Annotation of imach/src/imach.c, revision 1.197
1.197 ! brouard 1: /* $Id: imach.c,v 1.196 2015/08/18 23:17:52 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.197 ! brouard 4: Revision 1.196 2015/08/18 23:17:52 brouard
! 5: Summary: 0.98q5
! 6:
1.196 brouard 7: Revision 1.195 2015/08/18 16:28:39 brouard
8: Summary: Adding a hack for testing purpose
9:
10: After reading the title, ftol and model lines, if the comment line has
11: a q, starting with #q, the answer at the end of the run is quit. It
12: permits to run test files in batch with ctest. The former workaround was
13: $ echo q | imach foo.imach
14:
1.195 brouard 15: Revision 1.194 2015/08/18 13:32:00 brouard
16: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
17:
1.194 brouard 18: Revision 1.193 2015/08/04 07:17:42 brouard
19: Summary: 0.98q4
20:
1.193 brouard 21: Revision 1.192 2015/07/16 16:49:02 brouard
22: Summary: Fixing some outputs
23:
1.192 brouard 24: Revision 1.191 2015/07/14 10:00:33 brouard
25: Summary: Some fixes
26:
1.191 brouard 27: Revision 1.190 2015/05/05 08:51:13 brouard
28: Summary: Adding digits in output parameters (7 digits instead of 6)
29:
30: Fix 1+age+.
31:
1.190 brouard 32: Revision 1.189 2015/04/30 14:45:16 brouard
33: Summary: 0.98q2
34:
1.189 brouard 35: Revision 1.188 2015/04/30 08:27:53 brouard
36: *** empty log message ***
37:
1.188 brouard 38: Revision 1.187 2015/04/29 09:11:15 brouard
39: *** empty log message ***
40:
1.187 brouard 41: Revision 1.186 2015/04/23 12:01:52 brouard
42: Summary: V1*age is working now, version 0.98q1
43:
44: Some codes had been disabled in order to simplify and Vn*age was
45: working in the optimization phase, ie, giving correct MLE parameters,
46: but, as usual, outputs were not correct and program core dumped.
47:
1.186 brouard 48: Revision 1.185 2015/03/11 13:26:42 brouard
49: Summary: Inclusion of compile and links command line for Intel Compiler
50:
1.185 brouard 51: Revision 1.184 2015/03/11 11:52:39 brouard
52: Summary: Back from Windows 8. Intel Compiler
53:
1.184 brouard 54: Revision 1.183 2015/03/10 20:34:32 brouard
55: Summary: 0.98q0, trying with directest, mnbrak fixed
56:
57: We use directest instead of original Powell test; probably no
58: incidence on the results, but better justifications;
59: We fixed Numerical Recipes mnbrak routine which was wrong and gave
60: wrong results.
61:
1.183 brouard 62: Revision 1.182 2015/02/12 08:19:57 brouard
63: Summary: Trying to keep directest which seems simpler and more general
64: Author: Nicolas Brouard
65:
1.182 brouard 66: Revision 1.181 2015/02/11 23:22:24 brouard
67: Summary: Comments on Powell added
68:
69: Author:
70:
1.181 brouard 71: Revision 1.180 2015/02/11 17:33:45 brouard
72: Summary: Finishing move from main to function (hpijx and prevalence_limit)
73:
1.180 brouard 74: Revision 1.179 2015/01/04 09:57:06 brouard
75: Summary: back to OS/X
76:
1.179 brouard 77: Revision 1.178 2015/01/04 09:35:48 brouard
78: *** empty log message ***
79:
1.178 brouard 80: Revision 1.177 2015/01/03 18:40:56 brouard
81: Summary: Still testing ilc32 on OSX
82:
1.177 brouard 83: Revision 1.176 2015/01/03 16:45:04 brouard
84: *** empty log message ***
85:
1.176 brouard 86: Revision 1.175 2015/01/03 16:33:42 brouard
87: *** empty log message ***
88:
1.175 brouard 89: Revision 1.174 2015/01/03 16:15:49 brouard
90: Summary: Still in cross-compilation
91:
1.174 brouard 92: Revision 1.173 2015/01/03 12:06:26 brouard
93: Summary: trying to detect cross-compilation
94:
1.173 brouard 95: Revision 1.172 2014/12/27 12:07:47 brouard
96: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
97:
1.172 brouard 98: Revision 1.171 2014/12/23 13:26:59 brouard
99: Summary: Back from Visual C
100:
101: Still problem with utsname.h on Windows
102:
1.171 brouard 103: Revision 1.170 2014/12/23 11:17:12 brouard
104: Summary: Cleaning some \%% back to %%
105:
106: The escape was mandatory for a specific compiler (which one?), but too many warnings.
107:
1.170 brouard 108: Revision 1.169 2014/12/22 23:08:31 brouard
109: Summary: 0.98p
110:
111: Outputs some informations on compiler used, OS etc. Testing on different platforms.
112:
1.169 brouard 113: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 114: Summary: update
1.169 brouard 115:
1.168 brouard 116: Revision 1.167 2014/12/22 13:50:56 brouard
117: Summary: Testing uname and compiler version and if compiled 32 or 64
118:
119: Testing on Linux 64
120:
1.167 brouard 121: Revision 1.166 2014/12/22 11:40:47 brouard
122: *** empty log message ***
123:
1.166 brouard 124: Revision 1.165 2014/12/16 11:20:36 brouard
125: Summary: After compiling on Visual C
126:
127: * imach.c (Module): Merging 1.61 to 1.162
128:
1.165 brouard 129: Revision 1.164 2014/12/16 10:52:11 brouard
130: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
131:
132: * imach.c (Module): Merging 1.61 to 1.162
133:
1.164 brouard 134: Revision 1.163 2014/12/16 10:30:11 brouard
135: * imach.c (Module): Merging 1.61 to 1.162
136:
1.163 brouard 137: Revision 1.162 2014/09/25 11:43:39 brouard
138: Summary: temporary backup 0.99!
139:
1.162 brouard 140: Revision 1.1 2014/09/16 11:06:58 brouard
141: Summary: With some code (wrong) for nlopt
142:
143: Author:
144:
145: Revision 1.161 2014/09/15 20:41:41 brouard
146: Summary: Problem with macro SQR on Intel compiler
147:
1.161 brouard 148: Revision 1.160 2014/09/02 09:24:05 brouard
149: *** empty log message ***
150:
1.160 brouard 151: Revision 1.159 2014/09/01 10:34:10 brouard
152: Summary: WIN32
153: Author: Brouard
154:
1.159 brouard 155: Revision 1.158 2014/08/27 17:11:51 brouard
156: *** empty log message ***
157:
1.158 brouard 158: Revision 1.157 2014/08/27 16:26:55 brouard
159: Summary: Preparing windows Visual studio version
160: Author: Brouard
161:
162: In order to compile on Visual studio, time.h is now correct and time_t
163: and tm struct should be used. difftime should be used but sometimes I
164: just make the differences in raw time format (time(&now).
165: Trying to suppress #ifdef LINUX
166: Add xdg-open for __linux in order to open default browser.
167:
1.157 brouard 168: Revision 1.156 2014/08/25 20:10:10 brouard
169: *** empty log message ***
170:
1.156 brouard 171: Revision 1.155 2014/08/25 18:32:34 brouard
172: Summary: New compile, minor changes
173: Author: Brouard
174:
1.155 brouard 175: Revision 1.154 2014/06/20 17:32:08 brouard
176: Summary: Outputs now all graphs of convergence to period prevalence
177:
1.154 brouard 178: Revision 1.153 2014/06/20 16:45:46 brouard
179: Summary: If 3 live state, convergence to period prevalence on same graph
180: Author: Brouard
181:
1.153 brouard 182: Revision 1.152 2014/06/18 17:54:09 brouard
183: Summary: open browser, use gnuplot on same dir than imach if not found in the path
184:
1.152 brouard 185: Revision 1.151 2014/06/18 16:43:30 brouard
186: *** empty log message ***
187:
1.151 brouard 188: Revision 1.150 2014/06/18 16:42:35 brouard
189: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
190: Author: brouard
191:
1.150 brouard 192: Revision 1.149 2014/06/18 15:51:14 brouard
193: Summary: Some fixes in parameter files errors
194: Author: Nicolas Brouard
195:
1.149 brouard 196: Revision 1.148 2014/06/17 17:38:48 brouard
197: Summary: Nothing new
198: Author: Brouard
199:
200: Just a new packaging for OS/X version 0.98nS
201:
1.148 brouard 202: Revision 1.147 2014/06/16 10:33:11 brouard
203: *** empty log message ***
204:
1.147 brouard 205: Revision 1.146 2014/06/16 10:20:28 brouard
206: Summary: Merge
207: Author: Brouard
208:
209: Merge, before building revised version.
210:
1.146 brouard 211: Revision 1.145 2014/06/10 21:23:15 brouard
212: Summary: Debugging with valgrind
213: Author: Nicolas Brouard
214:
215: Lot of changes in order to output the results with some covariates
216: After the Edimburgh REVES conference 2014, it seems mandatory to
217: improve the code.
218: No more memory valgrind error but a lot has to be done in order to
219: continue the work of splitting the code into subroutines.
220: Also, decodemodel has been improved. Tricode is still not
221: optimal. nbcode should be improved. Documentation has been added in
222: the source code.
223:
1.144 brouard 224: Revision 1.143 2014/01/26 09:45:38 brouard
225: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
226:
227: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
228: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
229:
1.143 brouard 230: Revision 1.142 2014/01/26 03:57:36 brouard
231: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
232:
233: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
234:
1.142 brouard 235: Revision 1.141 2014/01/26 02:42:01 brouard
236: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
237:
1.141 brouard 238: Revision 1.140 2011/09/02 10:37:54 brouard
239: Summary: times.h is ok with mingw32 now.
240:
1.140 brouard 241: Revision 1.139 2010/06/14 07:50:17 brouard
242: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
243: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
244:
1.139 brouard 245: Revision 1.138 2010/04/30 18:19:40 brouard
246: *** empty log message ***
247:
1.138 brouard 248: Revision 1.137 2010/04/29 18:11:38 brouard
249: (Module): Checking covariates for more complex models
250: than V1+V2. A lot of change to be done. Unstable.
251:
1.137 brouard 252: Revision 1.136 2010/04/26 20:30:53 brouard
253: (Module): merging some libgsl code. Fixing computation
254: of likelione (using inter/intrapolation if mle = 0) in order to
255: get same likelihood as if mle=1.
256: Some cleaning of code and comments added.
257:
1.136 brouard 258: Revision 1.135 2009/10/29 15:33:14 brouard
259: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
260:
1.135 brouard 261: Revision 1.134 2009/10/29 13:18:53 brouard
262: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
263:
1.134 brouard 264: Revision 1.133 2009/07/06 10:21:25 brouard
265: just nforces
266:
1.133 brouard 267: Revision 1.132 2009/07/06 08:22:05 brouard
268: Many tings
269:
1.132 brouard 270: Revision 1.131 2009/06/20 16:22:47 brouard
271: Some dimensions resccaled
272:
1.131 brouard 273: Revision 1.130 2009/05/26 06:44:34 brouard
274: (Module): Max Covariate is now set to 20 instead of 8. A
275: lot of cleaning with variables initialized to 0. Trying to make
276: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
277:
1.130 brouard 278: Revision 1.129 2007/08/31 13:49:27 lievre
279: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
280:
1.129 lievre 281: Revision 1.128 2006/06/30 13:02:05 brouard
282: (Module): Clarifications on computing e.j
283:
1.128 brouard 284: Revision 1.127 2006/04/28 18:11:50 brouard
285: (Module): Yes the sum of survivors was wrong since
286: imach-114 because nhstepm was no more computed in the age
287: loop. Now we define nhstepma in the age loop.
288: (Module): In order to speed up (in case of numerous covariates) we
289: compute health expectancies (without variances) in a first step
290: and then all the health expectancies with variances or standard
291: deviation (needs data from the Hessian matrices) which slows the
292: computation.
293: In the future we should be able to stop the program is only health
294: expectancies and graph are needed without standard deviations.
295:
1.127 brouard 296: Revision 1.126 2006/04/28 17:23:28 brouard
297: (Module): Yes the sum of survivors was wrong since
298: imach-114 because nhstepm was no more computed in the age
299: loop. Now we define nhstepma in the age loop.
300: Version 0.98h
301:
1.126 brouard 302: Revision 1.125 2006/04/04 15:20:31 lievre
303: Errors in calculation of health expectancies. Age was not initialized.
304: Forecasting file added.
305:
306: Revision 1.124 2006/03/22 17:13:53 lievre
307: Parameters are printed with %lf instead of %f (more numbers after the comma).
308: The log-likelihood is printed in the log file
309:
310: Revision 1.123 2006/03/20 10:52:43 brouard
311: * imach.c (Module): <title> changed, corresponds to .htm file
312: name. <head> headers where missing.
313:
314: * imach.c (Module): Weights can have a decimal point as for
315: English (a comma might work with a correct LC_NUMERIC environment,
316: otherwise the weight is truncated).
317: Modification of warning when the covariates values are not 0 or
318: 1.
319: Version 0.98g
320:
321: Revision 1.122 2006/03/20 09:45:41 brouard
322: (Module): Weights can have a decimal point as for
323: English (a comma might work with a correct LC_NUMERIC environment,
324: otherwise the weight is truncated).
325: Modification of warning when the covariates values are not 0 or
326: 1.
327: Version 0.98g
328:
329: Revision 1.121 2006/03/16 17:45:01 lievre
330: * imach.c (Module): Comments concerning covariates added
331:
332: * imach.c (Module): refinements in the computation of lli if
333: status=-2 in order to have more reliable computation if stepm is
334: not 1 month. Version 0.98f
335:
336: Revision 1.120 2006/03/16 15:10:38 lievre
337: (Module): refinements in the computation of lli if
338: status=-2 in order to have more reliable computation if stepm is
339: not 1 month. Version 0.98f
340:
341: Revision 1.119 2006/03/15 17:42:26 brouard
342: (Module): Bug if status = -2, the loglikelihood was
343: computed as likelihood omitting the logarithm. Version O.98e
344:
345: Revision 1.118 2006/03/14 18:20:07 brouard
346: (Module): varevsij Comments added explaining the second
347: table of variances if popbased=1 .
348: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
349: (Module): Function pstamp added
350: (Module): Version 0.98d
351:
352: Revision 1.117 2006/03/14 17:16:22 brouard
353: (Module): varevsij Comments added explaining the second
354: table of variances if popbased=1 .
355: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
356: (Module): Function pstamp added
357: (Module): Version 0.98d
358:
359: Revision 1.116 2006/03/06 10:29:27 brouard
360: (Module): Variance-covariance wrong links and
361: varian-covariance of ej. is needed (Saito).
362:
363: Revision 1.115 2006/02/27 12:17:45 brouard
364: (Module): One freematrix added in mlikeli! 0.98c
365:
366: Revision 1.114 2006/02/26 12:57:58 brouard
367: (Module): Some improvements in processing parameter
368: filename with strsep.
369:
370: Revision 1.113 2006/02/24 14:20:24 brouard
371: (Module): Memory leaks checks with valgrind and:
372: datafile was not closed, some imatrix were not freed and on matrix
373: allocation too.
374:
375: Revision 1.112 2006/01/30 09:55:26 brouard
376: (Module): Back to gnuplot.exe instead of wgnuplot.exe
377:
378: Revision 1.111 2006/01/25 20:38:18 brouard
379: (Module): Lots of cleaning and bugs added (Gompertz)
380: (Module): Comments can be added in data file. Missing date values
381: can be a simple dot '.'.
382:
383: Revision 1.110 2006/01/25 00:51:50 brouard
384: (Module): Lots of cleaning and bugs added (Gompertz)
385:
386: Revision 1.109 2006/01/24 19:37:15 brouard
387: (Module): Comments (lines starting with a #) are allowed in data.
388:
389: Revision 1.108 2006/01/19 18:05:42 lievre
390: Gnuplot problem appeared...
391: To be fixed
392:
393: Revision 1.107 2006/01/19 16:20:37 brouard
394: Test existence of gnuplot in imach path
395:
396: Revision 1.106 2006/01/19 13:24:36 brouard
397: Some cleaning and links added in html output
398:
399: Revision 1.105 2006/01/05 20:23:19 lievre
400: *** empty log message ***
401:
402: Revision 1.104 2005/09/30 16:11:43 lievre
403: (Module): sump fixed, loop imx fixed, and simplifications.
404: (Module): If the status is missing at the last wave but we know
405: that the person is alive, then we can code his/her status as -2
406: (instead of missing=-1 in earlier versions) and his/her
407: contributions to the likelihood is 1 - Prob of dying from last
408: health status (= 1-p13= p11+p12 in the easiest case of somebody in
409: the healthy state at last known wave). Version is 0.98
410:
411: Revision 1.103 2005/09/30 15:54:49 lievre
412: (Module): sump fixed, loop imx fixed, and simplifications.
413:
414: Revision 1.102 2004/09/15 17:31:30 brouard
415: Add the possibility to read data file including tab characters.
416:
417: Revision 1.101 2004/09/15 10:38:38 brouard
418: Fix on curr_time
419:
420: Revision 1.100 2004/07/12 18:29:06 brouard
421: Add version for Mac OS X. Just define UNIX in Makefile
422:
423: Revision 1.99 2004/06/05 08:57:40 brouard
424: *** empty log message ***
425:
426: Revision 1.98 2004/05/16 15:05:56 brouard
427: New version 0.97 . First attempt to estimate force of mortality
428: directly from the data i.e. without the need of knowing the health
429: state at each age, but using a Gompertz model: log u =a + b*age .
430: This is the basic analysis of mortality and should be done before any
431: other analysis, in order to test if the mortality estimated from the
432: cross-longitudinal survey is different from the mortality estimated
433: from other sources like vital statistic data.
434:
435: The same imach parameter file can be used but the option for mle should be -3.
436:
1.133 brouard 437: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 438: former routines in order to include the new code within the former code.
439:
440: The output is very simple: only an estimate of the intercept and of
441: the slope with 95% confident intervals.
442:
443: Current limitations:
444: A) Even if you enter covariates, i.e. with the
445: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
446: B) There is no computation of Life Expectancy nor Life Table.
447:
448: Revision 1.97 2004/02/20 13:25:42 lievre
449: Version 0.96d. Population forecasting command line is (temporarily)
450: suppressed.
451:
452: Revision 1.96 2003/07/15 15:38:55 brouard
453: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
454: rewritten within the same printf. Workaround: many printfs.
455:
456: Revision 1.95 2003/07/08 07:54:34 brouard
457: * imach.c (Repository):
458: (Repository): Using imachwizard code to output a more meaningful covariance
459: matrix (cov(a12,c31) instead of numbers.
460:
461: Revision 1.94 2003/06/27 13:00:02 brouard
462: Just cleaning
463:
464: Revision 1.93 2003/06/25 16:33:55 brouard
465: (Module): On windows (cygwin) function asctime_r doesn't
466: exist so I changed back to asctime which exists.
467: (Module): Version 0.96b
468:
469: Revision 1.92 2003/06/25 16:30:45 brouard
470: (Module): On windows (cygwin) function asctime_r doesn't
471: exist so I changed back to asctime which exists.
472:
473: Revision 1.91 2003/06/25 15:30:29 brouard
474: * imach.c (Repository): Duplicated warning errors corrected.
475: (Repository): Elapsed time after each iteration is now output. It
476: helps to forecast when convergence will be reached. Elapsed time
477: is stamped in powell. We created a new html file for the graphs
478: concerning matrix of covariance. It has extension -cov.htm.
479:
480: Revision 1.90 2003/06/24 12:34:15 brouard
481: (Module): Some bugs corrected for windows. Also, when
482: mle=-1 a template is output in file "or"mypar.txt with the design
483: of the covariance matrix to be input.
484:
485: Revision 1.89 2003/06/24 12:30:52 brouard
486: (Module): Some bugs corrected for windows. Also, when
487: mle=-1 a template is output in file "or"mypar.txt with the design
488: of the covariance matrix to be input.
489:
490: Revision 1.88 2003/06/23 17:54:56 brouard
491: * 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.
492:
493: Revision 1.87 2003/06/18 12:26:01 brouard
494: Version 0.96
495:
496: Revision 1.86 2003/06/17 20:04:08 brouard
497: (Module): Change position of html and gnuplot routines and added
498: routine fileappend.
499:
500: Revision 1.85 2003/06/17 13:12:43 brouard
501: * imach.c (Repository): Check when date of death was earlier that
502: current date of interview. It may happen when the death was just
503: prior to the death. In this case, dh was negative and likelihood
504: was wrong (infinity). We still send an "Error" but patch by
505: assuming that the date of death was just one stepm after the
506: interview.
507: (Repository): Because some people have very long ID (first column)
508: we changed int to long in num[] and we added a new lvector for
509: memory allocation. But we also truncated to 8 characters (left
510: truncation)
511: (Repository): No more line truncation errors.
512:
513: Revision 1.84 2003/06/13 21:44:43 brouard
514: * imach.c (Repository): Replace "freqsummary" at a correct
515: place. It differs from routine "prevalence" which may be called
516: many times. Probs is memory consuming and must be used with
517: parcimony.
518: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
519:
520: Revision 1.83 2003/06/10 13:39:11 lievre
521: *** empty log message ***
522:
523: Revision 1.82 2003/06/05 15:57:20 brouard
524: Add log in imach.c and fullversion number is now printed.
