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Tue Aug 18 16:28:39 2015 UTC (9 years ago) by
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Summary: Adding a hack for testing purpose
After reading the title, ftol and model lines, if the comment line has
a q, starting with #q, the answer at the end of the run is quit. It
permits to run test files in batch with ctest. The former workaround was
$ echo q | imach foo.imach
1: /* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $
2: $State: Exp $
3: $Log: imach.c,v $
4: Revision 1.195 2015/08/18 16:28:39 brouard
5: Summary: Adding a hack for testing purpose
6:
7: After reading the title, ftol and model lines, if the comment line has
8: a q, starting with #q, the answer at the end of the run is quit. It
9: permits to run test files in batch with ctest. The former workaround was
10: $ echo q | imach foo.imach
11:
12: Revision 1.194 2015/08/18 13:32:00 brouard
13: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
14:
15: Revision 1.193 2015/08/04 07:17:42 brouard
16: Summary: 0.98q4
17:
18: Revision 1.192 2015/07/16 16:49:02 brouard
19: Summary: Fixing some outputs
20:
21: Revision 1.191 2015/07/14 10:00:33 brouard
22: Summary: Some fixes
23:
24: Revision 1.190 2015/05/05 08:51:13 brouard
25: Summary: Adding digits in output parameters (7 digits instead of 6)
26:
27: Fix 1+age+.
28:
29: Revision 1.189 2015/04/30 14:45:16 brouard
30: Summary: 0.98q2
31:
32: Revision 1.188 2015/04/30 08:27:53 brouard
33: *** empty log message ***
34:
35: Revision 1.187 2015/04/29 09:11:15 brouard
36: *** empty log message ***
37:
38: Revision 1.186 2015/04/23 12:01:52 brouard
39: Summary: V1*age is working now, version 0.98q1
40:
41: Some codes had been disabled in order to simplify and Vn*age was
42: working in the optimization phase, ie, giving correct MLE parameters,
43: but, as usual, outputs were not correct and program core dumped.
44:
45: Revision 1.185 2015/03/11 13:26:42 brouard
46: Summary: Inclusion of compile and links command line for Intel Compiler
47:
48: Revision 1.184 2015/03/11 11:52:39 brouard
49: Summary: Back from Windows 8. Intel Compiler
50:
51: Revision 1.183 2015/03/10 20:34:32 brouard
52: Summary: 0.98q0, trying with directest, mnbrak fixed
53:
54: We use directest instead of original Powell test; probably no
55: incidence on the results, but better justifications;
56: We fixed Numerical Recipes mnbrak routine which was wrong and gave
57: wrong results.
58:
59: Revision 1.182 2015/02/12 08:19:57 brouard
60: Summary: Trying to keep directest which seems simpler and more general
61: Author: Nicolas Brouard
62:
63: Revision 1.181 2015/02/11 23:22:24 brouard
64: Summary: Comments on Powell added
65:
66: Author:
67:
68: Revision 1.180 2015/02/11 17:33:45 brouard
69: Summary: Finishing move from main to function (hpijx and prevalence_limit)
70:
71: Revision 1.179 2015/01/04 09:57:06 brouard
72: Summary: back to OS/X
73:
74: Revision 1.178 2015/01/04 09:35:48 brouard
75: *** empty log message ***
76:
77: Revision 1.177 2015/01/03 18:40:56 brouard
78: Summary: Still testing ilc32 on OSX
79:
80: Revision 1.176 2015/01/03 16:45:04 brouard
81: *** empty log message ***
82:
83: Revision 1.175 2015/01/03 16:33:42 brouard
84: *** empty log message ***
85:
86: Revision 1.174 2015/01/03 16:15:49 brouard
87: Summary: Still in cross-compilation
88:
89: Revision 1.173 2015/01/03 12:06:26 brouard
90: Summary: trying to detect cross-compilation
91:
92: Revision 1.172 2014/12/27 12:07:47 brouard
93: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
94:
95: Revision 1.171 2014/12/23 13:26:59 brouard
96: Summary: Back from Visual C
97:
98: Still problem with utsname.h on Windows
99:
100: Revision 1.170 2014/12/23 11:17:12 brouard
101: Summary: Cleaning some \%% back to %%
102:
103: The escape was mandatory for a specific compiler (which one?), but too many warnings.
104:
105: Revision 1.169 2014/12/22 23:08:31 brouard
106: Summary: 0.98p
107:
108: Outputs some informations on compiler used, OS etc. Testing on different platforms.
109:
110: Revision 1.168 2014/12/22 15:17:42 brouard
111: Summary: update
112:
113: Revision 1.167 2014/12/22 13:50:56 brouard
114: Summary: Testing uname and compiler version and if compiled 32 or 64
115:
116: Testing on Linux 64
117:
118: Revision 1.166 2014/12/22 11:40:47 brouard
119: *** empty log message ***
120:
121: Revision 1.165 2014/12/16 11:20:36 brouard
122: Summary: After compiling on Visual C
123:
124: * imach.c (Module): Merging 1.61 to 1.162
125:
126: Revision 1.164 2014/12/16 10:52:11 brouard
127: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
128:
129: * imach.c (Module): Merging 1.61 to 1.162
130:
131: Revision 1.163 2014/12/16 10:30:11 brouard
132: * imach.c (Module): Merging 1.61 to 1.162
133:
134: Revision 1.162 2014/09/25 11:43:39 brouard
135: Summary: temporary backup 0.99!
136:
137: Revision 1.1 2014/09/16 11:06:58 brouard
138: Summary: With some code (wrong) for nlopt
139:
140: Author:
141:
142: Revision 1.161 2014/09/15 20:41:41 brouard
143: Summary: Problem with macro SQR on Intel compiler
144:
145: Revision 1.160 2014/09/02 09:24:05 brouard
146: *** empty log message ***
147:
148: Revision 1.159 2014/09/01 10:34:10 brouard
149: Summary: WIN32
150: Author: Brouard
151:
152: Revision 1.158 2014/08/27 17:11:51 brouard
153: *** empty log message ***
154:
155: Revision 1.157 2014/08/27 16:26:55 brouard
156: Summary: Preparing windows Visual studio version
157: Author: Brouard
158:
159: In order to compile on Visual studio, time.h is now correct and time_t
160: and tm struct should be used. difftime should be used but sometimes I
161: just make the differences in raw time format (time(&now).
162: Trying to suppress #ifdef LINUX
163: Add xdg-open for __linux in order to open default browser.
164:
165: Revision 1.156 2014/08/25 20:10:10 brouard
166: *** empty log message ***
167:
168: Revision 1.155 2014/08/25 18:32:34 brouard
169: Summary: New compile, minor changes
170: Author: Brouard
171:
172: Revision 1.154 2014/06/20 17:32:08 brouard
173: Summary: Outputs now all graphs of convergence to period prevalence
174:
175: Revision 1.153 2014/06/20 16:45:46 brouard
176: Summary: If 3 live state, convergence to period prevalence on same graph
177: Author: Brouard
178:
179: Revision 1.152 2014/06/18 17:54:09 brouard
180: Summary: open browser, use gnuplot on same dir than imach if not found in the path
181:
182: Revision 1.151 2014/06/18 16:43:30 brouard
183: *** empty log message ***
184:
185: Revision 1.150 2014/06/18 16:42:35 brouard
186: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
187: Author: brouard
188:
189: Revision 1.149 2014/06/18 15:51:14 brouard
190: Summary: Some fixes in parameter files errors
191: Author: Nicolas Brouard
192:
193: Revision 1.148 2014/06/17 17:38:48 brouard
194: Summary: Nothing new
195: Author: Brouard
196:
197: Just a new packaging for OS/X version 0.98nS
198:
199: Revision 1.147 2014/06/16 10:33:11 brouard
200: *** empty log message ***
201:
202: Revision 1.146 2014/06/16 10:20:28 brouard
203: Summary: Merge
204: Author: Brouard
205:
206: Merge, before building revised version.
207:
208: Revision 1.145 2014/06/10 21:23:15 brouard
209: Summary: Debugging with valgrind
210: Author: Nicolas Brouard
211:
212: Lot of changes in order to output the results with some covariates
213: After the Edimburgh REVES conference 2014, it seems mandatory to
214: improve the code.
215: No more memory valgrind error but a lot has to be done in order to
216: continue the work of splitting the code into subroutines.
217: Also, decodemodel has been improved. Tricode is still not
218: optimal. nbcode should be improved. Documentation has been added in
219: the source code.
220:
221: Revision 1.143 2014/01/26 09:45:38 brouard
222: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
223:
224: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
225: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
226:
227: Revision 1.142 2014/01/26 03:57:36 brouard
228: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
229:
230: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
231:
232: Revision 1.141 2014/01/26 02:42:01 brouard
233: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
234:
235: Revision 1.140 2011/09/02 10:37:54 brouard
236: Summary: times.h is ok with mingw32 now.
237:
238: Revision 1.139 2010/06/14 07:50:17 brouard
239: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
240: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
241:
242: Revision 1.138 2010/04/30 18:19:40 brouard
243: *** empty log message ***
244:
245: Revision 1.137 2010/04/29 18:11:38 brouard
246: (Module): Checking covariates for more complex models
247: than V1+V2. A lot of change to be done. Unstable.
248:
249: Revision 1.136 2010/04/26 20:30:53 brouard
250: (Module): merging some libgsl code. Fixing computation
251: of likelione (using inter/intrapolation if mle = 0) in order to
252: get same likelihood as if mle=1.
253: Some cleaning of code and comments added.
254:
255: Revision 1.135 2009/10/29 15:33:14 brouard
256: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
257:
258: Revision 1.134 2009/10/29 13:18:53 brouard
259: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
260:
261: Revision 1.133 2009/07/06 10:21:25 brouard
262: just nforces
263:
264: Revision 1.132 2009/07/06 08:22:05 brouard
265: Many tings
266:
267: Revision 1.131 2009/06/20 16:22:47 brouard
268: Some dimensions resccaled
269:
270: Revision 1.130 2009/05/26 06:44:34 brouard
271: (Module): Max Covariate is now set to 20 instead of 8. A
272: lot of cleaning with variables initialized to 0. Trying to make
273: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
274:
275: Revision 1.129 2007/08/31 13:49:27 lievre
276: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
277:
278: Revision 1.128 2006/06/30 13:02:05 brouard
279: (Module): Clarifications on computing e.j
280:
281: Revision 1.127 2006/04/28 18:11:50 brouard
282: (Module): Yes the sum of survivors was wrong since
283: imach-114 because nhstepm was no more computed in the age
284: loop. Now we define nhstepma in the age loop.
285: (Module): In order to speed up (in case of numerous covariates) we
286: compute health expectancies (without variances) in a first step
287: and then all the health expectancies with variances or standard
288: deviation (needs data from the Hessian matrices) which slows the
289: computation.
290: In the future we should be able to stop the program is only health
291: expectancies and graph are needed without standard deviations.
292:
293: Revision 1.126 2006/04/28 17:23:28 brouard
294: (Module): Yes the sum of survivors was wrong since
295: imach-114 because nhstepm was no more computed in the age
296: loop. Now we define nhstepma in the age loop.
297: Version 0.98h
298:
299: Revision 1.125 2006/04/04 15:20:31 lievre
300: Errors in calculation of health expectancies. Age was not initialized.
301: Forecasting file added.
302:
303: Revision 1.124 2006/03/22 17:13:53 lievre
304: Parameters are printed with %lf instead of %f (more numbers after the comma).
305: The log-likelihood is printed in the log file
306:
307: Revision 1.123 2006/03/20 10:52:43 brouard
308: * imach.c (Module): <title> changed, corresponds to .htm file
309: name. <head> headers where missing.
310:
311: * imach.c (Module): Weights can have a decimal point as for
312: English (a comma might work with a correct LC_NUMERIC environment,
313: otherwise the weight is truncated).
314: Modification of warning when the covariates values are not 0 or
315: 1.
316: Version 0.98g
317:
318: Revision 1.122 2006/03/20 09:45:41 brouard
319: (Module): Weights can have a decimal point as for
320: English (a comma might work with a correct LC_NUMERIC environment,
321: otherwise the weight is truncated).
322: Modification of warning when the covariates values are not 0 or
323: 1.
324: Version 0.98g
325:
326: Revision 1.121 2006/03/16 17:45:01 lievre
327: * imach.c (Module): Comments concerning covariates added
328:
329: * imach.c (Module): refinements in the computation of lli if
330: status=-2 in order to have more reliable computation if stepm is
331: not 1 month. Version 0.98f
332:
333: Revision 1.120 2006/03/16 15:10:38 lievre
334: (Module): refinements in the computation of lli if
335: status=-2 in order to have more reliable computation if stepm is
336: not 1 month. Version 0.98f
337:
338: Revision 1.119 2006/03/15 17:42:26 brouard
339: (Module): Bug if status = -2, the loglikelihood was
340: computed as likelihood omitting the logarithm. Version O.98e
341:
342: Revision 1.118 2006/03/14 18:20:07 brouard
343: (Module): varevsij Comments added explaining the second
344: table of variances if popbased=1 .
345: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
346: (Module): Function pstamp added
347: (Module): Version 0.98d
348:
349: Revision 1.117 2006/03/14 17:16:22 brouard
350: (Module): varevsij Comments added explaining the second
351: table of variances if popbased=1 .
352: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
353: (Module): Function pstamp added
354: (Module): Version 0.98d
355:
356: Revision 1.116 2006/03/06 10:29:27 brouard
357: (Module): Variance-covariance wrong links and
358: varian-covariance of ej. is needed (Saito).
359:
360: Revision 1.115 2006/02/27 12:17:45 brouard
361: (Module): One freematrix added in mlikeli! 0.98c
362:
363: Revision 1.114 2006/02/26 12:57:58 brouard
364: (Module): Some improvements in processing parameter
365: filename with strsep.
366:
367: Revision 1.113 2006/02/24 14:20:24 brouard
368: (Module): Memory leaks checks with valgrind and:
369: datafile was not closed, some imatrix were not freed and on matrix
370: allocation too.
371:
372: Revision 1.112 2006/01/30 09:55:26 brouard
373: (Module): Back to gnuplot.exe instead of wgnuplot.exe
374:
375: Revision 1.111 2006/01/25 20:38:18 brouard
376: (Module): Lots of cleaning and bugs added (Gompertz)
377: (Module): Comments can be added in data file. Missing date values
378: can be a simple dot '.'.
379:
380: Revision 1.110 2006/01/25 00:51:50 brouard
381: (Module): Lots of cleaning and bugs added (Gompertz)
382:
383: Revision 1.109 2006/01/24 19:37:15 brouard
384: (Module): Comments (lines starting with a #) are allowed in data.
385:
386: Revision 1.108 2006/01/19 18:05:42 lievre
387: Gnuplot problem appeared...
388: To be fixed
389:
390: Revision 1.107 2006/01/19 16:20:37 brouard
391: Test existence of gnuplot in imach path
392:
393: Revision 1.106 2006/01/19 13:24:36 brouard
394: Some cleaning and links added in html output
395:
396: Revision 1.105 2006/01/05 20:23:19 lievre
397: *** empty log message ***
398:
399: Revision 1.104 2005/09/30 16:11:43 lievre
400: (Module): sump fixed, loop imx fixed, and simplifications.
401: (Module): If the status is missing at the last wave but we know
402: that the person is alive, then we can code his/her status as -2
403: (instead of missing=-1 in earlier versions) and his/her
404: contributions to the likelihood is 1 - Prob of dying from last
405: health status (= 1-p13= p11+p12 in the easiest case of somebody in
406: the healthy state at last known wave). Version is 0.98
407:
408: Revision 1.103 2005/09/30 15:54:49 lievre
409: (Module): sump fixed, loop imx fixed, and simplifications.
410:
411: Revision 1.102 2004/09/15 17:31:30 brouard
412: Add the possibility to read data file including tab characters.
413:
414: Revision 1.101 2004/09/15 10:38:38 brouard
415: Fix on curr_time
416:
417: Revision 1.100 2004/07/12 18:29:06 brouard
418: Add version for Mac OS X. Just define UNIX in Makefile
419:
420: Revision 1.99 2004/06/05 08:57:40 brouard
421: *** empty log message ***
422:
423: Revision 1.98 2004/05/16 15:05:56 brouard
424: New version 0.97 . First attempt to estimate force of mortality
425: directly from the data i.e. without the need of knowing the health
426: state at each age, but using a Gompertz model: log u =a + b*age .
427: This is the basic analysis of mortality and should be done before any
428: other analysis, in order to test if the mortality estimated from the
429: cross-longitudinal survey is different from the mortality estimated
430: from other sources like vital statistic data.
431:
432: The same imach parameter file can be used but the option for mle should be -3.
433:
434: Agnès, who wrote this part of the code, tried to keep most of the
435: former routines in order to include the new code within the former code.
436:
437: The output is very simple: only an estimate of the intercept and of
438: the slope with 95% confident intervals.
439:
440: Current limitations:
441: A) Even if you enter covariates, i.e. with the
442: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
443: B) There is no computation of Life Expectancy nor Life Table.
444:
445: Revision 1.97 2004/02/20 13:25:42 lievre
446: Version 0.96d. Population forecasting command line is (temporarily)
447: suppressed.
448:
449: Revision 1.96 2003/07/15 15:38:55 brouard
450: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
451: rewritten within the same printf. Workaround: many printfs.
452:
453: Revision 1.95 2003/07/08 07:54:34 brouard
454: * imach.c (Repository):
455: (Repository): Using imachwizard code to output a more meaningful covariance
456: matrix (cov(a12,c31) instead of numbers.
457:
458: Revision 1.94 2003/06/27 13:00:02 brouard
459: Just cleaning
460:
461: Revision 1.93 2003/06/25 16:33:55 brouard
462: (Module): On windows (cygwin) function asctime_r doesn't
463: exist so I changed back to asctime which exists.
464: (Module): Version 0.96b
465:
466: Revision 1.92 2003/06/25 16:30:45 brouard
467: (Module): On windows (cygwin) function asctime_r doesn't
468: exist so I changed back to asctime which exists.
469:
470: Revision 1.91 2003/06/25 15:30:29 brouard
471: * imach.c (Repository): Duplicated warning errors corrected.
472: (Repository): Elapsed time after each iteration is now output. It
473: helps to forecast when convergence will be reached. Elapsed time
474: is stamped in powell. We created a new html file for the graphs
475: concerning matrix of covariance. It has extension -cov.htm.
476:
477: Revision 1.90 2003/06/24 12:34:15 brouard
478: (Module): Some bugs corrected for windows. Also, when
479: mle=-1 a template is output in file "or"mypar.txt with the design
480: of the covariance matrix to be input.
481:
482: Revision 1.89 2003/06/24 12:30:52 brouard
483: (Module): Some bugs corrected for windows. Also, when
484: mle=-1 a template is output in file "or"mypar.txt with the design
485: of the covariance matrix to be input.
486:
487: Revision 1.88 2003/06/23 17:54:56 brouard
488: * 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.
489:
490: Revision 1.87 2003/06/18 12:26:01 brouard
491: Version 0.96
492:
493: Revision 1.86 2003/06/17 20:04:08 brouard
494: (Module): Change position of html and gnuplot routines and added
495: routine fileappend.
496:
497: Revision 1.85 2003/06/17 13:12:43 brouard
498: * imach.c (Repository): Check when date of death was earlier that
499: current date of interview. It may happen when the death was just
500: prior to the death. In this case, dh was negative and likelihood
501: was wrong (infinity). We still send an "Error" but patch by
502: assuming that the date of death was just one stepm after the
503: interview.
504: (Repository): Because some people have very long ID (first column)
505: we changed int to long in num[] and we added a new lvector for
506: memory allocation. But we also truncated to 8 characters (left
507: truncation)
508: (Repository): No more line truncation errors.
509:
510: Revision 1.84 2003/06/13 21:44:43 brouard
511: * imach.c (Repository): Replace "freqsummary" at a correct
512: place. It differs from routine "prevalence" which may be called
513: many times. Probs is memory consuming and must be used with
514: parcimony.
515: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
516:
517: Revision 1.83 2003/06/10 13:39:11 lievre
518: *** empty log message ***
519:
520: Revision 1.82 2003/06/05 15:57:20 brouard
521: Add log in imach.c and fullversion number is now printed.
522:
523: */
524: /*
525: Interpolated Markov Chain
526:
527: Short summary of the programme:
528:
529: This program computes Healthy Life Expectancies from
530: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
531: first survey ("cross") where individuals from different ages are
532: interviewed on their health status or degree of disability (in the
533: case of a health survey which is our main interest) -2- at least a
534: second wave of interviews ("longitudinal") which measure each change
535: (if any) in individual health status. Health expectancies are
536: computed from the time spent in each health state according to a
537: model. More health states you consider, more time is necessary to reach the
538: Maximum Likelihood of the parameters involved in the model. The
539: simplest model is the multinomial logistic model where pij is the
540: probability to be observed in state j at the second wave
541: conditional to be observed in state i at the first wave. Therefore
542: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
543: 'age' is age and 'sex' is a covariate. If you want to have a more
544: complex model than "constant and age", you should modify the program
545: where the markup *Covariates have to be included here again* invites
546: you to do it. More covariates you add, slower the
547: convergence.
548:
549: The advantage of this computer programme, compared to a simple
550: multinomial logistic model, is clear when the delay between waves is not
551: identical for each individual. Also, if a individual missed an
552: intermediate interview, the information is lost, but taken into
553: account using an interpolation or extrapolation.
554:
555: hPijx is the probability to be observed in state i at age x+h
556: conditional to the observed state i at age x. The delay 'h' can be
557: split into an exact number (nh*stepm) of unobserved intermediate
558: states. This elementary transition (by month, quarter,
559: semester or year) is modelled as a multinomial logistic. The hPx
560: matrix is simply the matrix product of nh*stepm elementary matrices
561: and the contribution of each individual to the likelihood is simply
562: hPijx.
563:
564: Also this programme outputs the covariance matrix of the parameters but also
565: of the life expectancies. It also computes the period (stable) prevalence.
566:
567: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
568: Institut national d'études démographiques, Paris.
569: This software have been partly granted by Euro-REVES, a concerted action
570: from the European Union.
571: It is copyrighted identically to a GNU software product, ie programme and
572: software can be distributed freely for non commercial use. Latest version
573: can be accessed at http://euroreves.ined.fr/imach .
574:
575: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
576: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
577:
578: **********************************************************************/
579: /*
580: main
581: read parameterfile
582: read datafile
583: concatwav
584: freqsummary
585: if (mle >= 1)
586: mlikeli
587: print results files
588: if mle==1
589: computes hessian
590: read end of parameter file: agemin, agemax, bage, fage, estepm
591: begin-prev-date,...
592: open gnuplot file
593: open html file
594: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
595: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
596: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
597: freexexit2 possible for memory heap.
598:
599: h Pij x | pij_nom ficrestpij
600: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
601: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
602: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
603:
604: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
605: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
606: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
607: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
608: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
609:
610: forecasting if prevfcast==1 prevforecast call prevalence()
611: health expectancies
612: Variance-covariance of DFLE
613: prevalence()
614: movingaverage()
615: varevsij()
616: if popbased==1 varevsij(,popbased)
617: total life expectancies
618: Variance of period (stable) prevalence
619: end
620: */
621:
622: /* #define DEBUG */
623: /* #define DEBUGBRENT */
624: #define POWELL /* Instead of NLOPT */
625: #define POWELLF1F3 /* Skip test */
626: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
627: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
628:
629: #include <math.h>
630: #include <stdio.h>
631: #include <stdlib.h>
632: #include <string.h>
633:
634: #ifdef _WIN32
635: #include <io.h>
636: #include <windows.h>
637: #include <tchar.h>
638: #else
639: #include <unistd.h>
640: #endif
641:
642: #include <limits.h>
643: #include <sys/types.h>
644:
645: #if defined(__GNUC__)
646: #include <sys/utsname.h> /* Doesn't work on Windows */
647: #endif
648:
649: #include <sys/stat.h>
650: #include <errno.h>
651: /* extern int errno; */
652:
653: /* #ifdef LINUX */
654: /* #include <time.h> */
655: /* #include "timeval.h" */
656: /* #else */
657: /* #include <sys/time.h> */
658: /* #endif */
659:
660: #include <time.h>
661:
662: #ifdef GSL
663: #include <gsl/gsl_errno.h>
664: #include <gsl/gsl_multimin.h>
665: #endif
666:
667:
668: #ifdef NLOPT
669: #include <nlopt.h>
670: typedef struct {
671: double (* function)(double [] );
672: } myfunc_data ;
673: #endif
674:
675: /* #include <libintl.h> */
676: /* #define _(String) gettext (String) */
677:
678: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
679:
680: #define GNUPLOTPROGRAM "gnuplot"
681: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
682: #define FILENAMELENGTH 132
683:
684: #define GLOCK_ERROR_NOPATH -1 /* empty path */
685: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
686:
687: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
688: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
689:
690: #define NINTERVMAX 8
691: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
692: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
693: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
694: #define codtabm(h,k) 1 & (h-1) >> (k-1) ;
695: #define MAXN 20000
696: #define YEARM 12. /**< Number of months per year */
697: #define AGESUP 130
698: #define AGEBASE 40
699: #define AGEOVERFLOW 1.e20
700: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
701: #ifdef _WIN32
702: #define DIRSEPARATOR '\\'
703: #define CHARSEPARATOR "\\"
704: #define ODIRSEPARATOR '/'
705: #else
706: #define DIRSEPARATOR '/'
707: #define CHARSEPARATOR "/"
708: #define ODIRSEPARATOR '\\'
709: #endif
710:
711: /* $Id: imach.c,v 1.195 2015/08/18 16:28:39 brouard Exp $ */
712: /* $State: Exp $ */
713:
714: char version[]="Imach version 0.98q5, August 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
715: char fullversion[]="$Revision: 1.195 $ $Date: 2015/08/18 16:28:39 $";
716: char strstart[80];
717: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
718: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
719: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
720: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
721: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
722: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
723: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
724: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
725: int cptcovprodnoage=0; /**< Number of covariate products without age */
726: int cptcoveff=0; /* Total number of covariates to vary for printing results */
727: int cptcov=0; /* Working variable */
728: int npar=NPARMAX;
729: int nlstate=2; /* Number of live states */
730: int ndeath=1; /* Number of dead states */
731: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
732: int popbased=0;
733:
734: int *wav; /* Number of waves for this individuual 0 is possible */
735: int maxwav=0; /* Maxim number of waves */
736: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
737: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
738: int gipmx=0, gsw=0; /* Global variables on the number of contributions
739: to the likelihood and the sum of weights (done by funcone)*/
740: int mle=1, weightopt=0;
741: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
742: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
743: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
744: * wave mi and wave mi+1 is not an exact multiple of stepm. */
745: int countcallfunc=0; /* Count the number of calls to func */
746: double jmean=1; /* Mean space between 2 waves */
747: double **matprod2(); /* test */
748: double **oldm, **newm, **savm; /* Working pointers to matrices */
749: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
750: /*FILE *fic ; */ /* Used in readdata only */
751: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
752: FILE *ficlog, *ficrespow;
753: int globpr=0; /* Global variable for printing or not */
754: double fretone; /* Only one call to likelihood */
755: long ipmx=0; /* Number of contributions */
756: double sw; /* Sum of weights */
757: char filerespow[FILENAMELENGTH];
758: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
759: FILE *ficresilk;
760: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
761: FILE *ficresprobmorprev;
762: FILE *fichtm, *fichtmcov; /* Html File */
763: FILE *ficreseij;
764: char filerese[FILENAMELENGTH];
765: FILE *ficresstdeij;
766: char fileresstde[FILENAMELENGTH];
767: FILE *ficrescveij;
768: char filerescve[FILENAMELENGTH];
769: FILE *ficresvij;
770: char fileresv[FILENAMELENGTH];
771: FILE *ficresvpl;
772: char fileresvpl[FILENAMELENGTH];
773: char title[MAXLINE];
774: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
775: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
776: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
777: char command[FILENAMELENGTH];
778: int outcmd=0;
779:
780: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
781:
782: char filelog[FILENAMELENGTH]; /* Log file */
783: char filerest[FILENAMELENGTH];
784: char fileregp[FILENAMELENGTH];
785: char popfile[FILENAMELENGTH];
786:
787: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
788:
789: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
790: /* struct timezone tzp; */
791: /* extern int gettimeofday(); */
792: struct tm tml, *gmtime(), *localtime();
793:
794: extern time_t time();
795:
796: struct tm start_time, end_time, curr_time, last_time, forecast_time;
797: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
798: struct tm tm;
799:
800: char strcurr[80], strfor[80];
801:
802: char *endptr;
803: long lval;
804: double dval;
805:
806: #define NR_END 1
807: #define FREE_ARG char*
808: #define FTOL 1.0e-10
809:
810: #define NRANSI
811: #define ITMAX 200
812:
813: #define TOL 2.0e-4
814:
815: #define CGOLD 0.3819660
816: #define ZEPS 1.0e-10
817: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
818:
819: #define GOLD 1.618034
820: #define GLIMIT 100.0
821: #define TINY 1.0e-20
822:
823: static double maxarg1,maxarg2;
824: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
825: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
826:
827: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
828: #define rint(a) floor(a+0.5)
829: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
830: #define mytinydouble 1.0e-16
831: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
832: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
833: /* static double dsqrarg; */
834: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
835: static double sqrarg;
836: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
837: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
838: int agegomp= AGEGOMP;
839:
840: int imx;
841: int stepm=1;
842: /* Stepm, step in month: minimum step interpolation*/
843:
844: int estepm;
845: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
846:
847: int m,nb;
848: long *num;
849: int firstpass=0, lastpass=4,*cod, *Tage,*cens;
850: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
851: covariate for which somebody answered excluding
852: undefined. Usually 2: 0 and 1. */
853: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
854: covariate for which somebody answered including
855: undefined. Usually 3: -1, 0 and 1. */
856: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
857: double **pmmij, ***probs;
858: double *ageexmed,*agecens;
859: double dateintmean=0;
860:
861: double *weight;
862: int **s; /* Status */
863: double *agedc;
864: double **covar; /**< covar[j,i], value of jth covariate for individual i,
865: * covar=matrix(0,NCOVMAX,1,n);
866: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
867: double idx;
868: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
869: int *Ndum; /** Freq of modality (tricode */
870: int **codtab; /**< codtab=imatrix(1,100,1,10); */
871: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
872: double *lsurv, *lpop, *tpop;
873:
874: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
875: double ftolhess; /**< Tolerance for computing hessian */
876:
877: /**************** split *************************/
878: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
879: {
880: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
881: the name of the file (name), its extension only (ext) and its first part of the name (finame)
882: */
883: char *ss; /* pointer */
884: int l1=0, l2=0; /* length counters */
885:
886: l1 = strlen(path ); /* length of path */
887: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
888: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
889: if ( ss == NULL ) { /* no directory, so determine current directory */
890: strcpy( name, path ); /* we got the fullname name because no directory */
891: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
892: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
893: /* get current working directory */
894: /* extern char* getcwd ( char *buf , int len);*/
895: #ifdef WIN32
896: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
897: #else
898: if (getcwd(dirc, FILENAME_MAX) == NULL) {
899: #endif
900: return( GLOCK_ERROR_GETCWD );
901: }
902: /* got dirc from getcwd*/
903: printf(" DIRC = %s \n",dirc);
904: } else { /* strip direcotry from path */
905: ss++; /* after this, the filename */
906: l2 = strlen( ss ); /* length of filename */
907: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
908: strcpy( name, ss ); /* save file name */
909: strncpy( dirc, path, l1 - l2 ); /* now the directory */
910: dirc[l1-l2] = '\0'; /* add zero */
911: printf(" DIRC2 = %s \n",dirc);
912: }
913: /* We add a separator at the end of dirc if not exists */
914: l1 = strlen( dirc ); /* length of directory */
915: if( dirc[l1-1] != DIRSEPARATOR ){
916: dirc[l1] = DIRSEPARATOR;
917: dirc[l1+1] = 0;
918: printf(" DIRC3 = %s \n",dirc);
919: }
920: ss = strrchr( name, '.' ); /* find last / */
921: if (ss >0){
922: ss++;
923: strcpy(ext,ss); /* save extension */
924: l1= strlen( name);
925: l2= strlen(ss)+1;
926: strncpy( finame, name, l1-l2);
927: finame[l1-l2]= 0;
928: }
929:
930: return( 0 ); /* we're done */
931: }
932:
933:
934: /******************************************/
935:
936: void replace_back_to_slash(char *s, char*t)
937: {
938: int i;
939: int lg=0;
940: i=0;
941: lg=strlen(t);
942: for(i=0; i<= lg; i++) {
943: (s[i] = t[i]);
944: if (t[i]== '\\') s[i]='/';
945: }
946: }
947:
948: char *trimbb(char *out, char *in)
949: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
950: char *s;
951: s=out;
952: while (*in != '\0'){
953: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
954: in++;
955: }
956: *out++ = *in++;
957: }
958: *out='\0';
959: return s;
960: }
961:
962: /* char *substrchaine(char *out, char *in, char *chain) */
963: /* { */
964: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
965: /* char *s, *t; */
966: /* t=in;s=out; */
967: /* while ((*in != *chain) && (*in != '\0')){ */
968: /* *out++ = *in++; */
969: /* } */
970:
971: /* /\* *in matches *chain *\/ */
972: /* while ((*in++ == *chain++) && (*in != '\0')){ */
973: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
974: /* } */
975: /* in--; chain--; */
976: /* while ( (*in != '\0')){ */
977: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
978: /* *out++ = *in++; */
979: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
980: /* } */
981: /* *out='\0'; */
982: /* out=s; */
983: /* return out; */
984: /* } */
985: char *substrchaine(char *out, char *in, char *chain)
986: {
987: /* Substract chain 'chain' from 'in', return and output 'out' */
988: /* in="V1+V1*age+age*age+V2", chain="age*age" */
989:
990: char *strloc;
991:
992: strcpy (out, in);
993: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
994: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
995: if(strloc != NULL){
996: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
997: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
998: /* strcpy (strloc, strloc +strlen(chain));*/
999: }
1000: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1001: return out;
1002: }
1003:
1004:
1005: char *cutl(char *blocc, char *alocc, char *in, char occ)
1006: {
1007: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1008: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1009: gives blocc="abcdef" and alocc="ghi2j".
