <=nlstate;j++)
6868: vepp += vareij[i][j][(int)age];
6869: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
6870: for(j=1;j <=nlstate;j++){
6871: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
6872: }
6873: fprintf(ficrest,"\n");
6874: }
6875: }
6876: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6877: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
6878: free_vector(epj,1,nlstate+1);
6879: /*}*/
6880: }
6881: free_vector(weight,1,n);
6882: free_imatrix(Tvard,1,NCOVMAX,1,2);
6883: free_imatrix(s,1,maxwav+1,1,n);
6884: free_matrix(anint,1,maxwav,1,n);
6885: free_matrix(mint,1,maxwav,1,n);
6886: free_ivector(cod,1,n);
6887: free_ivector(tab,1,NCOVMAX);
6888: fclose(ficresstdeij);
6889: fclose(ficrescveij);
6890: fclose(ficresvij);
6891: fclose(ficrest);
6892: fclose(ficpar);
6893:
6894: /*------- Variance of period (stable) prevalence------*/
6895:
6896: strcpy(fileresvpl,"vpl");
6897: strcat(fileresvpl,fileres);
6898: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
6899: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
6900: exit(0);
6901: }
6902: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
6903:
6904: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6905: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
6906:
6907: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6908: fprintf(ficresvpl,"\n#****** ");
6909: for(j=1;j<=cptcoveff;j++)
6910: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6911: fprintf(ficresvpl,"******\n");
6912:
6913: varpl=matrix(1,nlstate,(int) bage, (int) fage);
6914: oldm=oldms;savm=savms;
6915: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
6916: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
6917: /*}*/
6918: }
6919:
6920: fclose(ficresvpl);
6921:
6922: /*---------- End : free ----------------*/
6923: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
6924: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
6925: } /* mle==-3 arrives here for freeing */
6926: /* endfree:*/
6927: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
6928: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
6929: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
6930: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
6931: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
6932: free_matrix(covar,0,NCOVMAX,1,n);
6933: free_matrix(matcov,1,npar,1,npar);
6934: /*free_vector(delti,1,npar);*/
6935: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6936: free_matrix(agev,1,maxwav,1,imx);
6937: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6938:
6939: free_ivector(ncodemax,1,NCOVMAX);
6940: free_ivector(Tvar,1,NCOVMAX);
6941: free_ivector(Tprod,1,NCOVMAX);
6942: free_ivector(Tvaraff,1,NCOVMAX);
6943: free_ivector(Tage,1,NCOVMAX);
6944:
6945: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
6946: free_imatrix(codtab,1,100,1,10);
6947: fflush(fichtm);
6948: fflush(ficgp);
6949:
6950:
6951: if((nberr >0) || (nbwarn>0)){
6952: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
6953: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
6954: }else{
6955: printf("End of Imach\n");
6956: fprintf(ficlog,"End of Imach\n");
6957: }
6958: printf("See log file on %s\n",filelog);
6959: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
6960: /*(void) gettimeofday(&end_time,&tzp);*/
6961: rend_time = time(NULL);
6962: end_time = *localtime(&rend_time);
6963: /* tml = *localtime(&end_time.tm_sec); */
6964: strcpy(strtend,asctime(&end_time));
6965: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
6966: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
6967: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6968:
6969: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6970: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
6971: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
6972: /* printf("Total time was %d uSec.\n", total_usecs);*/
6973: /* if(fileappend(fichtm,optionfilehtm)){ */
6974: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6975: fclose(fichtm);
6976: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
6977: fclose(fichtmcov);
6978: fclose(ficgp);
6979: fclose(ficlog);
6980: /*------ End -----------*/
6981:
6982:
6983: printf("Before Current directory %s!\n",pathcd);
6984: if(chdir(pathcd) != 0)
6985: printf("Can't move to directory %s!\n",path);
6986: if(getcwd(pathcd,MAXLINE) > 0)
6987: printf("Current directory %s!\n",pathcd);
6988: /*strcat(plotcmd,CHARSEPARATOR);*/
6989: sprintf(plotcmd,"gnuplot");
6990: #ifdef _WIN32
6991: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
6992: #endif
6993: if(!stat(plotcmd,&info)){
6994: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
6995: if(!stat(getenv("GNUPLOTBIN"),&info)){
6996: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
6997: }else
6998: strcpy(pplotcmd,plotcmd);
6999: #ifdef __unix
7000: strcpy(plotcmd,GNUPLOTPROGRAM);
7001: if(!stat(plotcmd,&info)){
7002: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7003: }else
7004: strcpy(pplotcmd,plotcmd);
7005: #endif
7006: }else
7007: strcpy(pplotcmd,plotcmd);
7008:
7009: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7010: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7011:
7012: if((outcmd=system(plotcmd)) != 0){
7013: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7014: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7015: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7016: if((outcmd=system(plotcmd)) != 0)
7017: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7018: }
7019: printf(" Successful, please wait...");
7020: while (z[0] != 'q') {
7021: /* chdir(path); */
7022: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7023: scanf("%s",z);
7024: /* if (z[0] == 'c') system("./imach"); */
7025: if (z[0] == 'e') {
7026: #ifdef __APPLE__
7027: sprintf(pplotcmd, "open %s", optionfilehtm);
7028: #elif __linux
7029: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7030: #else
7031: sprintf(pplotcmd, "%s", optionfilehtm);
7032: #endif
7033: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7034: system(pplotcmd);
7035: }
7036: else if (z[0] == 'g') system(plotcmd);
7037: else if (z[0] == 'q') exit(0);
7038: }
7039: end:
7040: while (z[0] != 'q') {
7041: printf("\nType q for exiting: ");
7042: scanf("%s",z);
7043: }
7044: }
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