525:
526: */
527: /*
528: Interpolated Markov Chain
529:
530: Short summary of the programme:
531:
532: This program computes Healthy Life Expectancies from
533: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
534: first survey ("cross") where individuals from different ages are
535: interviewed on their health status or degree of disability (in the
536: case of a health survey which is our main interest) -2- at least a
537: second wave of interviews ("longitudinal") which measure each change
538: (if any) in individual health status. Health expectancies are
539: computed from the time spent in each health state according to a
540: model. More health states you consider, more time is necessary to reach the
541: Maximum Likelihood of the parameters involved in the model. The
542: simplest model is the multinomial logistic model where pij is the
543: probability to be observed in state j at the second wave
544: conditional to be observed in state i at the first wave. Therefore
545: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
546: 'age' is age and 'sex' is a covariate. If you want to have a more
547: complex model than "constant and age", you should modify the program
548: where the markup *Covariates have to be included here again* invites
549: you to do it. More covariates you add, slower the
550: convergence.
551:
552: The advantage of this computer programme, compared to a simple
553: multinomial logistic model, is clear when the delay between waves is not
554: identical for each individual. Also, if a individual missed an
555: intermediate interview, the information is lost, but taken into
556: account using an interpolation or extrapolation.
557:
558: hPijx is the probability to be observed in state i at age x+h
559: conditional to the observed state i at age x. The delay 'h' can be
560: split into an exact number (nh*stepm) of unobserved intermediate
561: states. This elementary transition (by month, quarter,
562: semester or year) is modelled as a multinomial logistic. The hPx
563: matrix is simply the matrix product of nh*stepm elementary matrices
564: and the contribution of each individual to the likelihood is simply
565: hPijx.
566:
567: Also this programme outputs the covariance matrix of the parameters but also
568: of the life expectancies. It also computes the period (stable) prevalence.
569:
1.133 brouard 570: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
571: Institut national d'études démographiques, Paris.
1.126 brouard 572: This software have been partly granted by Euro-REVES, a concerted action
573: from the European Union.
574: It is copyrighted identically to a GNU software product, ie programme and
575: software can be distributed freely for non commercial use. Latest version
576: can be accessed at http://euroreves.ined.fr/imach .
577:
578: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
579: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
580:
581: **********************************************************************/
582: /*
583: main
584: read parameterfile
585: read datafile
586: concatwav
587: freqsummary
588: if (mle >= 1)
589: mlikeli
590: print results files
591: if mle==1
592: computes hessian
593: read end of parameter file: agemin, agemax, bage, fage, estepm
594: begin-prev-date,...
595: open gnuplot file
596: open html file
1.145 brouard 597: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
598: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
599: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
600: freexexit2 possible for memory heap.
601:
602: h Pij x | pij_nom ficrestpij
603: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
604: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
605: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
606:
607: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
608: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
609: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
610: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
611: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
612:
1.126 brouard 613: forecasting if prevfcast==1 prevforecast call prevalence()
614: health expectancies
615: Variance-covariance of DFLE
616: prevalence()
617: movingaverage()
618: varevsij()
619: if popbased==1 varevsij(,popbased)
620: total life expectancies
621: Variance of period (stable) prevalence
622: end
623: */
624:
1.187 brouard 625: /* #define DEBUG */
626: /* #define DEBUGBRENT */
1.165 brouard 627: #define POWELL /* Instead of NLOPT */
1.192 brouard 628: #define POWELLF1F3 /* Skip test */
1.186 brouard 629: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
630: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 631:
632: #include <math.h>
633: #include <stdio.h>
634: #include <stdlib.h>
635: #include <string.h>
1.159 brouard 636:
637: #ifdef _WIN32
638: #include <io.h>
1.172 brouard 639: #include <windows.h>
640: #include <tchar.h>
1.159 brouard 641: #else
1.126 brouard 642: #include <unistd.h>
1.159 brouard 643: #endif
1.126 brouard 644:
645: #include <limits.h>
646: #include <sys/types.h>
1.171 brouard 647:
648: #if defined(__GNUC__)
649: #include <sys/utsname.h> /* Doesn't work on Windows */
650: #endif
651:
1.126 brouard 652: #include <sys/stat.h>
653: #include <errno.h>
1.159 brouard 654: /* extern int errno; */
1.126 brouard 655:
1.157 brouard 656: /* #ifdef LINUX */
657: /* #include <time.h> */
658: /* #include "timeval.h" */
659: /* #else */
660: /* #include <sys/time.h> */
661: /* #endif */
662:
1.126 brouard 663: #include <time.h>
664:
1.136 brouard 665: #ifdef GSL
666: #include <gsl/gsl_errno.h>
667: #include <gsl/gsl_multimin.h>
668: #endif
669:
1.167 brouard 670:
1.162 brouard 671: #ifdef NLOPT
672: #include <nlopt.h>
673: typedef struct {
674: double (* function)(double [] );
675: } myfunc_data ;
676: #endif
677:
1.126 brouard 678: /* #include <libintl.h> */
679: /* #define _(String) gettext (String) */
680:
1.141 brouard 681: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 682:
683: #define GNUPLOTPROGRAM "gnuplot"
684: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
685: #define FILENAMELENGTH 132
686:
687: #define GLOCK_ERROR_NOPATH -1 /* empty path */
688: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
689:
1.144 brouard 690: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
691: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 692:
693: #define NINTERVMAX 8
1.144 brouard 694: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
695: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
696: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 ! brouard 697: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 698: #define MAXN 20000
1.144 brouard 699: #define YEARM 12. /**< Number of months per year */
1.126 brouard 700: #define AGESUP 130
701: #define AGEBASE 40
1.194 brouard 702: #define AGEOVERFLOW 1.e20
1.164 brouard 703: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 704: #ifdef _WIN32
705: #define DIRSEPARATOR '\\'
706: #define CHARSEPARATOR "\\"
707: #define ODIRSEPARATOR '/'
708: #else
1.126 brouard 709: #define DIRSEPARATOR '/'
710: #define CHARSEPARATOR "/"
711: #define ODIRSEPARATOR '\\'
712: #endif
713:
1.197 ! brouard 714: /* $Id: imach.c,v 1.196 2015/08/18 23:17:52 brouard Exp $ */
1.126 brouard 715: /* $State: Exp $ */
1.196 brouard 716: #include "version.h"
717: char version[]=__IMACH_VERSION__;
1.197 ! brouard 718: char copyright[]="September 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
! 719: char fullversion[]="$Revision: 1.196 $ $Date: 2015/08/18 23:17:52 $";
1.126 brouard 720: char strstart[80];
721: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 722: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 723: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 724: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
725: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
726: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
727: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
728: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
729: int cptcovprodnoage=0; /**< Number of covariate products without age */
730: int cptcoveff=0; /* Total number of covariates to vary for printing results */
731: int cptcov=0; /* Working variable */
1.126 brouard 732: int npar=NPARMAX;
733: int nlstate=2; /* Number of live states */
734: int ndeath=1; /* Number of dead states */
1.130 brouard 735: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 736: int popbased=0;
737:
738: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 739: int maxwav=0; /* Maxim number of waves */
740: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
741: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
742: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 743: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 744: int mle=1, weightopt=0;
1.126 brouard 745: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
746: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
747: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
748: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 749: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 750: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 751: double **matprod2(); /* test */
1.126 brouard 752: double **oldm, **newm, **savm; /* Working pointers to matrices */
753: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 754: /*FILE *fic ; */ /* Used in readdata only */
755: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 756: FILE *ficlog, *ficrespow;
1.130 brouard 757: int globpr=0; /* Global variable for printing or not */
1.126 brouard 758: double fretone; /* Only one call to likelihood */
1.130 brouard 759: long ipmx=0; /* Number of contributions */
1.126 brouard 760: double sw; /* Sum of weights */
761: char filerespow[FILENAMELENGTH];
762: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
763: FILE *ficresilk;
764: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
765: FILE *ficresprobmorprev;
766: FILE *fichtm, *fichtmcov; /* Html File */
767: FILE *ficreseij;
768: char filerese[FILENAMELENGTH];
769: FILE *ficresstdeij;
770: char fileresstde[FILENAMELENGTH];
771: FILE *ficrescveij;
772: char filerescve[FILENAMELENGTH];
773: FILE *ficresvij;
774: char fileresv[FILENAMELENGTH];
775: FILE *ficresvpl;
776: char fileresvpl[FILENAMELENGTH];
777: char title[MAXLINE];
778: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
779: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
780: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
781: char command[FILENAMELENGTH];
782: int outcmd=0;
783:
784: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
785:
786: char filelog[FILENAMELENGTH]; /* Log file */
787: char filerest[FILENAMELENGTH];
788: char fileregp[FILENAMELENGTH];
789: char popfile[FILENAMELENGTH];
790:
791: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
792:
1.157 brouard 793: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
794: /* struct timezone tzp; */
795: /* extern int gettimeofday(); */
796: struct tm tml, *gmtime(), *localtime();
797:
798: extern time_t time();
799:
800: struct tm start_time, end_time, curr_time, last_time, forecast_time;
801: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
802: struct tm tm;
803:
1.126 brouard 804: char strcurr[80], strfor[80];
805:
806: char *endptr;
807: long lval;
808: double dval;
809:
810: #define NR_END 1
811: #define FREE_ARG char*
812: #define FTOL 1.0e-10
813:
814: #define NRANSI
815: #define ITMAX 200
816:
817: #define TOL 2.0e-4
818:
819: #define CGOLD 0.3819660
820: #define ZEPS 1.0e-10
821: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
822:
823: #define GOLD 1.618034
824: #define GLIMIT 100.0
825: #define TINY 1.0e-20
826:
827: static double maxarg1,maxarg2;
828: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
829: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
830:
831: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
832: #define rint(a) floor(a+0.5)
1.166 brouard 833: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 834: #define mytinydouble 1.0e-16
1.166 brouard 835: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
836: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
837: /* static double dsqrarg; */
838: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 839: static double sqrarg;
840: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
841: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
842: int agegomp= AGEGOMP;
843:
844: int imx;
845: int stepm=1;
846: /* Stepm, step in month: minimum step interpolation*/
847:
848: int estepm;
849: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
850:
851: int m,nb;
852: long *num;
1.197 ! brouard 853: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 854: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
855: covariate for which somebody answered excluding
856: undefined. Usually 2: 0 and 1. */
857: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
858: covariate for which somebody answered including
859: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 860: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
861: double **pmmij, ***probs;
862: double *ageexmed,*agecens;
863: double dateintmean=0;
864:
865: double *weight;
866: int **s; /* Status */
1.141 brouard 867: double *agedc;
1.145 brouard 868: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 869: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 870: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 871: double idx;
872: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 ! brouard 873: int *Tage;
1.145 brouard 874: int *Ndum; /** Freq of modality (tricode */
1.141 brouard 875: int **codtab; /**< codtab=imatrix(1,100,1,10); */
876: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 877: double *lsurv, *lpop, *tpop;
878:
1.143 brouard 879: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
880: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 881:
882: /**************** split *************************/
883: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
884: {
885: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
886: the name of the file (name), its extension only (ext) and its first part of the name (finame)
887: */
888: char *ss; /* pointer */
1.186 brouard 889: int l1=0, l2=0; /* length counters */
1.126 brouard 890:
891: l1 = strlen(path ); /* length of path */
892: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
893: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
894: if ( ss == NULL ) { /* no directory, so determine current directory */
895: strcpy( name, path ); /* we got the fullname name because no directory */
896: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
897: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
898: /* get current working directory */
899: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 900: #ifdef WIN32
901: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
902: #else
903: if (getcwd(dirc, FILENAME_MAX) == NULL) {
904: #endif
1.126 brouard 905: return( GLOCK_ERROR_GETCWD );
906: }
907: /* got dirc from getcwd*/
908: printf(" DIRC = %s \n",dirc);
909: } else { /* strip direcotry from path */
910: ss++; /* after this, the filename */
911: l2 = strlen( ss ); /* length of filename */
912: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
913: strcpy( name, ss ); /* save file name */
914: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 915: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 916: printf(" DIRC2 = %s \n",dirc);
917: }
918: /* We add a separator at the end of dirc if not exists */
919: l1 = strlen( dirc ); /* length of directory */
920: if( dirc[l1-1] != DIRSEPARATOR ){
921: dirc[l1] = DIRSEPARATOR;
922: dirc[l1+1] = 0;
923: printf(" DIRC3 = %s \n",dirc);
924: }
925: ss = strrchr( name, '.' ); /* find last / */
926: if (ss >0){
927: ss++;
928: strcpy(ext,ss); /* save extension */
929: l1= strlen( name);
930: l2= strlen(ss)+1;
931: strncpy( finame, name, l1-l2);
932: finame[l1-l2]= 0;
933: }
934:
935: return( 0 ); /* we're done */
936: }
937:
938:
939: /******************************************/
940:
941: void replace_back_to_slash(char *s, char*t)
942: {
943: int i;
944: int lg=0;
945: i=0;
946: lg=strlen(t);
947: for(i=0; i<= lg; i++) {
948: (s[i] = t[i]);
949: if (t[i]== '\\') s[i]='/';
950: }
951: }
952:
1.132 brouard 953: char *trimbb(char *out, char *in)
1.137 brouard 954: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 955: char *s;
956: s=out;
957: while (*in != '\0'){
1.137 brouard 958: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 959: in++;
960: }
961: *out++ = *in++;
962: }
963: *out='\0';
964: return s;
965: }
966:
1.187 brouard 967: /* char *substrchaine(char *out, char *in, char *chain) */
968: /* { */
969: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
970: /* char *s, *t; */
971: /* t=in;s=out; */
972: /* while ((*in != *chain) && (*in != '\0')){ */
973: /* *out++ = *in++; */
974: /* } */
975:
976: /* /\* *in matches *chain *\/ */
977: /* while ((*in++ == *chain++) && (*in != '\0')){ */
978: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
979: /* } */
980: /* in--; chain--; */
981: /* while ( (*in != '\0')){ */
982: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
983: /* *out++ = *in++; */
984: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
985: /* } */
986: /* *out='\0'; */
987: /* out=s; */
988: /* return out; */
989: /* } */
990: char *substrchaine(char *out, char *in, char *chain)
991: {
992: /* Substract chain 'chain' from 'in', return and output 'out' */
993: /* in="V1+V1*age+age*age+V2", chain="age*age" */
994:
995: char *strloc;
996:
997: strcpy (out, in);
998: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
999: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1000: if(strloc != NULL){
1001: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1002: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1003: /* strcpy (strloc, strloc +strlen(chain));*/
1004: }
1005: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1006: return out;
1007: }
1008:
1009:
1.145 brouard 1010: char *cutl(char *blocc, char *alocc, char *in, char occ)
1011: {
1.187 brouard 1012: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1013: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1014: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1015: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1016: */
1.160 brouard 1017: char *s, *t;
1.145 brouard 1018: t=in;s=in;
1019: while ((*in != occ) && (*in != '\0')){
1020: *alocc++ = *in++;
1021: }
1022: if( *in == occ){
1023: *(alocc)='\0';
1024: s=++in;
1025: }
1026:
1027: if (s == t) {/* occ not found */
1028: *(alocc-(in-s))='\0';
1029: in=s;
1030: }
1031: while ( *in != '\0'){
1032: *blocc++ = *in++;
1033: }
1034:
1035: *blocc='\0';
1036: return t;
1037: }
1.137 brouard 1038: char *cutv(char *blocc, char *alocc, char *in, char occ)
1039: {
1.187 brouard 1040: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1041: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1042: gives blocc="abcdef2ghi" and alocc="j".
1043: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1044: */
1045: char *s, *t;
1046: t=in;s=in;
1047: while (*in != '\0'){
1048: while( *in == occ){
1049: *blocc++ = *in++;
1050: s=in;
1051: }
1052: *blocc++ = *in++;
1053: }
1054: if (s == t) /* occ not found */
1055: *(blocc-(in-s))='\0';
1056: else
1057: *(blocc-(in-s)-1)='\0';
1058: in=s;
1059: while ( *in != '\0'){
1060: *alocc++ = *in++;
1061: }
1062:
1063: *alocc='\0';
1064: return s;
1065: }
1066:
1.126 brouard 1067: int nbocc(char *s, char occ)
1068: {
1069: int i,j=0;
1070: int lg=20;
1071: i=0;
1072: lg=strlen(s);
1073: for(i=0; i<= lg; i++) {
1074: if (s[i] == occ ) j++;
1075: }
1076: return j;
1077: }
1078:
1.137 brouard 1079: /* void cutv(char *u,char *v, char*t, char occ) */
1080: /* { */
1081: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1082: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1083: /* gives u="abcdef2ghi" and v="j" *\/ */
1084: /* int i,lg,j,p=0; */
1085: /* i=0; */
1086: /* lg=strlen(t); */
1087: /* for(j=0; j<=lg-1; j++) { */
1088: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1089: /* } */
1.126 brouard 1090:
1.137 brouard 1091: /* for(j=0; j<p; j++) { */
1092: /* (u[j] = t[j]); */
1093: /* } */
1094: /* u[p]='\0'; */
1.126 brouard 1095:
1.137 brouard 1096: /* for(j=0; j<= lg; j++) { */
1097: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1098: /* } */
1099: /* } */
1.126 brouard 1100:
1.160 brouard 1101: #ifdef _WIN32
1102: char * strsep(char **pp, const char *delim)
1103: {
1104: char *p, *q;
1105:
1106: if ((p = *pp) == NULL)
1107: return 0;
1108: if ((q = strpbrk (p, delim)) != NULL)
1109: {
1110: *pp = q + 1;
1111: *q = '\0';
1112: }
1113: else
1114: *pp = 0;
1115: return p;
1116: }
1117: #endif
1118:
1.126 brouard 1119: /********************** nrerror ********************/
1120:
1121: void nrerror(char error_text[])
1122: {
1123: fprintf(stderr,"ERREUR ...\n");
1124: fprintf(stderr,"%s\n",error_text);
1125: exit(EXIT_FAILURE);
1126: }
1127: /*********************** vector *******************/
1128: double *vector(int nl, int nh)
1129: {
1130: double *v;
1131: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1132: if (!v) nrerror("allocation failure in vector");
1133: return v-nl+NR_END;
1134: }
1135:
1136: /************************ free vector ******************/
1137: void free_vector(double*v, int nl, int nh)
1138: {
1139: free((FREE_ARG)(v+nl-NR_END));
1140: }
1141:
1142: /************************ivector *******************************/
1143: int *ivector(long nl,long nh)
1144: {
1145: int *v;
1146: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1147: if (!v) nrerror("allocation failure in ivector");
1148: return v-nl+NR_END;
1149: }
1150:
1151: /******************free ivector **************************/
1152: void free_ivector(int *v, long nl, long nh)
1153: {
1154: free((FREE_ARG)(v+nl-NR_END));
1155: }
1156:
1157: /************************lvector *******************************/
1158: long *lvector(long nl,long nh)
1159: {
1160: long *v;
1161: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1162: if (!v) nrerror("allocation failure in ivector");
1163: return v-nl+NR_END;
1164: }
1165:
1166: /******************free lvector **************************/
1167: void free_lvector(long *v, long nl, long nh)
1168: {
1169: free((FREE_ARG)(v+nl-NR_END));
1170: }
1171:
1172: /******************* imatrix *******************************/
1173: int **imatrix(long nrl, long nrh, long ncl, long nch)
1174: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1175: {
1176: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1177: int **m;
1178:
1179: /* allocate pointers to rows */
1180: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1181: if (!m) nrerror("allocation failure 1 in matrix()");
1182: m += NR_END;
1183: m -= nrl;
1184:
1185:
1186: /* allocate rows and set pointers to them */
1187: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1188: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1189: m[nrl] += NR_END;
1190: m[nrl] -= ncl;
1191:
1192: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1193:
1194: /* return pointer to array of pointers to rows */
1195: return m;
1196: }
1197:
1198: /****************** free_imatrix *************************/
1199: void free_imatrix(m,nrl,nrh,ncl,nch)
1200: int **m;
1201: long nch,ncl,nrh,nrl;
1202: /* free an int matrix allocated by imatrix() */
1203: {
1204: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1205: free((FREE_ARG) (m+nrl-NR_END));
1206: }
1207:
1208: /******************* matrix *******************************/
1209: double **matrix(long nrl, long nrh, long ncl, long nch)
1210: {
1211: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1212: double **m;
1213:
1214: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1215: if (!m) nrerror("allocation failure 1 in matrix()");
1216: m += NR_END;
1217: m -= nrl;
1218:
1219: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1220: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1221: m[nrl] += NR_END;
1222: m[nrl] -= ncl;
1223:
1224: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1225: return m;
1.145 brouard 1226: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1227: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1228: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1229: */
1230: }
1231:
1232: /*************************free matrix ************************/
1233: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1234: {
1235: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1236: free((FREE_ARG)(m+nrl-NR_END));
1237: }
1238:
1239: /******************* ma3x *******************************/
1240: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1241: {
1242: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1243: double ***m;
1244:
1245: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1246: if (!m) nrerror("allocation failure 1 in matrix()");
1247: m += NR_END;
1248: m -= nrl;
1249:
1250: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1251: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1252: m[nrl] += NR_END;
1253: m[nrl] -= ncl;
1254:
1255: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1256:
1257: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1258: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1259: m[nrl][ncl] += NR_END;
1260: m[nrl][ncl] -= nll;
1261: for (j=ncl+1; j<=nch; j++)
1262: m[nrl][j]=m[nrl][j-1]+nlay;
1263:
1264: for (i=nrl+1; i<=nrh; i++) {
1265: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1266: for (j=ncl+1; j<=nch; j++)
1267: m[i][j]=m[i][j-1]+nlay;
1268: }
1269: return m;
1270: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1271: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1272: */
1273: }
1274:
1275: /*************************free ma3x ************************/
1276: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1277: {
1278: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1279: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1280: free((FREE_ARG)(m+nrl-NR_END));
1281: }
1282:
1283: /*************** function subdirf ***********/
1284: char *subdirf(char fileres[])
1285: {
1286: /* Caution optionfilefiname is hidden */
1287: strcpy(tmpout,optionfilefiname);
1288: strcat(tmpout,"/"); /* Add to the right */
1289: strcat(tmpout,fileres);
1290: return tmpout;
1291: }
1292:
1293: /*************** function subdirf2 ***********/
1294: char *subdirf2(char fileres[], char *preop)
1295: {
1296:
1297: /* Caution optionfilefiname is hidden */
1298: strcpy(tmpout,optionfilefiname);
1299: strcat(tmpout,"/");
1300: strcat(tmpout,preop);
1301: strcat(tmpout,fileres);
1302: return tmpout;
1303: }
1304:
1305: /*************** function subdirf3 ***********/
1306: char *subdirf3(char fileres[], char *preop, char *preop2)
1307: {
1308:
1309: /* Caution optionfilefiname is hidden */
1310: strcpy(tmpout,optionfilefiname);
1311: strcat(tmpout,"/");
1312: strcat(tmpout,preop);
1313: strcat(tmpout,preop2);
1314: strcat(tmpout,fileres);
1315: return tmpout;
1316: }
1317:
1.162 brouard 1318: char *asc_diff_time(long time_sec, char ascdiff[])
1319: {
1320: long sec_left, days, hours, minutes;
1321: days = (time_sec) / (60*60*24);
1322: sec_left = (time_sec) % (60*60*24);
1323: hours = (sec_left) / (60*60) ;
1324: sec_left = (sec_left) %(60*60);
1325: minutes = (sec_left) /60;
1326: sec_left = (sec_left) % (60);
1327: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1328: return ascdiff;
1329: }
1330:
1.126 brouard 1331: /***************** f1dim *************************/
1332: extern int ncom;
1333: extern double *pcom,*xicom;
1334: extern double (*nrfunc)(double []);
1335:
1336: double f1dim(double x)
1337: {
1338: int j;
1339: double f;
1340: double *xt;
1341:
1342: xt=vector(1,ncom);
1343: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1344: f=(*nrfunc)(xt);
1345: free_vector(xt,1,ncom);
1346: return f;
1347: }
1348:
1349: /*****************brent *************************/
1350: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1351: {
1352: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1353: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1354: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1355: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1356: * returned function value.