1010: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1011: */
1012: char *s, *t;
1013: t=in;s=in;
1014: while ((*in != occ) && (*in != '\0')){
1015: *alocc++ = *in++;
1016: }
1017: if( *in == occ){
1018: *(alocc)='\0';
1019: s=++in;
1020: }
1021:
1022: if (s == t) {/* occ not found */
1023: *(alocc-(in-s))='\0';
1024: in=s;
1025: }
1026: while ( *in != '\0'){
1027: *blocc++ = *in++;
1028: }
1029:
1030: *blocc='\0';
1031: return t;
1032: }
1033: char *cutv(char *blocc, char *alocc, char *in, char occ)
1034: {
1035: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1036: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1037: gives blocc="abcdef2ghi" and alocc="j".
1038: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1039: */
1040: char *s, *t;
1041: t=in;s=in;
1042: while (*in != '\0'){
1043: while( *in == occ){
1044: *blocc++ = *in++;
1045: s=in;
1046: }
1047: *blocc++ = *in++;
1048: }
1049: if (s == t) /* occ not found */
1050: *(blocc-(in-s))='\0';
1051: else
1052: *(blocc-(in-s)-1)='\0';
1053: in=s;
1054: while ( *in != '\0'){
1055: *alocc++ = *in++;
1056: }
1057:
1058: *alocc='\0';
1059: return s;
1060: }
1061:
1062: int nbocc(char *s, char occ)
1063: {
1064: int i,j=0;
1065: int lg=20;
1066: i=0;
1067: lg=strlen(s);
1068: for(i=0; i<= lg; i++) {
1069: if (s[i] == occ ) j++;
1070: }
1071: return j;
1072: }
1073:
1074: /* void cutv(char *u,char *v, char*t, char occ) */
1075: /* { */
1076: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1077: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1078: /* gives u="abcdef2ghi" and v="j" *\/ */
1079: /* int i,lg,j,p=0; */
1080: /* i=0; */
1081: /* lg=strlen(t); */
1082: /* for(j=0; j<=lg-1; j++) { */
1083: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1084: /* } */
1085:
1086: /* for(j=0; j<p; j++) { */
1087: /* (u[j] = t[j]); */
1088: /* } */
1089: /* u[p]='\0'; */
1090:
1091: /* for(j=0; j<= lg; j++) { */
1092: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1093: /* } */
1094: /* } */
1095:
1096: #ifdef _WIN32
1097: char * strsep(char **pp, const char *delim)
1098: {
1099: char *p, *q;
1100:
1101: if ((p = *pp) == NULL)
1102: return 0;
1103: if ((q = strpbrk (p, delim)) != NULL)
1104: {
1105: *pp = q + 1;
1106: *q = '\0';
1107: }
1108: else
1109: *pp = 0;
1110: return p;
1111: }
1112: #endif
1113:
1114: /********************** nrerror ********************/
1115:
1116: void nrerror(char error_text[])
1117: {
1118: fprintf(stderr,"ERREUR ...\n");
1119: fprintf(stderr,"%s\n",error_text);
1120: exit(EXIT_FAILURE);
1121: }
1122: /*********************** vector *******************/
1123: double *vector(int nl, int nh)
1124: {
1125: double *v;
1126: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1127: if (!v) nrerror("allocation failure in vector");
1128: return v-nl+NR_END;
1129: }
1130:
1131: /************************ free vector ******************/
1132: void free_vector(double*v, int nl, int nh)
1133: {
1134: free((FREE_ARG)(v+nl-NR_END));
1135: }
1136:
1137: /************************ivector *******************************/
1138: int *ivector(long nl,long nh)
1139: {
1140: int *v;
1141: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1142: if (!v) nrerror("allocation failure in ivector");
1143: return v-nl+NR_END;
1144: }
1145:
1146: /******************free ivector **************************/
1147: void free_ivector(int *v, long nl, long nh)
1148: {
1149: free((FREE_ARG)(v+nl-NR_END));
1150: }
1151:
1152: /************************lvector *******************************/
1153: long *lvector(long nl,long nh)
1154: {
1155: long *v;
1156: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1157: if (!v) nrerror("allocation failure in ivector");
1158: return v-nl+NR_END;
1159: }
1160:
1161: /******************free lvector **************************/
1162: void free_lvector(long *v, long nl, long nh)
1163: {
1164: free((FREE_ARG)(v+nl-NR_END));
1165: }
1166:
1167: /******************* imatrix *******************************/
1168: int **imatrix(long nrl, long nrh, long ncl, long nch)
1169: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1170: {
1171: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1172: int **m;
1173:
1174: /* allocate pointers to rows */
1175: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1176: if (!m) nrerror("allocation failure 1 in matrix()");
1177: m += NR_END;
1178: m -= nrl;
1179:
1180:
1181: /* allocate rows and set pointers to them */
1182: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1183: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1184: m[nrl] += NR_END;
1185: m[nrl] -= ncl;
1186:
1187: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1188:
1189: /* return pointer to array of pointers to rows */
1190: return m;
1191: }
1192:
1193: /****************** free_imatrix *************************/
1194: void free_imatrix(m,nrl,nrh,ncl,nch)
1195: int **m;
1196: long nch,ncl,nrh,nrl;
1197: /* free an int matrix allocated by imatrix() */
1198: {
1199: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1200: free((FREE_ARG) (m+nrl-NR_END));
1201: }
1202:
1203: /******************* matrix *******************************/
1204: double **matrix(long nrl, long nrh, long ncl, long nch)
1205: {
1206: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1207: double **m;
1208:
1209: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1210: if (!m) nrerror("allocation failure 1 in matrix()");
1211: m += NR_END;
1212: m -= nrl;
1213:
1214: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1215: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1216: m[nrl] += NR_END;
1217: m[nrl] -= ncl;
1218:
1219: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1220: return m;
1221: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1222: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1223: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1224: */
1225: }
1226:
1227: /*************************free matrix ************************/
1228: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1229: {
1230: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1231: free((FREE_ARG)(m+nrl-NR_END));
1232: }
1233:
1234: /******************* ma3x *******************************/
1235: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1236: {
1237: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1238: double ***m;
1239:
1240: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1241: if (!m) nrerror("allocation failure 1 in matrix()");
1242: m += NR_END;
1243: m -= nrl;
1244:
1245: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1246: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1247: m[nrl] += NR_END;
1248: m[nrl] -= ncl;
1249:
1250: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1251:
1252: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1253: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1254: m[nrl][ncl] += NR_END;
1255: m[nrl][ncl] -= nll;
1256: for (j=ncl+1; j<=nch; j++)
1257: m[nrl][j]=m[nrl][j-1]+nlay;
1258:
1259: for (i=nrl+1; i<=nrh; i++) {
1260: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1261: for (j=ncl+1; j<=nch; j++)
1262: m[i][j]=m[i][j-1]+nlay;
1263: }
1264: return m;
1265: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1266: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1267: */
1268: }
1269:
1270: /*************************free ma3x ************************/
1271: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1272: {
1273: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1274: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1275: free((FREE_ARG)(m+nrl-NR_END));
1276: }
1277:
1278: /*************** function subdirf ***********/
1279: char *subdirf(char fileres[])
1280: {
1281: /* Caution optionfilefiname is hidden */
1282: strcpy(tmpout,optionfilefiname);
1283: strcat(tmpout,"/"); /* Add to the right */
1284: strcat(tmpout,fileres);
1285: return tmpout;
1286: }
1287:
1288: /*************** function subdirf2 ***********/
1289: char *subdirf2(char fileres[], char *preop)
1290: {
1291:
1292: /* Caution optionfilefiname is hidden */
1293: strcpy(tmpout,optionfilefiname);
1294: strcat(tmpout,"/");
1295: strcat(tmpout,preop);
1296: strcat(tmpout,fileres);
1297: return tmpout;
1298: }
1299:
1300: /*************** function subdirf3 ***********/
1301: char *subdirf3(char fileres[], char *preop, char *preop2)
1302: {
1303:
1304: /* Caution optionfilefiname is hidden */
1305: strcpy(tmpout,optionfilefiname);
1306: strcat(tmpout,"/");
1307: strcat(tmpout,preop);
1308: strcat(tmpout,preop2);
1309: strcat(tmpout,fileres);
1310: return tmpout;
1311: }
1312:
1313: char *asc_diff_time(long time_sec, char ascdiff[])
1314: {
1315: long sec_left, days, hours, minutes;
1316: days = (time_sec) / (60*60*24);
1317: sec_left = (time_sec) % (60*60*24);
1318: hours = (sec_left) / (60*60) ;
1319: sec_left = (sec_left) %(60*60);
1320: minutes = (sec_left) /60;
1321: sec_left = (sec_left) % (60);
1322: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1323: return ascdiff;
1324: }
1325:
1326: /***************** f1dim *************************/
1327: extern int ncom;
1328: extern double *pcom,*xicom;
1329: extern double (*nrfunc)(double []);
1330:
1331: double f1dim(double x)
1332: {
1333: int j;
1334: double f;
1335: double *xt;
1336:
1337: xt=vector(1,ncom);
1338: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1339: f=(*nrfunc)(xt);
1340: free_vector(xt,1,ncom);
1341: return f;
1342: }
1343:
1344: /*****************brent *************************/
1345: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1346: {
1347: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1348: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1349: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1350: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1351: * returned function value.
1352: */
1353: int iter;
1354: double a,b,d,etemp;
1355: double fu=0,fv,fw,fx;
1356: double ftemp=0.;
1357: double p,q,r,tol1,tol2,u,v,w,x,xm;
1358: double e=0.0;
1359:
1360: a=(ax < cx ? ax : cx);
1361: b=(ax > cx ? ax : cx);
1362: x=w=v=bx;
1363: fw=fv=fx=(*f)(x);
1364: for (iter=1;iter<=ITMAX;iter++) {
1365: xm=0.5*(a+b);
1366: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1367: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1368: printf(".");fflush(stdout);
1369: fprintf(ficlog,".");fflush(ficlog);
1370: #ifdef DEBUGBRENT
1371: 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);
1372: 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);
1373: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1374: #endif
1375: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1376: *xmin=x;
1377: return fx;
1378: }
1379: ftemp=fu;
1380: if (fabs(e) > tol1) {
1381: r=(x-w)*(fx-fv);
1382: q=(x-v)*(fx-fw);
1383: p=(x-v)*q-(x-w)*r;
1384: q=2.0*(q-r);
1385: if (q > 0.0) p = -p;
1386: q=fabs(q);
1387: etemp=e;
1388: e=d;
1389: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1390: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1391: else {
1392: d=p/q;
1393: u=x+d;
1394: if (u-a < tol2 || b-u < tol2)
1395: d=SIGN(tol1,xm-x);
1396: }
1397: } else {
1398: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1399: }
1400: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1401: fu=(*f)(u);
1402: if (fu <= fx) {
1403: if (u >= x) a=x; else b=x;
1404: SHFT(v,w,x,u)
1405: SHFT(fv,fw,fx,fu)
1406: } else {
1407: if (u < x) a=u; else b=u;
1408: if (fu <= fw || w == x) {
1409: v=w;
1410: w=u;
1411: fv=fw;
1412: fw=fu;
1413: } else if (fu <= fv || v == x || v == w) {
1414: v=u;
1415: fv=fu;
1416: }
1417: }
1418: }
1419: nrerror("Too many iterations in brent");
1420: *xmin=x;
1421: return fx;
1422: }
1423:
1424: /****************** mnbrak ***********************/
1425:
1426: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1427: double (*func)(double))
1428: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1429: the downhill direction (defined by the function as evaluated at the initial points) and returns
1430: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1431: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1432: */
1433: double ulim,u,r,q, dum;
1434: double fu;
1435:
1436: double scale=10.;
1437: int iterscale=0;
1438:
1439: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1440: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1441:
1442:
1443: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1444: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1445: /* *bx = *ax - (*ax - *bx)/scale; */
1446: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1447: /* } */
1448:
1449: if (*fb > *fa) {
1450: SHFT(dum,*ax,*bx,dum)
1451: SHFT(dum,*fb,*fa,dum)
1452: }
1453: *cx=(*bx)+GOLD*(*bx-*ax);
1454: *fc=(*func)(*cx);
1455: #ifdef DEBUG
1456: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1457: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1458: #endif
1459: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1460: r=(*bx-*ax)*(*fb-*fc);
1461: q=(*bx-*cx)*(*fb-*fa);
1462: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1463: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1464: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1465: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1466: fu=(*func)(u);
1467: #ifdef DEBUG
1468: /* f(x)=A(x-u)**2+f(u) */
1469: double A, fparabu;
1470: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1471: fparabu= *fa - A*(*ax-u)*(*ax-u);
1472: 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);
1473: 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);
1474: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1475: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1476: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1477: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1478: #endif
1479: #ifdef MNBRAKORIGINAL
1480: #else
1481: /* if (fu > *fc) { */
1482: /* #ifdef DEBUG */
1483: /* printf("mnbrak4 fu > fc \n"); */
1484: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1485: /* #endif */
1486: /* /\* SHFT(u,*cx,*cx,u) /\\* ie a=c, c=u and u=c; in that case, next SHFT(a,b,c,u) will give a=b=b, b=c=u, c=u=c and *\\/ *\/ */
1487: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1488: /* dum=u; /\* Shifting c and u *\/ */
1489: /* u = *cx; */
1490: /* *cx = dum; */
1491: /* dum = fu; */
1492: /* fu = *fc; */
1493: /* *fc =dum; */
1494: /* } else { /\* end *\/ */
1495: /* #ifdef DEBUG */
1496: /* printf("mnbrak3 fu < fc \n"); */
1497: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1498: /* #endif */
1499: /* dum=u; /\* Shifting c and u *\/ */
1500: /* u = *cx; */
1501: /* *cx = dum; */
1502: /* dum = fu; */
1503: /* fu = *fc; */
1504: /* *fc =dum; */
1505: /* } */
1506: #ifdef DEBUG
1507: printf("mnbrak34 fu < or >= fc \n");
1508: fprintf(ficlog, "mnbrak34 fu < fc\n");
1509: #endif
1510: dum=u; /* Shifting c and u */
1511: u = *cx;
1512: *cx = dum;
1513: dum = fu;
1514: fu = *fc;
1515: *fc =dum;
1516: #endif
1517: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1518: #ifdef DEBUG
1519: printf("mnbrak2 u after c but before ulim\n");
1520: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1521: #endif
1522: fu=(*func)(u);
1523: if (fu < *fc) {
1524: #ifdef DEBUG
1525: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1526: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1527: #endif
1528: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1529: SHFT(*fb,*fc,fu,(*func)(u))
1530: }
1531: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1532: #ifdef DEBUG
1533: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1534: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1535: #endif
1536: u=ulim;
1537: fu=(*func)(u);
1538: } else { /* u could be left to b (if r > q parabola has a maximum) */
1539: #ifdef DEBUG
1540: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1541: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1542: #endif
1543: u=(*cx)+GOLD*(*cx-*bx);
1544: fu=(*func)(u);
1545: } /* end tests */
1546: SHFT(*ax,*bx,*cx,u)
1547: SHFT(*fa,*fb,*fc,fu)
1548: #ifdef DEBUG
1549: printf("mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1550: fprintf(ficlog, "mnbrak2 (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf), (*u=%.12f, fu=%.12lf)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu);
1551: #endif
1552: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1553: }
1554:
1555: /*************** linmin ************************/
1556: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1557: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1558: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1559: the value of func at the returned location p . This is actually all accomplished by calling the
1560: routines mnbrak and brent .*/
1561: int ncom;
1562: double *pcom,*xicom;
1563: double (*nrfunc)(double []);
1564:
1565: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1566: {
1567: double brent(double ax, double bx, double cx,
1568: double (*f)(double), double tol, double *xmin);
1569: double f1dim(double x);
1570: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1571: double *fc, double (*func)(double));
1572: int j;
1573: double xx,xmin,bx,ax;
1574: double fx,fb,fa;
1575:
1576: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1577:
1578: ncom=n;
1579: pcom=vector(1,n);
1580: xicom=vector(1,n);
1581: nrfunc=func;
1582: for (j=1;j<=n;j++) {
1583: pcom[j]=p[j];
1584: xicom[j]=xi[j];
1585: }
1586:
1587: /* axs=0.0; */
1588: /* xxss=1; /\* 1 and using scale *\/ */
1589: xxs=1;
1590: /* do{ */
1591: ax=0.;
1592: xx= xxs;
1593: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1594: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1595: /* xt[x,j]=pcom[j]+x*xicom[j] f(ax) = f(xt(a,j=1,n)) = f(p(j) + 0 * xi(j)) and f(xx) = f(xt(x, j=1,n)) = f(p(j) + 1 * xi(j)) */
1596: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1597: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1598: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1599: /* Find a bracket a,x,b in direction n=xi ie xicom, order may change. Scale is [0:xxs*xi[j]] et non plus [0:xi[j]]*/
1600: /* if (fx != fx){ */
1601: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1602: /* printf("\nLinmin NAN : input [axs=%lf:xxs=%lf], mnbrak outputs fx=%lf <(fb=%lf and fa=%lf) with xx=%lf in [ax=%lf:bx=%lf] \n", axs, xxs, fx,fb, fa, xx, ax, bx); */
1603: /* } */
1604: /* }while(fx != fx); */
1605:
1606: #ifdef DEBUGLINMIN
1607: printf("\nLinmin after mnbrak: ax=%12.7f xx=%12.7f bx=%12.7f fa=%12.2f fx=%12.2f fb=%12.2f\n", ax,xx,bx,fa,fx,fb);
1608: #endif
1609: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1610: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1611: /* fmin = f(p[j] + xmin * xi[j]) */
1612: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1613: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1614: #ifdef DEBUG
1615: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1616: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1617: #endif
1618: #ifdef DEBUGLINMIN
1619: printf("linmin end ");
1620: #endif
1621: for (j=1;j<=n;j++) {
1622: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1623: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1624: /* if(xxs <1.0) */
1625: /* printf(" after xi[%d]=%12.8f, xmin=%12.8f, ax=%12.8f, xx=%12.8f, bx=%12.8f, xxs=%12.8f", j,xi[j], xmin, ax, xx, bx,xxs ); */
1626: p[j] += xi[j]; /* Parameters values are updated accordingly */
1627: }
1628: /* printf("\n"); */
1629: #ifdef DEBUGLINMIN
1630: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1631: for (j=1;j<=n;j++) {
1632: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1633: if(j % ncovmodel == 0)
1634: printf("\n");
1635: }
1636: #endif
1637: free_vector(xicom,1,n);
1638: free_vector(pcom,1,n);
1639: }
1640:
1641:
1642: /*************** powell ************************/
1643: /*
1644: Minimization of a function func of n variables. Input consists of an initial starting point
1645: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1646: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1647: such that failure to decrease by more than this amount on one iteration signals doneness. On
1648: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1649: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1650: */
1651: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1652: double (*func)(double []))
1653: {
1654: void linmin(double p[], double xi[], int n, double *fret,
1655: double (*func)(double []));
1656: int i,ibig,j;
1657: double del,t,*pt,*ptt,*xit;
1658: double directest;
1659: double fp,fptt;
1660: double *xits;
1661: int niterf, itmp;
1662:
1663: pt=vector(1,n);
1664: ptt=vector(1,n);
1665: xit=vector(1,n);
1666: xits=vector(1,n);
1667: *fret=(*func)(p);
1668: for (j=1;j<=n;j++) pt[j]=p[j];
1669: rcurr_time = time(NULL);
1670: for (*iter=1;;++(*iter)) {
1671: fp=(*fret); /* From former iteration or initial value */
1672: ibig=0;
1673: del=0.0;
1674: rlast_time=rcurr_time;
1675: /* (void) gettimeofday(&curr_time,&tzp); */
1676: rcurr_time = time(NULL);
1677: curr_time = *localtime(&rcurr_time);
1678: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1679: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1680: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1681: for (i=1;i<=n;i++) {
1682: printf(" %d %.12f",i, p[i]);
1683: fprintf(ficlog," %d %.12lf",i, p[i]);
1684: fprintf(ficrespow," %.12lf", p[i]);
1685: }
1686: printf("\n");
1687: fprintf(ficlog,"\n");
1688: fprintf(ficrespow,"\n");fflush(ficrespow);
1689: if(*iter <=3){
1690: tml = *localtime(&rcurr_time);
1691: strcpy(strcurr,asctime(&tml));
1692: rforecast_time=rcurr_time;
1693: itmp = strlen(strcurr);
1694: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1695: strcurr[itmp-1]='\0';
1696: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1697: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1698: for(niterf=10;niterf<=30;niterf+=10){
1699: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1700: forecast_time = *localtime(&rforecast_time);
1701: strcpy(strfor,asctime(&forecast_time));
1702: itmp = strlen(strfor);
1703: if(strfor[itmp-1]=='\n')
1704: strfor[itmp-1]='\0';
1705: 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);
1706: 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);
1707: }
1708: }
1709: for (i=1;i<=n;i++) { /* For each direction i */
1710: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1711: fptt=(*fret);
1712: #ifdef DEBUG
1713: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1714: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1715: #endif
1716: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1717: fprintf(ficlog,"%d",i);fflush(ficlog);
1718: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1719: /* Outputs are fret(new point p) p is updated and xit rescaled */
1720: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1721: /* because that direction will be replaced unless the gain del is small */
1722: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1723: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1724: /* with the new direction. */
1725: del=fabs(fptt-(*fret));
1726: ibig=i;
1727: }
1728: #ifdef DEBUG
1729: printf("%d %.12e",i,(*fret));
1730: fprintf(ficlog,"%d %.12e",i,(*fret));
1731: for (j=1;j<=n;j++) {
1732: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1733: printf(" x(%d)=%.12e",j,xit[j]);
1734: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1735: }
1736: for(j=1;j<=n;j++) {
1737: printf(" p(%d)=%.12e",j,p[j]);
1738: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1739: }
1740: printf("\n");
1741: fprintf(ficlog,"\n");
1742: #endif
1743: } /* end loop on each direction i */
1744: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1745: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1746: /* New value of last point Pn is not computed, P(n-1) */
1747: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1748: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1749: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1750: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1751: /* decreased of more than 3.84 */
1752: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1753: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1754: /* By adding 10 parameters more the gain should be 18.31 */
1755:
1756: /* Starting the program with initial values given by a former maximization will simply change */
1757: /* the scales of the directions and the directions, because the are reset to canonical directions */
1758: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1759: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1760: #ifdef DEBUG
1761: int k[2],l;
1762: k[0]=1;
1763: k[1]=-1;
1764: printf("Max: %.12e",(*func)(p));
1765: fprintf(ficlog,"Max: %.12e",(*func)(p));
1766: for (j=1;j<=n;j++) {
1767: printf(" %.12e",p[j]);
1768: fprintf(ficlog," %.12e",p[j]);
1769: }
1770: printf("\n");
1771: fprintf(ficlog,"\n");
1772: for(l=0;l<=1;l++) {
1773: for (j=1;j<=n;j++) {
1774: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1775: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1776: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1777: }
1778: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1779: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1780: }
1781: #endif
1782:
1783:
1784: free_vector(xit,1,n);
1785: free_vector(xits,1,n);
1786: free_vector(ptt,1,n);
1787: free_vector(pt,1,n);
1788: return;
1789: } /* enough precision */
1790: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1791: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1792: ptt[j]=2.0*p[j]-pt[j];
1793: xit[j]=p[j]-pt[j];
1794: pt[j]=p[j];
1795: }
1796: fptt=(*func)(ptt); /* f_3 */
1797: #ifdef POWELLF1F3
1798: #else
1799: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1800: #endif
1801: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1802: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1803: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1804: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1805: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1806: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1807: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1808: #ifdef NRCORIGINAL
1809: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1810: #else
1811: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1812: t= t- del*SQR(fp-fptt);
1813: #endif
1814: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1815: #ifdef DEBUG
1816: printf("t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1817: fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf directest=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t,directest);
1818: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1819: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1820: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1821: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1822: 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);
1823: 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);
1824: #endif
1825: #ifdef POWELLORIGINAL
1826: if (t < 0.0) { /* Then we use it for new direction */
1827: #else
1828: if (directest*t < 0.0) { /* Contradiction between both tests */
1829: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1830: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1831: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1832: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1833: }
1834: if (directest < 0.0) { /* Then we use it for new direction */
1835: #endif
1836: #ifdef DEBUGLINMIN
1837: printf("Before linmin in direction P%d-P0\n",n);
1838: for (j=1;j<=n;j++) {
1839: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1840: if(j % ncovmodel == 0)
1841: printf("\n");
1842: }
1843: #endif
1844: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1845: #ifdef DEBUGLINMIN
1846: for (j=1;j<=n;j++) {
1847: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1848: if(j % ncovmodel == 0)
1849: printf("\n");
1850: }
1851: #endif
1852: for (j=1;j<=n;j++) {
1853: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1854: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1855: }
1856: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1857: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1858:
1859: #ifdef DEBUG
1860: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1861: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1862: for(j=1;j<=n;j++){
1863: printf(" %.12e",xit[j]);
1864: fprintf(ficlog," %.12e",xit[j]);
1865: }
1866: printf("\n");
1867: fprintf(ficlog,"\n");
1868: #endif
1869: } /* end of t or directest negative */
1870: #ifdef POWELLF1F3
1871: #else
1872: } /* end if (fptt < fp) */
1873: #endif
1874: } /* loop iteration */
1875: }
1876:
1877: /**** Prevalence limit (stable or period prevalence) ****************/
1878:
1879: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1880: {
1881: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1882: matrix by transitions matrix until convergence is reached */
1883:
1884: int i, ii,j,k;
1885: double min, max, maxmin, maxmax,sumnew=0.;
1886: /* double **matprod2(); */ /* test */
1887: double **out, cov[NCOVMAX+1], **pmij();
1888: double **newm;
1889: double agefin, delaymax=50 ; /* Max number of years to converge */
1890:
1891: for (ii=1;ii<=nlstate+ndeath;ii++)
1892: for (j=1;j<=nlstate+ndeath;j++){
1893: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1894: }
1895:
1896: cov[1]=1.;
1897:
1898: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1899: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1900: newm=savm;
1901: /* Covariates have to be included here again */
1902: cov[2]=agefin;
1903: if(nagesqr==1)
1904: cov[3]= agefin*agefin;;
1905: for (k=1; k<=cptcovn;k++) {
1906: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1907: /*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]]);*/
1908: }
1909: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1910: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1911: for (k=1; k<=cptcovprod;k++) /* Useless */
1912: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1913:
1914: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1915: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1916: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1917: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1918: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1919: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1920:
1921: savm=oldm;
1922: oldm=newm;
1923: maxmax=0.;
1924: for(j=1;j<=nlstate;j++){
1925: min=1.;
1926: max=0.;
1927: for(i=1; i<=nlstate; i++) {
1928: sumnew=0;
1929: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1930: prlim[i][j]= newm[i][j]/(1-sumnew);
1931: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1932: max=FMAX(max,prlim[i][j]);
1933: min=FMIN(min,prlim[i][j]);
1934: }
1935: maxmin=max-min;
1936: maxmax=FMAX(maxmax,maxmin);
1937: } /* j loop */
1938: if(maxmax < ftolpl){
1939: return prlim;
1940: }
1941: } /* age loop */
1942: return prlim; /* should not reach here */
1943: }
1944:
1945: /*************** transition probabilities ***************/
1946:
1947: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1948: {
1949: /* According to parameters values stored in x and the covariate's values stored in cov,
1950: computes the probability to be observed in state j being in state i by appying the
1951: model to the ncovmodel covariates (including constant and age).