1357: */
1.126 brouard 1358: int iter;
1359: double a,b,d,etemp;
1.159 brouard 1360: double fu=0,fv,fw,fx;
1.164 brouard 1361: double ftemp=0.;
1.126 brouard 1362: double p,q,r,tol1,tol2,u,v,w,x,xm;
1363: double e=0.0;
1364:
1365: a=(ax < cx ? ax : cx);
1366: b=(ax > cx ? ax : cx);
1367: x=w=v=bx;
1368: fw=fv=fx=(*f)(x);
1369: for (iter=1;iter<=ITMAX;iter++) {
1370: xm=0.5*(a+b);
1371: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1372: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1373: printf(".");fflush(stdout);
1374: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1375: #ifdef DEBUGBRENT
1.126 brouard 1376: 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);
1377: 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);
1378: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1379: #endif
1380: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1381: *xmin=x;
1382: return fx;
1383: }
1384: ftemp=fu;
1385: if (fabs(e) > tol1) {
1386: r=(x-w)*(fx-fv);
1387: q=(x-v)*(fx-fw);
1388: p=(x-v)*q-(x-w)*r;
1389: q=2.0*(q-r);
1390: if (q > 0.0) p = -p;
1391: q=fabs(q);
1392: etemp=e;
1393: e=d;
1394: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1395: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1396: else {
1397: d=p/q;
1398: u=x+d;
1399: if (u-a < tol2 || b-u < tol2)
1400: d=SIGN(tol1,xm-x);
1401: }
1402: } else {
1403: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1404: }
1405: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1406: fu=(*f)(u);
1407: if (fu <= fx) {
1408: if (u >= x) a=x; else b=x;
1409: SHFT(v,w,x,u)
1.183 brouard 1410: SHFT(fv,fw,fx,fu)
1411: } else {
1412: if (u < x) a=u; else b=u;
1413: if (fu <= fw || w == x) {
1414: v=w;
1415: w=u;
1416: fv=fw;
1417: fw=fu;
1418: } else if (fu <= fv || v == x || v == w) {
1419: v=u;
1420: fv=fu;
1421: }
1422: }
1.126 brouard 1423: }
1424: nrerror("Too many iterations in brent");
1425: *xmin=x;
1426: return fx;
1427: }
1428:
1429: /****************** mnbrak ***********************/
1430:
1431: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1432: double (*func)(double))
1.183 brouard 1433: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1434: the downhill direction (defined by the function as evaluated at the initial points) and returns
1435: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1436: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1437: */
1.126 brouard 1438: double ulim,u,r,q, dum;
1439: double fu;
1.187 brouard 1440:
1441: double scale=10.;
1442: int iterscale=0;
1443:
1444: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1445: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1446:
1447:
1448: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1449: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1450: /* *bx = *ax - (*ax - *bx)/scale; */
1451: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1452: /* } */
1453:
1.126 brouard 1454: if (*fb > *fa) {
1455: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1456: SHFT(dum,*fb,*fa,dum)
1457: }
1.126 brouard 1458: *cx=(*bx)+GOLD*(*bx-*ax);
1459: *fc=(*func)(*cx);
1.183 brouard 1460: #ifdef DEBUG
1461: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1462: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1463: #endif
1464: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1465: r=(*bx-*ax)*(*fb-*fc);
1466: q=(*bx-*cx)*(*fb-*fa);
1467: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1468: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1469: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1470: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1471: fu=(*func)(u);
1.163 brouard 1472: #ifdef DEBUG
1473: /* f(x)=A(x-u)**2+f(u) */
1474: double A, fparabu;
1475: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1476: fparabu= *fa - A*(*ax-u)*(*ax-u);
1477: 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);
1478: 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);
1.183 brouard 1479: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1480: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1481: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1482: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1483: #endif
1.184 brouard 1484: #ifdef MNBRAKORIGINAL
1.183 brouard 1485: #else
1.191 brouard 1486: /* if (fu > *fc) { */
1487: /* #ifdef DEBUG */
1488: /* printf("mnbrak4 fu > fc \n"); */
1489: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1490: /* #endif */
1491: /* /\* 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 *\\/ *\/ */
1492: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1493: /* dum=u; /\* Shifting c and u *\/ */
1494: /* u = *cx; */
1495: /* *cx = dum; */
1496: /* dum = fu; */
1497: /* fu = *fc; */
1498: /* *fc =dum; */
1499: /* } else { /\* end *\/ */
1500: /* #ifdef DEBUG */
1501: /* printf("mnbrak3 fu < fc \n"); */
1502: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1503: /* #endif */
1504: /* dum=u; /\* Shifting c and u *\/ */
1505: /* u = *cx; */
1506: /* *cx = dum; */
1507: /* dum = fu; */
1508: /* fu = *fc; */
1509: /* *fc =dum; */
1510: /* } */
1.183 brouard 1511: #ifdef DEBUG
1.191 brouard 1512: printf("mnbrak34 fu < or >= fc \n");
1513: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1514: #endif
1.191 brouard 1515: dum=u; /* Shifting c and u */
1516: u = *cx;
1517: *cx = dum;
1518: dum = fu;
1519: fu = *fc;
1520: *fc =dum;
1.183 brouard 1521: #endif
1.162 brouard 1522: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1523: #ifdef DEBUG
1524: printf("mnbrak2 u after c but before ulim\n");
1525: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1526: #endif
1.126 brouard 1527: fu=(*func)(u);
1528: if (fu < *fc) {
1.183 brouard 1529: #ifdef DEBUG
1530: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1531: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1532: #endif
1.126 brouard 1533: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1534: SHFT(*fb,*fc,fu,(*func)(u))
1535: }
1.162 brouard 1536: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1537: #ifdef DEBUG
1538: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1539: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1540: #endif
1.126 brouard 1541: u=ulim;
1542: fu=(*func)(u);
1.183 brouard 1543: } else { /* u could be left to b (if r > q parabola has a maximum) */
1544: #ifdef DEBUG
1545: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1546: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1547: #endif
1.126 brouard 1548: u=(*cx)+GOLD*(*cx-*bx);
1549: fu=(*func)(u);
1.183 brouard 1550: } /* end tests */
1.126 brouard 1551: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1552: SHFT(*fa,*fb,*fc,fu)
1553: #ifdef DEBUG
1554: 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);
1555: 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);
1556: #endif
1557: } /* end while; ie return (a, b, c, fa, fb, fc) such that a < b < c with f(a) > f(b) and fb < f(c) */
1.126 brouard 1558: }
1559:
1560: /*************** linmin ************************/
1.162 brouard 1561: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1562: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1563: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1564: the value of func at the returned location p . This is actually all accomplished by calling the
1565: routines mnbrak and brent .*/
1.126 brouard 1566: int ncom;
1567: double *pcom,*xicom;
1568: double (*nrfunc)(double []);
1569:
1570: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1571: {
1572: double brent(double ax, double bx, double cx,
1573: double (*f)(double), double tol, double *xmin);
1574: double f1dim(double x);
1575: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1576: double *fc, double (*func)(double));
1577: int j;
1578: double xx,xmin,bx,ax;
1579: double fx,fb,fa;
1.187 brouard 1580:
1581: double scale=10., axs, xxs, xxss; /* Scale added for infinity */
1.126 brouard 1582:
1583: ncom=n;
1584: pcom=vector(1,n);
1585: xicom=vector(1,n);
1586: nrfunc=func;
1587: for (j=1;j<=n;j++) {
1588: pcom[j]=p[j];
1589: xicom[j]=xi[j];
1590: }
1.187 brouard 1591:
1.192 brouard 1592: /* axs=0.0; */
1593: /* xxss=1; /\* 1 and using scale *\/ */
1.187 brouard 1594: xxs=1;
1.192 brouard 1595: /* do{ */
1.187 brouard 1596: ax=0.;
1597: xx= xxs;
1598: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1599: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1600: /* 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)) */
1601: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1602: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1603: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1604: /* 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]]*/
1.192 brouard 1605: /* if (fx != fx){ */
1606: /* xxs=xxs/scale; /\* Trying a smaller xx, closer to initial ax=0 *\/ */
1607: /* 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); */
1608: /* } */
1609: /* }while(fx != fx); */
1.187 brouard 1610:
1.191 brouard 1611: #ifdef DEBUGLINMIN
1612: 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);
1613: #endif
1.187 brouard 1614: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1615: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1616: /* fmin = f(p[j] + xmin * xi[j]) */
1617: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1618: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1619: #ifdef DEBUG
1620: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1621: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1622: #endif
1.191 brouard 1623: #ifdef DEBUGLINMIN
1624: printf("linmin end ");
1625: #endif
1.126 brouard 1626: for (j=1;j<=n;j++) {
1.188 brouard 1627: /* printf(" before xi[%d]=%12.8f", j,xi[j]); */
1.187 brouard 1628: xi[j] *= xmin; /* xi rescaled by xmin: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1.189 brouard 1629: /* if(xxs <1.0) */
1630: /* 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 ); */
1.187 brouard 1631: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1632: }
1.189 brouard 1633: /* printf("\n"); */
1.191 brouard 1634: #ifdef DEBUGLINMIN
1635: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1636: for (j=1;j<=n;j++) {
1637: printf(" xi[%d]= %12.7f p[%d]= %12.7f",j,xi[j],j,p[j]);
1638: if(j % ncovmodel == 0)
1639: printf("\n");
1640: }
1641: #endif
1.126 brouard 1642: free_vector(xicom,1,n);
1643: free_vector(pcom,1,n);
1644: }
1645:
1646:
1647: /*************** powell ************************/
1.162 brouard 1648: /*
1649: Minimization of a function func of n variables. Input consists of an initial starting point
1650: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1651: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1652: such that failure to decrease by more than this amount on one iteration signals doneness. On
1653: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1654: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1655: */
1.126 brouard 1656: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1657: double (*func)(double []))
1658: {
1659: void linmin(double p[], double xi[], int n, double *fret,
1660: double (*func)(double []));
1661: int i,ibig,j;
1662: double del,t,*pt,*ptt,*xit;
1.181 brouard 1663: double directest;
1.126 brouard 1664: double fp,fptt;
1665: double *xits;
1666: int niterf, itmp;
1667:
1668: pt=vector(1,n);
1669: ptt=vector(1,n);
1670: xit=vector(1,n);
1671: xits=vector(1,n);
1672: *fret=(*func)(p);
1673: for (j=1;j<=n;j++) pt[j]=p[j];
1.157 brouard 1674: rcurr_time = time(NULL);
1.126 brouard 1675: for (*iter=1;;++(*iter)) {
1.187 brouard 1676: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1677: ibig=0;
1678: del=0.0;
1.157 brouard 1679: rlast_time=rcurr_time;
1680: /* (void) gettimeofday(&curr_time,&tzp); */
1681: rcurr_time = time(NULL);
1682: curr_time = *localtime(&rcurr_time);
1683: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1684: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1685: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1686: for (i=1;i<=n;i++) {
1.126 brouard 1687: printf(" %d %.12f",i, p[i]);
1688: fprintf(ficlog," %d %.12lf",i, p[i]);
1689: fprintf(ficrespow," %.12lf", p[i]);
1690: }
1691: printf("\n");
1692: fprintf(ficlog,"\n");
1693: fprintf(ficrespow,"\n");fflush(ficrespow);
1694: if(*iter <=3){
1.157 brouard 1695: tml = *localtime(&rcurr_time);
1696: strcpy(strcurr,asctime(&tml));
1697: rforecast_time=rcurr_time;
1.126 brouard 1698: itmp = strlen(strcurr);
1699: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1700: strcurr[itmp-1]='\0';
1.162 brouard 1701: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1702: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1703: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1704: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1705: forecast_time = *localtime(&rforecast_time);
1706: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1707: itmp = strlen(strfor);
1708: if(strfor[itmp-1]=='\n')
1709: strfor[itmp-1]='\0';
1.157 brouard 1710: 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);
1711: fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
1.126 brouard 1712: }
1713: }
1.187 brouard 1714: for (i=1;i<=n;i++) { /* For each direction i */
1715: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1716: fptt=(*fret);
1717: #ifdef DEBUG
1.164 brouard 1718: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1719: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1720: #endif
1.187 brouard 1721: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1722: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1723: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1724: /* Outputs are fret(new point p) p is updated and xit rescaled */
1725: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1726: /* because that direction will be replaced unless the gain del is small */
1727: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1728: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1729: /* with the new direction. */
1.126 brouard 1730: del=fabs(fptt-(*fret));
1731: ibig=i;
1732: }
1733: #ifdef DEBUG
1734: printf("%d %.12e",i,(*fret));
1735: fprintf(ficlog,"%d %.12e",i,(*fret));
1736: for (j=1;j<=n;j++) {
1737: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1738: printf(" x(%d)=%.12e",j,xit[j]);
1739: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1740: }
1741: for(j=1;j<=n;j++) {
1.162 brouard 1742: printf(" p(%d)=%.12e",j,p[j]);
1743: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1744: }
1745: printf("\n");
1746: fprintf(ficlog,"\n");
1747: #endif
1.187 brouard 1748: } /* end loop on each direction i */
1749: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1750: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1751: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1752: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1753: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1754: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1755: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1756: /* decreased of more than 3.84 */
1757: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1758: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1759: /* By adding 10 parameters more the gain should be 18.31 */
1760:
1761: /* Starting the program with initial values given by a former maximization will simply change */
1762: /* the scales of the directions and the directions, because the are reset to canonical directions */
1763: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1764: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1765: #ifdef DEBUG
1766: int k[2],l;
1767: k[0]=1;
1768: k[1]=-1;
1769: printf("Max: %.12e",(*func)(p));
1770: fprintf(ficlog,"Max: %.12e",(*func)(p));
1771: for (j=1;j<=n;j++) {
1772: printf(" %.12e",p[j]);
1773: fprintf(ficlog," %.12e",p[j]);
1774: }
1775: printf("\n");
1776: fprintf(ficlog,"\n");
1777: for(l=0;l<=1;l++) {
1778: for (j=1;j<=n;j++) {
1779: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1780: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1781: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1782: }
1783: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1784: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1785: }
1786: #endif
1787:
1788:
1789: free_vector(xit,1,n);
1790: free_vector(xits,1,n);
1791: free_vector(ptt,1,n);
1792: free_vector(pt,1,n);
1793: return;
1.192 brouard 1794: } /* enough precision */
1.126 brouard 1795: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1796: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1797: ptt[j]=2.0*p[j]-pt[j];
1798: xit[j]=p[j]-pt[j];
1799: pt[j]=p[j];
1800: }
1.181 brouard 1801: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1802: #ifdef POWELLF1F3
1803: #else
1.161 brouard 1804: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1805: #endif
1.162 brouard 1806: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1807: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1808: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1809: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1810: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1811: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1812: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1813: #ifdef NRCORIGINAL
1814: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1815: #else
1816: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del); /* Intel compiler doesn't work on one line; bug reported */
1.161 brouard 1817: t= t- del*SQR(fp-fptt);
1.183 brouard 1818: #endif
1.182 brouard 1819: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If del was big enough we change it for a new direction */
1.161 brouard 1820: #ifdef DEBUG
1.181 brouard 1821: 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);
1822: 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);
1.161 brouard 1823: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1824: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1825: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1826: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1827: 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);
1828: 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);
1829: #endif
1.183 brouard 1830: #ifdef POWELLORIGINAL
1831: if (t < 0.0) { /* Then we use it for new direction */
1832: #else
1.182 brouard 1833: if (directest*t < 0.0) { /* Contradiction between both tests */
1.192 brouard 1834: printf("directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1835: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1836: fprintf(ficlog,"directest= %.12lf, t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1837: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1838: }
1.181 brouard 1839: if (directest < 0.0) { /* Then we use it for new direction */
1840: #endif
1.191 brouard 1841: #ifdef DEBUGLINMIN
1842: printf("Before linmin in direction P%d-P0\n",n);
1843: for (j=1;j<=n;j++) {
1844: printf("Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1845: if(j % ncovmodel == 0)
1846: printf("\n");
1847: }
1848: #endif
1.187 brouard 1849: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1850: #ifdef DEBUGLINMIN
1851: for (j=1;j<=n;j++) {
1852: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1853: if(j % ncovmodel == 0)
1854: printf("\n");
1855: }
1856: #endif
1.126 brouard 1857: for (j=1;j<=n;j++) {
1.181 brouard 1858: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1859: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1860: }
1.181 brouard 1861: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1862: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1863:
1.126 brouard 1864: #ifdef DEBUG
1.164 brouard 1865: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1866: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1867: for(j=1;j<=n;j++){
1868: printf(" %.12e",xit[j]);
1869: fprintf(ficlog," %.12e",xit[j]);
1870: }
1871: printf("\n");
1872: fprintf(ficlog,"\n");
1873: #endif
1.192 brouard 1874: } /* end of t or directest negative */
1875: #ifdef POWELLF1F3
1876: #else
1.162 brouard 1877: } /* end if (fptt < fp) */
1.192 brouard 1878: #endif
1879: } /* loop iteration */
1.126 brouard 1880: }
1881:
1882: /**** Prevalence limit (stable or period prevalence) ****************/
1883:
1884: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
1885: {
1886: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1887: matrix by transitions matrix until convergence is reached */
1.169 brouard 1888:
1.126 brouard 1889: int i, ii,j,k;
1890: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1891: /* double **matprod2(); */ /* test */
1.131 brouard 1892: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1893: double **newm;
1894: double agefin, delaymax=50 ; /* Max number of years to converge */
1.169 brouard 1895:
1.126 brouard 1896: for (ii=1;ii<=nlstate+ndeath;ii++)
1897: for (j=1;j<=nlstate+ndeath;j++){
1898: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1899: }
1.169 brouard 1900:
1901: cov[1]=1.;
1902:
1903: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.126 brouard 1904: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1905: newm=savm;
1906: /* Covariates have to be included here again */
1.138 brouard 1907: cov[2]=agefin;
1.187 brouard 1908: if(nagesqr==1)
1909: cov[3]= agefin*agefin;;
1.138 brouard 1910: for (k=1; k<=cptcovn;k++) {
1.187 brouard 1911: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.197 ! brouard 1912: /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtab[%d][Tvar[%d]]=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], ij, k, codtab[ij][Tvar[k]]);*/
1.138 brouard 1913: }
1.186 brouard 1914: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 1915: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]*cov[2];
1.186 brouard 1916: for (k=1; k<=cptcovprod;k++) /* Useless */
1.187 brouard 1917: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]] * nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.138 brouard 1918:
1919: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
1920: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
1921: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 1922: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1923: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 1924: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 1925:
1.126 brouard 1926: savm=oldm;
1927: oldm=newm;
1928: maxmax=0.;
1929: for(j=1;j<=nlstate;j++){
1930: min=1.;
1931: max=0.;
1932: for(i=1; i<=nlstate; i++) {
1933: sumnew=0;
1934: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
1935: prlim[i][j]= newm[i][j]/(1-sumnew);
1.145 brouard 1936: /*printf(" prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d \n", i, j, i, j, prlim[i][j],(int)agefin);*/
1.126 brouard 1937: max=FMAX(max,prlim[i][j]);
1938: min=FMIN(min,prlim[i][j]);
1939: }
1940: maxmin=max-min;
1941: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 1942: } /* j loop */
1.126 brouard 1943: if(maxmax < ftolpl){
1944: return prlim;
1945: }
1.169 brouard 1946: } /* age loop */
1947: return prlim; /* should not reach here */
1.126 brouard 1948: }
1949:
1950: /*************** transition probabilities ***************/
1951:
1952: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
1953: {
1.138 brouard 1954: /* According to parameters values stored in x and the covariate's values stored in cov,
1955: computes the probability to be observed in state j being in state i by appying the
1956: model to the ncovmodel covariates (including constant and age).
1957: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
1958: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
1959: ncth covariate in the global vector x is given by the formula:
1960: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
1961: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
1962: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
1963: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
1964: Outputs ps[i][j] the probability to be observed in j being in j according to
1965: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
1966: */
1967: double s1, lnpijopii;
1.126 brouard 1968: /*double t34;*/
1.164 brouard 1969: int i,j, nc, ii, jj;
1.126 brouard 1970:
1971: for(i=1; i<= nlstate; i++){
1972: for(j=1; j<i;j++){
1.138 brouard 1973: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1974: /*lnpijopii += param[i][j][nc]*cov[nc];*/
1975: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
1976: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1977: }
1.138 brouard 1978: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1979: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 1980: }
1981: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 1982: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
1983: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
1984: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
1985: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 1986: }
1.138 brouard 1987: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 1988: }
1989: }
1990:
1991: for(i=1; i<= nlstate; i++){
1992: s1=0;
1.131 brouard 1993: for(j=1; j<i; j++){
1.138 brouard 1994: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1995: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
1996: }
1997: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 1998: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 1999: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2000: }
1.138 brouard 2001: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2002: ps[i][i]=1./(s1+1.);
1.138 brouard 2003: /* Computing other pijs */
1.126 brouard 2004: for(j=1; j<i; j++)
2005: ps[i][j]= exp(ps[i][j])*ps[i][i];
2006: for(j=i+1; j<=nlstate+ndeath; j++)
2007: ps[i][j]= exp(ps[i][j])*ps[i][i];
2008: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2009: } /* end i */
2010:
2011: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2012: for(jj=1; jj<= nlstate+ndeath; jj++){
2013: ps[ii][jj]=0;
2014: ps[ii][ii]=1;
2015: }
2016: }
2017:
1.145 brouard 2018:
2019: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2020: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2021: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2022: /* } */
2023: /* printf("\n "); */
2024: /* } */
2025: /* printf("\n ");printf("%lf ",cov[2]);*/
2026: /*
1.126 brouard 2027: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2028: goto end;*/
2029: return ps;
2030: }
2031:
2032: /**************** Product of 2 matrices ******************/
2033:
1.145 brouard 2034: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2035: {
2036: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2037: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2038: /* in, b, out are matrice of pointers which should have been initialized
2039: before: only the contents of out is modified. The function returns
2040: a pointer to pointers identical to out */
1.145 brouard 2041: int i, j, k;
1.126 brouard 2042: for(i=nrl; i<= nrh; i++)
1.145 brouard 2043: for(k=ncolol; k<=ncoloh; k++){
2044: out[i][k]=0.;
2045: for(j=ncl; j<=nch; j++)
2046: out[i][k] +=in[i][j]*b[j][k];
2047: }
1.126 brouard 2048: return out;
2049: }
2050:
2051:
2052: /************* Higher Matrix Product ***************/
2053:
2054: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2055: {
2056: /* Computes the transition matrix starting at age 'age' over
2057: 'nhstepm*hstepm*stepm' months (i.e. until
2058: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2059: nhstepm*hstepm matrices.
2060: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2061: (typically every 2 years instead of every month which is too big
2062: for the memory).
2063: Model is determined by parameters x and covariates have to be
2064: included manually here.
2065:
2066: */
2067:
2068: int i, j, d, h, k;
1.131 brouard 2069: double **out, cov[NCOVMAX+1];
1.126 brouard 2070: double **newm;
1.187 brouard 2071: double agexact;
1.126 brouard 2072:
2073: /* Hstepm could be zero and should return the unit matrix */
2074: for (i=1;i<=nlstate+ndeath;i++)
2075: for (j=1;j<=nlstate+ndeath;j++){
2076: oldm[i][j]=(i==j ? 1.0 : 0.0);
2077: po[i][j][0]=(i==j ? 1.0 : 0.0);
2078: }
2079: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2080: for(h=1; h <=nhstepm; h++){
2081: for(d=1; d <=hstepm; d++){
2082: newm=savm;
2083: /* Covariates have to be included here again */
2084: cov[1]=1.;
1.187 brouard 2085: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2086: cov[2]=agexact;
2087: if(nagesqr==1)
2088: cov[3]= agexact*agexact;
1.131 brouard 2089: for (k=1; k<=cptcovn;k++)
1.187 brouard 2090: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
1.186 brouard 2091: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2092: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.187 brouard 2093: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.145 brouard 2094: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.187 brouard 2095: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 2096:
2097:
2098: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2099: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2100: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2101: pmij(pmmij,cov,ncovmodel,x,nlstate));
2102: savm=oldm;
2103: oldm=newm;
2104: }
2105: for(i=1; i<=nlstate+ndeath; i++)
2106: for(j=1;j<=nlstate+ndeath;j++) {
2107: po[i][j][h]=newm[i][j];
1.128 brouard 2108: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2109: }
1.128 brouard 2110: /*printf("h=%d ",h);*/
1.126 brouard 2111: } /* end h */
1.128 brouard 2112: /* printf("\n H=%d \n",h); */
1.126 brouard 2113: return po;
2114: }
2115:
1.162 brouard 2116: #ifdef NLOPT
2117: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2118: double fret;
2119: double *xt;
2120: int j;
2121: myfunc_data *d2 = (myfunc_data *) pd;
2122: /* xt = (p1-1); */
2123: xt=vector(1,n);
2124: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2125:
2126: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2127: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2128: printf("Function = %.12lf ",fret);
2129: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2130: printf("\n");
2131: free_vector(xt,1,n);
2132: return fret;
2133: }
2134: #endif
1.126 brouard 2135:
2136: /*************** log-likelihood *************/
2137: double func( double *x)
2138: {
2139: int i, ii, j, k, mi, d, kk;
1.131 brouard 2140: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2141: double **out;
2142: double sw; /* Sum of weights */
2143: double lli; /* Individual log likelihood */
2144: int s1, s2;
2145: double bbh, survp;
2146: long ipmx;
1.187 brouard 2147: double agexact;
1.126 brouard 2148: /*extern weight */
2149: /* We are differentiating ll according to initial status */
2150: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2151: /*for(i=1;i<imx;i++)
2152: printf(" %d\n",s[4][i]);
2153: */
1.162 brouard 2154:
2155: ++countcallfunc;
2156:
1.126 brouard 2157: cov[1]=1.;
2158:
2159: for(k=1; k<=nlstate; k++) ll[k]=0.;
2160:
2161: if(mle==1){
2162: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2163: /* Computes the values of the ncovmodel covariates of the model
2164: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2165: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2166: to be observed in j being in i according to the model.
2167: */
1.145 brouard 2168: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2169: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2170: }
1.137 brouard 2171: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2172: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2173: has been calculated etc */
1.126 brouard 2174: for(mi=1; mi<= wav[i]-1; mi++){
2175: for (ii=1;ii<=nlstate+ndeath;ii++)
2176: for (j=1;j<=nlstate+ndeath;j++){
2177: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2178: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2179: }
2180: for(d=0; d<dh[mi][i]; d++){
2181: newm=savm;
1.187 brouard 2182: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2183: cov[2]=agexact;
2184: if(nagesqr==1)
2185: cov[3]= agexact*agexact;
1.126 brouard 2186: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2187: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2188: }
2189: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2190: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2191: savm=oldm;
2192: oldm=newm;
2193: } /* end mult */
2194:
2195: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2196: /* But now since version 0.9 we anticipate for bias at large stepm.
2197: * If stepm is larger than one month (smallest stepm) and if the exact delay
2198: * (in months) between two waves is not a multiple of stepm, we rounded to
2199: * the nearest (and in case of equal distance, to the lowest) interval but now
2200: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2201: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2202: * probability in order to take into account the bias as a fraction of the way
2203: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2204: * -stepm/2 to stepm/2 .
2205: * For stepm=1 the results are the same as for previous versions of Imach.
2206: * For stepm > 1 the results are less biased than in previous versions.
2207: */
2208: s1=s[mw[mi][i]][i];
2209: s2=s[mw[mi+1][i]][i];
2210: bbh=(double)bh[mi][i]/(double)stepm;
2211: /* bias bh is positive if real duration
2212: * is higher than the multiple of stepm and negative otherwise.
2213: */
2214: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2215: if( s2 > nlstate){
2216: /* i.e. if s2 is a death state and if the date of death is known
2217: then the contribution to the likelihood is the probability to
2218: die between last step unit time and current step unit time,
2219: which is also equal to probability to die before dh
2220: minus probability to die before dh-stepm .
2221: In version up to 0.92 likelihood was computed
2222: as if date of death was unknown. Death was treated as any other
2223: health state: the date of the interview describes the actual state
2224: and not the date of a change in health state. The former idea was
2225: to consider that at each interview the state was recorded
2226: (healthy, disable or death) and IMaCh was corrected; but when we
2227: introduced the exact date of death then we should have modified
2228: the contribution of an exact death to the likelihood. This new
2229: contribution is smaller and very dependent of the step unit
2230: stepm. It is no more the probability to die between last interview
2231: and month of death but the probability to survive from last
2232: interview up to one month before death multiplied by the
2233: probability to die within a month. Thanks to Chris
2234: Jackson for correcting this bug. Former versions increased
2235: mortality artificially. The bad side is that we add another loop
2236: which slows down the processing. The difference can be up to 10%
2237: lower mortality.
2238: */
1.183 brouard 2239: /* If, at the beginning of the maximization mostly, the
2240: cumulative probability or probability to be dead is
2241: constant (ie = 1) over time d, the difference is equal to
2242: 0. out[s1][3] = savm[s1][3]: probability, being at state
2243: s1 at precedent wave, to be dead a month before current
2244: wave is equal to probability, being at state s1 at
2245: precedent wave, to be dead at mont of the current
2246: wave. Then the observed probability (that this person died)
2247: is null according to current estimated parameter. In fact,
2248: it should be very low but not zero otherwise the log go to
2249: infinity.
2250: */
2251: /* #ifdef INFINITYORIGINAL */
2252: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2253: /* #else */
2254: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2255: /* lli=log(mytinydouble); */
2256: /* else */
2257: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2258: /* #endif */
2259: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2260:
2261: } else if (s2==-2) {
2262: for (j=1,survp=0. ; j<=nlstate; j++)
2263: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2264: /*survp += out[s1][j]; */
2265: lli= log(survp);
2266: }
2267:
2268: else if (s2==-4) {
2269: for (j=3,survp=0. ; j<=nlstate; j++)
2270: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2271: lli= log(survp);
2272: }
2273:
2274: else if (s2==-5) {
2275: for (j=1,survp=0. ; j<=2; j++)
2276: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2277: lli= log(survp);
2278: }
2279:
2280: else{
2281: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2282: /* 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 */
2283: }
2284: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2285: /*if(lli ==000.0)*/
2286: /*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); */
2287: ipmx +=1;
2288: sw += weight[i];
2289: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2290: /* if (lli < log(mytinydouble)){ */
2291: /* 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); */
2292: /* 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]); */
2293: /* } */
1.126 brouard 2294: } /* end of wave */
2295: } /* end of individual */
2296: } else if(mle==2){
2297: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2298: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2299: for(mi=1; mi<= wav[i]-1; mi++){
2300: for (ii=1;ii<=nlstate+ndeath;ii++)
2301: for (j=1;j<=nlstate+ndeath;j++){
2302: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2303: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2304: }
2305: for(d=0; d<=dh[mi][i]; d++){
2306: newm=savm;
1.187 brouard 2307: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2308: cov[2]=agexact;
2309: if(nagesqr==1)
2310: cov[3]= agexact*agexact;
1.126 brouard 2311: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2312: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2313: }
2314: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2315: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2316: savm=oldm;
2317: oldm=newm;
2318: } /* end mult */
2319:
2320: s1=s[mw[mi][i]][i];
2321: s2=s[mw[mi+1][i]][i];
2322: bbh=(double)bh[mi][i]/(double)stepm;
2323: 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 */
2324: ipmx +=1;
2325: sw += weight[i];
2326: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2327: } /* end of wave */
2328: } /* end of individual */
2329: } else if(mle==3){ /* exponential inter-extrapolation */
2330: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2331: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2332: for(mi=1; mi<= wav[i]-1; mi++){
2333: for (ii=1;ii<=nlstate+ndeath;ii++)
2334: for (j=1;j<=nlstate+ndeath;j++){
2335: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2336: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2337: }
2338: for(d=0; d<dh[mi][i]; d++){
2339: newm=savm;
1.187 brouard 2340: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2341: cov[2]=agexact;
2342: if(nagesqr==1)
2343: cov[3]= agexact*agexact;
1.126 brouard 2344: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2345: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2346: }
2347: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2348: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2349: savm=oldm;
2350: oldm=newm;
2351: } /* end mult */
2352:
2353: s1=s[mw[mi][i]][i];
2354: s2=s[mw[mi+1][i]][i];
2355: bbh=(double)bh[mi][i]/(double)stepm;
2356: 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 */
2357: ipmx +=1;
2358: sw += weight[i];
2359: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2360: } /* end of wave */
2361: } /* end of individual */
2362: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2363: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2364: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2365: for(mi=1; mi<= wav[i]-1; mi++){
2366: for (ii=1;ii<=nlstate+ndeath;ii++)
2367: for (j=1;j<=nlstate+ndeath;j++){
2368: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2369: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2370: }
2371: for(d=0; d<dh[mi][i]; d++){
2372: newm=savm;
1.187 brouard 2373: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2374: cov[2]=agexact;
2375: if(nagesqr==1)
2376: cov[3]= agexact*agexact;
1.126 brouard 2377: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2378: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2379: }
2380:
2381: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2382: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2383: savm=oldm;
2384: oldm=newm;
2385: } /* end mult */
2386:
2387: s1=s[mw[mi][i]][i];
2388: s2=s[mw[mi+1][i]][i];
2389: if( s2 > nlstate){
2390: lli=log(out[s1][s2] - savm[s1][s2]);
2391: }else{
2392: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2393: }
2394: ipmx +=1;
2395: sw += weight[i];
2396: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2397: /* 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]); */
2398: } /* end of wave */
2399: } /* end of individual */
2400: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2401: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2402: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2403: for(mi=1; mi<= wav[i]-1; mi++){
2404: for (ii=1;ii<=nlstate+ndeath;ii++)
2405: for (j=1;j<=nlstate+ndeath;j++){
2406: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2407: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2408: }
2409: for(d=0; d<dh[mi][i]; d++){
2410: newm=savm;
1.187 brouard 2411: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2412: cov[2]=agexact;
2413: if(nagesqr==1)
2414: cov[3]= agexact*agexact;
1.126 brouard 2415: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2416: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2417: }
2418:
2419: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2420: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2421: savm=oldm;
2422: oldm=newm;
2423: } /* end mult */
2424:
2425: s1=s[mw[mi][i]][i];
2426: s2=s[mw[mi+1][i]][i];
2427: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2428: ipmx +=1;
2429: sw += weight[i];
2430: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2431: /*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]);*/
2432: } /* end of wave */
2433: } /* end of individual */
2434: } /* End of if */
2435: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2436: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2437: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2438: return -l;
2439: }
2440:
2441: /*************** log-likelihood *************/
2442: double funcone( double *x)
2443: {
2444: /* Same as likeli but slower because of a lot of printf and if */
2445: int i, ii, j, k, mi, d, kk;
1.131 brouard 2446: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2447: double **out;
2448: double lli; /* Individual log likelihood */
2449: double llt;
2450: int s1, s2;
2451: double bbh, survp;
1.187 brouard 2452: double agexact;
1.126 brouard 2453: /*extern weight */
2454: /* We are differentiating ll according to initial status */
2455: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2456: /*for(i=1;i<imx;i++)
2457: printf(" %d\n",s[4][i]);
2458: */
2459: cov[1]=1.;
2460:
2461: for(k=1; k<=nlstate; k++) ll[k]=0.;
2462:
2463: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2464: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2465: for(mi=1; mi<= wav[i]-1; mi++){
2466: for (ii=1;ii<=nlstate+ndeath;ii++)
2467: for (j=1;j<=nlstate+ndeath;j++){
2468: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2469: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2470: }
2471: for(d=0; d<dh[mi][i]; d++){
2472: newm=savm;
1.187 brouard 2473: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2474: cov[2]=agexact;
2475: if(nagesqr==1)
2476: cov[3]= agexact*agexact;
1.126 brouard 2477: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2478: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2479: }
1.187 brouard 2480:
1.145 brouard 2481: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2482: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2483: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2484: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2485: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2486: savm=oldm;
2487: oldm=newm;
2488: } /* end mult */
2489:
2490: s1=s[mw[mi][i]][i];
2491: s2=s[mw[mi+1][i]][i];
2492: bbh=(double)bh[mi][i]/(double)stepm;
2493: /* bias is positive if real duration
2494: * is higher than the multiple of stepm and negative otherwise.
2495: */
2496: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2497: lli=log(out[s1][s2] - savm[s1][s2]);
2498: } else if (s2==-2) {
2499: for (j=1,survp=0. ; j<=nlstate; j++)
2500: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2501: lli= log(survp);
2502: }else if (mle==1){
2503: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2504: } else if(mle==2){
2505: 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 */
2506: } else if(mle==3){ /* exponential inter-extrapolation */
2507: 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 */
2508: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2509: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2510: } else{ /* mle=0 back to 1 */
2511: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2512: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2513: } /* End of if */
2514: ipmx +=1;
2515: sw += weight[i];
2516: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2517: /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
1.126 brouard 2518: if(globpr){
1.141 brouard 2519: fprintf(ficresilk,"%9ld %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
1.126 brouard 2520: %11.6f %11.6f %11.6f ", \
2521: num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2522: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2523: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2524: llt +=ll[k]*gipmx/gsw;
2525: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2526: }
2527: fprintf(ficresilk," %10.6f\n", -llt);
2528: }
2529: } /* end of wave */
2530: } /* end of individual */
2531: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2532: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2533: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2534: if(globpr==0){ /* First time we count the contributions and weights */
2535: gipmx=ipmx;
2536: gsw=sw;
2537: }
2538: return -l;
2539: }
2540:
2541:
2542: /*************** function likelione ***********/
2543: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2544: {
2545: /* This routine should help understanding what is done with
2546: the selection of individuals/waves and
2547: to check the exact contribution to the likelihood.
2548: Plotting could be done.