1952: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1953: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1954: ncth covariate in the global vector x is given by the formula:
1955: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1956: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1957: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1958: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1959: Outputs ps[i][j] the probability to be observed in j being in j according to
1960: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1961: */
1962: double s1, lnpijopii;
1963: /*double t34;*/
1964: int i,j, nc, ii, jj;
1965:
1966: for(i=1; i<= nlstate; i++){
1967: for(j=1; j<i;j++){
1968: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1969: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1970: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1971: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1972: }
1973: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1974: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1975: }
1976: for(j=i+1; j<=nlstate+ndeath;j++){
1977: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1978: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1979: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1980: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1981: }
1982: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1983: }
1984: }
1985:
1986: for(i=1; i<= nlstate; i++){
1987: s1=0;
1988: for(j=1; j<i; j++){
1989: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1990: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1991: }
1992: for(j=i+1; j<=nlstate+ndeath; j++){
1993: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1994: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1995: }
1996: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1997: ps[i][i]=1./(s1+1.);
1998: /* Computing other pijs */
1999: for(j=1; j<i; j++)
2000: ps[i][j]= exp(ps[i][j])*ps[i][i];
2001: for(j=i+1; j<=nlstate+ndeath; j++)
2002: ps[i][j]= exp(ps[i][j])*ps[i][i];
2003: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2004: } /* end i */
2005:
2006: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2007: for(jj=1; jj<= nlstate+ndeath; jj++){
2008: ps[ii][jj]=0;
2009: ps[ii][ii]=1;
2010: }
2011: }
2012:
2013:
2014: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2015: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2016: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2017: /* } */
2018: /* printf("\n "); */
2019: /* } */
2020: /* printf("\n ");printf("%lf ",cov[2]);*/
2021: /*
2022: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2023: goto end;*/
2024: return ps;
2025: }
2026:
2027: /**************** Product of 2 matrices ******************/
2028:
2029: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
2030: {
2031: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2032: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2033: /* in, b, out are matrice of pointers which should have been initialized
2034: before: only the contents of out is modified. The function returns
2035: a pointer to pointers identical to out */
2036: int i, j, k;
2037: for(i=nrl; i<= nrh; i++)
2038: for(k=ncolol; k<=ncoloh; k++){
2039: out[i][k]=0.;
2040: for(j=ncl; j<=nch; j++)
2041: out[i][k] +=in[i][j]*b[j][k];
2042: }
2043: return out;
2044: }
2045:
2046:
2047: /************* Higher Matrix Product ***************/
2048:
2049: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2050: {
2051: /* Computes the transition matrix starting at age 'age' over
2052: 'nhstepm*hstepm*stepm' months (i.e. until
2053: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2054: nhstepm*hstepm matrices.
2055: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2056: (typically every 2 years instead of every month which is too big
2057: for the memory).
2058: Model is determined by parameters x and covariates have to be
2059: included manually here.
2060:
2061: */
2062:
2063: int i, j, d, h, k;
2064: double **out, cov[NCOVMAX+1];
2065: double **newm;
2066: double agexact;
2067:
2068: /* Hstepm could be zero and should return the unit matrix */
2069: for (i=1;i<=nlstate+ndeath;i++)
2070: for (j=1;j<=nlstate+ndeath;j++){
2071: oldm[i][j]=(i==j ? 1.0 : 0.0);
2072: po[i][j][0]=(i==j ? 1.0 : 0.0);
2073: }
2074: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2075: for(h=1; h <=nhstepm; h++){
2076: for(d=1; d <=hstepm; d++){
2077: newm=savm;
2078: /* Covariates have to be included here again */
2079: cov[1]=1.;
2080: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2081: cov[2]=agexact;
2082: if(nagesqr==1)
2083: cov[3]= agexact*agexact;
2084: for (k=1; k<=cptcovn;k++)
2085: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
2086: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2087: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
2088: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
2089: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
2090: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
2091:
2092:
2093: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2094: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2095: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2096: pmij(pmmij,cov,ncovmodel,x,nlstate));
2097: savm=oldm;
2098: oldm=newm;
2099: }
2100: for(i=1; i<=nlstate+ndeath; i++)
2101: for(j=1;j<=nlstate+ndeath;j++) {
2102: po[i][j][h]=newm[i][j];
2103: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
2104: }
2105: /*printf("h=%d ",h);*/
2106: } /* end h */
2107: /* printf("\n H=%d \n",h); */
2108: return po;
2109: }
2110:
2111: #ifdef NLOPT
2112: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2113: double fret;
2114: double *xt;
2115: int j;
2116: myfunc_data *d2 = (myfunc_data *) pd;
2117: /* xt = (p1-1); */
2118: xt=vector(1,n);
2119: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2120:
2121: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2122: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2123: printf("Function = %.12lf ",fret);
2124: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2125: printf("\n");
2126: free_vector(xt,1,n);
2127: return fret;
2128: }
2129: #endif
2130:
2131: /*************** log-likelihood *************/
2132: double func( double *x)
2133: {
2134: int i, ii, j, k, mi, d, kk;
2135: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2136: double **out;
2137: double sw; /* Sum of weights */
2138: double lli; /* Individual log likelihood */
2139: int s1, s2;
2140: double bbh, survp;
2141: long ipmx;
2142: double agexact;
2143: /*extern weight */
2144: /* We are differentiating ll according to initial status */
2145: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2146: /*for(i=1;i<imx;i++)
2147: printf(" %d\n",s[4][i]);
2148: */
2149:
2150: ++countcallfunc;
2151:
2152: cov[1]=1.;
2153:
2154: for(k=1; k<=nlstate; k++) ll[k]=0.;
2155:
2156: if(mle==1){
2157: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2158: /* Computes the values of the ncovmodel covariates of the model
2159: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2160: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2161: to be observed in j being in i according to the model.
2162: */
2163: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
2164: cov[2+nagesqr+k]=covar[Tvar[k]][i];
2165: }
2166: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
2167: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
2168: has been calculated etc */
2169: for(mi=1; mi<= wav[i]-1; mi++){
2170: for (ii=1;ii<=nlstate+ndeath;ii++)
2171: for (j=1;j<=nlstate+ndeath;j++){
2172: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2173: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2174: }
2175: for(d=0; d<dh[mi][i]; d++){
2176: newm=savm;
2177: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2178: cov[2]=agexact;
2179: if(nagesqr==1)
2180: cov[3]= agexact*agexact;
2181: for (kk=1; kk<=cptcovage;kk++) {
2182: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
2183: }
2184: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2185: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2186: savm=oldm;
2187: oldm=newm;
2188: } /* end mult */
2189:
2190: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2191: /* But now since version 0.9 we anticipate for bias at large stepm.
2192: * If stepm is larger than one month (smallest stepm) and if the exact delay
2193: * (in months) between two waves is not a multiple of stepm, we rounded to
2194: * the nearest (and in case of equal distance, to the lowest) interval but now
2195: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2196: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2197: * probability in order to take into account the bias as a fraction of the way
2198: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2199: * -stepm/2 to stepm/2 .
2200: * For stepm=1 the results are the same as for previous versions of Imach.
2201: * For stepm > 1 the results are less biased than in previous versions.
2202: */
2203: s1=s[mw[mi][i]][i];
2204: s2=s[mw[mi+1][i]][i];
2205: bbh=(double)bh[mi][i]/(double)stepm;
2206: /* bias bh is positive if real duration
2207: * is higher than the multiple of stepm and negative otherwise.
2208: */
2209: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2210: if( s2 > nlstate){
2211: /* i.e. if s2 is a death state and if the date of death is known
2212: then the contribution to the likelihood is the probability to
2213: die between last step unit time and current step unit time,
2214: which is also equal to probability to die before dh
2215: minus probability to die before dh-stepm .
2216: In version up to 0.92 likelihood was computed
2217: as if date of death was unknown. Death was treated as any other
2218: health state: the date of the interview describes the actual state
2219: and not the date of a change in health state. The former idea was
2220: to consider that at each interview the state was recorded
2221: (healthy, disable or death) and IMaCh was corrected; but when we
2222: introduced the exact date of death then we should have modified
2223: the contribution of an exact death to the likelihood. This new
2224: contribution is smaller and very dependent of the step unit
2225: stepm. It is no more the probability to die between last interview
2226: and month of death but the probability to survive from last
2227: interview up to one month before death multiplied by the
2228: probability to die within a month. Thanks to Chris
2229: Jackson for correcting this bug. Former versions increased
2230: mortality artificially. The bad side is that we add another loop
2231: which slows down the processing. The difference can be up to 10%
2232: lower mortality.
2233: */
2234: /* If, at the beginning of the maximization mostly, the
2235: cumulative probability or probability to be dead is
2236: constant (ie = 1) over time d, the difference is equal to
2237: 0. out[s1][3] = savm[s1][3]: probability, being at state
2238: s1 at precedent wave, to be dead a month before current
2239: wave is equal to probability, being at state s1 at
2240: precedent wave, to be dead at mont of the current
2241: wave. Then the observed probability (that this person died)
2242: is null according to current estimated parameter. In fact,
2243: it should be very low but not zero otherwise the log go to
2244: infinity.
2245: */
2246: /* #ifdef INFINITYORIGINAL */
2247: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2248: /* #else */
2249: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2250: /* lli=log(mytinydouble); */
2251: /* else */
2252: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2253: /* #endif */
2254: lli=log(out[s1][s2] - savm[s1][s2]);
2255:
2256: } else if (s2==-2) {
2257: for (j=1,survp=0. ; j<=nlstate; j++)
2258: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2259: /*survp += out[s1][j]; */
2260: lli= log(survp);
2261: }
2262:
2263: else if (s2==-4) {
2264: for (j=3,survp=0. ; j<=nlstate; j++)
2265: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2266: lli= log(survp);
2267: }
2268:
2269: else if (s2==-5) {
2270: for (j=1,survp=0. ; j<=2; j++)
2271: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2272: lli= log(survp);
2273: }
2274:
2275: else{
2276: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2277: /* 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 */
2278: }
2279: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2280: /*if(lli ==000.0)*/
2281: /*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); */
2282: ipmx +=1;
2283: sw += weight[i];
2284: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2285: /* if (lli < log(mytinydouble)){ */
2286: /* printf("Close to inf lli = %.10lf < %.10lf i= %d mi= %d, s[%d][i]=%d s1=%d s2=%d\n", lli,log(mytinydouble), i, mi,mw[mi][i], s[mw[mi][i]][i], s1,s2); */
2287: /* fprintf(ficlog,"Close to inf lli = %.10lf i= %d mi= %d, s[mw[mi][i]][i]=%d\n", lli, i, mi,s[mw[mi][i]][i]); */
2288: /* } */
2289: } /* end of wave */
2290: } /* end of individual */
2291: } else if(mle==2){
2292: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2293: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2294: for(mi=1; mi<= wav[i]-1; mi++){
2295: for (ii=1;ii<=nlstate+ndeath;ii++)
2296: for (j=1;j<=nlstate+ndeath;j++){
2297: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2298: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2299: }
2300: for(d=0; d<=dh[mi][i]; d++){
2301: newm=savm;
2302: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2303: cov[2]=agexact;
2304: if(nagesqr==1)
2305: cov[3]= agexact*agexact;
2306: for (kk=1; kk<=cptcovage;kk++) {
2307: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2308: }
2309: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2310: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2311: savm=oldm;
2312: oldm=newm;
2313: } /* end mult */
2314:
2315: s1=s[mw[mi][i]][i];
2316: s2=s[mw[mi+1][i]][i];
2317: bbh=(double)bh[mi][i]/(double)stepm;
2318: 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 */
2319: ipmx +=1;
2320: sw += weight[i];
2321: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2322: } /* end of wave */
2323: } /* end of individual */
2324: } else if(mle==3){ /* exponential inter-extrapolation */
2325: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2326: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2327: for(mi=1; mi<= wav[i]-1; mi++){
2328: for (ii=1;ii<=nlstate+ndeath;ii++)
2329: for (j=1;j<=nlstate+ndeath;j++){
2330: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2331: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2332: }
2333: for(d=0; d<dh[mi][i]; d++){
2334: newm=savm;
2335: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2336: cov[2]=agexact;
2337: if(nagesqr==1)
2338: cov[3]= agexact*agexact;
2339: for (kk=1; kk<=cptcovage;kk++) {
2340: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2341: }
2342: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2343: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2344: savm=oldm;
2345: oldm=newm;
2346: } /* end mult */
2347:
2348: s1=s[mw[mi][i]][i];
2349: s2=s[mw[mi+1][i]][i];
2350: bbh=(double)bh[mi][i]/(double)stepm;
2351: 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 */
2352: ipmx +=1;
2353: sw += weight[i];
2354: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2355: } /* end of wave */
2356: } /* end of individual */
2357: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2358: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2359: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2360: for(mi=1; mi<= wav[i]-1; mi++){
2361: for (ii=1;ii<=nlstate+ndeath;ii++)
2362: for (j=1;j<=nlstate+ndeath;j++){
2363: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2364: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2365: }
2366: for(d=0; d<dh[mi][i]; d++){
2367: newm=savm;
2368: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2369: cov[2]=agexact;
2370: if(nagesqr==1)
2371: cov[3]= agexact*agexact;
2372: for (kk=1; kk<=cptcovage;kk++) {
2373: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2374: }
2375:
2376: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2377: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2378: savm=oldm;
2379: oldm=newm;
2380: } /* end mult */
2381:
2382: s1=s[mw[mi][i]][i];
2383: s2=s[mw[mi+1][i]][i];
2384: if( s2 > nlstate){
2385: lli=log(out[s1][s2] - savm[s1][s2]);
2386: }else{
2387: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2388: }
2389: ipmx +=1;
2390: sw += weight[i];
2391: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2392: /* 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]); */
2393: } /* end of wave */
2394: } /* end of individual */
2395: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2396: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2397: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2398: for(mi=1; mi<= wav[i]-1; mi++){
2399: for (ii=1;ii<=nlstate+ndeath;ii++)
2400: for (j=1;j<=nlstate+ndeath;j++){
2401: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2402: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2403: }
2404: for(d=0; d<dh[mi][i]; d++){
2405: newm=savm;
2406: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2407: cov[2]=agexact;
2408: if(nagesqr==1)
2409: cov[3]= agexact*agexact;
2410: for (kk=1; kk<=cptcovage;kk++) {
2411: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2412: }
2413:
2414: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2415: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2416: savm=oldm;
2417: oldm=newm;
2418: } /* end mult */
2419:
2420: s1=s[mw[mi][i]][i];
2421: s2=s[mw[mi+1][i]][i];
2422: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2423: ipmx +=1;
2424: sw += weight[i];
2425: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2426: /*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]);*/
2427: } /* end of wave */
2428: } /* end of individual */
2429: } /* End of if */
2430: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2431: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2432: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2433: return -l;
2434: }
2435:
2436: /*************** log-likelihood *************/
2437: double funcone( double *x)
2438: {
2439: /* Same as likeli but slower because of a lot of printf and if */
2440: int i, ii, j, k, mi, d, kk;
2441: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
2442: double **out;
2443: double lli; /* Individual log likelihood */
2444: double llt;
2445: int s1, s2;
2446: double bbh, survp;
2447: double agexact;
2448: /*extern weight */
2449: /* We are differentiating ll according to initial status */
2450: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2451: /*for(i=1;i<imx;i++)
2452: printf(" %d\n",s[4][i]);
2453: */
2454: cov[1]=1.;
2455:
2456: for(k=1; k<=nlstate; k++) ll[k]=0.;
2457:
2458: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
2459: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
2460: for(mi=1; mi<= wav[i]-1; mi++){
2461: for (ii=1;ii<=nlstate+ndeath;ii++)
2462: for (j=1;j<=nlstate+ndeath;j++){
2463: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2464: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2465: }
2466: for(d=0; d<dh[mi][i]; d++){
2467: newm=savm;
2468: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2469: cov[2]=agexact;
2470: if(nagesqr==1)
2471: cov[3]= agexact*agexact;
2472: for (kk=1; kk<=cptcovage;kk++) {
2473: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
2474: }
2475:
2476: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2477: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2478: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2479: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2480: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
2481: savm=oldm;
2482: oldm=newm;
2483: } /* end mult */
2484:
2485: s1=s[mw[mi][i]][i];
2486: s2=s[mw[mi+1][i]][i];
2487: bbh=(double)bh[mi][i]/(double)stepm;
2488: /* bias is positive if real duration
2489: * is higher than the multiple of stepm and negative otherwise.
2490: */
2491: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2492: lli=log(out[s1][s2] - savm[s1][s2]);
2493: } else if (s2==-2) {
2494: for (j=1,survp=0. ; j<=nlstate; j++)
2495: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2496: lli= log(survp);
2497: }else if (mle==1){
2498: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2499: } else if(mle==2){
2500: 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 */
2501: } else if(mle==3){ /* exponential inter-extrapolation */
2502: 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 */
2503: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2504: lli=log(out[s1][s2]); /* Original formula */
2505: } else{ /* mle=0 back to 1 */
2506: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2507: /*lli=log(out[s1][s2]); */ /* Original formula */
2508: } /* End of if */
2509: ipmx +=1;
2510: sw += weight[i];
2511: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2512: /*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]); */
2513: if(globpr){
2514: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
2515: %11.6f %11.6f %11.6f ", \
2516: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2517: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2518: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2519: llt +=ll[k]*gipmx/gsw;
2520: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2521: }
2522: fprintf(ficresilk," %10.6f\n", -llt);
2523: }
2524: } /* end of wave */
2525: } /* end of individual */
2526: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2527: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2528: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2529: if(globpr==0){ /* First time we count the contributions and weights */
2530: gipmx=ipmx;
2531: gsw=sw;
2532: }
2533: return -l;
2534: }
2535:
2536:
2537: /*************** function likelione ***********/
2538: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2539: {
2540: /* This routine should help understanding what is done with
2541: the selection of individuals/waves and
2542: to check the exact contribution to the likelihood.
2543: Plotting could be done.
2544: */
2545: int k;
2546:
2547: if(*globpri !=0){ /* Just counts and sums, no printings */
2548: strcpy(fileresilk,"ilk");
2549: strcat(fileresilk,fileres);
2550: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2551: printf("Problem with resultfile: %s\n", fileresilk);
2552: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2553: }
2554: 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");
2555: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2556: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2557: for(k=1; k<=nlstate; k++)
2558: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2559: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2560: }
2561:
2562: *fretone=(*funcone)(p);
2563: if(*globpri !=0){
2564: fclose(ficresilk);
2565: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2566: fflush(fichtm);
2567: }
2568: return;
2569: }
2570:
2571:
2572: /*********** Maximum Likelihood Estimation ***************/
2573:
2574: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2575: {
2576: int i,j, iter=0;
2577: double **xi;
2578: double fret;
2579: double fretone; /* Only one call to likelihood */
2580: /* char filerespow[FILENAMELENGTH];*/
2581:
2582: #ifdef NLOPT
2583: int creturn;
2584: nlopt_opt opt;
2585: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2586: double *lb;
2587: double minf; /* the minimum objective value, upon return */
2588: double * p1; /* Shifted parameters from 0 instead of 1 */
2589: myfunc_data dinst, *d = &dinst;
2590: #endif
2591:
2592:
2593: xi=matrix(1,npar,1,npar);
2594: for (i=1;i<=npar;i++)
2595: for (j=1;j<=npar;j++)
2596: xi[i][j]=(i==j ? 1.0 : 0.0);
2597: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2598: strcpy(filerespow,"pow");
2599: strcat(filerespow,fileres);
2600: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2601: printf("Problem with resultfile: %s\n", filerespow);
2602: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2603: }
2604: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2605: for (i=1;i<=nlstate;i++)
2606: for(j=1;j<=nlstate+ndeath;j++)
2607: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2608: fprintf(ficrespow,"\n");
2609: #ifdef POWELL
2610: powell(p,xi,npar,ftol,&iter,&fret,func);
2611: #endif
2612:
2613: #ifdef NLOPT
2614: #ifdef NEWUOA
2615: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2616: #else
2617: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2618: #endif
2619: lb=vector(0,npar-1);
2620: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2621: nlopt_set_lower_bounds(opt, lb);
2622: nlopt_set_initial_step1(opt, 0.1);
2623:
2624: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2625: d->function = func;
2626: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2627: nlopt_set_min_objective(opt, myfunc, d);
2628: nlopt_set_xtol_rel(opt, ftol);
2629: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2630: printf("nlopt failed! %d\n",creturn);
2631: }
2632: else {
2633: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2634: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2635: iter=1; /* not equal */
2636: }
2637: nlopt_destroy(opt);
2638: #endif
2639: free_matrix(xi,1,npar,1,npar);
2640: fclose(ficrespow);
2641: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2642: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2643: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2644:
2645: }
2646:
2647: /**** Computes Hessian and covariance matrix ***/
2648: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2649: {
2650: double **a,**y,*x,pd;
2651: double **hess;
2652: int i, j;
2653: int *indx;
2654:
2655: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2656: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2657: void lubksb(double **a, int npar, int *indx, double b[]) ;
2658: void ludcmp(double **a, int npar, int *indx, double *d) ;
2659: double gompertz(double p[]);
2660: hess=matrix(1,npar,1,npar);
2661:
2662: printf("\nCalculation of the hessian matrix. Wait...\n");
2663: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2664: for (i=1;i<=npar;i++){
2665: printf("%d",i);fflush(stdout);
2666: fprintf(ficlog,"%d",i);fflush(ficlog);
2667:
2668: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2669:
2670: /* printf(" %f ",p[i]);
2671: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2672: }
2673:
2674: for (i=1;i<=npar;i++) {
2675: for (j=1;j<=npar;j++) {
2676: if (j>i) {
2677: printf(".%d%d",i,j);fflush(stdout);
2678: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2679: hess[i][j]=hessij(p,delti,i,j,func,npar);
2680:
2681: hess[j][i]=hess[i][j];
2682: /*printf(" %lf ",hess[i][j]);*/
2683: }
2684: }
2685: }
2686: printf("\n");
2687: fprintf(ficlog,"\n");
2688:
2689: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2690: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2691:
2692: a=matrix(1,npar,1,npar);
2693: y=matrix(1,npar,1,npar);
2694: x=vector(1,npar);
2695: indx=ivector(1,npar);
2696: for (i=1;i<=npar;i++)
2697: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2698: ludcmp(a,npar,indx,&pd);
2699:
2700: for (j=1;j<=npar;j++) {
2701: for (i=1;i<=npar;i++) x[i]=0;
2702: x[j]=1;
2703: lubksb(a,npar,indx,x);
2704: for (i=1;i<=npar;i++){
2705: matcov[i][j]=x[i];
2706: }
2707: }
2708:
2709: printf("\n#Hessian matrix#\n");
2710: fprintf(ficlog,"\n#Hessian matrix#\n");
2711: for (i=1;i<=npar;i++) {
2712: for (j=1;j<=npar;j++) {
2713: printf("%.3e ",hess[i][j]);
2714: fprintf(ficlog,"%.3e ",hess[i][j]);
2715: }
2716: printf("\n");
2717: fprintf(ficlog,"\n");
2718: }
2719:
2720: /* Recompute Inverse */
2721: for (i=1;i<=npar;i++)
2722: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2723: ludcmp(a,npar,indx,&pd);
2724:
2725: /* printf("\n#Hessian matrix recomputed#\n");
2726:
2727: for (j=1;j<=npar;j++) {
2728: for (i=1;i<=npar;i++) x[i]=0;
2729: x[j]=1;
2730: lubksb(a,npar,indx,x);
2731: for (i=1;i<=npar;i++){
2732: y[i][j]=x[i];
2733: printf("%.3e ",y[i][j]);
2734: fprintf(ficlog,"%.3e ",y[i][j]);
2735: }
2736: printf("\n");
2737: fprintf(ficlog,"\n");
2738: }
2739: */
2740:
2741: free_matrix(a,1,npar,1,npar);
2742: free_matrix(y,1,npar,1,npar);
2743: free_vector(x,1,npar);
2744: free_ivector(indx,1,npar);
2745: free_matrix(hess,1,npar,1,npar);
2746:
2747:
2748: }
2749:
2750: /*************** hessian matrix ****************/
2751: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2752: {
2753: int i;
2754: int l=1, lmax=20;
2755: double k1,k2;
2756: double p2[MAXPARM+1]; /* identical to x */
2757: double res;
2758: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2759: double fx;
2760: int k=0,kmax=10;
2761: double l1;
2762:
2763: fx=func(x);
2764: for (i=1;i<=npar;i++) p2[i]=x[i];
2765: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
2766: l1=pow(10,l);
2767: delts=delt;
2768: for(k=1 ; k <kmax; k=k+1){
2769: delt = delta*(l1*k);
2770: p2[theta]=x[theta] +delt;
2771: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
2772: p2[theta]=x[theta]-delt;
2773: k2=func(p2)-fx;
2774: /*res= (k1-2.0*fx+k2)/delt/delt; */
2775: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2776:
2777: #ifdef DEBUGHESS
2778: 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);
2779: 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);
2780: #endif
2781: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2782: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2783: k=kmax;
2784: }
2785: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
2786: k=kmax; l=lmax*10;
2787: }
2788: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2789: delts=delt;
2790: }
2791: }
2792: }
2793: delti[theta]=delts;
2794: return res;
2795:
2796: }
2797:
2798: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2799: {
2800: int i;
2801: int l=1, lmax=20;
2802: double k1,k2,k3,k4,res,fx;
2803: double p2[MAXPARM+1];
2804: int k;
2805:
2806: fx=func(x);
2807: for (k=1; k<=2; k++) {
2808: for (i=1;i<=npar;i++) p2[i]=x[i];
2809: p2[thetai]=x[thetai]+delti[thetai]/k;
2810: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2811: k1=func(p2)-fx;
2812:
2813: p2[thetai]=x[thetai]+delti[thetai]/k;
2814: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2815: k2=func(p2)-fx;
2816:
2817: p2[thetai]=x[thetai]-delti[thetai]/k;
2818: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2819: k3=func(p2)-fx;
2820:
2821: p2[thetai]=x[thetai]-delti[thetai]/k;
2822: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2823: k4=func(p2)-fx;
2824: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2825: #ifdef DEBUG
2826: 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);
2827: 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);
2828: #endif
2829: }
2830: return res;
2831: }
2832:
2833: /************** Inverse of matrix **************/
2834: void ludcmp(double **a, int n, int *indx, double *d)
2835: {
2836: int i,imax,j,k;
2837: double big,dum,sum,temp;
2838: double *vv;
2839:
2840: vv=vector(1,n);
2841: *d=1.0;
2842: for (i=1;i<=n;i++) {
2843: big=0.0;
2844: for (j=1;j<=n;j++)
2845: if ((temp=fabs(a[i][j])) > big) big=temp;
2846: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2847: vv[i]=1.0/big;
2848: }
2849: for (j=1;j<=n;j++) {
2850: for (i=1;i<j;i++) {
2851: sum=a[i][j];
2852: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2853: a[i][j]=sum;
2854: }
2855: big=0.0;
2856: for (i=j;i<=n;i++) {
2857: sum=a[i][j];
2858: for (k=1;k<j;k++)
2859: sum -= a[i][k]*a[k][j];
2860: a[i][j]=sum;
2861: if ( (dum=vv[i]*fabs(sum)) >= big) {
2862: big=dum;
2863: imax=i;
2864: }
2865: }
2866: if (j != imax) {
2867: for (k=1;k<=n;k++) {
2868: dum=a[imax][k];
2869: a[imax][k]=a[j][k];
2870: a[j][k]=dum;
2871: }
2872: *d = -(*d);
2873: vv[imax]=vv[j];
2874: }
2875: indx[j]=imax;
2876: if (a[j][j] == 0.0) a[j][j]=TINY;
2877: if (j != n) {
2878: dum=1.0/(a[j][j]);
2879: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2880: }
2881: }
2882: free_vector(vv,1,n); /* Doesn't work */
2883: ;
2884: }
2885:
2886: void lubksb(double **a, int n, int *indx, double b[])
2887: {
2888: int i,ii=0,ip,j;
2889: double sum;
2890:
2891: for (i=1;i<=n;i++) {
2892: ip=indx[i];
2893: sum=b[ip];
2894: b[ip]=b[i];
2895: if (ii)
2896: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2897: else if (sum) ii=i;
2898: b[i]=sum;
2899: }
2900: for (i=n;i>=1;i--) {
2901: sum=b[i];
2902: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2903: b[i]=sum/a[i][i];
2904: }
2905: }
2906:
2907: void pstamp(FILE *fichier)
2908: {
2909: fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
2910: }
2911:
2912: /************ Frequencies ********************/
2913: 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[])
2914: { /* Some frequencies */
2915:
2916: int i, m, jk, j1, bool, z1,j;
2917: int first;
2918: double ***freq; /* Frequencies */
2919: double *pp, **prop;
2920: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2921: char fileresp[FILENAMELENGTH];
2922:
2923: pp=vector(1,nlstate);
2924: prop=matrix(1,nlstate,iagemin,iagemax+3);
2925: strcpy(fileresp,"p");
2926: strcat(fileresp,fileres);
2927: if((ficresp=fopen(fileresp,"w"))==NULL) {
2928: printf("Problem with prevalence resultfile: %s\n", fileresp);
2929: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2930: exit(0);
2931: }
2932: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2933: j1=0;
2934:
2935: j=cptcoveff;
2936: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2937:
2938: first=1;
2939:
2940: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2941: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2942: /* j1++; */
2943: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
2944: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2945: scanf("%d", i);*/
2946: for (i=-5; i<=nlstate+ndeath; i++)
2947: for (jk=-5; jk<=nlstate+ndeath; jk++)
2948: for(m=iagemin; m <= iagemax+3; m++)
2949: freq[i][jk][m]=0;
2950:
2951: for (i=1; i<=nlstate; i++)
2952: for(m=iagemin; m <= iagemax+3; m++)
2953: prop[i][m]=0;
2954:
2955: dateintsum=0;
2956: k2cpt=0;
2957: for (i=1; i<=imx; i++) {
2958: bool=1;
2959: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2960: for (z1=1; z1<=cptcoveff; z1++)
2961: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
2962: /* Tests if the value of each of the covariates of i is equal to filter j1 */
2963: bool=0;
2964: /* 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",
2965: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2966: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
2967: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2968: }
2969: }
2970:
2971: if (bool==1){
2972: for(m=firstpass; m<=lastpass; m++){
2973: k2=anint[m][i]+(mint[m][i]/12.);
2974: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2975: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2976: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2977: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2978: if (m<lastpass) {
2979: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2980: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2981: }
2982:
2983: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2984: dateintsum=dateintsum+k2;
2985: k2cpt++;
2986: }
2987: /*}*/
2988: }
2989: }
2990: } /* end i */
2991:
2992: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2993: pstamp(ficresp);
2994: if (cptcovn>0) {
2995: fprintf(ficresp, "\n#********** Variable ");
2996: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
2997: fprintf(ficresp, "**********\n#");
2998: fprintf(ficlog, "\n#********** Variable ");
2999: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3000: fprintf(ficlog, "**********\n#");
3001: }
3002: for(i=1; i<=nlstate;i++)
3003: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3004: fprintf(ficresp, "\n");
3005:
3006: for(i=iagemin; i <= iagemax+3; i++){
3007: if(i==iagemax+3){
3008: fprintf(ficlog,"Total");
3009: }else{
3010: if(first==1){
3011: first=0;
3012: printf("See log file for details...\n");
3013: }
3014: fprintf(ficlog,"Age %d", i);
3015: }
3016: for(jk=1; jk <=nlstate ; jk++){
3017: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3018: pp[jk] += freq[jk][m][i];
3019: }
3020: for(jk=1; jk <=nlstate ; jk++){
3021: for(m=-1, pos=0; m <=0 ; m++)
3022: pos += freq[jk][m][i];
3023: if(pp[jk]>=1.e-10){
3024: if(first==1){
3025: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3026: }
3027: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3028: }else{
3029: if(first==1)
3030: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3031: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3032: }
3033: }
3034:
3035: for(jk=1; jk <=nlstate ; jk++){
3036: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3037: pp[jk] += freq[jk][m][i];
3038: }
3039: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3040: pos += pp[jk];
3041: posprop += prop[jk][i];
3042: }
3043: for(jk=1; jk <=nlstate ; jk++){
3044: if(pos>=1.e-5){
3045: if(first==1)
3046: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3047: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3048: }else{
3049: if(first==1)
3050: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3051: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3052: }
3053: if( i <= iagemax){
3054: if(pos>=1.e-5){
3055: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3056: /*probs[i][jk][j1]= pp[jk]/pos;*/
3057: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3058: }
3059: else
3060: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3061: }
3062: }
3063:
3064: for(jk=-1; jk <=nlstate+ndeath; jk++)
3065: for(m=-1; m <=nlstate+ndeath; m++)
3066: if(freq[jk][m][i] !=0 ) {
3067: if(first==1)
3068: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3069: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3070: }
3071: if(i <= iagemax)
3072: fprintf(ficresp,"\n");
3073: if(first==1)
3074: printf("Others in log...\n");
3075: fprintf(ficlog,"\n");
3076: }
3077: /*}*/
3078: }
3079: dateintmean=dateintsum/k2cpt;
3080:
3081: fclose(ficresp);
3082: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3083: free_vector(pp,1,nlstate);
3084: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3085: /* End of Freq */
3086: }
3087:
3088: /************ Prevalence ********************/
3089: 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)
3090: {
3091: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3092: in each health status at the date of interview (if between dateprev1 and dateprev2).
3093: We still use firstpass and lastpass as another selection.
3094: */
3095:
3096: int i, m, jk, j1, bool, z1,j;
3097:
3098: double **prop;
3099: double posprop;
3100: double y2; /* in fractional years */
3101: int iagemin, iagemax;
3102: int first; /** to stop verbosity which is redirected to log file */
3103:
3104: iagemin= (int) agemin;
3105: iagemax= (int) agemax;
3106: /*pp=vector(1,nlstate);*/
3107: prop=matrix(1,nlstate,iagemin,iagemax+3);
3108: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3109: j1=0;
3110:
3111: /*j=cptcoveff;*/
3112: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3113:
3114: first=1;
3115: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3116: /*for(i1=1; i1<=ncodemax[k1];i1++){
3117: j1++;*/
3118:
3119: for (i=1; i<=nlstate; i++)
3120: for(m=iagemin; m <= iagemax+3; m++)
3121: prop[i][m]=0.0;
3122:
3123: for (i=1; i<=imx; i++) { /* Each individual */
3124: bool=1;
3125: if (cptcovn>0) {
3126: for (z1=1; z1<=cptcoveff; z1++)
3127: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3128: bool=0;
3129: }
3130: if (bool==1) {
3131: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3132: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3133: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3134: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3135: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3136: 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);
3137: if (s[m][i]>0 && s[m][i]<=nlstate) {
3138: /*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]]);*/
3139: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3140: prop[s[m][i]][iagemax+3] += weight[i];
3141: }
3142: }
3143: } /* end selection of waves */
3144: }
3145: }
3146: for(i=iagemin; i <= iagemax+3; i++){
3147: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3148: posprop += prop[jk][i];
3149: }
3150:
3151: for(jk=1; jk <=nlstate ; jk++){
3152: if( i <= iagemax){
3153: if(posprop>=1.e-5){
3154: probs[i][jk][j1]= prop[jk][i]/posprop;
3155: } else{
3156: if(first==1){
3157: first=0;
3158: 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]);
3159: }
3160: }
3161: }
3162: }/* end jk */
3163: }/* end i */
3164: /*} *//* end i1 */
3165: } /* end j1 */
3166:
3167: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3168: /*free_vector(pp,1,nlstate);*/
3169: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3170: } /* End of prevalence */
3171:
3172: /************* Waves Concatenation ***************/
3173:
3174: 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)
3175: {
3176: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3177: Death is a valid wave (if date is known).
3178: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3179: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3180: and mw[mi+1][i]. dh depends on stepm.
3181: */
3182:
3183: int i, mi, m;
3184: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3185: double sum=0., jmean=0.;*/
3186: int first;
3187: int j, k=0,jk, ju, jl;
3188: double sum=0.;
3189: first=0;
3190: jmin=100000;
3191: jmax=-1;
3192: jmean=0.;
3193: for(i=1; i<=imx; i++){
3194: mi=0;
3195: m=firstpass;
3196: while(s[m][i] <= nlstate){
3197: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3198: mw[++mi][i]=m;
3199: if(m >=lastpass)
3200: break;
3201: else
3202: m++;
3203: }/* end while */
3204: if (s[m][i] > nlstate){
3205: mi++; /* Death is another wave */
3206: /* if(mi==0) never been interviewed correctly before death */
3207: /* Only death is a correct wave */
3208: mw[mi][i]=m;
3209: }
3210:
3211: wav[i]=mi;
3212: if(mi==0){
3213: nbwarn++;
3214: if(first==0){
3215: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3216: first=1;
3217: }
3218: if(first==1){
3219: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3220: }
3221: } /* end mi==0 */
3222: } /* End individuals */
3223:
3224: for(i=1; i<=imx; i++){
3225: for(mi=1; mi<wav[i];mi++){
3226: if (stepm <=0)
3227: dh[mi][i]=1;
3228: else{
3229: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3230: if (agedc[i] < 2*AGESUP) {
3231: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3232: if(j==0) j=1; /* Survives at least one month after exam */
3233: else if(j<0){
3234: nberr++;
3235: 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]);
3236: j=1; /* Temporary Dangerous patch */
3237: 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);
3238: 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]);
3239: 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);
3240: }
3241: k=k+1;
3242: if (j >= jmax){
3243: jmax=j;
3244: ijmax=i;
3245: }
3246: if (j <= jmin){
3247: jmin=j;
3248: ijmin=i;
3249: }
3250: sum=sum+j;
3251: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3252: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3253: }
3254: }
3255: else{
3256: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3257: /* 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]); */
3258:
3259: k=k+1;
3260: if (j >= jmax) {
3261: jmax=j;
3262: ijmax=i;
3263: }
3264: else if (j <= jmin){
3265: jmin=j;
3266: ijmin=i;
3267: }
3268: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3269: /*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]);*/
3270: if(j<0){
3271: nberr++;
3272: 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]);
3273: 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]);
3274: }
3275: sum=sum+j;
3276: }
3277: jk= j/stepm;
3278: jl= j -jk*stepm;
3279: ju= j -(jk+1)*stepm;
3280: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3281: if(jl==0){
3282: dh[mi][i]=jk;
3283: bh[mi][i]=0;
3284: }else{ /* We want a negative bias in order to only have interpolation ie
3285: * to avoid the price of an extra matrix product in likelihood */
3286: dh[mi][i]=jk+1;
3287: bh[mi][i]=ju;
3288: }
3289: }else{
3290: if(jl <= -ju){
3291: dh[mi][i]=jk;
3292: bh[mi][i]=jl; /* bias is positive if real duration
3293: * is higher than the multiple of stepm and negative otherwise.
3294: */
3295: }
3296: else{
3297: dh[mi][i]=jk+1;
3298: bh[mi][i]=ju;
3299: }
3300: if(dh[mi][i]==0){
3301: dh[mi][i]=1; /* At least one step */
3302: bh[mi][i]=ju; /* At least one step */
3303: /* 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);*/
3304: }
3305: } /* end if mle */
3306: }
3307: } /* end wave */
3308: }
3309: jmean=sum/k;
3310: 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);
3311: 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);
3312: }
3313:
3314: /*********** Tricode ****************************/
3315: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
3316: {
3317: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3318: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
3319: * Boring subroutine which should only output nbcode[Tvar[j]][k]
3320: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
3321: * nbcode[Tvar[j]][1]=
3322: */
3323:
3324: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
3325: int modmaxcovj=0; /* Modality max of covariates j */
3326: int cptcode=0; /* Modality max of covariates j */
3327: int modmincovj=0; /* Modality min of covariates j */
3328:
3329:
3330: cptcoveff=0;
3331:
3332: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
3333:
3334: /* Loop on covariates without age and products */
3335: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
3336: for (k=-1; k < maxncov; k++) Ndum[k]=0;
3337: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
3338: modality of this covariate Vj*/
3339: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3340: * If product of Vn*Vm, still boolean *:
3341: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3342: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3343: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
3344: modality of the nth covariate of individual i. */
3345: if (ij > modmaxcovj)
3346: modmaxcovj=ij;
3347: else if (ij < modmincovj)
3348: modmincovj=ij;
3349: if ((ij < -1) && (ij > NCOVMAX)){
3350: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3351: exit(1);
3352: }else
3353: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
3354: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
3355: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
3356: /* getting the maximum value of the modality of the covariate
3357: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3358: female is 1, then modmaxcovj=1.*/
3359: } /* end for loop on individuals i */
3360: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3361: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
3362: cptcode=modmaxcovj;
3363: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
3364: /*for (i=0; i<=cptcode; i++) {*/
3365: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3366: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3367: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3368: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3369: if( k != -1){
3370: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3371: covariate for which somebody answered excluding
3372: undefined. Usually 2: 0 and 1. */
3373: }
3374: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3375: covariate for which somebody answered including
3376: undefined. Usually 3: -1, 0 and 1. */
3377: }
3378: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3379: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
3380: } /* Ndum[-1] number of undefined modalities */
3381:
3382: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
3383: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3384: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
3385: modmincovj=3; modmaxcovj = 7;
3386: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3387: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3388: defining two dummy variables: variables V1_1 and V1_2.
3389: nbcode[Tvar[j]][ij]=k;
3390: nbcode[Tvar[j]][1]=0;
3391: nbcode[Tvar[j]][2]=1;
3392: nbcode[Tvar[j]][3]=2;
3393: */
3394: ij=0; /* ij is similar to i but can jumps over null modalities */
3395: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 to 1*/
3396: if (Ndum[i] == 0) { /* If at least one individual responded to this modality k */
3397: break;
3398: }
3399: ij++;
3400: nbcode[Tvar[j]][ij]=i; /* stores the original modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
3401: cptcode = ij; /* New max modality for covar j */
3402: } /* end of loop on modality i=-1 to 1 or more */
3403:
3404: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3405: /* /\*recode from 0 *\/ */
3406: /* k is a modality. If we have model=V1+V1*sex */
3407: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3408: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3409: /* } */
3410: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3411: /* if (ij > ncodemax[j]) { */
3412: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3413: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3414: /* break; */
3415: /* } */
3416: /* } /\* end of loop on modality k *\/ */
3417: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3418:
3419: for (k=-1; k< maxncov; k++) Ndum[k]=0;
3420:
3421: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
3422: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3423: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
3424: Ndum[ij]++; /* Might be supersed V1 + V1*age */
3425: }
3426:
3427: ij=0;
3428: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3429: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
3430: if((Ndum[i]!=0) && (i<=ncovcol)){
3431: ij++;
3432: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3433: Tvaraff[ij]=i; /*For printing (unclear) */
3434: }else{
3435: /* Tvaraff[ij]=0; */
3436: }
3437: }
3438: /* ij--; */
3439: cptcoveff=ij; /*Number of total covariates*/
3440:
3441: }
3442:
3443:
3444: /*********** Health Expectancies ****************/
3445:
3446: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
3447:
3448: {
3449: /* Health expectancies, no variances */
3450: int i, j, nhstepm, hstepm, h, nstepm;
3451: int nhstepma, nstepma; /* Decreasing with age */
3452: double age, agelim, hf;
3453: double ***p3mat;
3454: double eip;
3455:
3456: pstamp(ficreseij);
3457: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3458: fprintf(ficreseij,"# Age");
3459: for(i=1; i<=nlstate;i++){
3460: for(j=1; j<=nlstate;j++){
3461: fprintf(ficreseij," e%1d%1d ",i,j);
3462: }
3463: fprintf(ficreseij," e%1d. ",i);
3464: }
3465: fprintf(ficreseij,"\n");
3466:
3467:
3468: if(estepm < stepm){
3469: printf ("Problem %d lower than %d\n",estepm, stepm);
3470: }
3471: else hstepm=estepm;
3472: /* We compute the life expectancy from trapezoids spaced every estepm months
3473: * This is mainly to measure the difference between two models: for example
3474: * if stepm=24 months pijx are given only every 2 years and by summing them
3475: * we are calculating an estimate of the Life Expectancy assuming a linear
3476: * progression in between and thus overestimating or underestimating according
3477: * to the curvature of the survival function. If, for the same date, we
3478: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3479: * to compare the new estimate of Life expectancy with the same linear
3480: * hypothesis. A more precise result, taking into account a more precise
3481: * curvature will be obtained if estepm is as small as stepm. */
3482:
3483: /* For example we decided to compute the life expectancy with the smallest unit */
3484: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3485: nhstepm is the number of hstepm from age to agelim
3486: nstepm is the number of stepm from age to agelin.
3487: Look at hpijx to understand the reason of that which relies in memory size
3488: and note for a fixed period like estepm months */
3489: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3490: survival function given by stepm (the optimization length). Unfortunately it
3491: means that if the survival funtion is printed only each two years of age and if
3492: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3493: results. So we changed our mind and took the option of the best precision.
3494: */
3495: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3496:
3497: agelim=AGESUP;
3498: /* If stepm=6 months */
3499: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3500: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3501:
3502: /* nhstepm age range expressed in number of stepm */
3503: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3504: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3505: /* if (stepm >= YEARM) hstepm=1;*/
3506: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3507: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3508:
3509: for (age=bage; age<=fage; age ++){
3510: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3511: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3512: /* if (stepm >= YEARM) hstepm=1;*/
3513: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3514:
3515: /* If stepm=6 months */
3516: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3517: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3518:
3519: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3520:
3521: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3522:
3523: printf("%d|",(int)age);fflush(stdout);
3524: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3525:
3526: /* Computing expectancies */
3527: for(i=1; i<=nlstate;i++)
3528: for(j=1; j<=nlstate;j++)
3529: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3530: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3531:
3532: /* 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]);*/
3533:
3534: }
3535:
3536: fprintf(ficreseij,"%3.0f",age );
3537: for(i=1; i<=nlstate;i++){
3538: eip=0;
3539: for(j=1; j<=nlstate;j++){
3540: eip +=eij[i][j][(int)age];
3541: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3542: }
3543: fprintf(ficreseij,"%9.4f", eip );
3544: }
3545: fprintf(ficreseij,"\n");
3546:
3547: }
3548: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3549: printf("\n");
3550: fprintf(ficlog,"\n");
3551:
3552: }
3553:
3554: 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[] )
3555:
3556: {
3557: /* Covariances of health expectancies eij and of total life expectancies according
3558: to initial status i, ei. .
3559: */
3560: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3561: int nhstepma, nstepma; /* Decreasing with age */
3562: double age, agelim, hf;
3563: double ***p3matp, ***p3matm, ***varhe;
3564: double **dnewm,**doldm;
3565: double *xp, *xm;
3566: double **gp, **gm;
3567: double ***gradg, ***trgradg;
3568: int theta;
3569:
3570: double eip, vip;
3571:
3572: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3573: xp=vector(1,npar);
3574: xm=vector(1,npar);
3575: dnewm=matrix(1,nlstate*nlstate,1,npar);
3576: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3577:
3578: pstamp(ficresstdeij);
3579: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3580: fprintf(ficresstdeij,"# Age");
3581: for(i=1; i<=nlstate;i++){
3582: for(j=1; j<=nlstate;j++)
3583: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3584: fprintf(ficresstdeij," e%1d. ",i);
3585: }
3586: fprintf(ficresstdeij,"\n");
3587:
3588: pstamp(ficrescveij);
3589: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3590: fprintf(ficrescveij,"# Age");
3591: for(i=1; i<=nlstate;i++)
3592: for(j=1; j<=nlstate;j++){
3593: cptj= (j-1)*nlstate+i;
3594: for(i2=1; i2<=nlstate;i2++)
3595: for(j2=1; j2<=nlstate;j2++){
3596: cptj2= (j2-1)*nlstate+i2;
3597: if(cptj2 <= cptj)
3598: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3599: }
3600: }
3601: fprintf(ficrescveij,"\n");
3602:
3603: if(estepm < stepm){
3604: printf ("Problem %d lower than %d\n",estepm, stepm);
3605: }
3606: else hstepm=estepm;
3607: /* We compute the life expectancy from trapezoids spaced every estepm months
3608: * This is mainly to measure the difference between two models: for example
3609: * if stepm=24 months pijx are given only every 2 years and by summing them
3610: * we are calculating an estimate of the Life Expectancy assuming a linear
3611: * progression in between and thus overestimating or underestimating according
3612: * to the curvature of the survival function. If, for the same date, we
3613: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3614: * to compare the new estimate of Life expectancy with the same linear
3615: * hypothesis. A more precise result, taking into account a more precise
3616: * curvature will be obtained if estepm is as small as stepm. */
3617:
3618: /* For example we decided to compute the life expectancy with the smallest unit */
3619: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3620: nhstepm is the number of hstepm from age to agelim
3621: nstepm is the number of stepm from age to agelin.
3622: Look at hpijx to understand the reason of that which relies in memory size
3623: and note for a fixed period like estepm months */
3624: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3625: survival function given by stepm (the optimization length). Unfortunately it
3626: means that if the survival funtion is printed only each two years of age and if
3627: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3628: results. So we changed our mind and took the option of the best precision.
3629: */
3630: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3631:
3632: /* If stepm=6 months */
3633: /* nhstepm age range expressed in number of stepm */
3634: agelim=AGESUP;
3635: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3636: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3637: /* if (stepm >= YEARM) hstepm=1;*/
3638: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3639:
3640: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3641: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3642: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3643: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3644: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3645: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3646:
3647: for (age=bage; age<=fage; age ++){
3648: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3649: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3650: /* if (stepm >= YEARM) hstepm=1;*/
3651: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3652:
3653: /* If stepm=6 months */
3654: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3655: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3656:
3657: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3658:
3659: /* Computing Variances of health expectancies */
3660: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3661: decrease memory allocation */
3662: for(theta=1; theta <=npar; theta++){
3663: for(i=1; i<=npar; i++){
3664: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3665: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3666: }
3667: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3668: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3669:
3670: for(j=1; j<= nlstate; j++){
3671: for(i=1; i<=nlstate; i++){
3672: for(h=0; h<=nhstepm-1; h++){
3673: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3674: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3675: }
3676: }
3677: }
3678:
3679: for(ij=1; ij<= nlstate*nlstate; ij++)
3680: for(h=0; h<=nhstepm-1; h++){
3681: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3682: }
3683: }/* End theta */
3684:
3685:
3686: for(h=0; h<=nhstepm-1; h++)
3687: for(j=1; j<=nlstate*nlstate;j++)
3688: for(theta=1; theta <=npar; theta++)
3689: trgradg[h][j][theta]=gradg[h][theta][j];
3690:
3691:
3692: for(ij=1;ij<=nlstate*nlstate;ij++)
3693: for(ji=1;ji<=nlstate*nlstate;ji++)
3694: varhe[ij][ji][(int)age] =0.;
3695:
3696: printf("%d|",(int)age);fflush(stdout);
3697: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3698: for(h=0;h<=nhstepm-1;h++){
3699: for(k=0;k<=nhstepm-1;k++){
3700: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3701: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3702: for(ij=1;ij<=nlstate*nlstate;ij++)
3703: for(ji=1;ji<=nlstate*nlstate;ji++)
3704: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3705: }
3706: }
3707:
3708: /* Computing expectancies */
3709: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3710: for(i=1; i<=nlstate;i++)
3711: for(j=1; j<=nlstate;j++)
3712: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3713: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3714:
3715: /* 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]);*/
3716:
3717: }
3718:
3719: fprintf(ficresstdeij,"%3.0f",age );
3720: for(i=1; i<=nlstate;i++){
3721: eip=0.;
3722: vip=0.;
3723: for(j=1; j<=nlstate;j++){
3724: eip += eij[i][j][(int)age];
3725: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3726: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3727: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3728: }
3729: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3730: }
3731: fprintf(ficresstdeij,"\n");
3732:
3733: fprintf(ficrescveij,"%3.0f",age );
3734: for(i=1; i<=nlstate;i++)
3735: for(j=1; j<=nlstate;j++){
3736: cptj= (j-1)*nlstate+i;
3737: for(i2=1; i2<=nlstate;i2++)
3738: for(j2=1; j2<=nlstate;j2++){
3739: cptj2= (j2-1)*nlstate+i2;
3740: if(cptj2 <= cptj)
3741: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3742: }
3743: }
3744: fprintf(ficrescveij,"\n");
3745:
3746: }
3747: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3748: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3749: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3750: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3751: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3752: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3753: printf("\n");
3754: fprintf(ficlog,"\n");
3755:
3756: free_vector(xm,1,npar);
3757: free_vector(xp,1,npar);
3758: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3759: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3760: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3761: }
3762:
3763: /************ Variance ******************/
3764: 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[])
3765: {
3766: /* Variance of health expectancies */
3767: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3768: /* double **newm;*/
3769: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3770:
3771: int movingaverage();
3772: double **dnewm,**doldm;
3773: double **dnewmp,**doldmp;
3774: int i, j, nhstepm, hstepm, h, nstepm ;
3775: int k;
3776: double *xp;
3777: double **gp, **gm; /* for var eij */
3778: double ***gradg, ***trgradg; /*for var eij */
3779: double **gradgp, **trgradgp; /* for var p point j */
3780: double *gpp, *gmp; /* for var p point j */
3781: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3782: double ***p3mat;
3783: double age,agelim, hf;
3784: double ***mobaverage;
3785: int theta;
3786: char digit[4];
3787: char digitp[25];
3788:
3789: char fileresprobmorprev[FILENAMELENGTH];
3790:
3791: if(popbased==1){
3792: if(mobilav!=0)
3793: strcpy(digitp,"-populbased-mobilav-");
3794: else strcpy(digitp,"-populbased-nomobil-");
3795: }
3796: else
3797: strcpy(digitp,"-stablbased-");
3798:
3799: if (mobilav!=0) {
3800: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3801: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3802: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3803: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3804: }
3805: }
3806:
3807: strcpy(fileresprobmorprev,"prmorprev");
3808: sprintf(digit,"%-d",ij);
3809: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3810: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3811: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3812: strcat(fileresprobmorprev,fileres);
3813: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3814: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3815: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3816: }
3817: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3818:
3819: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3820: pstamp(ficresprobmorprev);
3821: 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);
3822: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3823: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3824: fprintf(ficresprobmorprev," p.%-d SE",j);
3825: for(i=1; i<=nlstate;i++)
3826: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3827: }
3828: fprintf(ficresprobmorprev,"\n");
3829: fprintf(ficgp,"\n# Routine varevsij");
3830: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3831: 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");
3832: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3833: /* } */
3834: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3835: pstamp(ficresvij);
3836: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3837: if(popbased==1)
3838: 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);
3839: else
3840: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3841: fprintf(ficresvij,"# Age");
3842: for(i=1; i<=nlstate;i++)
3843: for(j=1; j<=nlstate;j++)
3844: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3845: fprintf(ficresvij,"\n");
3846:
3847: xp=vector(1,npar);
3848: dnewm=matrix(1,nlstate,1,npar);
3849: doldm=matrix(1,nlstate,1,nlstate);
3850: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3851: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3852:
3853: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3854: gpp=vector(nlstate+1,nlstate+ndeath);
3855: gmp=vector(nlstate+1,nlstate+ndeath);
3856: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3857:
3858: if(estepm < stepm){
3859: printf ("Problem %d lower than %d\n",estepm, stepm);
3860: }
3861: else hstepm=estepm;
3862: /* For example we decided to compute the life expectancy with the smallest unit */
3863: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3864: nhstepm is the number of hstepm from age to agelim
3865: nstepm is the number of stepm from age to agelin.