2549: */
2550: int k;
2551:
2552: if(*globpri !=0){ /* Just counts and sums, no printings */
2553: strcpy(fileresilk,"ilk");
2554: strcat(fileresilk,fileres);
2555: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2556: printf("Problem with resultfile: %s\n", fileresilk);
2557: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2558: }
2559: 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");
2560: fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
2561: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2562: for(k=1; k<=nlstate; k++)
2563: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2564: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2565: }
2566:
2567: *fretone=(*funcone)(p);
2568: if(*globpri !=0){
2569: fclose(ficresilk);
2570: fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
2571: fflush(fichtm);
2572: }
2573: return;
2574: }
2575:
2576:
2577: /*********** Maximum Likelihood Estimation ***************/
2578:
2579: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2580: {
1.165 brouard 2581: int i,j, iter=0;
1.126 brouard 2582: double **xi;
2583: double fret;
2584: double fretone; /* Only one call to likelihood */
2585: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2586:
2587: #ifdef NLOPT
2588: int creturn;
2589: nlopt_opt opt;
2590: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2591: double *lb;
2592: double minf; /* the minimum objective value, upon return */
2593: double * p1; /* Shifted parameters from 0 instead of 1 */
2594: myfunc_data dinst, *d = &dinst;
2595: #endif
2596:
2597:
1.126 brouard 2598: xi=matrix(1,npar,1,npar);
2599: for (i=1;i<=npar;i++)
2600: for (j=1;j<=npar;j++)
2601: xi[i][j]=(i==j ? 1.0 : 0.0);
2602: printf("Powell\n"); fprintf(ficlog,"Powell\n");
2603: strcpy(filerespow,"pow");
2604: strcat(filerespow,fileres);
2605: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2606: printf("Problem with resultfile: %s\n", filerespow);
2607: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2608: }
2609: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2610: for (i=1;i<=nlstate;i++)
2611: for(j=1;j<=nlstate+ndeath;j++)
2612: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2613: fprintf(ficrespow,"\n");
1.162 brouard 2614: #ifdef POWELL
1.126 brouard 2615: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2616: #endif
1.126 brouard 2617:
1.162 brouard 2618: #ifdef NLOPT
2619: #ifdef NEWUOA
2620: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2621: #else
2622: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2623: #endif
2624: lb=vector(0,npar-1);
2625: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2626: nlopt_set_lower_bounds(opt, lb);
2627: nlopt_set_initial_step1(opt, 0.1);
2628:
2629: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2630: d->function = func;
2631: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2632: nlopt_set_min_objective(opt, myfunc, d);
2633: nlopt_set_xtol_rel(opt, ftol);
2634: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2635: printf("nlopt failed! %d\n",creturn);
2636: }
2637: else {
2638: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2639: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2640: iter=1; /* not equal */
2641: }
2642: nlopt_destroy(opt);
2643: #endif
1.126 brouard 2644: free_matrix(xi,1,npar,1,npar);
2645: fclose(ficrespow);
1.180 brouard 2646: printf("#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2647: fprintf(ficlog,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2648: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2649:
2650: }
2651:
2652: /**** Computes Hessian and covariance matrix ***/
2653: void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
2654: {
2655: double **a,**y,*x,pd;
2656: double **hess;
1.164 brouard 2657: int i, j;
1.126 brouard 2658: int *indx;
2659:
2660: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
2661: double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
2662: void lubksb(double **a, int npar, int *indx, double b[]) ;
2663: void ludcmp(double **a, int npar, int *indx, double *d) ;
2664: double gompertz(double p[]);
2665: hess=matrix(1,npar,1,npar);
2666:
2667: printf("\nCalculation of the hessian matrix. Wait...\n");
2668: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2669: for (i=1;i<=npar;i++){
2670: printf("%d",i);fflush(stdout);
2671: fprintf(ficlog,"%d",i);fflush(ficlog);
2672:
2673: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2674:
2675: /* printf(" %f ",p[i]);
2676: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2677: }
2678:
2679: for (i=1;i<=npar;i++) {
2680: for (j=1;j<=npar;j++) {
2681: if (j>i) {
2682: printf(".%d%d",i,j);fflush(stdout);
2683: fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
2684: hess[i][j]=hessij(p,delti,i,j,func,npar);
2685:
2686: hess[j][i]=hess[i][j];
2687: /*printf(" %lf ",hess[i][j]);*/
2688: }
2689: }
2690: }
2691: printf("\n");
2692: fprintf(ficlog,"\n");
2693:
2694: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2695: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2696:
2697: a=matrix(1,npar,1,npar);
2698: y=matrix(1,npar,1,npar);
2699: x=vector(1,npar);
2700: indx=ivector(1,npar);
2701: for (i=1;i<=npar;i++)
2702: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2703: ludcmp(a,npar,indx,&pd);
2704:
2705: for (j=1;j<=npar;j++) {
2706: for (i=1;i<=npar;i++) x[i]=0;
2707: x[j]=1;
2708: lubksb(a,npar,indx,x);
2709: for (i=1;i<=npar;i++){
2710: matcov[i][j]=x[i];
2711: }
2712: }
2713:
2714: printf("\n#Hessian matrix#\n");
2715: fprintf(ficlog,"\n#Hessian matrix#\n");
2716: for (i=1;i<=npar;i++) {
2717: for (j=1;j<=npar;j++) {
2718: printf("%.3e ",hess[i][j]);
2719: fprintf(ficlog,"%.3e ",hess[i][j]);
2720: }
2721: printf("\n");
2722: fprintf(ficlog,"\n");
2723: }
2724:
2725: /* Recompute Inverse */
2726: for (i=1;i<=npar;i++)
2727: for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
2728: ludcmp(a,npar,indx,&pd);
2729:
2730: /* printf("\n#Hessian matrix recomputed#\n");
2731:
2732: for (j=1;j<=npar;j++) {
2733: for (i=1;i<=npar;i++) x[i]=0;
2734: x[j]=1;
2735: lubksb(a,npar,indx,x);
2736: for (i=1;i<=npar;i++){
2737: y[i][j]=x[i];
2738: printf("%.3e ",y[i][j]);
2739: fprintf(ficlog,"%.3e ",y[i][j]);
2740: }
2741: printf("\n");
2742: fprintf(ficlog,"\n");
2743: }
2744: */
2745:
2746: free_matrix(a,1,npar,1,npar);
2747: free_matrix(y,1,npar,1,npar);
2748: free_vector(x,1,npar);
2749: free_ivector(indx,1,npar);
2750: free_matrix(hess,1,npar,1,npar);
2751:
2752:
2753: }
2754:
2755: /*************** hessian matrix ****************/
2756: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
2757: {
2758: int i;
2759: int l=1, lmax=20;
2760: double k1,k2;
1.132 brouard 2761: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2762: double res;
2763: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2764: double fx;
2765: int k=0,kmax=10;
2766: double l1;
2767:
2768: fx=func(x);
2769: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2770: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2771: l1=pow(10,l);
2772: delts=delt;
2773: for(k=1 ; k <kmax; k=k+1){
2774: delt = delta*(l1*k);
2775: p2[theta]=x[theta] +delt;
1.145 brouard 2776: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2777: p2[theta]=x[theta]-delt;
2778: k2=func(p2)-fx;
2779: /*res= (k1-2.0*fx+k2)/delt/delt; */
2780: res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
2781:
1.132 brouard 2782: #ifdef DEBUGHESS
1.126 brouard 2783: 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);
2784: 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);
2785: #endif
2786: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2787: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2788: k=kmax;
2789: }
2790: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2791: k=kmax; l=lmax*10;
1.126 brouard 2792: }
2793: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2794: delts=delt;
2795: }
2796: }
2797: }
2798: delti[theta]=delts;
2799: return res;
2800:
2801: }
2802:
2803: double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
2804: {
2805: int i;
1.164 brouard 2806: int l=1, lmax=20;
1.126 brouard 2807: double k1,k2,k3,k4,res,fx;
1.132 brouard 2808: double p2[MAXPARM+1];
1.126 brouard 2809: int k;
2810:
2811: fx=func(x);
2812: for (k=1; k<=2; k++) {
2813: for (i=1;i<=npar;i++) p2[i]=x[i];
2814: p2[thetai]=x[thetai]+delti[thetai]/k;
2815: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2816: k1=func(p2)-fx;
2817:
2818: p2[thetai]=x[thetai]+delti[thetai]/k;
2819: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2820: k2=func(p2)-fx;
2821:
2822: p2[thetai]=x[thetai]-delti[thetai]/k;
2823: p2[thetaj]=x[thetaj]+delti[thetaj]/k;
2824: k3=func(p2)-fx;
2825:
2826: p2[thetai]=x[thetai]-delti[thetai]/k;
2827: p2[thetaj]=x[thetaj]-delti[thetaj]/k;
2828: k4=func(p2)-fx;
2829: res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
2830: #ifdef DEBUG
2831: 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);
2832: 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);
2833: #endif
2834: }
2835: return res;
2836: }
2837:
2838: /************** Inverse of matrix **************/
2839: void ludcmp(double **a, int n, int *indx, double *d)
2840: {
2841: int i,imax,j,k;
2842: double big,dum,sum,temp;
2843: double *vv;
2844:
2845: vv=vector(1,n);
2846: *d=1.0;
2847: for (i=1;i<=n;i++) {
2848: big=0.0;
2849: for (j=1;j<=n;j++)
2850: if ((temp=fabs(a[i][j])) > big) big=temp;
2851: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
2852: vv[i]=1.0/big;
2853: }
2854: for (j=1;j<=n;j++) {
2855: for (i=1;i<j;i++) {
2856: sum=a[i][j];
2857: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
2858: a[i][j]=sum;
2859: }
2860: big=0.0;
2861: for (i=j;i<=n;i++) {
2862: sum=a[i][j];
2863: for (k=1;k<j;k++)
2864: sum -= a[i][k]*a[k][j];
2865: a[i][j]=sum;
2866: if ( (dum=vv[i]*fabs(sum)) >= big) {
2867: big=dum;
2868: imax=i;
2869: }
2870: }
2871: if (j != imax) {
2872: for (k=1;k<=n;k++) {
2873: dum=a[imax][k];
2874: a[imax][k]=a[j][k];
2875: a[j][k]=dum;
2876: }
2877: *d = -(*d);
2878: vv[imax]=vv[j];
2879: }
2880: indx[j]=imax;
2881: if (a[j][j] == 0.0) a[j][j]=TINY;
2882: if (j != n) {
2883: dum=1.0/(a[j][j]);
2884: for (i=j+1;i<=n;i++) a[i][j] *= dum;
2885: }
2886: }
2887: free_vector(vv,1,n); /* Doesn't work */
2888: ;
2889: }
2890:
2891: void lubksb(double **a, int n, int *indx, double b[])
2892: {
2893: int i,ii=0,ip,j;
2894: double sum;
2895:
2896: for (i=1;i<=n;i++) {
2897: ip=indx[i];
2898: sum=b[ip];
2899: b[ip]=b[i];
2900: if (ii)
2901: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
2902: else if (sum) ii=i;
2903: b[i]=sum;
2904: }
2905: for (i=n;i>=1;i--) {
2906: sum=b[i];
2907: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
2908: b[i]=sum/a[i][i];
2909: }
2910: }
2911:
2912: void pstamp(FILE *fichier)
2913: {
1.196 brouard 2914: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 2915: }
2916:
2917: /************ Frequencies ********************/
2918: 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[])
2919: { /* Some frequencies */
2920:
1.164 brouard 2921: int i, m, jk, j1, bool, z1,j;
1.126 brouard 2922: int first;
2923: double ***freq; /* Frequencies */
2924: double *pp, **prop;
2925: double pos,posprop, k2, dateintsum=0,k2cpt=0;
2926: char fileresp[FILENAMELENGTH];
2927:
2928: pp=vector(1,nlstate);
2929: prop=matrix(1,nlstate,iagemin,iagemax+3);
2930: strcpy(fileresp,"p");
2931: strcat(fileresp,fileres);
2932: if((ficresp=fopen(fileresp,"w"))==NULL) {
2933: printf("Problem with prevalence resultfile: %s\n", fileresp);
2934: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
2935: exit(0);
2936: }
2937: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
2938: j1=0;
2939:
2940: j=cptcoveff;
2941: if (cptcovn<1) {j=1;ncodemax[1]=1;}
2942:
2943: first=1;
2944:
1.169 brouard 2945: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
2946: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
2947: /* j1++; */
1.145 brouard 2948: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 2949: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
2950: scanf("%d", i);*/
2951: for (i=-5; i<=nlstate+ndeath; i++)
2952: for (jk=-5; jk<=nlstate+ndeath; jk++)
2953: for(m=iagemin; m <= iagemax+3; m++)
2954: freq[i][jk][m]=0;
1.143 brouard 2955:
2956: for (i=1; i<=nlstate; i++)
2957: for(m=iagemin; m <= iagemax+3; m++)
2958: prop[i][m]=0;
1.126 brouard 2959:
2960: dateintsum=0;
2961: k2cpt=0;
2962: for (i=1; i<=imx; i++) {
2963: bool=1;
1.144 brouard 2964: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
2965: for (z1=1; z1<=cptcoveff; z1++)
2966: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]){
1.145 brouard 2967: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 2968: bool=0;
1.145 brouard 2969: /* 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",
2970: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtab[j1][z1],
2971: j1,z1,nbcode[Tvaraff[z1]][codtab[j1][z1]],j1);*/
1.144 brouard 2972: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtab[7][3]=1 and nbcde[3][?]=1*/
2973: }
1.126 brouard 2974: }
1.144 brouard 2975:
1.126 brouard 2976: if (bool==1){
2977: for(m=firstpass; m<=lastpass; m++){
2978: k2=anint[m][i]+(mint[m][i]/12.);
2979: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
2980: if(agev[m][i]==0) agev[m][i]=iagemax+1;
2981: if(agev[m][i]==1) agev[m][i]=iagemax+2;
2982: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
2983: if (m<lastpass) {
2984: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
2985: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
2986: }
2987:
2988: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
2989: dateintsum=dateintsum+k2;
2990: k2cpt++;
2991: }
2992: /*}*/
2993: }
2994: }
1.145 brouard 2995: } /* end i */
1.126 brouard 2996:
2997: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
2998: pstamp(ficresp);
2999: if (cptcovn>0) {
3000: fprintf(ficresp, "\n#********** Variable ");
3001: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3002: fprintf(ficresp, "**********\n#");
1.143 brouard 3003: fprintf(ficlog, "\n#********** Variable ");
3004: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
3005: fprintf(ficlog, "**********\n#");
1.126 brouard 3006: }
3007: for(i=1; i<=nlstate;i++)
3008: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3009: fprintf(ficresp, "\n");
3010:
3011: for(i=iagemin; i <= iagemax+3; i++){
3012: if(i==iagemax+3){
3013: fprintf(ficlog,"Total");
3014: }else{
3015: if(first==1){
3016: first=0;
3017: printf("See log file for details...\n");
3018: }
3019: fprintf(ficlog,"Age %d", i);
3020: }
3021: for(jk=1; jk <=nlstate ; jk++){
3022: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3023: pp[jk] += freq[jk][m][i];
3024: }
3025: for(jk=1; jk <=nlstate ; jk++){
3026: for(m=-1, pos=0; m <=0 ; m++)
3027: pos += freq[jk][m][i];
3028: if(pp[jk]>=1.e-10){
3029: if(first==1){
1.132 brouard 3030: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3031: }
3032: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3033: }else{
3034: if(first==1)
3035: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3036: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3037: }
3038: }
3039:
3040: for(jk=1; jk <=nlstate ; jk++){
3041: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3042: pp[jk] += freq[jk][m][i];
3043: }
3044: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3045: pos += pp[jk];
3046: posprop += prop[jk][i];
3047: }
3048: for(jk=1; jk <=nlstate ; jk++){
3049: if(pos>=1.e-5){
3050: if(first==1)
3051: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3052: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3053: }else{
3054: if(first==1)
3055: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3056: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3057: }
3058: if( i <= iagemax){
3059: if(pos>=1.e-5){
3060: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3061: /*probs[i][jk][j1]= pp[jk]/pos;*/
3062: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3063: }
3064: else
3065: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3066: }
3067: }
3068:
3069: for(jk=-1; jk <=nlstate+ndeath; jk++)
3070: for(m=-1; m <=nlstate+ndeath; m++)
3071: if(freq[jk][m][i] !=0 ) {
3072: if(first==1)
3073: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3074: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3075: }
3076: if(i <= iagemax)
3077: fprintf(ficresp,"\n");
3078: if(first==1)
3079: printf("Others in log...\n");
3080: fprintf(ficlog,"\n");
3081: }
1.145 brouard 3082: /*}*/
1.126 brouard 3083: }
3084: dateintmean=dateintsum/k2cpt;
3085:
3086: fclose(ficresp);
3087: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3088: free_vector(pp,1,nlstate);
3089: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3090: /* End of Freq */
3091: }
3092:
3093: /************ Prevalence ********************/
3094: 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)
3095: {
3096: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3097: in each health status at the date of interview (if between dateprev1 and dateprev2).
3098: We still use firstpass and lastpass as another selection.
3099: */
3100:
1.164 brouard 3101: int i, m, jk, j1, bool, z1,j;
3102:
3103: double **prop;
3104: double posprop;
1.126 brouard 3105: double y2; /* in fractional years */
3106: int iagemin, iagemax;
1.145 brouard 3107: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3108:
3109: iagemin= (int) agemin;
3110: iagemax= (int) agemax;
3111: /*pp=vector(1,nlstate);*/
3112: prop=matrix(1,nlstate,iagemin,iagemax+3);
3113: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3114: j1=0;
3115:
1.145 brouard 3116: /*j=cptcoveff;*/
1.126 brouard 3117: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3118:
1.145 brouard 3119: first=1;
3120: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3121: /*for(i1=1; i1<=ncodemax[k1];i1++){
3122: j1++;*/
1.126 brouard 3123:
3124: for (i=1; i<=nlstate; i++)
3125: for(m=iagemin; m <= iagemax+3; m++)
3126: prop[i][m]=0.0;
3127:
3128: for (i=1; i<=imx; i++) { /* Each individual */
3129: bool=1;
3130: if (cptcovn>0) {
3131: for (z1=1; z1<=cptcoveff; z1++)
3132: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
3133: bool=0;
3134: }
3135: if (bool==1) {
3136: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3137: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3138: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3139: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3140: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3141: 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);
3142: if (s[m][i]>0 && s[m][i]<=nlstate) {
3143: /*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]]);*/
3144: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3145: prop[s[m][i]][iagemax+3] += weight[i];
3146: }
3147: }
3148: } /* end selection of waves */
3149: }
3150: }
3151: for(i=iagemin; i <= iagemax+3; i++){
3152: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3153: posprop += prop[jk][i];
3154: }
1.145 brouard 3155:
1.126 brouard 3156: for(jk=1; jk <=nlstate ; jk++){
3157: if( i <= iagemax){
3158: if(posprop>=1.e-5){
3159: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3160: } else{
3161: if(first==1){
3162: first=0;
3163: 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]);
3164: }
3165: }
1.126 brouard 3166: }
3167: }/* end jk */
3168: }/* end i */
1.145 brouard 3169: /*} *//* end i1 */
3170: } /* end j1 */
1.126 brouard 3171:
3172: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3173: /*free_vector(pp,1,nlstate);*/
3174: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3175: } /* End of prevalence */
3176:
3177: /************* Waves Concatenation ***************/
3178:
3179: 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)
3180: {
3181: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3182: Death is a valid wave (if date is known).
3183: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3184: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3185: and mw[mi+1][i]. dh depends on stepm.
3186: */
3187:
3188: int i, mi, m;
3189: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3190: double sum=0., jmean=0.;*/
3191: int first;
3192: int j, k=0,jk, ju, jl;
3193: double sum=0.;
3194: first=0;
1.164 brouard 3195: jmin=100000;
1.126 brouard 3196: jmax=-1;
3197: jmean=0.;
3198: for(i=1; i<=imx; i++){
3199: mi=0;
3200: m=firstpass;
3201: while(s[m][i] <= nlstate){
3202: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3203: mw[++mi][i]=m;
3204: if(m >=lastpass)
3205: break;
3206: else
3207: m++;
3208: }/* end while */
3209: if (s[m][i] > nlstate){
3210: mi++; /* Death is another wave */
3211: /* if(mi==0) never been interviewed correctly before death */
3212: /* Only death is a correct wave */
3213: mw[mi][i]=m;
3214: }
3215:
3216: wav[i]=mi;
3217: if(mi==0){
3218: nbwarn++;
3219: if(first==0){
3220: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3221: first=1;
3222: }
3223: if(first==1){
3224: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3225: }
3226: } /* end mi==0 */
3227: } /* End individuals */
3228:
3229: for(i=1; i<=imx; i++){
3230: for(mi=1; mi<wav[i];mi++){
3231: if (stepm <=0)
3232: dh[mi][i]=1;
3233: else{
3234: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3235: if (agedc[i] < 2*AGESUP) {
3236: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3237: if(j==0) j=1; /* Survives at least one month after exam */
3238: else if(j<0){
3239: nberr++;
3240: 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]);
3241: j=1; /* Temporary Dangerous patch */
3242: 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);
3243: 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]);
3244: 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);
3245: }
3246: k=k+1;
3247: if (j >= jmax){
3248: jmax=j;
3249: ijmax=i;
3250: }
3251: if (j <= jmin){
3252: jmin=j;
3253: ijmin=i;
3254: }
3255: sum=sum+j;
3256: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3257: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3258: }
3259: }
3260: else{
3261: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3262: /* 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]); */
3263:
3264: k=k+1;
3265: if (j >= jmax) {
3266: jmax=j;
3267: ijmax=i;
3268: }
3269: else if (j <= jmin){
3270: jmin=j;
3271: ijmin=i;
3272: }
3273: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3274: /*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]);*/
3275: if(j<0){
3276: nberr++;
3277: 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]);
3278: 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]);
3279: }
3280: sum=sum+j;
3281: }
3282: jk= j/stepm;
3283: jl= j -jk*stepm;
3284: ju= j -(jk+1)*stepm;
3285: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3286: if(jl==0){
3287: dh[mi][i]=jk;
3288: bh[mi][i]=0;
3289: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3290: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3291: dh[mi][i]=jk+1;
3292: bh[mi][i]=ju;
3293: }
3294: }else{
3295: if(jl <= -ju){
3296: dh[mi][i]=jk;
3297: bh[mi][i]=jl; /* bias is positive if real duration
3298: * is higher than the multiple of stepm and negative otherwise.
3299: */
3300: }
3301: else{
3302: dh[mi][i]=jk+1;
3303: bh[mi][i]=ju;
3304: }
3305: if(dh[mi][i]==0){
3306: dh[mi][i]=1; /* At least one step */
3307: bh[mi][i]=ju; /* At least one step */
3308: /* 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);*/
3309: }
3310: } /* end if mle */
3311: }
3312: } /* end wave */
3313: }
3314: jmean=sum/k;
3315: printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
1.141 brouard 3316: fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %d) Max=%d (%d) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
1.126 brouard 3317: }
3318:
3319: /*********** Tricode ****************************/
1.145 brouard 3320: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3321: {
1.144 brouard 3322: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3323: /* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
1.169 brouard 3324: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3325: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3326: * nbcode[Tvar[j]][1]=
1.144 brouard 3327: */
1.130 brouard 3328:
1.145 brouard 3329: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3330: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3331: int cptcode=0; /* Modality max of covariates j */
3332: int modmincovj=0; /* Modality min of covariates j */
3333:
3334:
1.126 brouard 3335: cptcoveff=0;
3336:
1.144 brouard 3337: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3338:
1.145 brouard 3339: /* Loop on covariates without age and products */
1.186 brouard 3340: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3341: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3342: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3343: modality of this covariate Vj*/
1.145 brouard 3344: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3345: * If product of Vn*Vm, still boolean *:
3346: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3347: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3348: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3349: modality of the nth covariate of individual i. */
1.145 brouard 3350: if (ij > modmaxcovj)
3351: modmaxcovj=ij;
3352: else if (ij < modmincovj)
3353: modmincovj=ij;
3354: if ((ij < -1) && (ij > NCOVMAX)){
3355: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3356: exit(1);
3357: }else
1.136 brouard 3358: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3359: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3360: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3361: /* getting the maximum value of the modality of the covariate
3362: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3363: female is 1, then modmaxcovj=1.*/
1.192 brouard 3364: } /* end for loop on individuals i */
1.145 brouard 3365: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3366: fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.145 brouard 3367: cptcode=modmaxcovj;
1.137 brouard 3368: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3369: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3370: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3371: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3372: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3373: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3374: if( k != -1){
3375: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3376: covariate for which somebody answered excluding
3377: undefined. Usually 2: 0 and 1. */
3378: }
3379: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3380: covariate for which somebody answered including
3381: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3382: }
3383: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3384: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3385: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3386:
1.136 brouard 3387: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3388: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3389: If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125;
1.145 brouard 3390: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3391: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3392: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3393: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3394: nbcode[Tvar[j]][ij]=k;
3395: nbcode[Tvar[j]][1]=0;
3396: nbcode[Tvar[j]][2]=1;
3397: nbcode[Tvar[j]][3]=2;
1.197 ! brouard 3398: To be continued (not working yet).