3866: Look at function hpijx to understand why (it is linked to memory size questions) */
3867: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3868: survival function given by stepm (the optimization length). Unfortunately it
3869: means that if the survival funtion is printed every two years of age and if
3870: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3871: results. So we changed our mind and took the option of the best precision.
3872: */
3873: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3874: agelim = AGESUP;
3875: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3876: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3877: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3878: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3879: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3880: gp=matrix(0,nhstepm,1,nlstate);
3881: gm=matrix(0,nhstepm,1,nlstate);
3882:
3883:
3884: for(theta=1; theta <=npar; theta++){
3885: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3886: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3887: }
3888: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3889: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3890:
3891: if (popbased==1) {
3892: if(mobilav ==0){
3893: for(i=1; i<=nlstate;i++)
3894: prlim[i][i]=probs[(int)age][i][ij];
3895: }else{ /* mobilav */
3896: for(i=1; i<=nlstate;i++)
3897: prlim[i][i]=mobaverage[(int)age][i][ij];
3898: }
3899: }
3900:
3901: for(j=1; j<= nlstate; j++){
3902: for(h=0; h<=nhstepm; h++){
3903: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3904: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3905: }
3906: }
3907: /* This for computing probability of death (h=1 means
3908: computed over hstepm matrices product = hstepm*stepm months)
3909: as a weighted average of prlim.
3910: */
3911: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3912: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3913: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3914: }
3915: /* end probability of death */
3916:
3917: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3918: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3919: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3920: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3921:
3922: if (popbased==1) {
3923: if(mobilav ==0){
3924: for(i=1; i<=nlstate;i++)
3925: prlim[i][i]=probs[(int)age][i][ij];
3926: }else{ /* mobilav */
3927: for(i=1; i<=nlstate;i++)
3928: prlim[i][i]=mobaverage[(int)age][i][ij];
3929: }
3930: }
3931:
3932: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
3933: for(h=0; h<=nhstepm; h++){
3934: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3935: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3936: }
3937: }
3938: /* This for computing probability of death (h=1 means
3939: computed over hstepm matrices product = hstepm*stepm months)
3940: as a weighted average of prlim.
3941: */
3942: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3943: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3944: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3945: }
3946: /* end probability of death */
3947:
3948: for(j=1; j<= nlstate; j++) /* vareij */
3949: for(h=0; h<=nhstepm; h++){
3950: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3951: }
3952:
3953: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3954: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3955: }
3956:
3957: } /* End theta */
3958:
3959: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3960:
3961: for(h=0; h<=nhstepm; h++) /* veij */
3962: for(j=1; j<=nlstate;j++)
3963: for(theta=1; theta <=npar; theta++)
3964: trgradg[h][j][theta]=gradg[h][theta][j];
3965:
3966: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3967: for(theta=1; theta <=npar; theta++)
3968: trgradgp[j][theta]=gradgp[theta][j];
3969:
3970:
3971: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3972: for(i=1;i<=nlstate;i++)
3973: for(j=1;j<=nlstate;j++)
3974: vareij[i][j][(int)age] =0.;
3975:
3976: for(h=0;h<=nhstepm;h++){
3977: for(k=0;k<=nhstepm;k++){
3978: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3979: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3980: for(i=1;i<=nlstate;i++)
3981: for(j=1;j<=nlstate;j++)
3982: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3983: }
3984: }
3985:
3986: /* pptj */
3987: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3988: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3989: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3990: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3991: varppt[j][i]=doldmp[j][i];
3992: /* end ppptj */
3993: /* x centered again */
3994: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
3995: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
3996:
3997: if (popbased==1) {
3998: if(mobilav ==0){
3999: for(i=1; i<=nlstate;i++)
4000: prlim[i][i]=probs[(int)age][i][ij];
4001: }else{ /* mobilav */
4002: for(i=1; i<=nlstate;i++)
4003: prlim[i][i]=mobaverage[(int)age][i][ij];
4004: }
4005: }
4006:
4007: /* This for computing probability of death (h=1 means
4008: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4009: as a weighted average of prlim.
4010: */
4011: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4012: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4013: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4014: }
4015: /* end probability of death */
4016:
4017: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4018: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4019: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4020: for(i=1; i<=nlstate;i++){
4021: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4022: }
4023: }
4024: fprintf(ficresprobmorprev,"\n");
4025:
4026: fprintf(ficresvij,"%.0f ",age );
4027: for(i=1; i<=nlstate;i++)
4028: for(j=1; j<=nlstate;j++){
4029: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4030: }
4031: fprintf(ficresvij,"\n");
4032: free_matrix(gp,0,nhstepm,1,nlstate);
4033: free_matrix(gm,0,nhstepm,1,nlstate);
4034: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4035: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4036: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4037: } /* End age */
4038: free_vector(gpp,nlstate+1,nlstate+ndeath);
4039: free_vector(gmp,nlstate+1,nlstate+ndeath);
4040: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4041: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4042: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
4043: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
4044: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
4045: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4046: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4047: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
4048: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
4049: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
4050: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
4051: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4052: 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);
4053: /* 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);
4054: */
4055: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4056: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4057:
4058: free_vector(xp,1,npar);
4059: free_matrix(doldm,1,nlstate,1,nlstate);
4060: free_matrix(dnewm,1,nlstate,1,npar);
4061: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4062: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4063: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4064: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4065: fclose(ficresprobmorprev);
4066: fflush(ficgp);
4067: fflush(fichtm);
4068: } /* end varevsij */
4069:
4070: /************ Variance of prevlim ******************/
4071: 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[])
4072: {
4073: /* Variance of prevalence limit */
4074: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
4075:
4076: double **dnewm,**doldm;
4077: int i, j, nhstepm, hstepm;
4078: double *xp;
4079: double *gp, *gm;
4080: double **gradg, **trgradg;
4081: double age,agelim;
4082: int theta;
4083:
4084: pstamp(ficresvpl);
4085: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4086: fprintf(ficresvpl,"# Age");
4087: for(i=1; i<=nlstate;i++)
4088: fprintf(ficresvpl," %1d-%1d",i,i);
4089: fprintf(ficresvpl,"\n");
4090:
4091: xp=vector(1,npar);
4092: dnewm=matrix(1,nlstate,1,npar);
4093: doldm=matrix(1,nlstate,1,nlstate);
4094:
4095: hstepm=1*YEARM; /* Every year of age */
4096: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4097: agelim = AGESUP;
4098: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4099: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4100: if (stepm >= YEARM) hstepm=1;
4101: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4102: gradg=matrix(1,npar,1,nlstate);
4103: gp=vector(1,nlstate);
4104: gm=vector(1,nlstate);
4105:
4106: for(theta=1; theta <=npar; theta++){
4107: for(i=1; i<=npar; i++){ /* Computes gradient */
4108: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4109: }
4110: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4111: for(i=1;i<=nlstate;i++)
4112: gp[i] = prlim[i][i];
4113:
4114: for(i=1; i<=npar; i++) /* Computes gradient */
4115: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4117: for(i=1;i<=nlstate;i++)
4118: gm[i] = prlim[i][i];
4119:
4120: for(i=1;i<=nlstate;i++)
4121: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4122: } /* End theta */
4123:
4124: trgradg =matrix(1,nlstate,1,npar);
4125:
4126: for(j=1; j<=nlstate;j++)
4127: for(theta=1; theta <=npar; theta++)
4128: trgradg[j][theta]=gradg[theta][j];
4129:
4130: for(i=1;i<=nlstate;i++)
4131: varpl[i][(int)age] =0.;
4132: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4133: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4134: for(i=1;i<=nlstate;i++)
4135: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4136:
4137: fprintf(ficresvpl,"%.0f ",age );
4138: for(i=1; i<=nlstate;i++)
4139: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4140: fprintf(ficresvpl,"\n");
4141: free_vector(gp,1,nlstate);
4142: free_vector(gm,1,nlstate);
4143: free_matrix(gradg,1,npar,1,nlstate);
4144: free_matrix(trgradg,1,nlstate,1,npar);
4145: } /* End age */
4146:
4147: free_vector(xp,1,npar);
4148: free_matrix(doldm,1,nlstate,1,npar);
4149: free_matrix(dnewm,1,nlstate,1,nlstate);
4150:
4151: }
4152:
4153: /************ Variance of one-step probabilities ******************/
4154: 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[])
4155: {
4156: int i, j=0, k1, l1, tj;
4157: int k2, l2, j1, z1;
4158: int k=0, l;
4159: int first=1, first1, first2;
4160: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4161: double **dnewm,**doldm;
4162: double *xp;
4163: double *gp, *gm;
4164: double **gradg, **trgradg;
4165: double **mu;
4166: double age, cov[NCOVMAX+1];
4167: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4168: int theta;
4169: char fileresprob[FILENAMELENGTH];
4170: char fileresprobcov[FILENAMELENGTH];
4171: char fileresprobcor[FILENAMELENGTH];
4172: double ***varpij;
4173:
4174: strcpy(fileresprob,"prob");
4175: strcat(fileresprob,fileres);
4176: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4177: printf("Problem with resultfile: %s\n", fileresprob);
4178: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4179: }
4180: strcpy(fileresprobcov,"probcov");
4181: strcat(fileresprobcov,fileres);
4182: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4183: printf("Problem with resultfile: %s\n", fileresprobcov);
4184: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4185: }
4186: strcpy(fileresprobcor,"probcor");
4187: strcat(fileresprobcor,fileres);
4188: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4189: printf("Problem with resultfile: %s\n", fileresprobcor);
4190: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4191: }
4192: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4193: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4194: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4195: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4196: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4197: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4198: pstamp(ficresprob);
4199: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4200: fprintf(ficresprob,"# Age");
4201: pstamp(ficresprobcov);
4202: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4203: fprintf(ficresprobcov,"# Age");
4204: pstamp(ficresprobcor);
4205: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4206: fprintf(ficresprobcor,"# Age");
4207:
4208:
4209: for(i=1; i<=nlstate;i++)
4210: for(j=1; j<=(nlstate+ndeath);j++){
4211: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4212: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4213: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4214: }
4215: /* fprintf(ficresprob,"\n");
4216: fprintf(ficresprobcov,"\n");
4217: fprintf(ficresprobcor,"\n");
4218: */
4219: xp=vector(1,npar);
4220: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4221: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4222: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4223: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4224: first=1;
4225: fprintf(ficgp,"\n# Routine varprob");
4226: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4227: fprintf(fichtm,"\n");
4228:
4229: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
4230: fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
4231: file %s<br>\n",optionfilehtmcov);
4232: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
4233: and drawn. It helps understanding how is the covariance between two incidences.\
4234: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4235: 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. \
4236: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4237: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4238: standard deviations wide on each axis. <br>\
4239: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4240: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4241: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4242:
4243: cov[1]=1;
4244: /* tj=cptcoveff; */
4245: tj = (int) pow(2,cptcoveff);
4246: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4247: j1=0;
4248: for(j1=1; j1<=tj;j1++){
4249: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4250: /*j1++;*/
4251: if (cptcovn>0) {
4252: fprintf(ficresprob, "\n#********** Variable ");
4253: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4254: fprintf(ficresprob, "**********\n#\n");
4255: fprintf(ficresprobcov, "\n#********** Variable ");
4256: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4257: fprintf(ficresprobcov, "**********\n#\n");
4258:
4259: fprintf(ficgp, "\n#********** Variable ");
4260: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4261: fprintf(ficgp, "**********\n#\n");
4262:
4263:
4264: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4265: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4266: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4267:
4268: fprintf(ficresprobcor, "\n#********** Variable ");
4269: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4270: fprintf(ficresprobcor, "**********\n#");
4271: }
4272:
4273: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4274: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4275: gp=vector(1,(nlstate)*(nlstate+ndeath));
4276: gm=vector(1,(nlstate)*(nlstate+ndeath));
4277: for (age=bage; age<=fage; age ++){
4278: cov[2]=age;
4279: if(nagesqr==1)
4280: cov[3]= age*age;
4281: for (k=1; k<=cptcovn;k++) {
4282: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
4283: * 1 1 1 1 1
4284: * 2 2 1 1 1
4285: * 3 1 2 1 1
4286: */
4287: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
4288: }
4289: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4290: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
4291: for (k=1; k<=cptcovprod;k++)
4292: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
4293:
4294:
4295: for(theta=1; theta <=npar; theta++){
4296: for(i=1; i<=npar; i++)
4297: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4298:
4299: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4300:
4301: k=0;
4302: for(i=1; i<= (nlstate); i++){
4303: for(j=1; j<=(nlstate+ndeath);j++){
4304: k=k+1;
4305: gp[k]=pmmij[i][j];
4306: }
4307: }
4308:
4309: for(i=1; i<=npar; i++)
4310: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4311:
4312: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4313: k=0;
4314: for(i=1; i<=(nlstate); i++){
4315: for(j=1; j<=(nlstate+ndeath);j++){
4316: k=k+1;
4317: gm[k]=pmmij[i][j];
4318: }
4319: }
4320:
4321: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4322: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4323: }
4324:
4325: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4326: for(theta=1; theta <=npar; theta++)
4327: trgradg[j][theta]=gradg[theta][j];
4328:
4329: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4330: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4331:
4332: pmij(pmmij,cov,ncovmodel,x,nlstate);
4333:
4334: k=0;
4335: for(i=1; i<=(nlstate); i++){
4336: for(j=1; j<=(nlstate+ndeath);j++){
4337: k=k+1;
4338: mu[k][(int) age]=pmmij[i][j];
4339: }
4340: }
4341: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4342: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4343: varpij[i][j][(int)age] = doldm[i][j];
4344:
4345: /*printf("\n%d ",(int)age);
4346: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4347: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4348: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4349: }*/
4350:
4351: fprintf(ficresprob,"\n%d ",(int)age);
4352: fprintf(ficresprobcov,"\n%d ",(int)age);
4353: fprintf(ficresprobcor,"\n%d ",(int)age);
4354:
4355: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4356: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4357: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4358: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4359: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4360: }
4361: i=0;
4362: for (k=1; k<=(nlstate);k++){
4363: for (l=1; l<=(nlstate+ndeath);l++){
4364: i++;
4365: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4366: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4367: for (j=1; j<=i;j++){
4368: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
4369: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4370: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4371: }
4372: }
4373: }/* end of loop for state */
4374: } /* end of loop for age */
4375: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4376: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4377: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4378: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4379:
4380: /* Confidence intervalle of pij */
4381: /*
4382: fprintf(ficgp,"\nunset parametric;unset label");
4383: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4384: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4385: 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);
4386: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4387: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4388: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4389: */
4390:
4391: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
4392: first1=1;first2=2;
4393: for (k2=1; k2<=(nlstate);k2++){
4394: for (l2=1; l2<=(nlstate+ndeath);l2++){
4395: if(l2==k2) continue;
4396: j=(k2-1)*(nlstate+ndeath)+l2;
4397: for (k1=1; k1<=(nlstate);k1++){
4398: for (l1=1; l1<=(nlstate+ndeath);l1++){
4399: if(l1==k1) continue;
4400: i=(k1-1)*(nlstate+ndeath)+l1;
4401: if(i<=j) continue;
4402: for (age=bage; age<=fage; age ++){
4403: if ((int)age %5==0){
4404: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4405: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4406: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4407: mu1=mu[i][(int) age]/stepm*YEARM ;
4408: mu2=mu[j][(int) age]/stepm*YEARM;
4409: c12=cv12/sqrt(v1*v2);
4410: /* Computing eigen value of matrix of covariance */
4411: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4412: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4413: if ((lc2 <0) || (lc1 <0) ){
4414: if(first2==1){
4415: first1=0;
4416: 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);
4417: }
4418: 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);
4419: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4420: /* lc2=fabs(lc2); */
4421: }
4422:
4423: /* Eigen vectors */
4424: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4425: /*v21=sqrt(1.-v11*v11); *//* error */
4426: v21=(lc1-v1)/cv12*v11;
4427: v12=-v21;
4428: v22=v11;
4429: tnalp=v21/v11;
4430: if(first1==1){
4431: first1=0;
4432: 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);
4433: }
4434: 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);
4435: /*printf(fignu*/
4436: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4437: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4438: if(first==1){
4439: first=0;
4440: fprintf(ficgp,"\nset parametric;unset label");
4441: 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);
4442: fprintf(ficgp,"\nset ter png small size 320, 240");
4443: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4444: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4445: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4446: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4447: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4448: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4449: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4450: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4451: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4452: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4453: 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",\
4454: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4455: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4456: }else{
4457: first=0;
4458: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4459: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4460: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4461: 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",\
4462: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4463: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4464: }/* if first */
4465: } /* age mod 5 */
4466: } /* end loop age */
4467: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4468: first=1;
4469: } /*l12 */
4470: } /* k12 */
4471: } /*l1 */
4472: }/* k1 */
4473: /* } */ /* loop covariates */
4474: }
4475: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4476: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4477: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4478: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4479: free_vector(xp,1,npar);
4480: fclose(ficresprob);
4481: fclose(ficresprobcov);
4482: fclose(ficresprobcor);
4483: fflush(ficgp);
4484: fflush(fichtmcov);
4485: }
4486:
4487:
4488: /******************* Printing html file ***********/
4489: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4490: int lastpass, int stepm, int weightopt, char model[],\
4491: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4492: int popforecast, int estepm ,\
4493: double jprev1, double mprev1,double anprev1, \
4494: double jprev2, double mprev2,double anprev2){
4495: int jj1, k1, i1, cpt;
4496:
4497: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4498: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4499: </ul>");
4500: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4501: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4502: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4503: fprintf(fichtm,"\
4504: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4505: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4506: fprintf(fichtm,"\
4507: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4508: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4509: fprintf(fichtm,"\
4510: - (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): \
4511: <a href=\"%s\">%s</a> <br>\n",
4512: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4513: fprintf(fichtm,"\
4514: - Population projections by age and states: \
4515: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4516:
4517: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4518:
4519: m=pow(2,cptcoveff);
4520: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4521:
4522: jj1=0;
4523: for(k1=1; k1<=m;k1++){
4524: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
4525: jj1++;
4526: if (cptcovn > 0) {
4527: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4528: for (cpt=1; cpt<=cptcoveff;cpt++){
4529: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4530: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4531: }
4532: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4533: }
4534: /* Pij */
4535: 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> \
4536: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4537: /* Quasi-incidences */
4538: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4539: 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> \
4540: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
4541: /* Period (stable) prevalence in each health state */
4542: for(cpt=1; cpt<=nlstate;cpt++){
4543: 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> \
4544: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
4545: }
4546: for(cpt=1; cpt<=nlstate;cpt++) {
4547: 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> \
4548: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
4549: }
4550: /* } /\* end i1 *\/ */
4551: }/* End k1 */
4552: fprintf(fichtm,"</ul>");
4553:
4554: fprintf(fichtm,"\
4555: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
4556: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
4557: - 95%% confidence intervals and T statistics are in the log file.<br>\n", rfileres,rfileres);
4558:
4559: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4560: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4561: fprintf(fichtm,"\
4562: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4563: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4564:
4565: fprintf(fichtm,"\
4566: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4567: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4568: fprintf(fichtm,"\
4569: - 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): \
4570: <a href=\"%s\">%s</a> <br>\n</li>",
4571: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4572: fprintf(fichtm,"\
4573: - (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): \
4574: <a href=\"%s\">%s</a> <br>\n</li>",
4575: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4576: fprintf(fichtm,"\
4577: - 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",
4578: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4579: fprintf(fichtm,"\
4580: - 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",
4581: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
4582: fprintf(fichtm,"\
4583: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4584: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4585:
4586: /* if(popforecast==1) fprintf(fichtm,"\n */
4587: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4588: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4589: /* <br>",fileres,fileres,fileres,fileres); */
4590: /* else */
4591: /* 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); */
4592: fflush(fichtm);
4593: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4594:
4595: m=pow(2,cptcoveff);
4596: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4597:
4598: jj1=0;
4599: for(k1=1; k1<=m;k1++){
4600: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
4601: jj1++;
4602: if (cptcovn > 0) {
4603: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4604: for (cpt=1; cpt<=cptcoveff;cpt++)
4605: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4606: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4607: }
4608: for(cpt=1; cpt<=nlstate;cpt++) {
4609: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
4610: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4611: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
4612: }
4613: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
4614: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4615: true period expectancies (those weighted with period prevalences are also\
4616: drawn in addition to the population based expectancies computed using\
4617: observed and cahotic prevalences: %s%d.png<br>\
4618: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
4619: /* } /\* end i1 *\/ */
4620: }/* End k1 */
4621: fprintf(fichtm,"</ul>");
4622: fflush(fichtm);
4623: }
4624:
4625: /******************* Gnuplot file **************/
4626: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4627:
4628: char dirfileres[132],optfileres[132];
4629: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
4630: int ng=0;
4631: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4632: /* printf("Problem with file %s",optionfilegnuplot); */
4633: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4634: /* } */
4635:
4636: /*#ifdef windows */
4637: fprintf(ficgp,"cd \"%s\" \n",pathc);
4638: /*#endif */
4639: m=pow(2,cptcoveff);
4640:
4641: strcpy(dirfileres,optionfilefiname);
4642: strcpy(optfileres,"vpl");
4643: /* 1eme*/
4644: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
4645: for (cpt=1; cpt<= nlstate ; cpt ++) {
4646: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4647: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4648: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
4649: fprintf(ficgp,"set xlabel \"Age\" \n\
4650: set ylabel \"Probability\" \n\
4651: set ter png small size 320, 240\n\
4652: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
4653:
4654: for (i=1; i<= nlstate ; i ++) {
4655: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4656: else fprintf(ficgp," %%*lf (%%*lf)");
4657: }
4658: 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);
4659: for (i=1; i<= nlstate ; i ++) {
4660: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4661: else fprintf(ficgp," %%*lf (%%*lf)");
4662: }
4663: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
4664: for (i=1; i<= nlstate ; i ++) {
4665: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4666: else fprintf(ficgp," %%*lf (%%*lf)");
4667: }
4668: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
4669: }
4670: }
4671: /*2 eme*/
4672: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
4673: for (k1=1; k1<= m ; k1 ++) {
4674: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
4675: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
4676:
4677: for (i=1; i<= nlstate+1 ; i ++) {
4678: k=2*i;
4679: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4680: for (j=1; j<= nlstate+1 ; j ++) {
4681: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4682: else fprintf(ficgp," %%*lf (%%*lf)");
4683: }
4684: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4685: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
4686: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4687: for (j=1; j<= nlstate+1 ; j ++) {
4688: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4689: else fprintf(ficgp," %%*lf (%%*lf)");
4690: }
4691: fprintf(ficgp,"\" t\"\" w l lt 0,");
4692: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
4693: for (j=1; j<= nlstate+1 ; j ++) {
4694: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4695: else fprintf(ficgp," %%*lf (%%*lf)");
4696: }
4697: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4698: else fprintf(ficgp,"\" t\"\" w l lt 0,");
4699: }
4700: }
4701:
4702: /*3eme*/
4703:
4704: for (k1=1; k1<= m ; k1 ++) {
4705: for (cpt=1; cpt<= nlstate ; cpt ++) {
4706: /* k=2+nlstate*(2*cpt-2); */
4707: k=2+(nlstate+1)*(cpt-1);
4708: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
4709: fprintf(ficgp,"set ter png small size 320, 240\n\
4710: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4711: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4712: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4713: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4714: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4715: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4716: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4717:
4718: */
4719: for (i=1; i< nlstate ; i ++) {
4720: 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);
4721: /* 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);*/
4722:
4723: }
4724: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4725: }
4726: }
4727:
4728: /* CV preval stable (period) */
4729: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4730: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
4731: k=3;
4732: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
4733: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
4734: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
4735: set ter png small size 320, 240\n\
4736: unset log y\n\
4737: plot [%.f:%.f] ", ageminpar, agemaxpar);
4738: for (i=1; i<= nlstate ; i ++){
4739: if(i==1)
4740: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4741: else
4742: fprintf(ficgp,", '' ");
4743: l=(nlstate+ndeath)*(i-1)+1;
4744: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
4745: for (j=1; j<= (nlstate-1) ; j ++)
4746: fprintf(ficgp,"+$%d",k+l+j);
4747: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4748: } /* nlstate */
4749: fprintf(ficgp,"\n");
4750: } /* end cpt state*/
4751: } /* end covariate */
4752:
4753: /* proba elementaires */
4754: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
4755: for(i=1,jk=1; i <=nlstate; i++){
4756: fprintf(ficgp,"# initial state %d\n",i);
4757: for(k=1; k <=(nlstate+ndeath); k++){
4758: if (k != i) {
4759: fprintf(ficgp,"# current state %d\n",k);
4760: for(j=1; j <=ncovmodel; j++){
4761: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
4762: jk++;
4763: }
4764: fprintf(ficgp,"\n");
4765: }
4766: }
4767: }
4768: fprintf(ficgp,"##############\n#\n");
4769:
4770: /*goto avoid;*/
4771: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4772: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4773: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4774: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4775: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4776: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4777: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4778: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4779: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4780: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4781: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4782: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4783: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4784: fprintf(ficgp,"#\n");
4785: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
4786: fprintf(ficgp,"# ng=%d\n",ng);
4787: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
4788: for(jk=1; jk <=m; jk++) {
4789: fprintf(ficgp,"# jk=%d\n",jk);
4790: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
4791: if (ng==2)
4792: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4793: else
4794: fprintf(ficgp,"\nset title \"Probability\"\n");
4795: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
4796: i=1;
4797: for(k2=1; k2<=nlstate; k2++) {
4798: k3=i;
4799: for(k=1; k<=(nlstate+ndeath); k++) {
4800: if (k != k2){
4801: if(ng==2)
4802: if(nagesqr==0)
4803: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4804: else /* nagesqr =1 */
4805: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
4806: else
4807: if(nagesqr==0)
4808: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4809: else /* nagesqr =1 */
4810: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
4811: ij=1;/* To be checked else nbcode[0][0] wrong */
4812: for(j=3; j <=ncovmodel-nagesqr; j++) {
4813: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) { /* Bug valgrind */
4814: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4815: ij++;
4816: }
4817: else
4818: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4819: }
4820: fprintf(ficgp,")/(1");
4821:
4822: for(k1=1; k1 <=nlstate; k1++){
4823: if(nagesqr==0)
4824: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4825: else /* nagesqr =1 */
4826: fprintf(ficgp,"+exp(p%d+p%d*x+p%d*x*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1,k3+(k1-1)*ncovmodel+1+nagesqr);
4827:
4828: ij=1;
4829: for(j=3; j <=ncovmodel-nagesqr; j++){
4830: if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
4831: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
4832: ij++;
4833: }
4834: else
4835: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
4836: }
4837: fprintf(ficgp,")");
4838: }
4839: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4840: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4841: i=i+ncovmodel;
4842: }
4843: } /* end k */
4844: } /* end k2 */
4845: } /* end jk */
4846: } /* end ng */
4847: /* avoid: */
4848: fflush(ficgp);
4849: } /* end gnuplot */
4850:
4851:
4852: /*************** Moving average **************/
4853: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4854:
4855: int i, cpt, cptcod;
4856: int modcovmax =1;
4857: int mobilavrange, mob;
4858: double age;
4859:
4860: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4861: a covariate has 2 modalities */
4862: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4863:
4864: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4865: if(mobilav==1) mobilavrange=5; /* default */
4866: else mobilavrange=mobilav;
4867: for (age=bage; age<=fage; age++)
4868: for (i=1; i<=nlstate;i++)
4869: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4870: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4871: /* We keep the original values on the extreme ages bage, fage and for
4872: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4873: we use a 5 terms etc. until the borders are no more concerned.