1.145 brouard 3399: */
1.197 ! brouard 3400: ij=0; /* ij is similar to i but can jump over null modalities */
! 3401: for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
! 3402: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3403: break;
3404: }
3405: ij++;
1.197 ! brouard 3406: nbcode[Tvar[j]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality.*/
1.192 brouard 3407: cptcode = ij; /* New max modality for covar j */
3408: } /* end of loop on modality i=-1 to 1 or more */
3409:
3410: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3411: /* /\*recode from 0 *\/ */
3412: /* k is a modality. If we have model=V1+V1*sex */
3413: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3414: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3415: /* } */
3416: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3417: /* if (ij > ncodemax[j]) { */
3418: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3419: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3420: /* break; */
3421: /* } */
3422: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3423: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3424:
1.145 brouard 3425: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3426:
1.187 brouard 3427: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3428: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3429: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3430: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3431: }
1.126 brouard 3432:
1.192 brouard 3433: ij=0;
1.145 brouard 3434: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3435: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3436: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3437: ij++;
1.145 brouard 3438: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3439: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3440: }else{
3441: /* Tvaraff[ij]=0; */
3442: }
1.126 brouard 3443: }
1.192 brouard 3444: /* ij--; */
1.144 brouard 3445: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3446:
1.126 brouard 3447: }
3448:
1.145 brouard 3449:
1.126 brouard 3450: /*********** Health Expectancies ****************/
3451:
1.127 brouard 3452: void evsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
1.126 brouard 3453:
3454: {
3455: /* Health expectancies, no variances */
1.164 brouard 3456: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3457: int nhstepma, nstepma; /* Decreasing with age */
3458: double age, agelim, hf;
3459: double ***p3mat;
3460: double eip;
3461:
3462: pstamp(ficreseij);
3463: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3464: fprintf(ficreseij,"# Age");
3465: for(i=1; i<=nlstate;i++){
3466: for(j=1; j<=nlstate;j++){
3467: fprintf(ficreseij," e%1d%1d ",i,j);
3468: }
3469: fprintf(ficreseij," e%1d. ",i);
3470: }
3471: fprintf(ficreseij,"\n");
3472:
3473:
3474: if(estepm < stepm){
3475: printf ("Problem %d lower than %d\n",estepm, stepm);
3476: }
3477: else hstepm=estepm;
3478: /* We compute the life expectancy from trapezoids spaced every estepm months
3479: * This is mainly to measure the difference between two models: for example
3480: * if stepm=24 months pijx are given only every 2 years and by summing them
3481: * we are calculating an estimate of the Life Expectancy assuming a linear
3482: * progression in between and thus overestimating or underestimating according
3483: * to the curvature of the survival function. If, for the same date, we
3484: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3485: * to compare the new estimate of Life expectancy with the same linear
3486: * hypothesis. A more precise result, taking into account a more precise
3487: * curvature will be obtained if estepm is as small as stepm. */
3488:
3489: /* For example we decided to compute the life expectancy with the smallest unit */
3490: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3491: nhstepm is the number of hstepm from age to agelim
3492: nstepm is the number of stepm from age to agelin.
3493: Look at hpijx to understand the reason of that which relies in memory size
3494: and note for a fixed period like estepm months */
3495: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3496: survival function given by stepm (the optimization length). Unfortunately it
3497: means that if the survival funtion is printed only each two years of age and if
3498: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3499: results. So we changed our mind and took the option of the best precision.
3500: */
3501: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3502:
3503: agelim=AGESUP;
3504: /* If stepm=6 months */
3505: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3506: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3507:
3508: /* nhstepm age range expressed in number of stepm */
3509: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3510: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3511: /* if (stepm >= YEARM) hstepm=1;*/
3512: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3513: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3514:
3515: for (age=bage; age<=fage; age ++){
3516: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3517: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3518: /* if (stepm >= YEARM) hstepm=1;*/
3519: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3520:
3521: /* If stepm=6 months */
3522: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3523: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3524:
3525: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3526:
3527: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3528:
3529: printf("%d|",(int)age);fflush(stdout);
3530: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3531:
3532: /* Computing expectancies */
3533: for(i=1; i<=nlstate;i++)
3534: for(j=1; j<=nlstate;j++)
3535: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3536: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3537:
3538: /* 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]);*/
3539:
3540: }
3541:
3542: fprintf(ficreseij,"%3.0f",age );
3543: for(i=1; i<=nlstate;i++){
3544: eip=0;
3545: for(j=1; j<=nlstate;j++){
3546: eip +=eij[i][j][(int)age];
3547: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3548: }
3549: fprintf(ficreseij,"%9.4f", eip );
3550: }
3551: fprintf(ficreseij,"\n");
3552:
3553: }
3554: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3555: printf("\n");
3556: fprintf(ficlog,"\n");
3557:
3558: }
3559:
1.127 brouard 3560: void cvevsij(double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
1.126 brouard 3561:
3562: {
3563: /* Covariances of health expectancies eij and of total life expectancies according
3564: to initial status i, ei. .
3565: */
3566: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3567: int nhstepma, nstepma; /* Decreasing with age */
3568: double age, agelim, hf;
3569: double ***p3matp, ***p3matm, ***varhe;
3570: double **dnewm,**doldm;
3571: double *xp, *xm;
3572: double **gp, **gm;
3573: double ***gradg, ***trgradg;
3574: int theta;
3575:
3576: double eip, vip;
3577:
3578: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3579: xp=vector(1,npar);
3580: xm=vector(1,npar);
3581: dnewm=matrix(1,nlstate*nlstate,1,npar);
3582: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3583:
3584: pstamp(ficresstdeij);
3585: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3586: fprintf(ficresstdeij,"# Age");
3587: for(i=1; i<=nlstate;i++){
3588: for(j=1; j<=nlstate;j++)
3589: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3590: fprintf(ficresstdeij," e%1d. ",i);
3591: }
3592: fprintf(ficresstdeij,"\n");
3593:
3594: pstamp(ficrescveij);
3595: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3596: fprintf(ficrescveij,"# Age");
3597: for(i=1; i<=nlstate;i++)
3598: for(j=1; j<=nlstate;j++){
3599: cptj= (j-1)*nlstate+i;
3600: for(i2=1; i2<=nlstate;i2++)
3601: for(j2=1; j2<=nlstate;j2++){
3602: cptj2= (j2-1)*nlstate+i2;
3603: if(cptj2 <= cptj)
3604: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3605: }
3606: }
3607: fprintf(ficrescveij,"\n");
3608:
3609: if(estepm < stepm){
3610: printf ("Problem %d lower than %d\n",estepm, stepm);
3611: }
3612: else hstepm=estepm;
3613: /* We compute the life expectancy from trapezoids spaced every estepm months
3614: * This is mainly to measure the difference between two models: for example
3615: * if stepm=24 months pijx are given only every 2 years and by summing them
3616: * we are calculating an estimate of the Life Expectancy assuming a linear
3617: * progression in between and thus overestimating or underestimating according
3618: * to the curvature of the survival function. If, for the same date, we
3619: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3620: * to compare the new estimate of Life expectancy with the same linear
3621: * hypothesis. A more precise result, taking into account a more precise
3622: * curvature will be obtained if estepm is as small as stepm. */
3623:
3624: /* For example we decided to compute the life expectancy with the smallest unit */
3625: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3626: nhstepm is the number of hstepm from age to agelim
3627: nstepm is the number of stepm from age to agelin.
3628: Look at hpijx to understand the reason of that which relies in memory size
3629: and note for a fixed period like estepm months */
3630: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3631: survival function given by stepm (the optimization length). Unfortunately it
3632: means that if the survival funtion is printed only each two years of age and if
3633: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3634: results. So we changed our mind and took the option of the best precision.
3635: */
3636: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3637:
3638: /* If stepm=6 months */
3639: /* nhstepm age range expressed in number of stepm */
3640: agelim=AGESUP;
3641: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3642: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3643: /* if (stepm >= YEARM) hstepm=1;*/
3644: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3645:
3646: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3647: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3648: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3649: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3650: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3651: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3652:
3653: for (age=bage; age<=fage; age ++){
3654: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3655: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3656: /* if (stepm >= YEARM) hstepm=1;*/
3657: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3658:
3659: /* If stepm=6 months */
3660: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3661: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3662:
3663: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3664:
3665: /* Computing Variances of health expectancies */
3666: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3667: decrease memory allocation */
3668: for(theta=1; theta <=npar; theta++){
3669: for(i=1; i<=npar; i++){
3670: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3671: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3672: }
3673: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3674: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3675:
3676: for(j=1; j<= nlstate; j++){
3677: for(i=1; i<=nlstate; i++){
3678: for(h=0; h<=nhstepm-1; h++){
3679: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3680: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3681: }
3682: }
3683: }
3684:
3685: for(ij=1; ij<= nlstate*nlstate; ij++)
3686: for(h=0; h<=nhstepm-1; h++){
3687: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3688: }
3689: }/* End theta */
3690:
3691:
3692: for(h=0; h<=nhstepm-1; h++)
3693: for(j=1; j<=nlstate*nlstate;j++)
3694: for(theta=1; theta <=npar; theta++)
3695: trgradg[h][j][theta]=gradg[h][theta][j];
3696:
3697:
3698: for(ij=1;ij<=nlstate*nlstate;ij++)
3699: for(ji=1;ji<=nlstate*nlstate;ji++)
3700: varhe[ij][ji][(int)age] =0.;
3701:
3702: printf("%d|",(int)age);fflush(stdout);
3703: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3704: for(h=0;h<=nhstepm-1;h++){
3705: for(k=0;k<=nhstepm-1;k++){
3706: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3707: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3708: for(ij=1;ij<=nlstate*nlstate;ij++)
3709: for(ji=1;ji<=nlstate*nlstate;ji++)
3710: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3711: }
3712: }
3713:
3714: /* Computing expectancies */
3715: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3716: for(i=1; i<=nlstate;i++)
3717: for(j=1; j<=nlstate;j++)
3718: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3719: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3720:
3721: /* 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]);*/
3722:
3723: }
3724:
3725: fprintf(ficresstdeij,"%3.0f",age );
3726: for(i=1; i<=nlstate;i++){
3727: eip=0.;
3728: vip=0.;
3729: for(j=1; j<=nlstate;j++){
3730: eip += eij[i][j][(int)age];
3731: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3732: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3733: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3734: }
3735: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3736: }
3737: fprintf(ficresstdeij,"\n");
3738:
3739: fprintf(ficrescveij,"%3.0f",age );
3740: for(i=1; i<=nlstate;i++)
3741: for(j=1; j<=nlstate;j++){
3742: cptj= (j-1)*nlstate+i;
3743: for(i2=1; i2<=nlstate;i2++)
3744: for(j2=1; j2<=nlstate;j2++){
3745: cptj2= (j2-1)*nlstate+i2;
3746: if(cptj2 <= cptj)
3747: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3748: }
3749: }
3750: fprintf(ficrescveij,"\n");
3751:
3752: }
3753: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3754: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3755: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3756: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3757: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3758: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3759: printf("\n");
3760: fprintf(ficlog,"\n");
3761:
3762: free_vector(xm,1,npar);
3763: free_vector(xp,1,npar);
3764: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3765: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3766: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3767: }
3768:
3769: /************ Variance ******************/
3770: 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[])
3771: {
3772: /* Variance of health expectancies */
3773: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3774: /* double **newm;*/
1.169 brouard 3775: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3776:
3777: int movingaverage();
1.126 brouard 3778: double **dnewm,**doldm;
3779: double **dnewmp,**doldmp;
3780: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 3781: int k;
1.126 brouard 3782: double *xp;
3783: double **gp, **gm; /* for var eij */
3784: double ***gradg, ***trgradg; /*for var eij */
3785: double **gradgp, **trgradgp; /* for var p point j */
3786: double *gpp, *gmp; /* for var p point j */
3787: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
3788: double ***p3mat;
3789: double age,agelim, hf;
3790: double ***mobaverage;
3791: int theta;
3792: char digit[4];
3793: char digitp[25];
3794:
3795: char fileresprobmorprev[FILENAMELENGTH];
3796:
3797: if(popbased==1){
3798: if(mobilav!=0)
3799: strcpy(digitp,"-populbased-mobilav-");
3800: else strcpy(digitp,"-populbased-nomobil-");
3801: }
3802: else
3803: strcpy(digitp,"-stablbased-");
3804:
3805: if (mobilav!=0) {
3806: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
3807: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
3808: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
3809: printf(" Error in movingaverage mobilav=%d\n",mobilav);
3810: }
3811: }
3812:
3813: strcpy(fileresprobmorprev,"prmorprev");
3814: sprintf(digit,"%-d",ij);
3815: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
3816: strcat(fileresprobmorprev,digit); /* Tvar to be done */
3817: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
3818: strcat(fileresprobmorprev,fileres);
3819: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
3820: printf("Problem with resultfile: %s\n", fileresprobmorprev);
3821: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
3822: }
3823: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3824:
3825: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
3826: pstamp(ficresprobmorprev);
3827: 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);
3828: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
3829: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
3830: fprintf(ficresprobmorprev," p.%-d SE",j);
3831: for(i=1; i<=nlstate;i++)
3832: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
3833: }
3834: fprintf(ficresprobmorprev,"\n");
3835: fprintf(ficgp,"\n# Routine varevsij");
3836: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
3837: 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");
3838: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
3839: /* } */
3840: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3841: pstamp(ficresvij);
3842: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
3843: if(popbased==1)
1.128 brouard 3844: fprintf(ficresvij,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
1.126 brouard 3845: else
3846: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
3847: fprintf(ficresvij,"# Age");
3848: for(i=1; i<=nlstate;i++)
3849: for(j=1; j<=nlstate;j++)
3850: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
3851: fprintf(ficresvij,"\n");
3852:
3853: xp=vector(1,npar);
3854: dnewm=matrix(1,nlstate,1,npar);
3855: doldm=matrix(1,nlstate,1,nlstate);
3856: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
3857: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
3858:
3859: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
3860: gpp=vector(nlstate+1,nlstate+ndeath);
3861: gmp=vector(nlstate+1,nlstate+ndeath);
3862: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
3863:
3864: if(estepm < stepm){
3865: printf ("Problem %d lower than %d\n",estepm, stepm);
3866: }
3867: else hstepm=estepm;
3868: /* For example we decided to compute the life expectancy with the smallest unit */
3869: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3870: nhstepm is the number of hstepm from age to agelim
3871: nstepm is the number of stepm from age to agelin.
1.128 brouard 3872: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 3873: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3874: survival function given by stepm (the optimization length). Unfortunately it
3875: means that if the survival funtion is printed every two years of age and if
3876: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3877: results. So we changed our mind and took the option of the best precision.
3878: */
3879: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3880: agelim = AGESUP;
3881: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
3882: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
3883: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3884: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3885: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
3886: gp=matrix(0,nhstepm,1,nlstate);
3887: gm=matrix(0,nhstepm,1,nlstate);
3888:
3889:
3890: for(theta=1; theta <=npar; theta++){
3891: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
3892: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3893: }
3894: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3895: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3896:
3897: if (popbased==1) {
3898: if(mobilav ==0){
3899: for(i=1; i<=nlstate;i++)
3900: prlim[i][i]=probs[(int)age][i][ij];
3901: }else{ /* mobilav */
3902: for(i=1; i<=nlstate;i++)
3903: prlim[i][i]=mobaverage[(int)age][i][ij];
3904: }
3905: }
3906:
3907: for(j=1; j<= nlstate; j++){
3908: for(h=0; h<=nhstepm; h++){
3909: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
3910: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
3911: }
3912: }
3913: /* This for computing probability of death (h=1 means
3914: computed over hstepm matrices product = hstepm*stepm months)
3915: as a weighted average of prlim.
3916: */
3917: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3918: for(i=1,gpp[j]=0.; i<= nlstate; i++)
3919: gpp[j] += prlim[i][i]*p3mat[i][j][1];
3920: }
3921: /* end probability of death */
3922:
3923: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
3924: xp[i] = x[i] - (i==theta ?delti[theta]:0);
3925: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
3926: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
3927:
3928: if (popbased==1) {
3929: if(mobilav ==0){
3930: for(i=1; i<=nlstate;i++)
3931: prlim[i][i]=probs[(int)age][i][ij];
3932: }else{ /* mobilav */
3933: for(i=1; i<=nlstate;i++)
3934: prlim[i][i]=mobaverage[(int)age][i][ij];
3935: }
3936: }
3937:
1.128 brouard 3938: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 3939: for(h=0; h<=nhstepm; h++){
3940: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
3941: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
3942: }
3943: }
3944: /* This for computing probability of death (h=1 means
3945: computed over hstepm matrices product = hstepm*stepm months)
3946: as a weighted average of prlim.
3947: */
3948: for(j=nlstate+1;j<=nlstate+ndeath;j++){
3949: for(i=1,gmp[j]=0.; i<= nlstate; i++)
3950: gmp[j] += prlim[i][i]*p3mat[i][j][1];
3951: }
3952: /* end probability of death */
3953:
3954: for(j=1; j<= nlstate; j++) /* vareij */
3955: for(h=0; h<=nhstepm; h++){
3956: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
3957: }
3958:
3959: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
3960: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
3961: }
3962:
3963: } /* End theta */
3964:
3965: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
3966:
3967: for(h=0; h<=nhstepm; h++) /* veij */
3968: for(j=1; j<=nlstate;j++)
3969: for(theta=1; theta <=npar; theta++)
3970: trgradg[h][j][theta]=gradg[h][theta][j];
3971:
3972: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
3973: for(theta=1; theta <=npar; theta++)
3974: trgradgp[j][theta]=gradgp[theta][j];
3975:
3976:
3977: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3978: for(i=1;i<=nlstate;i++)
3979: for(j=1;j<=nlstate;j++)
3980: vareij[i][j][(int)age] =0.;
3981:
3982: for(h=0;h<=nhstepm;h++){
3983: for(k=0;k<=nhstepm;k++){
3984: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
3985: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
3986: for(i=1;i<=nlstate;i++)
3987: for(j=1;j<=nlstate;j++)
3988: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
3989: }
3990: }
3991:
3992: /* pptj */
3993: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
3994: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
3995: for(j=nlstate+1;j<=nlstate+ndeath;j++)
3996: for(i=nlstate+1;i<=nlstate+ndeath;i++)
3997: varppt[j][i]=doldmp[j][i];
3998: /* end ppptj */
3999: /* x centered again */
4000: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
4001: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
4002:
4003: if (popbased==1) {
4004: if(mobilav ==0){
4005: for(i=1; i<=nlstate;i++)
4006: prlim[i][i]=probs[(int)age][i][ij];
4007: }else{ /* mobilav */
4008: for(i=1; i<=nlstate;i++)
4009: prlim[i][i]=mobaverage[(int)age][i][ij];
4010: }
4011: }
4012:
4013: /* This for computing probability of death (h=1 means
4014: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4015: as a weighted average of prlim.