4874: */
4875: for (mob=3;mob <=mobilavrange;mob=mob+2){
4876: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4877: for (i=1; i<=nlstate;i++){
4878: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4879: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4880: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4881: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4882: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4883: }
4884: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4885: }
4886: }
4887: }/* end age */
4888: }/* end mob */
4889: }else return -1;
4890: return 0;
4891: }/* End movingaverage */
4892:
4893:
4894: /************** Forecasting ******************/
4895: 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){
4896: /* proj1, year, month, day of starting projection
4897: agemin, agemax range of age
4898: dateprev1 dateprev2 range of dates during which prevalence is computed
4899: anproj2 year of en of projection (same day and month as proj1).
4900: */
4901: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
4902: double agec; /* generic age */
4903: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4904: double *popeffectif,*popcount;
4905: double ***p3mat;
4906: double ***mobaverage;
4907: char fileresf[FILENAMELENGTH];
4908:
4909: agelim=AGESUP;
4910: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4911:
4912: strcpy(fileresf,"f");
4913: strcat(fileresf,fileres);
4914: if((ficresf=fopen(fileresf,"w"))==NULL) {
4915: printf("Problem with forecast resultfile: %s\n", fileresf);
4916: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4917: }
4918: printf("Computing forecasting: result on file '%s' \n", fileresf);
4919: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4920:
4921: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4922:
4923: if (mobilav!=0) {
4924: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4925: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4926: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4927: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4928: }
4929: }
4930:
4931: stepsize=(int) (stepm+YEARM-1)/YEARM;
4932: if (stepm<=12) stepsize=1;
4933: if(estepm < stepm){
4934: printf ("Problem %d lower than %d\n",estepm, stepm);
4935: }
4936: else hstepm=estepm;
4937:
4938: hstepm=hstepm/stepm;
4939: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4940: fractional in yp1 */
4941: anprojmean=yp;
4942: yp2=modf((yp1*12),&yp);
4943: mprojmean=yp;
4944: yp1=modf((yp2*30.5),&yp);
4945: jprojmean=yp;
4946: if(jprojmean==0) jprojmean=1;
4947: if(mprojmean==0) jprojmean=1;
4948:
4949: i1=cptcoveff;
4950: if (cptcovn < 1){i1=1;}
4951:
4952: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4953:
4954: fprintf(ficresf,"#****** Routine prevforecast **\n");
4955:
4956: /* if (h==(int)(YEARM*yearp)){ */
4957: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4958: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4959: k=k+1;
4960: fprintf(ficresf,"\n#******");
4961: for(j=1;j<=cptcoveff;j++) {
4962: 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]]);
4963: }
4964: fprintf(ficresf,"******\n");
4965: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4966: for(j=1; j<=nlstate+ndeath;j++){
4967: for(i=1; i<=nlstate;i++)
4968: fprintf(ficresf," p%d%d",i,j);
4969: fprintf(ficresf," p.%d",j);
4970: }
4971: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4972: fprintf(ficresf,"\n");
4973: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4974:
4975: for (agec=fage; agec>=(ageminpar-1); agec--){
4976: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4977: nhstepm = nhstepm/hstepm;
4978: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4979: oldm=oldms;savm=savms;
4980: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4981:
4982: for (h=0; h<=nhstepm; h++){
4983: if (h*hstepm/YEARM*stepm ==yearp) {
4984: fprintf(ficresf,"\n");
4985: for(j=1;j<=cptcoveff;j++)
4986: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
4987: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
4988: }
4989: for(j=1; j<=nlstate+ndeath;j++) {
4990: ppij=0.;
4991: for(i=1; i<=nlstate;i++) {
4992: if (mobilav==1)
4993: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
4994: else {
4995: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
4996: }
4997: if (h*hstepm/YEARM*stepm== yearp) {
4998: fprintf(ficresf," %.3f", p3mat[i][j][h]);
4999: }
5000: } /* end i */
5001: if (h*hstepm/YEARM*stepm==yearp) {
5002: fprintf(ficresf," %.3f", ppij);
5003: }
5004: }/* end j */
5005: } /* end h */
5006: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5007: } /* end agec */
5008: } /* end yearp */
5009: } /* end cptcod */
5010: } /* end cptcov */
5011:
5012: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5013:
5014: fclose(ficresf);
5015: }
5016:
5017: /************** Forecasting *****not tested NB*************/
5018: 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){
5019:
5020: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5021: int *popage;
5022: double calagedatem, agelim, kk1, kk2;
5023: double *popeffectif,*popcount;
5024: double ***p3mat,***tabpop,***tabpopprev;
5025: double ***mobaverage;
5026: char filerespop[FILENAMELENGTH];
5027:
5028: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5029: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5030: agelim=AGESUP;
5031: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5032:
5033: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5034:
5035:
5036: strcpy(filerespop,"pop");
5037: strcat(filerespop,fileres);
5038: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5039: printf("Problem with forecast resultfile: %s\n", filerespop);
5040: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5041: }
5042: printf("Computing forecasting: result on file '%s' \n", filerespop);
5043: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5044:
5045: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5046:
5047: if (mobilav!=0) {
5048: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5049: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5050: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5051: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5052: }
5053: }
5054:
5055: stepsize=(int) (stepm+YEARM-1)/YEARM;
5056: if (stepm<=12) stepsize=1;
5057:
5058: agelim=AGESUP;
5059:
5060: hstepm=1;
5061: hstepm=hstepm/stepm;
5062:
5063: if (popforecast==1) {
5064: if((ficpop=fopen(popfile,"r"))==NULL) {
5065: printf("Problem with population file : %s\n",popfile);exit(0);
5066: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5067: }
5068: popage=ivector(0,AGESUP);
5069: popeffectif=vector(0,AGESUP);
5070: popcount=vector(0,AGESUP);
5071:
5072: i=1;
5073: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5074:
5075: imx=i;
5076: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5077: }
5078:
5079: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5080: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5081: k=k+1;
5082: fprintf(ficrespop,"\n#******");
5083: for(j=1;j<=cptcoveff;j++) {
5084: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5085: }
5086: fprintf(ficrespop,"******\n");
5087: fprintf(ficrespop,"# Age");
5088: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5089: if (popforecast==1) fprintf(ficrespop," [Population]");
5090:
5091: for (cpt=0; cpt<=0;cpt++) {
5092: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5093:
5094: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5095: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5096: nhstepm = nhstepm/hstepm;
5097:
5098: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5099: oldm=oldms;savm=savms;
5100: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5101:
5102: for (h=0; h<=nhstepm; h++){
5103: if (h==(int) (calagedatem+YEARM*cpt)) {
5104: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5105: }
5106: for(j=1; j<=nlstate+ndeath;j++) {
5107: kk1=0.;kk2=0;
5108: for(i=1; i<=nlstate;i++) {
5109: if (mobilav==1)
5110: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5111: else {
5112: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5113: }
5114: }
5115: if (h==(int)(calagedatem+12*cpt)){
5116: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5117: /*fprintf(ficrespop," %.3f", kk1);
5118: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5119: }
5120: }
5121: for(i=1; i<=nlstate;i++){
5122: kk1=0.;
5123: for(j=1; j<=nlstate;j++){
5124: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5125: }
5126: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5127: }
5128:
5129: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5130: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5131: }
5132: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5133: }
5134: }
5135:
5136: /******/
5137:
5138: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5139: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5140: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5141: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5142: nhstepm = nhstepm/hstepm;
5143:
5144: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5145: oldm=oldms;savm=savms;
5146: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5147: for (h=0; h<=nhstepm; h++){
5148: if (h==(int) (calagedatem+YEARM*cpt)) {
5149: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5150: }
5151: for(j=1; j<=nlstate+ndeath;j++) {
5152: kk1=0.;kk2=0;
5153: for(i=1; i<=nlstate;i++) {
5154: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5155: }
5156: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5157: }
5158: }
5159: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5160: }
5161: }
5162: }
5163: }
5164:
5165: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5166:
5167: if (popforecast==1) {
5168: free_ivector(popage,0,AGESUP);
5169: free_vector(popeffectif,0,AGESUP);
5170: free_vector(popcount,0,AGESUP);
5171: }
5172: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5173: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5174: fclose(ficrespop);
5175: } /* End of popforecast */
5176:
5177: int fileappend(FILE *fichier, char *optionfich)
5178: {
5179: if((fichier=fopen(optionfich,"a"))==NULL) {
5180: printf("Problem with file: %s\n", optionfich);
5181: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5182: return (0);
5183: }
5184: fflush(fichier);
5185: return (1);
5186: }
5187:
5188:
5189: /**************** function prwizard **********************/
5190: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5191: {
5192:
5193: /* Wizard to print covariance matrix template */
5194:
5195: char ca[32], cb[32];
5196: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
5197: int numlinepar;
5198:
5199: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5200: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5201: for(i=1; i <=nlstate; i++){
5202: jj=0;
5203: for(j=1; j <=nlstate+ndeath; j++){
5204: if(j==i) continue;
5205: jj++;
5206: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5207: printf("%1d%1d",i,j);
5208: fprintf(ficparo,"%1d%1d",i,j);
5209: for(k=1; k<=ncovmodel;k++){
5210: /* printf(" %lf",param[i][j][k]); */
5211: /* fprintf(ficparo," %lf",param[i][j][k]); */
5212: printf(" 0.");
5213: fprintf(ficparo," 0.");
5214: }
5215: printf("\n");
5216: fprintf(ficparo,"\n");
5217: }
5218: }
5219: printf("# Scales (for hessian or gradient estimation)\n");
5220: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5221: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5222: for(i=1; i <=nlstate; i++){
5223: jj=0;
5224: for(j=1; j <=nlstate+ndeath; j++){
5225: if(j==i) continue;
5226: jj++;
5227: fprintf(ficparo,"%1d%1d",i,j);
5228: printf("%1d%1d",i,j);
5229: fflush(stdout);
5230: for(k=1; k<=ncovmodel;k++){
5231: /* printf(" %le",delti3[i][j][k]); */
5232: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5233: printf(" 0.");
5234: fprintf(ficparo," 0.");
5235: }
5236: numlinepar++;
5237: printf("\n");
5238: fprintf(ficparo,"\n");
5239: }
5240: }
5241: printf("# Covariance matrix\n");
5242: /* # 121 Var(a12)\n\ */
5243: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5244: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5245: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5246: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5247: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5248: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5249: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5250: fflush(stdout);
5251: fprintf(ficparo,"# Covariance matrix\n");
5252: /* # 121 Var(a12)\n\ */
5253: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5254: /* # ...\n\ */
5255: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5256:
5257: for(itimes=1;itimes<=2;itimes++){
5258: jj=0;
5259: for(i=1; i <=nlstate; i++){
5260: for(j=1; j <=nlstate+ndeath; j++){
5261: if(j==i) continue;
5262: for(k=1; k<=ncovmodel;k++){
5263: jj++;
5264: ca[0]= k+'a'-1;ca[1]='\0';
5265: if(itimes==1){
5266: printf("#%1d%1d%d",i,j,k);
5267: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5268: }else{
5269: printf("%1d%1d%d",i,j,k);
5270: fprintf(ficparo,"%1d%1d%d",i,j,k);
5271: /* printf(" %.5le",matcov[i][j]); */
5272: }
5273: ll=0;
5274: for(li=1;li <=nlstate; li++){
5275: for(lj=1;lj <=nlstate+ndeath; lj++){
5276: if(lj==li) continue;
5277: for(lk=1;lk<=ncovmodel;lk++){
5278: ll++;
5279: if(ll<=jj){
5280: cb[0]= lk +'a'-1;cb[1]='\0';
5281: if(ll<jj){
5282: if(itimes==1){
5283: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5284: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5285: }else{
5286: printf(" 0.");
5287: fprintf(ficparo," 0.");
5288: }
5289: }else{
5290: if(itimes==1){
5291: printf(" Var(%s%1d%1d)",ca,i,j);
5292: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5293: }else{
5294: printf(" 0.");
5295: fprintf(ficparo," 0.");
5296: }
5297: }
5298: }
5299: } /* end lk */
5300: } /* end lj */
5301: } /* end li */
5302: printf("\n");
5303: fprintf(ficparo,"\n");
5304: numlinepar++;
5305: } /* end k*/
5306: } /*end j */
5307: } /* end i */
5308: } /* end itimes */
5309:
5310: } /* end of prwizard */
5311: /******************* Gompertz Likelihood ******************************/
5312: double gompertz(double x[])
5313: {
5314: double A,B,L=0.0,sump=0.,num=0.;
5315: int i,n=0; /* n is the size of the sample */
5316:
5317: for (i=0;i<=imx-1 ; i++) {
5318: sump=sump+weight[i];
5319: /* sump=sump+1;*/
5320: num=num+1;
5321: }
5322:
5323:
5324: /* for (i=0; i<=imx; i++)
5325: 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]);*/
5326:
5327: for (i=1;i<=imx ; i++)
5328: {
5329: if (cens[i] == 1 && wav[i]>1)
5330: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5331:
5332: if (cens[i] == 0 && wav[i]>1)
5333: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5334: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5335:
5336: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5337: if (wav[i] > 1 ) { /* ??? */
5338: L=L+A*weight[i];
5339: /* 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]);*/
5340: }
5341: }
5342:
5343: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5344:
5345: return -2*L*num/sump;
5346: }
5347:
5348: #ifdef GSL
5349: /******************* Gompertz_f Likelihood ******************************/
5350: double gompertz_f(const gsl_vector *v, void *params)
5351: {
5352: double A,B,LL=0.0,sump=0.,num=0.;
5353: double *x= (double *) v->data;
5354: int i,n=0; /* n is the size of the sample */
5355:
5356: for (i=0;i<=imx-1 ; i++) {
5357: sump=sump+weight[i];
5358: /* sump=sump+1;*/
5359: num=num+1;
5360: }
5361:
5362:
5363: /* for (i=0; i<=imx; i++)
5364: 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]);*/
5365: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5366: for (i=1;i<=imx ; i++)
5367: {
5368: if (cens[i] == 1 && wav[i]>1)
5369: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5370:
5371: if (cens[i] == 0 && wav[i]>1)
5372: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5373: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5374:
5375: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5376: if (wav[i] > 1 ) { /* ??? */
5377: LL=LL+A*weight[i];
5378: /* 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]);*/
5379: }
5380: }
5381:
5382: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5383: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5384:
5385: return -2*LL*num/sump;
5386: }
5387: #endif
5388:
5389: /******************* Printing html file ***********/
5390: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5391: int lastpass, int stepm, int weightopt, char model[],\
5392: int imx, double p[],double **matcov,double agemortsup){
5393: int i,k;
5394:
5395: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5396: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5397: for (i=1;i<=2;i++)
5398: 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]));
5399: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5400: fprintf(fichtm,"</ul>");
5401:
5402: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5403:
5404: 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>");
5405:
5406: for (k=agegomp;k<(agemortsup-2);k++)
5407: 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]);
5408:
5409:
5410: fflush(fichtm);
5411: }
5412:
5413: /******************* Gnuplot file **************/
5414: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5415:
5416: char dirfileres[132],optfileres[132];
5417:
5418: int ng;
5419:
5420:
5421: /*#ifdef windows */
5422: fprintf(ficgp,"cd \"%s\" \n",pathc);
5423: /*#endif */
5424:
5425:
5426: strcpy(dirfileres,optionfilefiname);
5427: strcpy(optfileres,"vpl");
5428: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5429: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
5430: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5431: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
5432: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5433:
5434: }
5435:
5436: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5437: {
5438:
5439: /*-------- data file ----------*/
5440: FILE *fic;
5441: char dummy[]=" ";
5442: int i=0, j=0, n=0;
5443: int linei, month, year,iout;
5444: char line[MAXLINE], linetmp[MAXLINE];
5445: char stra[MAXLINE], strb[MAXLINE];
5446: char *stratrunc;
5447: int lstra;
5448:
5449:
5450: if((fic=fopen(datafile,"r"))==NULL) {
5451: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5452: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
5453: }
5454:
5455: i=1;
5456: linei=0;
5457: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5458: linei=linei+1;
5459: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5460: if(line[j] == '\t')
5461: line[j] = ' ';
5462: }
5463: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5464: ;
5465: };
5466: line[j+1]=0; /* Trims blanks at end of line */
5467: if(line[0]=='#'){
5468: fprintf(ficlog,"Comment line\n%s\n",line);
5469: printf("Comment line\n%s\n",line);
5470: continue;
5471: }
5472: trimbb(linetmp,line); /* Trims multiple blanks in line */
5473: strcpy(line, linetmp);
5474:
5475:
5476: for (j=maxwav;j>=1;j--){
5477: cutv(stra, strb, line, ' ');
5478: if(strb[0]=='.') { /* Missing status */
5479: lval=-1;
5480: }else{
5481: errno=0;
5482: lval=strtol(strb,&endptr,10);
5483: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5484: if( strb[0]=='\0' || (*endptr != '\0')){
5485: 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);
5486: 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);
5487: return 1;
5488: }
5489: }
5490: s[j][i]=lval;
5491:
5492: strcpy(line,stra);
5493: cutv(stra, strb,line,' ');
5494: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5495: }
5496: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5497: month=99;
5498: year=9999;
5499: }else{
5500: 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);
5501: 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);
5502: return 1;
5503: }
5504: anint[j][i]= (double) year;
5505: mint[j][i]= (double)month;
5506: strcpy(line,stra);
5507: } /* ENd Waves */
5508:
5509: cutv(stra, strb,line,' ');
5510: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5511: }
5512: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
5513: month=99;
5514: year=9999;
5515: }else{
5516: 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);
5517: 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);
5518: return 1;
5519: }
5520: andc[i]=(double) year;
5521: moisdc[i]=(double) month;
5522: strcpy(line,stra);
5523:
5524: cutv(stra, strb,line,' ');
5525: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
5526: }
5527: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
5528: month=99;
5529: year=9999;
5530: }else{
5531: 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);
5532: 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);
5533: return 1;
5534: }
5535: if (year==9999) {
5536: 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);
5537: 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);
5538: return 1;
5539:
5540: }
5541: annais[i]=(double)(year);
5542: moisnais[i]=(double)(month);
5543: strcpy(line,stra);
5544:
5545: cutv(stra, strb,line,' ');
5546: errno=0;
5547: dval=strtod(strb,&endptr);
5548: if( strb[0]=='\0' || (*endptr != '\0')){
5549: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5550: 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);
5551: fflush(ficlog);
5552: return 1;
5553: }
5554: weight[i]=dval;
5555: strcpy(line,stra);
5556:
5557: for (j=ncovcol;j>=1;j--){
5558: cutv(stra, strb,line,' ');
5559: if(strb[0]=='.') { /* Missing status */
5560: lval=-1;
5561: }else{
5562: errno=0;
5563: lval=strtol(strb,&endptr,10);
5564: if( strb[0]=='\0' || (*endptr != '\0')){
5565: 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);
5566: 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);
5567: return 1;
5568: }
5569: }
5570: if(lval <-1 || lval >1){
5571: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5572: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5573: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5574: For example, for multinomial values like 1, 2 and 3,\n \
5575: build V1=0 V2=0 for the reference value (1),\n \
5576: V1=1 V2=0 for (2) \n \
5577: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5578: output of IMaCh is often meaningless.\n \
5579: Exiting.\n",lval,linei, i,line,j);
5580: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
5581: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5582: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5583: For example, for multinomial values like 1, 2 and 3,\n \
5584: build V1=0 V2=0 for the reference value (1),\n \
5585: V1=1 V2=0 for (2) \n \
5586: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5587: output of IMaCh is often meaningless.\n \
5588: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5589: return 1;
5590: }
5591: covar[j][i]=(double)(lval);
5592: strcpy(line,stra);
5593: }
5594: lstra=strlen(stra);
5595:
5596: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5597: stratrunc = &(stra[lstra-9]);
5598: num[i]=atol(stratrunc);
5599: }
5600: else
5601: num[i]=atol(stra);
5602: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5603: 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;}*/
5604:
5605: i=i+1;
5606: } /* End loop reading data */
5607:
5608: *imax=i-1; /* Number of individuals */
5609: fclose(fic);
5610:
5611: return (0);
5612: /* endread: */
5613: printf("Exiting readdata: ");
5614: fclose(fic);
5615: return (1);
5616:
5617:
5618:
5619: }
5620: void removespace(char *str) {
5621: char *p1 = str, *p2 = str;
5622: do
5623: while (*p2 == ' ')
5624: p2++;
5625: while (*p1++ == *p2++);
5626: }
5627:
5628: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
5629: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5630: * - nagesqr = 1 if age*age in the model, otherwise 0.
5631: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5632: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
5633: * - cptcovage number of covariates with age*products =2
5634: * - cptcovs number of simple covariates
5635: * - 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
5636: * which is a new column after the 9 (ncovcol) variables.
5637: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5638: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5639: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5640: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5641: */
5642: {
5643: int i, j, k, ks;
5644: int j1, k1, k2;
5645: char modelsav[80];
5646: char stra[80], strb[80], strc[80], strd[80],stre[80];
5647: char *strpt;
5648:
5649: /*removespace(model);*/
5650: if (strlen(model) >1){ /* If there is at least 1 covariate */
5651: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
5652: if (strstr(model,"AGE") !=0){
5653: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5654: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
5655: return 1;
5656: }
5657: if (strstr(model,"v") !=0){
5658: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5659: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5660: return 1;
5661: }
5662: strcpy(modelsav,model);
5663: if ((strpt=strstr(model,"age*age")) !=0){
5664: printf(" strpt=%s, model=%s\n",strpt, model);
5665: if(strpt != model){
5666: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5667: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
5668: corresponding column of parameters.\n",model);
5669: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
5670: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
5671: corresponding column of parameters.\n",model); fflush(ficlog);
5672: return 1;
5673: }
5674:
5675: nagesqr=1;
5676: if (strstr(model,"+age*age") !=0)
5677: substrchaine(modelsav, model, "+age*age");
5678: else if (strstr(model,"age*age+") !=0)
5679: substrchaine(modelsav, model, "age*age+");
5680: else
5681: substrchaine(modelsav, model, "age*age");
5682: }else
5683: nagesqr=0;
5684: if (strlen(modelsav) >1){
5685: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5686: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5687: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5688: cptcovt= j+1; /* Number of total covariates in the model, not including
5689: * cst, age and age*age
5690: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5691: /* including age products which are counted in cptcovage.
5692: * but the covariates which are products must be treated
5693: * separately: ncovn=4- 2=2 (V1+V3). */
5694: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5695: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5696:
5697:
5698: /* Design
5699: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5700: * < ncovcol=8 >
5701: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5702: * k= 1 2 3 4 5 6 7 8
5703: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5704: * covar[k,i], value of kth covariate if not including age for individual i:
5705: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5706: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5707: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5708: * Tage[++cptcovage]=k
5709: * if products, new covar are created after ncovcol with k1
5710: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5711: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5712: * 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
5713: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5714: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5715: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5716: * < ncovcol=8 >
5717: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5718: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5719: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5720: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5721: * p Tprod[1]@2={ 6, 5}
5722: *p Tvard[1][1]@4= {7, 8, 5, 6}
5723: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5724: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5725: *How to reorganize?
5726: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5727: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5728: * {2, 1, 4, 8, 5, 6, 3, 7}
5729: * Struct []
5730: */
5731:
5732: /* This loop fills the array Tvar from the string 'model'.*/
5733: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5734: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5735: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5736: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5737: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5738: /* k=1 Tvar[1]=2 (from V2) */
5739: /* k=5 Tvar[5] */
5740: /* for (k=1; k<=cptcovn;k++) { */
5741: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5742: /* } */
5743: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5744: /*
5745: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5746: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
5747: Tvar[k]=0;
5748: cptcovage=0;
5749: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5750: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5751: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5752: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5753: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5754: /*scanf("%d",i);*/
5755: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5756: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5757: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5758: /* covar is not filled and then is empty */
5759: cptcovprod--;
5760: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5761: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5762: cptcovage++; /* Sums the number of covariates which include age as a product */
5763: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5764: /*printf("stre=%s ", stre);*/
5765: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5766: cptcovprod--;
5767: cutl(stre,strb,strc,'V');
5768: Tvar[k]=atoi(stre);
5769: cptcovage++;
5770: Tage[cptcovage]=k;
5771: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5772: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5773: cptcovn++;
5774: cptcovprodnoage++;k1++;
5775: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5776: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5777: because this model-covariate is a construction we invent a new column
5778: ncovcol + k1
5779: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5780: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5781: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5782: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5783: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5784: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5785: k2=k2+2;
5786: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5787: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5788: for (i=1; i<=lastobs;i++){
5789: /* Computes the new covariate which is a product of
5790: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5791: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5792: }
5793: } /* End age is not in the model */
5794: } /* End if model includes a product */
5795: else { /* no more sum */
5796: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5797: /* scanf("%d",i);*/
5798: cutl(strd,strc,strb,'V');
5799: ks++; /**< Number of simple covariates */
5800: cptcovn++;
5801: Tvar[k]=atoi(strd);
5802: }
5803: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5804: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5805: scanf("%d",i);*/
5806: } /* end of loop + on total covariates */
5807: } /* end if strlen(modelsave == 0) age*age might exist */
5808: } /* end if strlen(model == 0) */
5809:
5810: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5811: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5812:
5813: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5814: printf("cptcovprod=%d ", cptcovprod);
5815: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5816:
5817: scanf("%d ",i);*/
5818:
5819:
5820: return (0); /* with covar[new additional covariate if product] and Tage if age */
5821: /*endread:*/
5822: printf("Exiting decodemodel: ");
5823: return (1);
5824: }
5825:
5826: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
5827: {
5828: int i, m;
5829:
5830: for (i=1; i<=imx; i++) {
5831: for(m=2; (m<= maxwav); m++) {
5832: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5833: anint[m][i]=9999;
5834: s[m][i]=-1;
5835: }
5836: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
5837: *nberr = *nberr + 1;
5838: 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);
5839: 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);
5840: s[m][i]=-1;
5841: }
5842: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
5843: (*nberr)++;
5844: 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]);
5845: 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]);
5846: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5847: }
5848: }
5849: }
5850:
5851: for (i=1; i<=imx; i++) {
5852: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5853: for(m=firstpass; (m<= lastpass); m++){
5854: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5855: if (s[m][i] >= nlstate+1) {
5856: if(agedc[i]>0){
5857: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
5858: agev[m][i]=agedc[i];
5859: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
5860: }else {
5861: if ((int)andc[i]!=9999){
5862: nbwarn++;
5863: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5864: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5865: agev[m][i]=-1;
5866: }
5867: }
5868: } /* agedc > 0 */
5869: }
5870: else if(s[m][i] !=9){ /* Standard case, age in fractional
5871: years but with the precision of a month */
5872: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5873: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5874: agev[m][i]=1;
5875: else if(agev[m][i] < *agemin){
5876: *agemin=agev[m][i];
5877: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5878: }
5879: else if(agev[m][i] >*agemax){
5880: *agemax=agev[m][i];
5881: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
5882: }
5883: /*agev[m][i]=anint[m][i]-annais[i];*/
5884: /* agev[m][i] = age[i]+2*m;*/
5885: }
5886: else { /* =9 */
5887: agev[m][i]=1;
5888: s[m][i]=-1;
5889: }
5890: }
5891: else /*= 0 Unknown */
5892: agev[m][i]=1;
5893: }
5894:
5895: }
5896: for (i=1; i<=imx; i++) {
5897: for(m=firstpass; (m<=lastpass); m++){
5898: if (s[m][i] > (nlstate+ndeath)) {
5899: (*nberr)++;
5900: 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);
5901: 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);
5902: return 1;
5903: }
5904: }
5905: }
5906:
5907: /*for (i=1; i<=imx; i++){
5908: for (m=firstpass; (m<lastpass); m++){
5909: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5910: }
5911:
5912: }*/
5913:
5914:
5915: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5916: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5917:
5918: return (0);
5919: /* endread:*/
5920: printf("Exiting calandcheckages: ");
5921: return (1);
5922: }
5923:
5924: #if defined(_MSC_VER)
5925: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5926: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5927: //#include "stdafx.h"
5928: //#include <stdio.h>
5929: //#include <tchar.h>
5930: //#include <windows.h>
5931: //#include <iostream>
5932: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5933:
5934: LPFN_ISWOW64PROCESS fnIsWow64Process;
5935:
5936: BOOL IsWow64()
5937: {
5938: BOOL bIsWow64 = FALSE;
5939:
5940: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5941: // (HANDLE, PBOOL);
5942:
5943: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5944:
5945: HMODULE module = GetModuleHandle(_T("kernel32"));
5946: const char funcName[] = "IsWow64Process";
5947: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5948: GetProcAddress(module, funcName);
5949:
5950: if (NULL != fnIsWow64Process)
5951: {
5952: if (!fnIsWow64Process(GetCurrentProcess(),
5953: &bIsWow64))
5954: //throw std::exception("Unknown error");
5955: printf("Unknown error\n");
5956: }
5957: return bIsWow64 != FALSE;
5958: }
5959: #endif
5960:
5961: void syscompilerinfo(int logged)
5962: {
5963: /* #include "syscompilerinfo.h"*/
5964: /* command line Intel compiler 32bit windows, XP compatible:*/
5965: /* /GS /W3 /Gy
5966: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5967: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5968: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
5969: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5970: */
5971: /* 64 bits */
5972: /*
5973: /GS /W3 /Gy
5974: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5975: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5976: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5977: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5978: /* Optimization are useless and O3 is slower than O2 */
5979: /*
5980: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5981: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5982: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
5983: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
5984: */
5985: /* Link is */ /* /OUT:"visual studio
5986: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
5987: /PDB:"visual studio
5988: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
5989: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
5990: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
5991: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
5992: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
5993: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
5994: uiAccess='false'"
5995: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
5996: /NOLOGO /TLBID:1
5997: */
5998: #if defined __INTEL_COMPILER
5999: #if defined(__GNUC__)
6000: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6001: #endif
6002: #elif defined(__GNUC__)
6003: #ifndef __APPLE__
6004: #include <gnu/libc-version.h> /* Only on gnu */
6005: #endif
6006: struct utsname sysInfo;
6007: int cross = CROSS;
6008: if (cross){
6009: printf("Cross-");
6010: if(logged) fprintf(ficlog, "Cross-");
6011: }
6012: #endif
6013:
6014: #include <stdint.h>
6015:
6016: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
6017: #if defined(__clang__)
6018: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
6019: #endif
6020: #if defined(__ICC) || defined(__INTEL_COMPILER)
6021: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
6022: #endif
6023: #if defined(__GNUC__) || defined(__GNUG__)
6024: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
6025: #endif
6026: #if defined(__HP_cc) || defined(__HP_aCC)
6027: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
6028: #endif
6029: #if defined(__IBMC__) || defined(__IBMCPP__)
6030: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
6031: #endif
6032: #if defined(_MSC_VER)
6033: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
6034: #endif
6035: #if defined(__PGI)
6036: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
6037: #endif
6038: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
6039: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
6040: #endif
6041: printf(" for "); if (logged) fprintf(ficlog, " for ");
6042:
6043: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6044: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6045: // Windows (x64 and x86)
6046: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
6047: #elif __unix__ // all unices, not all compilers
6048: // Unix
6049: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
6050: #elif __linux__
6051: // linux
6052: printf("linux ");if(logged) fprintf(ficlog,"linux ");
6053: #elif __APPLE__
6054: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
6055: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
6056: #endif
6057:
6058: /* __MINGW32__ */
6059: /* __CYGWIN__ */
6060: /* __MINGW64__ */
6061: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6062: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6063: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6064: /* _WIN64 // Defined for applications for Win64. */
6065: /* _M_X64 // Defined for compilations that target x64 processors. */
6066: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
6067:
6068: #if UINTPTR_MAX == 0xffffffff
6069: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
6070: #elif UINTPTR_MAX == 0xffffffffffffffff
6071: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
6072: #else
6073: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
6074: #endif
6075:
6076: #if defined(__GNUC__)
6077: # if defined(__GNUC_PATCHLEVEL__)
6078: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6079: + __GNUC_MINOR__ * 100 \
6080: + __GNUC_PATCHLEVEL__)
6081: # else
6082: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6083: + __GNUC_MINOR__ * 100)
6084: # endif
6085: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
6086: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
6087:
6088: if (uname(&sysInfo) != -1) {
6089: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
6090: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
6091: }
6092: else
6093: perror("uname() error");
6094: //#ifndef __INTEL_COMPILER
6095: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
6096: printf("GNU libc version: %s\n", gnu_get_libc_version());
6097: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
6098: #endif
6099: #endif
6100:
6101: // void main()
6102: // {
6103: #if defined(_MSC_VER)
6104: if (IsWow64()){
6105: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6106: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6107: }
6108: else{
6109: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6110: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6111: }
6112: // printf("\nPress Enter to continue...");
6113: // getchar();
6114: // }
6115:
6116: #endif
6117:
6118:
6119: }
6120:
6121: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6122: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6123: int i, j, k, i1 ;
6124: double ftolpl = 1.e-10;
6125: double age, agebase, agelim;
6126:
6127: strcpy(filerespl,"pl");
6128: strcat(filerespl,fileres);
6129: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6130: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6131: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6132: }
6133: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6134: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6135: pstamp(ficrespl);
6136: fprintf(ficrespl,"# Period (stable) prevalence \n");
6137: fprintf(ficrespl,"#Age ");
6138: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6139: fprintf(ficrespl,"\n");
6140:
6141: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6142:
6143: agebase=ageminpar;
6144: agelim=agemaxpar;
6145:
6146: i1=pow(2,cptcoveff);
6147: if (cptcovn < 1){i1=1;}
6148:
6149: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6150: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6151: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6152: k=k+1;
6153: /* to clean */
6154: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6155: fprintf(ficrespl,"\n#******");
6156: printf("\n#******");
6157: fprintf(ficlog,"\n#******");
6158: for(j=1;j<=cptcoveff;j++) {
6159: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6160: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6161: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6162: }
6163: fprintf(ficrespl,"******\n");
6164: printf("******\n");
6165: fprintf(ficlog,"******\n");
6166:
6167: fprintf(ficrespl,"#Age ");
6168: for(j=1;j<=cptcoveff;j++) {
6169: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6170: }
6171: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6172: fprintf(ficrespl,"\n");
6173:
6174: for (age=agebase; age<=agelim; age++){
6175: /* for (age=agebase; age<=agebase; age++){ */
6176: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6177: fprintf(ficrespl,"%.0f ",age );
6178: for(j=1;j<=cptcoveff;j++)
6179: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6180: for(i=1; i<=nlstate;i++)
6181: fprintf(ficrespl," %.5f", prlim[i][i]);
6182: fprintf(ficrespl,"\n");
6183: } /* Age */
6184: /* was end of cptcod */
6185: } /* cptcov */
6186: return 0;
6187: }
6188:
6189: int hPijx(double *p, int bage, int fage){
6190: /*------------- h Pij x at various ages ------------*/
6191:
6192: int stepsize;
6193: int agelim;
6194: int hstepm;
6195: int nhstepm;
6196: int h, i, i1, j, k;
6197:
6198: double agedeb;
6199: double ***p3mat;
6200:
6201: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6202: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6203: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6204: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6205: }
6206: printf("Computing pij: result on file '%s' \n", filerespij);
6207: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6208:
6209: stepsize=(int) (stepm+YEARM-1)/YEARM;
6210: /*if (stepm<=24) stepsize=2;*/
6211:
6212: agelim=AGESUP;
6213: hstepm=stepsize*YEARM; /* Every year of age */
6214: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6215:
6216: /* hstepm=1; aff par mois*/
6217: pstamp(ficrespij);
6218: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6219: i1= pow(2,cptcoveff);
6220: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6221: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6222: /* k=k+1; */
6223: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6224: fprintf(ficrespij,"\n#****** ");
6225: for(j=1;j<=cptcoveff;j++)
6226: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6227: fprintf(ficrespij,"******\n");
6228:
6229: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6230: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6231: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6232:
6233: /* nhstepm=nhstepm*YEARM; aff par mois*/
6234:
6235: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6236: oldm=oldms;savm=savms;
6237: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6238: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6239: for(i=1; i<=nlstate;i++)
6240: for(j=1; j<=nlstate+ndeath;j++)
6241: fprintf(ficrespij," %1d-%1d",i,j);
6242: fprintf(ficrespij,"\n");
6243: for (h=0; h<=nhstepm; h++){
6244: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6245: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
6246: for(i=1; i<=nlstate;i++)
6247: for(j=1; j<=nlstate+ndeath;j++)
6248: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
6249: fprintf(ficrespij,"\n");
6250: }
6251: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6252: fprintf(ficrespij,"\n");
6253: }
6254: /*}*/
6255: }
6256: return 0;
6257: }
6258:
6259:
6260: /***********************************************/
6261: /**************** Main Program *****************/
6262: /***********************************************/
6263:
6264: int main(int argc, char *argv[])
6265: {
6266: #ifdef GSL
6267: const gsl_multimin_fminimizer_type *T;
6268: size_t iteri = 0, it;
6269: int rval = GSL_CONTINUE;
6270: int status = GSL_SUCCESS;
6271: double ssval;
6272: #endif
6273: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
6274: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6275:
6276: int jj, ll, li, lj, lk;
6277: int numlinepar=0; /* Current linenumber of parameter file */
6278: int itimes;
6279: int NDIM=2;
6280: int vpopbased=0;
6281:
6282: char ca[32], cb[32];
6283: /* FILE *fichtm; *//* Html File */
6284: /* FILE *ficgp;*/ /*Gnuplot File */
6285: struct stat info;
6286: double agedeb=0.;
6287:
6288: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
6289:
6290: double fret;
6291: double dum=0.; /* Dummy variable */
6292: double ***p3mat;
6293: double ***mobaverage;
6294:
6295: char line[MAXLINE];
6296: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
6297: char pathr[MAXLINE], pathimach[MAXLINE];
6298: char *tok, *val; /* pathtot */
6299: int firstobs=1, lastobs=10;
6300: int c, h , cpt, c2;
6301: int jl=0;
6302: int i1, j1, jk, stepsize=0;
6303: int count=0;
6304:
6305: int *tab;
6306: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6307: int mobilav=0,popforecast=0;
6308: int hstepm=0, nhstepm=0;
6309: int agemortsup;
6310: float sumlpop=0.;
6311: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6312: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6313:
6314: double bage=0, fage=110., age, agelim=0., agebase=0.;
6315: double ftolpl=FTOL;
6316: double **prlim;
6317: double ***param; /* Matrix of parameters */
6318: double *p;
6319: double **matcov; /* Matrix of covariance */
6320: double ***delti3; /* Scale */
6321: double *delti; /* Scale */
6322: double ***eij, ***vareij;
6323: double **varpl; /* Variances of prevalence limits by age */
6324: double *epj, vepp;
6325:
6326: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6327: double **ximort;
6328: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
6329: int *dcwave;
6330:
6331: char z[1]="c";
6332:
6333: /*char *strt;*/
6334: char strtend[80];
6335:
6336:
6337: /* setlocale (LC_ALL, ""); */
6338: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6339: /* textdomain (PACKAGE); */
6340: /* setlocale (LC_CTYPE, ""); */
6341: /* setlocale (LC_MESSAGES, ""); */
6342:
6343: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
6344: rstart_time = time(NULL);
6345: /* (void) gettimeofday(&start_time,&tzp);*/
6346: start_time = *localtime(&rstart_time);
6347: curr_time=start_time;
6348: /*tml = *localtime(&start_time.tm_sec);*/
6349: /* strcpy(strstart,asctime(&tml)); */
6350: strcpy(strstart,asctime(&start_time));
6351:
6352: /* printf("Localtime (at start)=%s",strstart); */
6353: /* tp.tm_sec = tp.tm_sec +86400; */
6354: /* tm = *localtime(&start_time.tm_sec); */
6355: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6356: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6357: /* tmg.tm_hour=tmg.tm_hour + 1; */
6358: /* tp.tm_sec = mktime(&tmg); */
6359: /* strt=asctime(&tmg); */
6360: /* printf("Time(after) =%s",strstart); */
6361: /* (void) time (&time_value);
6362: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6363: * tm = *localtime(&time_value);
6364: * strstart=asctime(&tm);
6365: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6366: */
6367:
6368: nberr=0; /* Number of errors and warnings */
6369: nbwarn=0;
6370: #ifdef WIN32
6371: _getcwd(pathcd, size);
6372: #else
6373: getcwd(pathcd, size);
6374: #endif
6375: syscompilerinfo(0);
6376: printf("\n%s\n%s",version,fullversion);
6377: if(argc <=1){
6378: printf("\nEnter the parameter file name: ");
6379: fgets(pathr,FILENAMELENGTH,stdin);
6380: i=strlen(pathr);
6381: if(pathr[i-1]=='\n')
6382: pathr[i-1]='\0';
6383: i=strlen(pathr);
6384: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6385: pathr[i-1]='\0';
6386: for (tok = pathr; tok != NULL; ){
6387: printf("Pathr |%s|\n",pathr);
6388: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6389: printf("val= |%s| pathr=%s\n",val,pathr);
6390: strcpy (pathtot, val);
6391: if(pathr[0] == '\0') break; /* Dirty */
6392: }
6393: }
6394: else{
6395: strcpy(pathtot,argv[1]);
6396: }
6397: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6398: /*cygwin_split_path(pathtot,path,optionfile);
6399: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6400: /* cutv(path,optionfile,pathtot,'\\');*/
6401:
6402: /* Split argv[0], imach program to get pathimach */
6403: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6404: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6405: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6406: /* strcpy(pathimach,argv[0]); */
6407: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6408: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6409: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
6410: #ifdef WIN32
6411: _chdir(path); /* Can be a relative path */
6412: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6413: #else
6414: chdir(path); /* Can be a relative path */
6415: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6416: #endif
6417: printf("Current directory %s!\n",pathcd);
6418: strcpy(command,"mkdir ");
6419: strcat(command,optionfilefiname);
6420: if((outcmd=system(command)) != 0){
6421: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
6422: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6423: /* fclose(ficlog); */
6424: /* exit(1); */
6425: }
6426: /* if((imk=mkdir(optionfilefiname))<0){ */
6427: /* perror("mkdir"); */
6428: /* } */
6429:
6430: /*-------- arguments in the command line --------*/
6431:
6432: /* Main Log file */
6433: strcat(filelog, optionfilefiname);
6434: strcat(filelog,".log"); /* */
6435: if((ficlog=fopen(filelog,"w"))==NULL) {
6436: printf("Problem with logfile %s\n",filelog);
6437: goto end;
6438: }
6439: fprintf(ficlog,"Log filename:%s\n",filelog);
6440: fprintf(ficlog,"\n%s\n%s",version,fullversion);
6441: fprintf(ficlog,"\nEnter the parameter file name: \n");
6442: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6443: path=%s \n\
6444: optionfile=%s\n\
6445: optionfilext=%s\n\
6446: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
6447:
6448: syscompilerinfo(0);
6449:
6450: printf("Local time (at start):%s",strstart);
6451: fprintf(ficlog,"Local time (at start): %s",strstart);
6452: fflush(ficlog);
6453: /* (void) gettimeofday(&curr_time,&tzp); */
6454: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
6455:
6456: /* */
6457: strcpy(fileres,"r");
6458: strcat(fileres, optionfilefiname);
6459: strcat(fileres,".txt"); /* Other files have txt extension */
6460:
6461: /* Main ---------arguments file --------*/
6462:
6463: if((ficpar=fopen(optionfile,"r"))==NULL) {
6464: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6465: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6466: fflush(ficlog);
6467: /* goto end; */
6468: exit(70);
6469: }
6470:
6471:
6472:
6473: strcpy(filereso,"o");
6474: strcat(filereso,fileres);
6475: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6476: printf("Problem with Output resultfile: %s\n", filereso);
6477: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6478: fflush(ficlog);
6479: goto end;
6480: }
6481:
6482: /* Reads comments: lines beginning with '#' */
6483: numlinepar=0;
6484: while((c=getc(ficpar))=='#' && c!= EOF){
6485: ungetc(c,ficpar);
6486: fgets(line, MAXLINE, ficpar);
6487: numlinepar++;
6488: fputs(line,stdout);
6489: fputs(line,ficparo);
6490: fputs(line,ficlog);
6491: }
6492: ungetc(c,ficpar);
6493:
6494: 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=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
6495: numlinepar=numlinepar+3; /* In general */
6496: 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=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
6497: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6498: model[strlen(model)-1]='\0';
6499: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6500: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
6501: fflush(ficlog);
6502: /* if(model[0]=='#'|| model[0]== '\0'){ */
6503: if(model[0]=='#'){
6504: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6505: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6506: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6507: if(mle != -1){
6508: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6509: exit(1);
6510: }
6511: }
6512: while((c=getc(ficpar))=='#' && c!= EOF){
6513: ungetc(c,ficpar);
6514: fgets(line, MAXLINE, ficpar);
6515: numlinepar++;
6516: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6517: z[0]=line[1];
6518: }
6519: /* printf("****line [1] = %c \n",line[1]); */
6520: fputs(line, stdout);
6521: //puts(line);
6522: fputs(line,ficparo);
6523: fputs(line,ficlog);
6524: }
6525: ungetc(c,ficpar);
6526:
6527:
6528: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
6529: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6530: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6531: v1+v2*age+v2*v3 makes cptcovn = 3
6532: */
6533: if (strlen(model)>1)
6534: 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,age*age makes 3*/
6535: else
6536: ncovmodel=2; /* Constant and age */
6537: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6538: npar= nforce*ncovmodel; /* Number of parameters like aij*/
6539: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6540: 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);
6541: 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);
6542: fflush(stdout);
6543: fclose (ficlog);
6544: goto end;
6545: }
6546: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6547: delti=delti3[1][1];
6548: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6549: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6550: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6551: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6552: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6553: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6554: fclose (ficparo);
6555: fclose (ficlog);
6556: goto end;
6557: exit(0);
6558: }
6559: else if(mle==-3) { /* Main Wizard */
6560: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
6561: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6562: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6563: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6564: matcov=matrix(1,npar,1,npar);
6565: }
6566: else{
6567: /* Read guessed parameters */
6568: /* Reads comments: lines beginning with '#' */
6569: while((c=getc(ficpar))=='#' && c!= EOF){
6570: ungetc(c,ficpar);
6571: fgets(line, MAXLINE, ficpar);
6572: numlinepar++;
6573: fputs(line,stdout);
6574: fputs(line,ficparo);
6575: fputs(line,ficlog);
6576: }
6577: ungetc(c,ficpar);
6578:
6579: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6580: for(i=1; i <=nlstate; i++){
6581: j=0;
6582: for(jj=1; jj <=nlstate+ndeath; jj++){
6583: if(jj==i) continue;
6584: j++;
6585: fscanf(ficpar,"%1d%1d",&i1,&j1);
6586: if ((i1 != i) || (j1 != jj)){
6587: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6588: It might be a problem of design; if ncovcol and the model are correct\n \
6589: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6590: exit(1);
6591: }
6592: fprintf(ficparo,"%1d%1d",i1,j1);
6593: if(mle==1)
6594: printf("%1d%1d",i,jj);
6595: fprintf(ficlog,"%1d%1d",i,jj);
6596: for(k=1; k<=ncovmodel;k++){
6597: fscanf(ficpar," %lf",¶m[i][j][k]);
6598: if(mle==1){
6599: printf(" %lf",param[i][j][k]);
6600: fprintf(ficlog," %lf",param[i][j][k]);
6601: }
6602: else
6603: fprintf(ficlog," %lf",param[i][j][k]);
6604: fprintf(ficparo," %lf",param[i][j][k]);
6605: }
6606: fscanf(ficpar,"\n");
6607: numlinepar++;
6608: if(mle==1)
6609: printf("\n");
6610: fprintf(ficlog,"\n");
6611: fprintf(ficparo,"\n");
6612: }
6613: }
6614: fflush(ficlog);
6615:
6616: /* Reads scales values */
6617: p=param[1][1];
6618:
6619: /* Reads comments: lines beginning with '#' */
6620: while((c=getc(ficpar))=='#' && c!= EOF){
6621: ungetc(c,ficpar);
6622: fgets(line, MAXLINE, ficpar);
6623: numlinepar++;
6624: fputs(line,stdout);
6625: fputs(line,ficparo);
6626: fputs(line,ficlog);
6627: }
6628: ungetc(c,ficpar);
6629:
6630: for(i=1; i <=nlstate; i++){
6631: for(j=1; j <=nlstate+ndeath-1; j++){
6632: fscanf(ficpar,"%1d%1d",&i1,&j1);
6633: if ( (i1-i) * (j1-j) != 0){
6634: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6635: exit(1);
6636: }
6637: printf("%1d%1d",i,j);
6638: fprintf(ficparo,"%1d%1d",i1,j1);
6639: fprintf(ficlog,"%1d%1d",i1,j1);
6640: for(k=1; k<=ncovmodel;k++){
6641: fscanf(ficpar,"%le",&delti3[i][j][k]);
6642: printf(" %le",delti3[i][j][k]);
6643: fprintf(ficparo," %le",delti3[i][j][k]);
6644: fprintf(ficlog," %le",delti3[i][j][k]);
6645: }
6646: fscanf(ficpar,"\n");
6647: numlinepar++;
6648: printf("\n");
6649: fprintf(ficparo,"\n");
6650: fprintf(ficlog,"\n");
6651: }
6652: }
6653: fflush(ficlog);
6654:
6655: /* Reads covariance matrix */
6656: delti=delti3[1][1];
6657:
6658:
6659: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6660:
6661: /* Reads comments: lines beginning with '#' */
6662: while((c=getc(ficpar))=='#' && c!= EOF){
6663: ungetc(c,ficpar);
6664: fgets(line, MAXLINE, ficpar);
6665: numlinepar++;
6666: fputs(line,stdout);
6667: fputs(line,ficparo);
6668: fputs(line,ficlog);
6669: }
6670: ungetc(c,ficpar);
6671:
6672: matcov=matrix(1,npar,1,npar);
6673: for(i=1; i <=npar; i++)
6674: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6675:
6676: /* Scans npar lines */
6677: for(i=1; i <=npar; i++){
6678: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6679: if(count != 3){
6680: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6681: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6682: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6683: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6684: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6685: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6686: exit(1);
6687: }else
6688: if(mle==1)
6689: printf("%1d%1d%1d",i1,j1,jk);
6690: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6691: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
6692: for(j=1; j <=i; j++){
6693: fscanf(ficpar," %le",&matcov[i][j]);
6694: if(mle==1){
6695: printf(" %.5le",matcov[i][j]);
6696: }
6697: fprintf(ficlog," %.5le",matcov[i][j]);
6698: fprintf(ficparo," %.5le",matcov[i][j]);
6699: }
6700: fscanf(ficpar,"\n");
6701: numlinepar++;
6702: if(mle==1)
6703: printf("\n");
6704: fprintf(ficlog,"\n");
6705: fprintf(ficparo,"\n");
6706: }
6707: /* End of read covariance matrix npar lines */
6708: for(i=1; i <=npar; i++)
6709: for(j=i+1;j<=npar;j++)
6710: matcov[i][j]=matcov[j][i];
6711:
6712: if(mle==1)
6713: printf("\n");
6714: fprintf(ficlog,"\n");
6715:
6716: fflush(ficlog);
6717:
6718: /*-------- Rewriting parameter file ----------*/
6719: strcpy(rfileres,"r"); /* "Rparameterfile */
6720: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6721: strcat(rfileres,"."); /* */
6722: strcat(rfileres,optionfilext); /* Other files have txt extension */
6723: if((ficres =fopen(rfileres,"w"))==NULL) {
6724: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6725: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6726: }
6727: fprintf(ficres,"#%s\n",version);
6728: } /* End of mle != -3 */
6729:
6730: /* Main data
6731: */
6732: n= lastobs;
6733: num=lvector(1,n);
6734: moisnais=vector(1,n);
6735: annais=vector(1,n);
6736: moisdc=vector(1,n);
6737: andc=vector(1,n);
6738: agedc=vector(1,n);
6739: cod=ivector(1,n);
6740: weight=vector(1,n);
6741: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6742: mint=matrix(1,maxwav,1,n);
6743: anint=matrix(1,maxwav,1,n);
6744: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
6745: tab=ivector(1,NCOVMAX);
6746: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6747: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
6748:
6749: /* Reads data from file datafile */
6750: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6751: goto end;
6752:
6753: /* Calculation of the number of parameters from char model */
6754: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6755: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6756: k=3 V4 Tvar[k=3]= 4 (from V4)
6757: k=2 V1 Tvar[k=2]= 1 (from V1)
6758: k=1 Tvar[1]=2 (from V2)
6759: */
6760: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6761: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6762: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6763: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6764: */
6765: /* For model-covariate k tells which data-covariate to use but
6766: because this model-covariate is a construction we invent a new column
6767: ncovcol + k1
6768: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6769: Tvar[3=V1*V4]=4+1 etc */
6770: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
6771: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6772: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6773: */
6774: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6775: 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
6776: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6777: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
6778: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
6779: 4 covariates (3 plus signs)
6780: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6781: */
6782:
6783: /* Main decodemodel */