4016: */
4017: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4018: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4019: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4020: }
4021: /* end probability of death */
4022:
4023: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4024: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4025: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4026: for(i=1; i<=nlstate;i++){
4027: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4028: }
4029: }
4030: fprintf(ficresprobmorprev,"\n");
4031:
4032: fprintf(ficresvij,"%.0f ",age );
4033: for(i=1; i<=nlstate;i++)
4034: for(j=1; j<=nlstate;j++){
4035: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4036: }
4037: fprintf(ficresvij,"\n");
4038: free_matrix(gp,0,nhstepm,1,nlstate);
4039: free_matrix(gm,0,nhstepm,1,nlstate);
4040: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4041: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4042: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4043: } /* End age */
4044: free_vector(gpp,nlstate+1,nlstate+ndeath);
4045: free_vector(gmp,nlstate+1,nlstate+ndeath);
4046: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4047: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.145 brouard 4048: fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240");
1.126 brouard 4049: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4050: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.126 brouard 4051: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4052: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4053: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4054: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4055: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4056: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4057: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
4058: 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);
4059: /* 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);
4060: */
4061: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
4062: fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
4063:
4064: free_vector(xp,1,npar);
4065: free_matrix(doldm,1,nlstate,1,nlstate);
4066: free_matrix(dnewm,1,nlstate,1,npar);
4067: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4068: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4069: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4070: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4071: fclose(ficresprobmorprev);
4072: fflush(ficgp);
4073: fflush(fichtm);
4074: } /* end varevsij */
4075:
4076: /************ Variance of prevlim ******************/
4077: 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[])
4078: {
4079: /* Variance of prevalence limit */
4080: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4081:
1.126 brouard 4082: double **dnewm,**doldm;
4083: int i, j, nhstepm, hstepm;
4084: double *xp;
4085: double *gp, *gm;
4086: double **gradg, **trgradg;
4087: double age,agelim;
4088: int theta;
4089:
4090: pstamp(ficresvpl);
4091: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4092: fprintf(ficresvpl,"# Age");
4093: for(i=1; i<=nlstate;i++)
4094: fprintf(ficresvpl," %1d-%1d",i,i);
4095: fprintf(ficresvpl,"\n");
4096:
4097: xp=vector(1,npar);
4098: dnewm=matrix(1,nlstate,1,npar);
4099: doldm=matrix(1,nlstate,1,nlstate);
4100:
4101: hstepm=1*YEARM; /* Every year of age */
4102: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4103: agelim = AGESUP;
4104: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4105: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4106: if (stepm >= YEARM) hstepm=1;
4107: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4108: gradg=matrix(1,npar,1,nlstate);
4109: gp=vector(1,nlstate);
4110: gm=vector(1,nlstate);
4111:
4112: for(theta=1; theta <=npar; theta++){
4113: for(i=1; i<=npar; i++){ /* Computes gradient */
4114: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4115: }
4116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4117: for(i=1;i<=nlstate;i++)
4118: gp[i] = prlim[i][i];
4119:
4120: for(i=1; i<=npar; i++) /* Computes gradient */
4121: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4122: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
4123: for(i=1;i<=nlstate;i++)
4124: gm[i] = prlim[i][i];
4125:
4126: for(i=1;i<=nlstate;i++)
4127: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4128: } /* End theta */
4129:
4130: trgradg =matrix(1,nlstate,1,npar);
4131:
4132: for(j=1; j<=nlstate;j++)
4133: for(theta=1; theta <=npar; theta++)
4134: trgradg[j][theta]=gradg[theta][j];
4135:
4136: for(i=1;i<=nlstate;i++)
4137: varpl[i][(int)age] =0.;
4138: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4139: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4140: for(i=1;i<=nlstate;i++)
4141: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4142:
4143: fprintf(ficresvpl,"%.0f ",age );
4144: for(i=1; i<=nlstate;i++)
4145: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4146: fprintf(ficresvpl,"\n");
4147: free_vector(gp,1,nlstate);
4148: free_vector(gm,1,nlstate);
4149: free_matrix(gradg,1,npar,1,nlstate);
4150: free_matrix(trgradg,1,nlstate,1,npar);
4151: } /* End age */
4152:
4153: free_vector(xp,1,npar);
4154: free_matrix(doldm,1,nlstate,1,npar);
4155: free_matrix(dnewm,1,nlstate,1,nlstate);
4156:
4157: }
4158:
4159: /************ Variance of one-step probabilities ******************/
4160: 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[])
4161: {
1.164 brouard 4162: int i, j=0, k1, l1, tj;
1.126 brouard 4163: int k2, l2, j1, z1;
1.164 brouard 4164: int k=0, l;
1.145 brouard 4165: int first=1, first1, first2;
1.126 brouard 4166: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4167: double **dnewm,**doldm;
4168: double *xp;
4169: double *gp, *gm;
4170: double **gradg, **trgradg;
4171: double **mu;
1.164 brouard 4172: double age, cov[NCOVMAX+1];
1.126 brouard 4173: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4174: int theta;
4175: char fileresprob[FILENAMELENGTH];
4176: char fileresprobcov[FILENAMELENGTH];
4177: char fileresprobcor[FILENAMELENGTH];
4178: double ***varpij;
4179:
4180: strcpy(fileresprob,"prob");
4181: strcat(fileresprob,fileres);
4182: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4183: printf("Problem with resultfile: %s\n", fileresprob);
4184: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4185: }
4186: strcpy(fileresprobcov,"probcov");
4187: strcat(fileresprobcov,fileres);
4188: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4189: printf("Problem with resultfile: %s\n", fileresprobcov);
4190: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4191: }
4192: strcpy(fileresprobcor,"probcor");
4193: strcat(fileresprobcor,fileres);
4194: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4195: printf("Problem with resultfile: %s\n", fileresprobcor);
4196: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4197: }
4198: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4199: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4200: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4201: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4202: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4203: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4204: pstamp(ficresprob);
4205: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4206: fprintf(ficresprob,"# Age");
4207: pstamp(ficresprobcov);
4208: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4209: fprintf(ficresprobcov,"# Age");
4210: pstamp(ficresprobcor);
4211: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4212: fprintf(ficresprobcor,"# Age");
4213:
4214:
4215: for(i=1; i<=nlstate;i++)
4216: for(j=1; j<=(nlstate+ndeath);j++){
4217: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4218: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4219: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4220: }
4221: /* fprintf(ficresprob,"\n");
4222: fprintf(ficresprobcov,"\n");
4223: fprintf(ficresprobcor,"\n");
4224: */
1.131 brouard 4225: xp=vector(1,npar);
1.126 brouard 4226: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4227: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4228: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4229: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4230: first=1;
4231: fprintf(ficgp,"\n# Routine varprob");
4232: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4233: fprintf(fichtm,"\n");
4234:
1.197 ! brouard 4235: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4></br>this page is important in order to visualize confidence intervals and especially correlation between disability and recovery</li>\n",optionfilehtmcov);
! 4236: fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
! 4237: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4238: and drawn. It helps understanding how is the covariance between two incidences.\
4239: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4240: 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. \
4241: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4242: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4243: standard deviations wide on each axis. <br>\
4244: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4245: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4246: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4247:
4248: cov[1]=1;
1.145 brouard 4249: /* tj=cptcoveff; */
4250: tj = (int) pow(2,cptcoveff);
1.126 brouard 4251: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4252: j1=0;
1.145 brouard 4253: for(j1=1; j1<=tj;j1++){
4254: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4255: /*j1++;*/
1.126 brouard 4256: if (cptcovn>0) {
4257: fprintf(ficresprob, "\n#********** Variable ");
4258: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4259: fprintf(ficresprob, "**********\n#\n");
4260: fprintf(ficresprobcov, "\n#********** Variable ");
4261: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4262: fprintf(ficresprobcov, "**********\n#\n");
4263:
4264: fprintf(ficgp, "\n#********** Variable ");
4265: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4266: fprintf(ficgp, "**********\n#\n");
4267:
4268:
4269: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
4270: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4271: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4272:
4273: fprintf(ficresprobcor, "\n#********** Variable ");
4274: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
4275: fprintf(ficresprobcor, "**********\n#");
4276: }
4277:
1.145 brouard 4278: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4279: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4280: gp=vector(1,(nlstate)*(nlstate+ndeath));
4281: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4282: for (age=bage; age<=fage; age ++){
4283: cov[2]=age;
1.187 brouard 4284: if(nagesqr==1)
4285: cov[3]= age*age;
1.126 brouard 4286: for (k=1; k<=cptcovn;k++) {
1.187 brouard 4287: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];/* j1 1 2 3 4
1.145 brouard 4288: * 1 1 1 1 1
4289: * 2 2 1 1 1
4290: * 3 1 2 1 1
4291: */
4292: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4293: }
1.186 brouard 4294: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
4295: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2];
1.126 brouard 4296: for (k=1; k<=cptcovprod;k++)
1.187 brouard 4297: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
1.126 brouard 4298:
4299:
4300: for(theta=1; theta <=npar; theta++){
4301: for(i=1; i<=npar; i++)
4302: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4303:
4304: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4305:
4306: k=0;
4307: for(i=1; i<= (nlstate); i++){
4308: for(j=1; j<=(nlstate+ndeath);j++){
4309: k=k+1;
4310: gp[k]=pmmij[i][j];
4311: }
4312: }
4313:
4314: for(i=1; i<=npar; i++)
4315: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4316:
4317: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4318: k=0;
4319: for(i=1; i<=(nlstate); i++){
4320: for(j=1; j<=(nlstate+ndeath);j++){
4321: k=k+1;
4322: gm[k]=pmmij[i][j];
4323: }
4324: }
4325:
4326: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4327: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4328: }
4329:
4330: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4331: for(theta=1; theta <=npar; theta++)
4332: trgradg[j][theta]=gradg[theta][j];
4333:
4334: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4335: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4336:
4337: pmij(pmmij,cov,ncovmodel,x,nlstate);
4338:
4339: k=0;
4340: for(i=1; i<=(nlstate); i++){
4341: for(j=1; j<=(nlstate+ndeath);j++){
4342: k=k+1;
4343: mu[k][(int) age]=pmmij[i][j];
4344: }
4345: }
4346: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4347: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4348: varpij[i][j][(int)age] = doldm[i][j];
4349:
4350: /*printf("\n%d ",(int)age);
4351: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4352: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4353: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4354: }*/
4355:
4356: fprintf(ficresprob,"\n%d ",(int)age);
4357: fprintf(ficresprobcov,"\n%d ",(int)age);
4358: fprintf(ficresprobcor,"\n%d ",(int)age);
4359:
4360: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4361: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4362: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4363: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4364: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4365: }
4366: i=0;
4367: for (k=1; k<=(nlstate);k++){
4368: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4369: i++;
1.126 brouard 4370: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4371: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4372: for (j=1; j<=i;j++){
1.145 brouard 4373: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4374: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4375: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4376: }
4377: }
4378: }/* end of loop for state */
4379: } /* end of loop for age */
1.145 brouard 4380: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4381: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4382: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4383: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4384:
1.126 brouard 4385: /* Confidence intervalle of pij */
4386: /*
1.131 brouard 4387: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4388: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4389: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4390: 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);
4391: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4392: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4393: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4394: */
4395:
4396: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4397: first1=1;first2=2;
1.126 brouard 4398: for (k2=1; k2<=(nlstate);k2++){
4399: for (l2=1; l2<=(nlstate+ndeath);l2++){
4400: if(l2==k2) continue;
4401: j=(k2-1)*(nlstate+ndeath)+l2;
4402: for (k1=1; k1<=(nlstate);k1++){
4403: for (l1=1; l1<=(nlstate+ndeath);l1++){
4404: if(l1==k1) continue;
4405: i=(k1-1)*(nlstate+ndeath)+l1;
4406: if(i<=j) continue;
4407: for (age=bage; age<=fage; age ++){
4408: if ((int)age %5==0){
4409: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4410: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4411: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4412: mu1=mu[i][(int) age]/stepm*YEARM ;
4413: mu2=mu[j][(int) age]/stepm*YEARM;
4414: c12=cv12/sqrt(v1*v2);
4415: /* Computing eigen value of matrix of covariance */
4416: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4417: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4418: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4419: if(first2==1){
4420: first1=0;
4421: 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);
4422: }
4423: 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);
4424: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4425: /* lc2=fabs(lc2); */
1.135 brouard 4426: }
4427:
1.126 brouard 4428: /* Eigen vectors */
4429: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4430: /*v21=sqrt(1.-v11*v11); *//* error */
4431: v21=(lc1-v1)/cv12*v11;
4432: v12=-v21;
4433: v22=v11;
4434: tnalp=v21/v11;
4435: if(first1==1){
4436: first1=0;
4437: 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);
4438: }
4439: 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);
4440: /*printf(fignu*/
4441: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4442: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4443: if(first==1){
4444: first=0;
4445: fprintf(ficgp,"\nset parametric;unset label");
4446: fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
1.145 brouard 4447: fprintf(ficgp,"\nset ter png small size 320, 240");
1.126 brouard 4448: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
4449: :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
4450: %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
4451: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
4452: subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4453: fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4454: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
4455: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4456: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4457: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4458: 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",\
4459: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4460: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4461: }else{
4462: first=0;
4463: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4464: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4465: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4466: 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",\
4467: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4468: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4469: }/* if first */
4470: } /* age mod 5 */
4471: } /* end loop age */
4472: fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
4473: first=1;
4474: } /*l12 */
4475: } /* k12 */
4476: } /*l1 */
4477: }/* k1 */
1.169 brouard 4478: /* } */ /* loop covariates */
1.126 brouard 4479: }
4480: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4481: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4482: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4483: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4484: free_vector(xp,1,npar);
4485: fclose(ficresprob);
4486: fclose(ficresprobcov);
4487: fclose(ficresprobcor);
4488: fflush(ficgp);
4489: fflush(fichtmcov);
4490: }
4491:
4492:
4493: /******************* Printing html file ***********/
4494: void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
4495: int lastpass, int stepm, int weightopt, char model[],\
4496: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4497: int popforecast, int estepm ,\
4498: double jprev1, double mprev1,double anprev1, \
4499: double jprev2, double mprev2,double anprev2){
4500: int jj1, k1, i1, cpt;
4501:
4502: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4503: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4504: </ul>");
4505: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4506: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
4507: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
4508: fprintf(fichtm,"\
4509: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
4510: stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
4511: fprintf(fichtm,"\
4512: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
4513: subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
4514: fprintf(fichtm,"\
1.128 brouard 4515: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4516: <a href=\"%s\">%s</a> <br>\n",
4517: estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
4518: fprintf(fichtm,"\
4519: - Population projections by age and states: \
4520: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));
4521:
4522: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4523:
1.145 brouard 4524: m=pow(2,cptcoveff);
1.126 brouard 4525: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4526:
4527: jj1=0;
4528: for(k1=1; k1<=m;k1++){
1.192 brouard 4529: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4530: jj1++;
4531: if (cptcovn > 0) {
4532: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4533: for (cpt=1; cpt<=cptcoveff;cpt++){
1.126 brouard 4534: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
1.192 brouard 4535: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);fflush(stdout);
4536: }
1.126 brouard 4537: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4538: }
4539: /* Pij */
1.145 brouard 4540: 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> \
4541: <img src=\"%s%d_1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4542: /* Quasi-incidences */
4543: fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.145 brouard 4544: 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> \
4545: <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
1.126 brouard 4546: /* Period (stable) prevalence in each health state */
1.154 brouard 4547: for(cpt=1; cpt<=nlstate;cpt++){
1.166 brouard 4548: 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> \
4549: <img src=\"%s%d_%d.png\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
1.126 brouard 4550: }
4551: for(cpt=1; cpt<=nlstate;cpt++) {
1.154 brouard 4552: 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> \
4553: <img src=\"%s%d%d.png\">",cpt,nlstate,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
1.126 brouard 4554: }
1.192 brouard 4555: /* } /\* end i1 *\/ */
1.126 brouard 4556: }/* End k1 */
4557: fprintf(fichtm,"</ul>");
4558:
4559: fprintf(fichtm,"\
4560: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4561: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.197 ! brouard 4562: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file.<br> \
! 4563: But because parameters are usually highly correlated (a higher incidence of disability \
! 4564: and a higher incidence of recovery can give very close observed transition) it might \
! 4565: be very useful to look not only at linear confidence intervals estimated from the \
! 4566: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
! 4567: (parameters) of the logistic regression, it might be more meaningful to visualize the \
! 4568: covariance matrix of the one-step probabilities. \
! 4569: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4570:
1.193 brouard 4571: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.126 brouard 4572: subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
4573: fprintf(fichtm,"\
4574: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4575: subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
4576:
4577: fprintf(fichtm,"\
4578: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
4579: subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
4580: fprintf(fichtm,"\
4581: - 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): \
4582: <a href=\"%s\">%s</a> <br>\n</li>",
4583: estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
4584: fprintf(fichtm,"\
4585: - (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): \
4586: <a href=\"%s\">%s</a> <br>\n</li>",
4587: estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
4588: fprintf(fichtm,"\
1.128 brouard 4589: - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
1.126 brouard 4590: estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
4591: fprintf(fichtm,"\
1.128 brouard 4592: - 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",
4593: estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
1.126 brouard 4594: fprintf(fichtm,"\
4595: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
4596: subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
4597:
4598: /* if(popforecast==1) fprintf(fichtm,"\n */
4599: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4600: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4601: /* <br>",fileres,fileres,fileres,fileres); */
4602: /* else */
4603: /* 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); */
4604: fflush(fichtm);
4605: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4606:
1.145 brouard 4607: m=pow(2,cptcoveff);
1.126 brouard 4608: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4609:
4610: jj1=0;
4611: for(k1=1; k1<=m;k1++){
1.192 brouard 4612: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4613: jj1++;
4614: if (cptcovn > 0) {
4615: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4616: for (cpt=1; cpt<=cptcoveff;cpt++)
4617: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
4618: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4619: }
4620: for(cpt=1; cpt<=nlstate;cpt++) {
4621: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.145 brouard 4622: prevalence (with 95%% confidence interval) in state (%d): %s%d_%d.png <br>\
4623: <img src=\"%s%d_%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
1.126 brouard 4624: }
4625: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4626: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4627: true period expectancies (those weighted with period prevalences are also\
4628: drawn in addition to the population based expectancies computed using\
4629: observed and cahotic prevalences: %s%d.png<br>\
1.126 brouard 4630: <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
1.192 brouard 4631: /* } /\* end i1 *\/ */
1.126 brouard 4632: }/* End k1 */
4633: fprintf(fichtm,"</ul>");
4634: fflush(fichtm);
4635: }
4636:
4637: /******************* Gnuplot file **************/
4638: void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
4639:
4640: char dirfileres[132],optfileres[132];
1.164 brouard 4641: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4642: int ng=0;
1.126 brouard 4643: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4644: /* printf("Problem with file %s",optionfilegnuplot); */
4645: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4646: /* } */
4647:
4648: /*#ifdef windows */
4649: fprintf(ficgp,"cd \"%s\" \n",pathc);
4650: /*#endif */
4651: m=pow(2,cptcoveff);
4652:
4653: strcpy(dirfileres,optionfilefiname);
4654: strcpy(optfileres,"vpl");
4655: /* 1eme*/
1.153 brouard 4656: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'vpl' files\n");
1.126 brouard 4657: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4658: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
4659: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
4660: fprintf(ficgp,"\n#set out \"v%s%d_%d.png\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4661: fprintf(ficgp,"set xlabel \"Age\" \n\
4662: set ylabel \"Probability\" \n\
1.145 brouard 4663: set ter png small size 320, 240\n\
1.170 brouard 4664: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4665:
4666: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4667: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4668: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4669: }
1.170 brouard 4670: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4671: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4672: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4673: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4674: }
1.170 brouard 4675: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
1.126 brouard 4676: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4677: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4678: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4679: }
1.145 brouard 4680: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
1.126 brouard 4681: }
4682: }
4683: /*2 eme*/
1.153 brouard 4684: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4685: for (k1=1; k1<= m ; k1 ++) {
4686: fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
1.145 brouard 4687: fprintf(ficgp,"set ylabel \"Years\" \nset ter png small size 320, 240\nplot [%.f:%.f] ",ageminpar,fage);
1.126 brouard 4688:
4689: for (i=1; i<= nlstate+1 ; i ++) {
4690: k=2*i;
1.170 brouard 4691: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4692: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4693: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4694: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4695: }
4696: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
4697: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
1.170 brouard 4698: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4699: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4700: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4701: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4702: }
1.145 brouard 4703: fprintf(ficgp,"\" t\"\" w l lt 0,");
1.170 brouard 4704: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
1.126 brouard 4705: for (j=1; j<= nlstate+1 ; j ++) {
1.170 brouard 4706: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4707: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4708: }
1.145 brouard 4709: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4710: else fprintf(ficgp,"\" t\"\" w l lt 0,");
1.126 brouard 4711: }
4712: }
4713:
4714: /*3eme*/
4715:
4716: for (k1=1; k1<= m ; k1 ++) {
4717: for (cpt=1; cpt<= nlstate ; cpt ++) {
4718: /* k=2+nlstate*(2*cpt-2); */
4719: k=2+(nlstate+1)*(cpt-1);
4720: fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
1.145 brouard 4721: fprintf(ficgp,"set ter png small size 320, 240\n\
1.126 brouard 4722: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
4723: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4724: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4725: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4726: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
4727: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
4728: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
4729:
4730: */
4731: for (i=1; i< nlstate ; i ++) {
4732: 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);
4733: /* 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);*/
4734:
4735: }
4736: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
4737: }
4738: }
4739:
4740: /* CV preval stable (period) */
1.153 brouard 4741: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
4742: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 4743: k=3;
1.153 brouard 4744: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.145 brouard 4745: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
1.126 brouard 4746: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.145 brouard 4747: set ter png small size 320, 240\n\
1.126 brouard 4748: unset log y\n\
1.153 brouard 4749: plot [%.f:%.f] ", ageminpar, agemaxpar);
4750: for (i=1; i<= nlstate ; i ++){
4751: if(i==1)
4752: fprintf(ficgp,"\"%s\"",subdirf2(fileres,"pij"));
4753: else
4754: fprintf(ficgp,", '' ");
1.154 brouard 4755: l=(nlstate+ndeath)*(i-1)+1;
4756: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.153 brouard 4757: for (j=1; j<= (nlstate-1) ; j ++)
4758: fprintf(ficgp,"+$%d",k+l+j);
4759: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
4760: } /* nlstate */
4761: fprintf(ficgp,"\n");
4762: } /* end cpt state*/
4763: } /* end covariate */
1.126 brouard 4764:
4765: /* proba elementaires */
1.187 brouard 4766: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 4767: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 4768: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 4769: for(k=1; k <=(nlstate+ndeath); k++){
4770: if (k != i) {
1.187 brouard 4771: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 4772: for(j=1; j <=ncovmodel; j++){
1.187 brouard 4773: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 4774: jk++;
4775: }
1.187 brouard 4776: fprintf(ficgp,"\n");
1.126 brouard 4777: }
4778: }
4779: }
1.187 brouard 4780: fprintf(ficgp,"##############\n#\n");
4781:
1.145 brouard 4782: /*goto avoid;*/
1.187 brouard 4783: fprintf(ficgp,"\n##############\n#Graphics of of probabilities or incidences\n#############\n");
4784: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
4785: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
4786: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
4787: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
4788: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4789: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4790: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4791: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
4792: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
4793: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
4794: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
4795: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
4796: fprintf(ficgp,"#\n");
1.126 brouard 4797: for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
1.187 brouard 4798: fprintf(ficgp,"# ng=%d\n",ng);
4799: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 4800: for(jk=1; jk <=m; jk++) {
1.187 brouard 4801: fprintf(ficgp,"# jk=%d\n",jk);
1.145 brouard 4802: fprintf(ficgp,"\nset out \"%s%d_%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
1.126 brouard 4803: if (ng==2)
4804: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
4805: else
4806: fprintf(ficgp,"\nset title \"Probability\"\n");
1.145 brouard 4807: fprintf(ficgp,"\nset ter png small size 320, 240\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 4808: i=1;
4809: for(k2=1; k2<=nlstate; k2++) {
4810: k3=i;
4811: for(k=1; k<=(nlstate+ndeath); k++) {
4812: if (k != k2){
4813: if(ng==2)
1.187 brouard 4814: if(nagesqr==0)
4815: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
4816: else /* nagesqr =1 */
4817: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
1.126 brouard 4818: else
1.187 brouard 4819: if(nagesqr==0)
4820: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
4821: else /* nagesqr =1 */
4822: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
1.141 brouard 4823: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 4824: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 ! brouard 4825: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
! 4826: if(ij <=cptcovage) { /* Bug valgrind */
! 4827: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 4828: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 4829: ij++;
! 4830: }
1.186 brouard 4831: }
4832: else
1.187 brouard 4833: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4834: }
4835: fprintf(ficgp,")/(1");
4836:
1.187 brouard 4837: for(k1=1; k1 <=nlstate; k1++){
4838: if(nagesqr==0)
4839: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
4840: else /* nagesqr =1 */
4841: 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);
4842:
1.126 brouard 4843: ij=1;
1.187 brouard 4844: for(j=3; j <=ncovmodel-nagesqr; j++){
1.197 ! brouard 4845: if(ij <=cptcovage) { /* Bug valgrind */
! 4846: if((j-2)==Tage[ij]) { /* Bug valgrind */
! 4847: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
! 4848: ij++;
! 4849: }
1.186 brouard 4850: }
4851: else
1.187 brouard 4852: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
1.126 brouard 4853: }
4854: fprintf(ficgp,")");
4855: }
4856: fprintf(ficgp,") t \"p%d%d\" ", k2,k);
4857: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
4858: i=i+ncovmodel;
4859: }
4860: } /* end k */
4861: } /* end k2 */
4862: } /* end jk */
4863: } /* end ng */
1.164 brouard 4864: /* avoid: */
1.126 brouard 4865: fflush(ficgp);
4866: } /* end gnuplot */
4867:
4868:
4869: /*************** Moving average **************/
4870: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
4871:
4872: int i, cpt, cptcod;
4873: int modcovmax =1;
4874: int mobilavrange, mob;
4875: double age;
4876:
4877: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
4878: a covariate has 2 modalities */
4879: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
4880:
4881: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
4882: if(mobilav==1) mobilavrange=5; /* default */
4883: else mobilavrange=mobilav;
4884: for (age=bage; age<=fage; age++)
4885: for (i=1; i<=nlstate;i++)
4886: for (cptcod=1;cptcod<=modcovmax;cptcod++)
4887: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
4888: /* We keep the original values on the extreme ages bage, fage and for
4889: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
4890: we use a 5 terms etc. until the borders are no more concerned.