6784:
6785:
6786: if(decodemodel(model, lastobs) == 1)
6787: goto end;
6788:
6789: if((double)(lastobs-imx)/(double)imx > 1.10){
6790: nbwarn++;
6791: 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);
6792: 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);
6793: }
6794: /* if(mle==1){*/
6795: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6796: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
6797: }
6798:
6799: /*-calculation of age at interview from date of interview and age at death -*/
6800: agev=matrix(1,maxwav,1,imx);
6801:
6802: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6803: goto end;
6804:
6805:
6806: agegomp=(int)agemin;
6807: free_vector(moisnais,1,n);
6808: free_vector(annais,1,n);
6809: /* free_matrix(mint,1,maxwav,1,n);
6810: free_matrix(anint,1,maxwav,1,n);*/
6811: free_vector(moisdc,1,n);
6812: free_vector(andc,1,n);
6813: /* */
6814:
6815: wav=ivector(1,imx);
6816: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6817: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6818: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6819:
6820: /* Concatenates waves */
6821: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
6822: /* */
6823:
6824: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6825:
6826: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6827: ncodemax[1]=1;
6828: Ndum =ivector(-1,NCOVMAX);
6829: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
6830: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
6831: /* Nbcode gives the value of the lth modality of jth covariate, in
6832: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6833: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
6834:
6835: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6836: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
6837: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
6838: h=0;
6839:
6840:
6841: /*if (cptcovn > 0) */
6842:
6843:
6844: m=pow(2,cptcoveff);
6845:
6846: for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
6847: 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 */
6848: for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate ncodemax=2*/
6849: for(cpt=1; cpt <=pow(2,k-1); cpt++){ /* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 */
6850: h++;
6851: if (h>m)
6852: h=1;
6853: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
6854: * For k=4 covariates, h goes from 1 to 2**k
6855: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6856: * h\k 1 2 3 4
6857: *______________________________
6858: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6859: * 2 2 1 1 1
6860: * 3 i=2 1 2 1 1
6861: * 4 2 2 1 1
6862: * 5 i=3 1 i=2 1 2 1
6863: * 6 2 1 2 1
6864: * 7 i=4 1 2 2 1
6865: * 8 2 2 2 1
6866: * 9 i=5 1 i=3 1 i=2 1 1
6867: * 10 2 1 1 1
6868: * 11 i=6 1 2 1 1
6869: * 12 2 2 1 1
6870: * 13 i=7 1 i=4 1 2 1
6871: * 14 2 1 2 1
6872: * 15 i=8 1 2 2 1
6873: * 16 2 2 2 1
6874: */
6875: codtab[h][k]=j;
6876: /* codtab[12][3]=1; */
6877: /*codtab[h][Tvar[k]]=j;*/
6878: 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]]);
6879: }
6880: }
6881: }
6882: }
6883: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6884: codtab[1][2]=1;codtab[2][2]=2; */
6885: /* for(i=1; i <=m ;i++){
6886: for(k=1; k <=cptcovn; k++){
6887: printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
6888: }
6889: printf("\n");
6890: }
6891: scanf("%d",i);*/
6892:
6893: free_ivector(Ndum,-1,NCOVMAX);
6894:
6895:
6896:
6897: /* Initialisation of ----------- gnuplot -------------*/
6898: strcpy(optionfilegnuplot,optionfilefiname);
6899: if(mle==-3)
6900: strcat(optionfilegnuplot,"-mort");
6901: strcat(optionfilegnuplot,".gp");
6902:
6903: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6904: printf("Problem with file %s",optionfilegnuplot);
6905: }
6906: else{
6907: fprintf(ficgp,"\n# %s\n", version);
6908: fprintf(ficgp,"# %s\n", optionfilegnuplot);
6909: //fprintf(ficgp,"set missing 'NaNq'\n");
6910: fprintf(ficgp,"set datafile missing 'NaNq'\n");
6911: }
6912: /* fclose(ficgp);*/
6913:
6914:
6915: /* Initialisation of --------- index.htm --------*/
6916:
6917: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
6918: if(mle==-3)
6919: strcat(optionfilehtm,"-mort");
6920: strcat(optionfilehtm,".htm");
6921: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
6922: printf("Problem with %s \n",optionfilehtm);
6923: exit(0);
6924: }
6925:
6926: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
6927: strcat(optionfilehtmcov,"-cov.htm");
6928: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
6929: printf("Problem with %s \n",optionfilehtmcov), exit(0);
6930: }
6931: else{
6932: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6933: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6934: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
6935: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
6936: }
6937:
6938: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
6939: <hr size=\"2\" color=\"#EC5E5E\"> \n\
6940: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
6941: \n\
6942: <hr size=\"2\" color=\"#EC5E5E\">\
6943: <ul><li><h4>Parameter files</h4>\n\
6944: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
6945: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
6946: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
6947: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
6948: - Date and time at start: %s</ul>\n",\
6949: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
6950: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
6951: fileres,fileres,\
6952: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
6953: fflush(fichtm);
6954:
6955: strcpy(pathr,path);
6956: strcat(pathr,optionfilefiname);
6957: #ifdef WIN32
6958: _chdir(optionfilefiname); /* Move to directory named optionfile */
6959: #else
6960: chdir(optionfilefiname); /* Move to directory named optionfile */
6961: #endif
6962:
6963:
6964: /* Calculates basic frequencies. Computes observed prevalence at single age
6965: and prints on file fileres'p'. */
6966: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
6967:
6968: fprintf(fichtm,"\n");
6969: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
6970: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
6971: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
6972: imx,agemin,agemax,jmin,jmax,jmean);
6973: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6974: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6975: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6976: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
6977: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
6978:
6979:
6980: /* For Powell, parameters are in a vector p[] starting at p[1]
6981: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
6982: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
6983:
6984: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
6985: /* For mortality only */
6986: if (mle==-3){
6987: ximort=matrix(1,NDIM,1,NDIM);
6988: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
6989: cens=ivector(1,n);
6990: ageexmed=vector(1,n);
6991: agecens=vector(1,n);
6992: dcwave=ivector(1,n);
6993:
6994: for (i=1; i<=imx; i++){
6995: dcwave[i]=-1;
6996: for (m=firstpass; m<=lastpass; m++)
6997: if (s[m][i]>nlstate) {
6998: dcwave[i]=m;
6999: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7000: break;
7001: }
7002: }
7003:
7004: for (i=1; i<=imx; i++) {
7005: if (wav[i]>0){
7006: ageexmed[i]=agev[mw[1][i]][i];
7007: j=wav[i];
7008: agecens[i]=1.;
7009:
7010: if (ageexmed[i]> 1 && wav[i] > 0){
7011: agecens[i]=agev[mw[j][i]][i];
7012: cens[i]= 1;
7013: }else if (ageexmed[i]< 1)
7014: cens[i]= -1;
7015: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7016: cens[i]=0 ;
7017: }
7018: else cens[i]=-1;
7019: }
7020:
7021: for (i=1;i<=NDIM;i++) {
7022: for (j=1;j<=NDIM;j++)
7023: ximort[i][j]=(i == j ? 1.0 : 0.0);
7024: }
7025:
7026: /*p[1]=0.0268; p[NDIM]=0.083;*/
7027: /*printf("%lf %lf", p[1], p[2]);*/
7028:
7029:
7030: #ifdef GSL
7031: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
7032: #else
7033: printf("Powell\n"); fprintf(ficlog,"Powell\n");
7034: #endif
7035: strcpy(filerespow,"pow-mort");
7036: strcat(filerespow,fileres);
7037: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7038: printf("Problem with resultfile: %s\n", filerespow);
7039: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7040: }
7041: #ifdef GSL
7042: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
7043: #else
7044: fprintf(ficrespow,"# Powell\n# iter -2*LL");
7045: #endif
7046: /* for (i=1;i<=nlstate;i++)
7047: for(j=1;j<=nlstate+ndeath;j++)
7048: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7049: */
7050: fprintf(ficrespow,"\n");
7051: #ifdef GSL
7052: /* gsl starts here */
7053: T = gsl_multimin_fminimizer_nmsimplex;
7054: gsl_multimin_fminimizer *sfm = NULL;
7055: gsl_vector *ss, *x;
7056: gsl_multimin_function minex_func;
7057:
7058: /* Initial vertex size vector */
7059: ss = gsl_vector_alloc (NDIM);
7060:
7061: if (ss == NULL){
7062: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7063: }
7064: /* Set all step sizes to 1 */
7065: gsl_vector_set_all (ss, 0.001);
7066:
7067: /* Starting point */
7068:
7069: x = gsl_vector_alloc (NDIM);
7070:
7071: if (x == NULL){
7072: gsl_vector_free(ss);
7073: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7074: }
7075:
7076: /* Initialize method and iterate */
7077: /* p[1]=0.0268; p[NDIM]=0.083; */
7078: /* gsl_vector_set(x, 0, 0.0268); */
7079: /* gsl_vector_set(x, 1, 0.083); */
7080: gsl_vector_set(x, 0, p[1]);
7081: gsl_vector_set(x, 1, p[2]);
7082:
7083: minex_func.f = &gompertz_f;
7084: minex_func.n = NDIM;
7085: minex_func.params = (void *)&p; /* ??? */
7086:
7087: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7088: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7089:
7090: printf("Iterations beginning .....\n\n");
7091: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7092:
7093: iteri=0;
7094: while (rval == GSL_CONTINUE){
7095: iteri++;
7096: status = gsl_multimin_fminimizer_iterate(sfm);
7097:
7098: if (status) printf("error: %s\n", gsl_strerror (status));
7099: fflush(0);
7100:
7101: if (status)
7102: break;
7103:
7104: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7105: ssval = gsl_multimin_fminimizer_size (sfm);
7106:
7107: if (rval == GSL_SUCCESS)
7108: printf ("converged to a local maximum at\n");
7109:
7110: printf("%5d ", iteri);
7111: for (it = 0; it < NDIM; it++){
7112: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7113: }
7114: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7115: }
7116:
7117: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7118:
7119: gsl_vector_free(x); /* initial values */
7120: gsl_vector_free(ss); /* inital step size */
7121: for (it=0; it<NDIM; it++){
7122: p[it+1]=gsl_vector_get(sfm->x,it);
7123: fprintf(ficrespow," %.12lf", p[it]);
7124: }
7125: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7126: #endif
7127: #ifdef POWELL
7128: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7129: #endif
7130: fclose(ficrespow);
7131:
7132: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7133:
7134: for(i=1; i <=NDIM; i++)
7135: for(j=i+1;j<=NDIM;j++)
7136: matcov[i][j]=matcov[j][i];
7137:
7138: printf("\nCovariance matrix\n ");
7139: for(i=1; i <=NDIM; i++) {
7140: for(j=1;j<=NDIM;j++){
7141: printf("%f ",matcov[i][j]);
7142: }
7143: printf("\n ");
7144: }
7145:
7146: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
7147: for (i=1;i<=NDIM;i++) {
7148: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7149: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7150: }
7151: lsurv=vector(1,AGESUP);
7152: lpop=vector(1,AGESUP);
7153: tpop=vector(1,AGESUP);
7154: lsurv[agegomp]=100000;
7155:
7156: for (k=agegomp;k<=AGESUP;k++) {
7157: agemortsup=k;
7158: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7159: }
7160:
7161: for (k=agegomp;k<agemortsup;k++)
7162: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7163:
7164: for (k=agegomp;k<agemortsup;k++){
7165: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7166: sumlpop=sumlpop+lpop[k];
7167: }
7168:
7169: tpop[agegomp]=sumlpop;
7170: for (k=agegomp;k<(agemortsup-3);k++){
7171: /* tpop[k+1]=2;*/
7172: tpop[k+1]=tpop[k]-lpop[k];
7173: }
7174:
7175:
7176: printf("\nAge lx qx dx Lx Tx e(x)\n");
7177: for (k=agegomp;k<(agemortsup-2);k++)
7178: 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]);
7179:
7180:
7181: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7182: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7183: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7184: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7185: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7186: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7187: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7188: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7189: }else
7190: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7191: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7192: stepm, weightopt,\
7193: model,imx,p,matcov,agemortsup);
7194:
7195: free_vector(lsurv,1,AGESUP);
7196: free_vector(lpop,1,AGESUP);
7197: free_vector(tpop,1,AGESUP);
7198: #ifdef GSL
7199: free_ivector(cens,1,n);
7200: free_vector(agecens,1,n);
7201: free_ivector(dcwave,1,n);
7202: free_matrix(ximort,1,NDIM,1,NDIM);
7203: #endif
7204: } /* Endof if mle==-3 mortality only */
7205: /* Standard maximisation */
7206: else{ /* For mle >=1 */
7207: globpr=0;/* debug */
7208: /* Computes likelihood for initial parameters */
7209: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7210: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7211: for (k=1; k<=npar;k++)
7212: printf(" %d %8.5f",k,p[k]);
7213: printf("\n");
7214: globpr=1; /* again, to print the contributions */
7215: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7216: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7217: for (k=1; k<=npar;k++)
7218: printf(" %d %8.5f",k,p[k]);
7219: printf("\n");
7220: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
7221: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7222: }
7223:
7224: /*--------- results files --------------*/
7225: 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=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
7226:
7227:
7228: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7229: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7230: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7231: for(i=1,jk=1; i <=nlstate; i++){
7232: for(k=1; k <=(nlstate+ndeath); k++){
7233: if (k != i) {
7234: printf("%d%d ",i,k);
7235: fprintf(ficlog,"%d%d ",i,k);
7236: fprintf(ficres,"%1d%1d ",i,k);
7237: for(j=1; j <=ncovmodel; j++){
7238: printf("%12.7f ",p[jk]);
7239: fprintf(ficlog,"%12.7f ",p[jk]);
7240: fprintf(ficres,"%12.7f ",p[jk]);
7241: jk++;
7242: }
7243: printf("\n");
7244: fprintf(ficlog,"\n");
7245: fprintf(ficres,"\n");
7246: }
7247: }
7248: }
7249: if(mle!=0){
7250: /* Computing hessian and covariance matrix */
7251: ftolhess=ftol; /* Usually correct */
7252: hesscov(matcov, p, npar, delti, ftolhess, func);
7253: }
7254: printf("Parameters and 95%% confidence intervals\n");
7255: fprintf(ficlog, "Parameters, T and confidence intervals\n");
7256: for(i=1,jk=1; i <=nlstate; i++){
7257: for(k=1; k <=(nlstate+ndeath); k++){
7258: if (k != i) {
7259: printf("%d%d ",i,k);
7260: fprintf(ficlog,"%d%d ",i,k);
7261: for(j=1; j <=ncovmodel; j++){
7262: printf("%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7263: fprintf(ficlog,"%12.7f T=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-2*sqrt(matcov[jk][jk]),p[jk]+2*sqrt(matcov[jk][jk]));
7264: jk++;
7265: }
7266: printf("\n");
7267: fprintf(ficlog,"\n");
7268: }
7269: }
7270: }
7271:
7272: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7273: printf("# Scales (for hessian or gradient estimation)\n");
7274: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7275: for(i=1,jk=1; i <=nlstate; i++){
7276: for(j=1; j <=nlstate+ndeath; j++){
7277: if (j!=i) {
7278: fprintf(ficres,"%1d%1d",i,j);
7279: printf("%1d%1d",i,j);
7280: fprintf(ficlog,"%1d%1d",i,j);
7281: for(k=1; k<=ncovmodel;k++){
7282: printf(" %.5e",delti[jk]);
7283: fprintf(ficlog," %.5e",delti[jk]);
7284: fprintf(ficres," %.5e",delti[jk]);
7285: jk++;
7286: }
7287: printf("\n");
7288: fprintf(ficlog,"\n");
7289: fprintf(ficres,"\n");
7290: }
7291: }
7292: }
7293:
7294: 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");
7295: if(mle>=1)
7296: 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");
7297: 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");
7298: /* # 121 Var(a12)\n\ */
7299: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7300: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7301: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7302: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7303: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7304: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7305: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7306:
7307:
7308: /* Just to have a covariance matrix which will be more understandable
7309: even is we still don't want to manage dictionary of variables
7310: */
7311: for(itimes=1;itimes<=2;itimes++){
7312: jj=0;
7313: for(i=1; i <=nlstate; i++){
7314: for(j=1; j <=nlstate+ndeath; j++){
7315: if(j==i) continue;
7316: for(k=1; k<=ncovmodel;k++){
7317: jj++;
7318: ca[0]= k+'a'-1;ca[1]='\0';
7319: if(itimes==1){
7320: if(mle>=1)
7321: printf("#%1d%1d%d",i,j,k);
7322: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7323: fprintf(ficres,"#%1d%1d%d",i,j,k);
7324: }else{
7325: if(mle>=1)
7326: printf("%1d%1d%d",i,j,k);
7327: fprintf(ficlog,"%1d%1d%d",i,j,k);
7328: fprintf(ficres,"%1d%1d%d",i,j,k);
7329: }
7330: ll=0;
7331: for(li=1;li <=nlstate; li++){
7332: for(lj=1;lj <=nlstate+ndeath; lj++){
7333: if(lj==li) continue;
7334: for(lk=1;lk<=ncovmodel;lk++){
7335: ll++;
7336: if(ll<=jj){
7337: cb[0]= lk +'a'-1;cb[1]='\0';
7338: if(ll<jj){
7339: if(itimes==1){
7340: if(mle>=1)
7341: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7342: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7343: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7344: }else{
7345: if(mle>=1)
7346: printf(" %.5e",matcov[jj][ll]);
7347: fprintf(ficlog," %.5e",matcov[jj][ll]);
7348: fprintf(ficres," %.5e",matcov[jj][ll]);
7349: }
7350: }else{
7351: if(itimes==1){
7352: if(mle>=1)
7353: printf(" Var(%s%1d%1d)",ca,i,j);
7354: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7355: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7356: }else{
7357: if(mle>=1)
7358: printf(" %.5e",matcov[jj][ll]);
7359: fprintf(ficlog," %.5e",matcov[jj][ll]);
7360: fprintf(ficres," %.5e",matcov[jj][ll]);
7361: }
7362: }
7363: }
7364: } /* end lk */
7365: } /* end lj */
7366: } /* end li */
7367: if(mle>=1)
7368: printf("\n");
7369: fprintf(ficlog,"\n");
7370: fprintf(ficres,"\n");
7371: numlinepar++;
7372: } /* end k*/
7373: } /*end j */
7374: } /* end i */
7375: } /* end itimes */
7376:
7377: fflush(ficlog);
7378: fflush(ficres);
7379:
7380: while((c=getc(ficpar))=='#' && c!= EOF){
7381: ungetc(c,ficpar);
7382: fgets(line, MAXLINE, ficpar);
7383: fputs(line,stdout);
7384: fputs(line,ficparo);
7385: }
7386: ungetc(c,ficpar);
7387:
7388: estepm=0;
7389: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7390: if (estepm==0 || estepm < stepm) estepm=stepm;
7391: if (fage <= 2) {
7392: bage = ageminpar;
7393: fage = agemaxpar;
7394: }
7395:
7396: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7397: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7398: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7399:
7400: /* Other stuffs, more or less useful */
7401: while((c=getc(ficpar))=='#' && c!= EOF){
7402: ungetc(c,ficpar);
7403: fgets(line, MAXLINE, ficpar);
7404: fputs(line,stdout);
7405: fputs(line,ficparo);
7406: }
7407: ungetc(c,ficpar);
7408:
7409: 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);
7410: 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);
7411: 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);
7412: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7413: 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);
7414:
7415: while((c=getc(ficpar))=='#' && c!= EOF){
7416: ungetc(c,ficpar);
7417: fgets(line, MAXLINE, ficpar);
7418: fputs(line,stdout);
7419: fputs(line,ficparo);
7420: }
7421: ungetc(c,ficpar);
7422:
7423:
7424: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7425: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7426:
7427: fscanf(ficpar,"pop_based=%d\n",&popbased);
7428: fprintf(ficlog,"pop_based=%d\n",popbased);
7429: fprintf(ficparo,"pop_based=%d\n",popbased);
7430: fprintf(ficres,"pop_based=%d\n",popbased);
7431:
7432: while((c=getc(ficpar))=='#' && c!= EOF){
7433: ungetc(c,ficpar);
7434: fgets(line, MAXLINE, ficpar);
7435: fputs(line,stdout);
7436: fputs(line,ficparo);
7437: }
7438: ungetc(c,ficpar);
7439:
7440: 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);
7441: 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);
7442: 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);
7443: 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);
7444: 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);
7445: /* day and month of proj2 are not used but only year anproj2.*/
7446:
7447:
7448:
7449: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7450: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
7451:
7452: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
7453: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7454: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7455: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7456: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7457: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7458: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7459: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7460: }else
7461: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7462:
7463: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7464: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7465: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7466:
7467: /*------------ free_vector -------------*/
7468: /* chdir(path); */
7469:
7470: free_ivector(wav,1,imx);
7471: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7472: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7473: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7474: free_lvector(num,1,n);
7475: free_vector(agedc,1,n);
7476: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7477: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7478: fclose(ficparo);
7479: fclose(ficres);
7480:
7481:
7482: /* Other results (useful)*/
7483:
7484:
7485: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
7486: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7487: prlim=matrix(1,nlstate,1,nlstate);
7488: prevalence_limit(p, prlim, ageminpar, agemaxpar);
7489: fclose(ficrespl);
7490:
7491: #ifdef FREEEXIT2
7492: #include "freeexit2.h"
7493: #endif
7494:
7495: /*------------- h Pij x at various ages ------------*/
7496: /*#include "hpijx.h"*/
7497: hPijx(p, bage, fage);
7498: fclose(ficrespij);
7499:
7500: /*-------------- Variance of one-step probabilities---*/
7501: k=1;
7502: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7503:
7504:
7505: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7506: for(i=1;i<=AGESUP;i++)
7507: for(j=1;j<=NCOVMAX;j++)
7508: for(k=1;k<=NCOVMAX;k++)
7509: probs[i][j][k]=0.;
7510:
7511: /*---------- Forecasting ------------------*/
7512: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7513: if(prevfcast==1){
7514: /* if(stepm ==1){*/
7515: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7516: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7517: /* } */
7518: /* else{ */
7519: /* erreur=108; */
7520: /* 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); */
7521: /* 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); */
7522: /* } */
7523: }
7524:
7525: /* ------ Other prevalence ratios------------ */
7526:
7527: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7528:
7529: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7530: /* 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",\
7531: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7532: */
7533:
7534: if (mobilav!=0) {
7535: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7536: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7537: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7538: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7539: }
7540: }
7541:
7542:
7543: /*---------- Health expectancies, no variances ------------*/
7544:
7545: strcpy(filerese,"e");
7546: strcat(filerese,fileres);
7547: if((ficreseij=fopen(filerese,"w"))==NULL) {
7548: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7549: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7550: }
7551: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7552: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
7553: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7554: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7555:
7556: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7557: fprintf(ficreseij,"\n#****** ");
7558: for(j=1;j<=cptcoveff;j++) {
7559: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7560: }
7561: fprintf(ficreseij,"******\n");
7562:
7563: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7564: oldm=oldms;savm=savms;
7565: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7566:
7567: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7568: /*}*/
7569: }
7570: fclose(ficreseij);
7571:
7572:
7573: /*---------- Health expectancies and variances ------------*/
7574:
7575:
7576: strcpy(filerest,"t");
7577: strcat(filerest,fileres);
7578: if((ficrest=fopen(filerest,"w"))==NULL) {
7579: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7580: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7581: }
7582: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7583: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7584:
7585:
7586: strcpy(fileresstde,"stde");
7587: strcat(fileresstde,fileres);
7588: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7589: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7590: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7591: }
7592: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7593: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7594:
7595: strcpy(filerescve,"cve");
7596: strcat(filerescve,fileres);
7597: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7598: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7599: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7600: }
7601: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7602: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7603:
7604: strcpy(fileresv,"v");
7605: strcat(fileresv,fileres);
7606: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7607: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7608: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7609: }
7610: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7611: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7612:
7613: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7614: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7615:
7616: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7617: fprintf(ficrest,"\n#****** ");
7618: for(j=1;j<=cptcoveff;j++)
7619: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7620: fprintf(ficrest,"******\n");
7621:
7622: fprintf(ficresstdeij,"\n#****** ");
7623: fprintf(ficrescveij,"\n#****** ");
7624: for(j=1;j<=cptcoveff;j++) {
7625: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7626: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7627: }
7628: fprintf(ficresstdeij,"******\n");
7629: fprintf(ficrescveij,"******\n");
7630:
7631: fprintf(ficresvij,"\n#****** ");
7632: for(j=1;j<=cptcoveff;j++)
7633: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7634: fprintf(ficresvij,"******\n");
7635:
7636: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7637: oldm=oldms;savm=savms;
7638: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
7639: /*
7640: */
7641: /* goto endfree; */
7642:
7643: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7644: pstamp(ficrest);
7645:
7646:
7647: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
7648: oldm=oldms;savm=savms; /* Segmentation fault */
7649: cptcod= 0; /* To be deleted */
7650: 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 */
7651: 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 ");
7652: if(vpopbased==1)
7653: 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);
7654: else
7655: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7656: fprintf(ficrest,"# Age e.. (std) ");
7657: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7658: fprintf(ficrest,"\n");
7659:
7660: epj=vector(1,nlstate+1);
7661: for(age=bage; age <=fage ;age++){
7662: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7663: if (vpopbased==1) {
7664: if(mobilav ==0){
7665: for(i=1; i<=nlstate;i++)
7666: prlim[i][i]=probs[(int)age][i][k];
7667: }else{ /* mobilav */
7668: for(i=1; i<=nlstate;i++)
7669: prlim[i][i]=mobaverage[(int)age][i][k];
7670: }
7671: }
7672:
7673: fprintf(ficrest," %4.0f",age);
7674: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7675: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7676: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7677: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7678: }
7679: epj[nlstate+1] +=epj[j];
7680: }
7681:
7682: for(i=1, vepp=0.;i <=nlstate;i++)
7683: for(j=1;j <=nlstate;j++)
7684: vepp += vareij[i][j][(int)age];
7685: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7686: for(j=1;j <=nlstate;j++){
7687: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7688: }
7689: fprintf(ficrest,"\n");
7690: }
7691: }
7692: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7693: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7694: free_vector(epj,1,nlstate+1);
7695: /*}*/
7696: }
7697: free_vector(weight,1,n);
7698: free_imatrix(Tvard,1,NCOVMAX,1,2);
7699: free_imatrix(s,1,maxwav+1,1,n);
7700: free_matrix(anint,1,maxwav,1,n);
7701: free_matrix(mint,1,maxwav,1,n);
7702: free_ivector(cod,1,n);
7703: free_ivector(tab,1,NCOVMAX);
7704: fclose(ficresstdeij);
7705: fclose(ficrescveij);
7706: fclose(ficresvij);
7707: fclose(ficrest);
7708: fclose(ficpar);
7709:
7710: /*------- Variance of period (stable) prevalence------*/
7711:
7712: strcpy(fileresvpl,"vpl");
7713: strcat(fileresvpl,fileres);
7714: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7715: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7716: exit(0);
7717: }
7718: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7719:
7720: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7721: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7722:
7723: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7724: fprintf(ficresvpl,"\n#****** ");
7725: for(j=1;j<=cptcoveff;j++)
7726: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7727: fprintf(ficresvpl,"******\n");
7728:
7729: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7730: oldm=oldms;savm=savms;
7731: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7732: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
7733: /*}*/
7734: }
7735:
7736: fclose(ficresvpl);
7737:
7738: /*---------- End : free ----------------*/
7739: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7740: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7741: } /* mle==-3 arrives here for freeing */
7742: /* endfree:*/
7743: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
7744: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7745: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7746: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7747: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7748: free_matrix(covar,0,NCOVMAX,1,n);
7749: free_matrix(matcov,1,npar,1,npar);
7750: /*free_vector(delti,1,npar);*/
7751: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7752: free_matrix(agev,1,maxwav,1,imx);
7753: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7754:
7755: free_ivector(ncodemax,1,NCOVMAX);
7756: free_ivector(ncodemaxwundef,1,NCOVMAX);
7757: free_ivector(Tvar,1,NCOVMAX);
7758: free_ivector(Tprod,1,NCOVMAX);
7759: free_ivector(Tvaraff,1,NCOVMAX);
7760: free_ivector(Tage,1,NCOVMAX);
7761:
7762: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7763: free_imatrix(codtab,1,100,1,10);
7764: fflush(fichtm);
7765: fflush(ficgp);
7766:
7767:
7768: if((nberr >0) || (nbwarn>0)){
7769: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7770: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7771: }else{
7772: printf("End of Imach\n");
7773: fprintf(ficlog,"End of Imach\n");
7774: }
7775: printf("See log file on %s\n",filelog);
7776: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
7777: /*(void) gettimeofday(&end_time,&tzp);*/
7778: rend_time = time(NULL);
7779: end_time = *localtime(&rend_time);
7780: /* tml = *localtime(&end_time.tm_sec); */
7781: strcpy(strtend,asctime(&end_time));
7782: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7783: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
7784: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7785:
7786: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7787: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7788: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7789: /* printf("Total time was %d uSec.\n", total_usecs);*/
7790: /* if(fileappend(fichtm,optionfilehtm)){ */
7791: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7792: fclose(fichtm);
7793: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7794: fclose(fichtmcov);
7795: fclose(ficgp);
7796: fclose(ficlog);
7797: /*------ End -----------*/
7798:
7799:
7800: printf("Before Current directory %s!\n",pathcd);
7801: #ifdef WIN32
7802: if (_chdir(pathcd) != 0)
7803: printf("Can't move to directory %s!\n",path);
7804: if(_getcwd(pathcd,MAXLINE) > 0)
7805: #else
7806: if(chdir(pathcd) != 0)
7807: printf("Can't move to directory %s!\n", path);
7808: if (getcwd(pathcd, MAXLINE) > 0)
7809: #endif
7810: printf("Current directory %s!\n",pathcd);
7811: /*strcat(plotcmd,CHARSEPARATOR);*/
7812: sprintf(plotcmd,"gnuplot");
7813: #ifdef _WIN32
7814: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7815: #endif
7816: if(!stat(plotcmd,&info)){
7817: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7818: if(!stat(getenv("GNUPLOTBIN"),&info)){
7819: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
7820: }else
7821: strcpy(pplotcmd,plotcmd);
7822: #ifdef __unix
7823: strcpy(plotcmd,GNUPLOTPROGRAM);
7824: if(!stat(plotcmd,&info)){
7825: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
7826: }else
7827: strcpy(pplotcmd,plotcmd);
7828: #endif
7829: }else
7830: strcpy(pplotcmd,plotcmd);
7831:
7832: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
7833: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
7834:
7835: if((outcmd=system(plotcmd)) != 0){
7836: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
7837: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
7838: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
7839: if((outcmd=system(plotcmd)) != 0)
7840: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
7841: }
7842: printf(" Successful, please wait...");
7843: while (z[0] != 'q') {
7844: /* chdir(path); */
7845: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
7846: scanf("%s",z);
7847: /* if (z[0] == 'c') system("./imach"); */
7848: if (z[0] == 'e') {
7849: #ifdef __APPLE__
7850: sprintf(pplotcmd, "open %s", optionfilehtm);
7851: #elif __linux
7852: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
7853: #else
7854: sprintf(pplotcmd, "%s", optionfilehtm);
7855: #endif
7856: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7857: system(pplotcmd);
7858: }
7859: else if (z[0] == 'g') system(plotcmd);
7860: else if (z[0] == 'q') exit(0);
7861: }
7862: end:
7863: while (z[0] != 'q') {
7864: printf("\nType q for exiting: "); fflush(stdout);
7865: scanf("%s",z);
7866: }
7867: }
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