4891: */
4892: for (mob=3;mob <=mobilavrange;mob=mob+2){
4893: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
4894: for (i=1; i<=nlstate;i++){
4895: for (cptcod=1;cptcod<=modcovmax;cptcod++){
4896: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
4897: for (cpt=1;cpt<=(mob-1)/2;cpt++){
4898: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
4899: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
4900: }
4901: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
4902: }
4903: }
4904: }/* end age */
4905: }/* end mob */
4906: }else return -1;
4907: return 0;
4908: }/* End movingaverage */
4909:
4910:
4911: /************** Forecasting ******************/
1.169 brouard 4912: 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){
1.126 brouard 4913: /* proj1, year, month, day of starting projection
4914: agemin, agemax range of age
4915: dateprev1 dateprev2 range of dates during which prevalence is computed
4916: anproj2 year of en of projection (same day and month as proj1).
4917: */
1.164 brouard 4918: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 4919: double agec; /* generic age */
4920: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
4921: double *popeffectif,*popcount;
4922: double ***p3mat;
4923: double ***mobaverage;
4924: char fileresf[FILENAMELENGTH];
4925:
4926: agelim=AGESUP;
4927: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
4928:
4929: strcpy(fileresf,"f");
4930: strcat(fileresf,fileres);
4931: if((ficresf=fopen(fileresf,"w"))==NULL) {
4932: printf("Problem with forecast resultfile: %s\n", fileresf);
4933: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
4934: }
4935: printf("Computing forecasting: result on file '%s' \n", fileresf);
4936: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
4937:
4938: if (cptcoveff==0) ncodemax[cptcoveff]=1;
4939:
4940: if (mobilav!=0) {
4941: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4942: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
4943: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4944: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4945: }
4946: }
4947:
4948: stepsize=(int) (stepm+YEARM-1)/YEARM;
4949: if (stepm<=12) stepsize=1;
4950: if(estepm < stepm){
4951: printf ("Problem %d lower than %d\n",estepm, stepm);
4952: }
4953: else hstepm=estepm;
4954:
4955: hstepm=hstepm/stepm;
4956: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
4957: fractional in yp1 */
4958: anprojmean=yp;
4959: yp2=modf((yp1*12),&yp);
4960: mprojmean=yp;
4961: yp1=modf((yp2*30.5),&yp);
4962: jprojmean=yp;
4963: if(jprojmean==0) jprojmean=1;
4964: if(mprojmean==0) jprojmean=1;
4965:
4966: i1=cptcoveff;
4967: if (cptcovn < 1){i1=1;}
4968:
4969: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
4970:
4971: fprintf(ficresf,"#****** Routine prevforecast **\n");
4972:
4973: /* if (h==(int)(YEARM*yearp)){ */
4974: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
4975: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
4976: k=k+1;
4977: fprintf(ficresf,"\n#******");
4978: for(j=1;j<=cptcoveff;j++) {
4979: 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]]);
4980: }
4981: fprintf(ficresf,"******\n");
4982: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
4983: for(j=1; j<=nlstate+ndeath;j++){
4984: for(i=1; i<=nlstate;i++)
4985: fprintf(ficresf," p%d%d",i,j);
4986: fprintf(ficresf," p.%d",j);
4987: }
4988: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
4989: fprintf(ficresf,"\n");
4990: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
4991:
4992: for (agec=fage; agec>=(ageminpar-1); agec--){
4993: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
4994: nhstepm = nhstepm/hstepm;
4995: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4996: oldm=oldms;savm=savms;
4997: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
4998:
4999: for (h=0; h<=nhstepm; h++){
5000: if (h*hstepm/YEARM*stepm ==yearp) {
5001: fprintf(ficresf,"\n");
5002: for(j=1;j<=cptcoveff;j++)
5003: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5004: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5005: }
5006: for(j=1; j<=nlstate+ndeath;j++) {
5007: ppij=0.;
5008: for(i=1; i<=nlstate;i++) {
5009: if (mobilav==1)
5010: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5011: else {
5012: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5013: }
5014: if (h*hstepm/YEARM*stepm== yearp) {
5015: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5016: }
5017: } /* end i */
5018: if (h*hstepm/YEARM*stepm==yearp) {
5019: fprintf(ficresf," %.3f", ppij);
5020: }
5021: }/* end j */
5022: } /* end h */
5023: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5024: } /* end agec */
5025: } /* end yearp */
5026: } /* end cptcod */
5027: } /* end cptcov */
5028:
5029: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5030:
5031: fclose(ficresf);
5032: }
5033:
5034: /************** Forecasting *****not tested NB*************/
1.169 brouard 5035: 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){
1.126 brouard 5036:
5037: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5038: int *popage;
5039: double calagedatem, agelim, kk1, kk2;
5040: double *popeffectif,*popcount;
5041: double ***p3mat,***tabpop,***tabpopprev;
5042: double ***mobaverage;
5043: char filerespop[FILENAMELENGTH];
5044:
5045: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5046: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5047: agelim=AGESUP;
5048: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5049:
5050: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5051:
5052:
5053: strcpy(filerespop,"pop");
5054: strcat(filerespop,fileres);
5055: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5056: printf("Problem with forecast resultfile: %s\n", filerespop);
5057: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5058: }
5059: printf("Computing forecasting: result on file '%s' \n", filerespop);
5060: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5061:
5062: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5063:
5064: if (mobilav!=0) {
5065: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5066: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5067: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5068: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5069: }
5070: }
5071:
5072: stepsize=(int) (stepm+YEARM-1)/YEARM;
5073: if (stepm<=12) stepsize=1;
5074:
5075: agelim=AGESUP;
5076:
5077: hstepm=1;
5078: hstepm=hstepm/stepm;
5079:
5080: if (popforecast==1) {
5081: if((ficpop=fopen(popfile,"r"))==NULL) {
5082: printf("Problem with population file : %s\n",popfile);exit(0);
5083: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5084: }
5085: popage=ivector(0,AGESUP);
5086: popeffectif=vector(0,AGESUP);
5087: popcount=vector(0,AGESUP);
5088:
5089: i=1;
5090: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5091:
5092: imx=i;
5093: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5094: }
5095:
5096: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5097: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5098: k=k+1;
5099: fprintf(ficrespop,"\n#******");
5100: for(j=1;j<=cptcoveff;j++) {
5101: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
5102: }
5103: fprintf(ficrespop,"******\n");
5104: fprintf(ficrespop,"# Age");
5105: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5106: if (popforecast==1) fprintf(ficrespop," [Population]");
5107:
5108: for (cpt=0; cpt<=0;cpt++) {
5109: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5110:
5111: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5112: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5113: nhstepm = nhstepm/hstepm;
5114:
5115: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5116: oldm=oldms;savm=savms;
5117: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5118:
5119: for (h=0; h<=nhstepm; h++){
5120: if (h==(int) (calagedatem+YEARM*cpt)) {
5121: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5122: }
5123: for(j=1; j<=nlstate+ndeath;j++) {
5124: kk1=0.;kk2=0;
5125: for(i=1; i<=nlstate;i++) {
5126: if (mobilav==1)
5127: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5128: else {
5129: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5130: }
5131: }
5132: if (h==(int)(calagedatem+12*cpt)){
5133: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5134: /*fprintf(ficrespop," %.3f", kk1);
5135: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5136: }
5137: }
5138: for(i=1; i<=nlstate;i++){
5139: kk1=0.;
5140: for(j=1; j<=nlstate;j++){
5141: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5142: }
5143: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5144: }
5145:
5146: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5147: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5148: }
5149: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5150: }
5151: }
5152:
5153: /******/
5154:
5155: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5156: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5157: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5158: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5159: nhstepm = nhstepm/hstepm;
5160:
5161: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5162: oldm=oldms;savm=savms;
5163: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5164: for (h=0; h<=nhstepm; h++){
5165: if (h==(int) (calagedatem+YEARM*cpt)) {
5166: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5167: }
5168: for(j=1; j<=nlstate+ndeath;j++) {
5169: kk1=0.;kk2=0;
5170: for(i=1; i<=nlstate;i++) {
5171: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5172: }
5173: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5174: }
5175: }
5176: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5177: }
5178: }
5179: }
5180: }
5181:
5182: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5183:
5184: if (popforecast==1) {
5185: free_ivector(popage,0,AGESUP);
5186: free_vector(popeffectif,0,AGESUP);
5187: free_vector(popcount,0,AGESUP);
5188: }
5189: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5190: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5191: fclose(ficrespop);
5192: } /* End of popforecast */
5193:
5194: int fileappend(FILE *fichier, char *optionfich)
5195: {
5196: if((fichier=fopen(optionfich,"a"))==NULL) {
5197: printf("Problem with file: %s\n", optionfich);
5198: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5199: return (0);
5200: }
5201: fflush(fichier);
5202: return (1);
5203: }
5204:
5205:
5206: /**************** function prwizard **********************/
5207: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5208: {
5209:
5210: /* Wizard to print covariance matrix template */
5211:
1.164 brouard 5212: char ca[32], cb[32];
5213: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5214: int numlinepar;
5215:
5216: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5217: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5218: for(i=1; i <=nlstate; i++){
5219: jj=0;
5220: for(j=1; j <=nlstate+ndeath; j++){
5221: if(j==i) continue;
5222: jj++;
5223: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5224: printf("%1d%1d",i,j);
5225: fprintf(ficparo,"%1d%1d",i,j);
5226: for(k=1; k<=ncovmodel;k++){
5227: /* printf(" %lf",param[i][j][k]); */
5228: /* fprintf(ficparo," %lf",param[i][j][k]); */
5229: printf(" 0.");
5230: fprintf(ficparo," 0.");
5231: }
5232: printf("\n");
5233: fprintf(ficparo,"\n");
5234: }
5235: }
5236: printf("# Scales (for hessian or gradient estimation)\n");
5237: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5238: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5239: for(i=1; i <=nlstate; i++){
5240: jj=0;
5241: for(j=1; j <=nlstate+ndeath; j++){
5242: if(j==i) continue;
5243: jj++;
5244: fprintf(ficparo,"%1d%1d",i,j);
5245: printf("%1d%1d",i,j);
5246: fflush(stdout);
5247: for(k=1; k<=ncovmodel;k++){
5248: /* printf(" %le",delti3[i][j][k]); */
5249: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5250: printf(" 0.");
5251: fprintf(ficparo," 0.");
5252: }
5253: numlinepar++;
5254: printf("\n");
5255: fprintf(ficparo,"\n");
5256: }
5257: }
5258: printf("# Covariance matrix\n");
5259: /* # 121 Var(a12)\n\ */
5260: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5261: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5262: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5263: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5264: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5265: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5266: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5267: fflush(stdout);
5268: fprintf(ficparo,"# Covariance matrix\n");
5269: /* # 121 Var(a12)\n\ */
5270: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5271: /* # ...\n\ */
5272: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5273:
5274: for(itimes=1;itimes<=2;itimes++){
5275: jj=0;
5276: for(i=1; i <=nlstate; i++){
5277: for(j=1; j <=nlstate+ndeath; j++){
5278: if(j==i) continue;
5279: for(k=1; k<=ncovmodel;k++){
5280: jj++;
5281: ca[0]= k+'a'-1;ca[1]='\0';
5282: if(itimes==1){
5283: printf("#%1d%1d%d",i,j,k);
5284: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5285: }else{
5286: printf("%1d%1d%d",i,j,k);
5287: fprintf(ficparo,"%1d%1d%d",i,j,k);
5288: /* printf(" %.5le",matcov[i][j]); */
5289: }
5290: ll=0;
5291: for(li=1;li <=nlstate; li++){
5292: for(lj=1;lj <=nlstate+ndeath; lj++){
5293: if(lj==li) continue;
5294: for(lk=1;lk<=ncovmodel;lk++){
5295: ll++;
5296: if(ll<=jj){
5297: cb[0]= lk +'a'-1;cb[1]='\0';
5298: if(ll<jj){
5299: if(itimes==1){
5300: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5301: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5302: }else{
5303: printf(" 0.");
5304: fprintf(ficparo," 0.");
5305: }
5306: }else{
5307: if(itimes==1){
5308: printf(" Var(%s%1d%1d)",ca,i,j);
5309: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5310: }else{
5311: printf(" 0.");
5312: fprintf(ficparo," 0.");
5313: }
5314: }
5315: }
5316: } /* end lk */
5317: } /* end lj */
5318: } /* end li */
5319: printf("\n");
5320: fprintf(ficparo,"\n");
5321: numlinepar++;
5322: } /* end k*/
5323: } /*end j */
5324: } /* end i */
5325: } /* end itimes */
5326:
5327: } /* end of prwizard */
5328: /******************* Gompertz Likelihood ******************************/
5329: double gompertz(double x[])
5330: {
5331: double A,B,L=0.0,sump=0.,num=0.;
5332: int i,n=0; /* n is the size of the sample */
5333:
5334: for (i=0;i<=imx-1 ; i++) {
5335: sump=sump+weight[i];
5336: /* sump=sump+1;*/
5337: num=num+1;
5338: }
5339:
5340:
5341: /* for (i=0; i<=imx; i++)
5342: 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]);*/
5343:
5344: for (i=1;i<=imx ; i++)
5345: {
5346: if (cens[i] == 1 && wav[i]>1)
5347: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5348:
5349: if (cens[i] == 0 && wav[i]>1)
5350: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5351: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5352:
5353: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5354: if (wav[i] > 1 ) { /* ??? */
5355: L=L+A*weight[i];
5356: /* 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]);*/
5357: }
5358: }
5359:
5360: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5361:
5362: return -2*L*num/sump;
5363: }
5364:
1.136 brouard 5365: #ifdef GSL
5366: /******************* Gompertz_f Likelihood ******************************/
5367: double gompertz_f(const gsl_vector *v, void *params)
5368: {
5369: double A,B,LL=0.0,sump=0.,num=0.;
5370: double *x= (double *) v->data;
5371: int i,n=0; /* n is the size of the sample */
5372:
5373: for (i=0;i<=imx-1 ; i++) {
5374: sump=sump+weight[i];
5375: /* sump=sump+1;*/
5376: num=num+1;
5377: }
5378:
5379:
5380: /* for (i=0; i<=imx; i++)
5381: 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]);*/
5382: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5383: for (i=1;i<=imx ; i++)
5384: {
5385: if (cens[i] == 1 && wav[i]>1)
5386: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5387:
5388: if (cens[i] == 0 && wav[i]>1)
5389: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5390: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5391:
5392: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5393: if (wav[i] > 1 ) { /* ??? */
5394: LL=LL+A*weight[i];
5395: /* 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]);*/
5396: }
5397: }
5398:
5399: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5400: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5401:
5402: return -2*LL*num/sump;
5403: }
5404: #endif
5405:
1.126 brouard 5406: /******************* Printing html file ***********/
5407: void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
5408: int lastpass, int stepm, int weightopt, char model[],\
5409: int imx, double p[],double **matcov,double agemortsup){
5410: int i,k;
5411:
5412: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5413: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5414: for (i=1;i<=2;i++)
5415: 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]));
5416: fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
5417: fprintf(fichtm,"</ul>");
5418:
5419: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5420:
5421: 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>");
5422:
5423: for (k=agegomp;k<(agemortsup-2);k++)
5424: 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]);
5425:
5426:
5427: fflush(fichtm);
5428: }
5429:
5430: /******************* Gnuplot file **************/
5431: void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
5432:
5433: char dirfileres[132],optfileres[132];
1.164 brouard 5434:
1.126 brouard 5435: int ng;
5436:
5437:
5438: /*#ifdef windows */
5439: fprintf(ficgp,"cd \"%s\" \n",pathc);
5440: /*#endif */
5441:
5442:
5443: strcpy(dirfileres,optionfilefiname);
5444: strcpy(optfileres,"vpl");
5445: fprintf(ficgp,"set out \"graphmort.png\"\n ");
5446: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.145 brouard 5447: fprintf(ficgp, "set ter png small size 320, 240\n set log y\n");
5448: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5449: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5450:
5451: }
5452:
1.136 brouard 5453: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5454: {
1.126 brouard 5455:
1.136 brouard 5456: /*-------- data file ----------*/
5457: FILE *fic;
5458: char dummy[]=" ";
1.164 brouard 5459: int i=0, j=0, n=0;
1.136 brouard 5460: int linei, month, year,iout;
5461: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5462: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5463: char *stratrunc;
5464: int lstra;
1.126 brouard 5465:
5466:
1.136 brouard 5467: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5468: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5469: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5470: }
1.126 brouard 5471:
1.136 brouard 5472: i=1;
5473: linei=0;
5474: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5475: linei=linei+1;
5476: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5477: if(line[j] == '\t')
5478: line[j] = ' ';
5479: }
5480: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5481: ;
5482: };
5483: line[j+1]=0; /* Trims blanks at end of line */
5484: if(line[0]=='#'){
5485: fprintf(ficlog,"Comment line\n%s\n",line);
5486: printf("Comment line\n%s\n",line);
5487: continue;
5488: }
5489: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5490: strcpy(line, linetmp);
1.136 brouard 5491:
1.126 brouard 5492:
1.136 brouard 5493: for (j=maxwav;j>=1;j--){
1.137 brouard 5494: cutv(stra, strb, line, ' ');
1.136 brouard 5495: if(strb[0]=='.') { /* Missing status */
5496: lval=-1;
5497: }else{
5498: errno=0;
5499: lval=strtol(strb,&endptr,10);
5500: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5501: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5502: 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);
5503: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
1.136 brouard 5504: return 1;
5505: }
5506: }
5507: s[j][i]=lval;
5508:
5509: strcpy(line,stra);
5510: cutv(stra, strb,line,' ');
1.169 brouard 5511: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5512: }
1.169 brouard 5513: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5514: month=99;
5515: year=9999;
5516: }else{
1.141 brouard 5517: 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);
5518: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
1.136 brouard 5519: return 1;
5520: }
5521: anint[j][i]= (double) year;
5522: mint[j][i]= (double)month;
5523: strcpy(line,stra);
5524: } /* ENd Waves */
5525:
5526: cutv(stra, strb,line,' ');
1.169 brouard 5527: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5528: }
1.169 brouard 5529: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5530: month=99;
5531: year=9999;
5532: }else{
1.141 brouard 5533: 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);
5534: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5535: return 1;
5536: }
5537: andc[i]=(double) year;
5538: moisdc[i]=(double) month;
5539: strcpy(line,stra);
5540:
5541: cutv(stra, strb,line,' ');
1.169 brouard 5542: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5543: }
1.169 brouard 5544: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5545: month=99;
5546: year=9999;
5547: }else{
1.141 brouard 5548: 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);
5549: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5550: return 1;
5551: }
5552: if (year==9999) {
1.141 brouard 5553: 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);
5554: fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a date of birth (mm/yyyy) but at least the year of birth should be given. Exiting.\n",strb, linei,i,line);fflush(ficlog);
1.136 brouard 5555: return 1;
1.126 brouard 5556:
1.136 brouard 5557: }
5558: annais[i]=(double)(year);
5559: moisnais[i]=(double)(month);
5560: strcpy(line,stra);
5561:
5562: cutv(stra, strb,line,' ');
5563: errno=0;
5564: dval=strtod(strb,&endptr);
5565: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5566: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5567: fprintf(ficlog,"Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
1.136 brouard 5568: fflush(ficlog);
5569: return 1;
5570: }
5571: weight[i]=dval;
5572: strcpy(line,stra);
5573:
5574: for (j=ncovcol;j>=1;j--){
5575: cutv(stra, strb,line,' ');
5576: if(strb[0]=='.') { /* Missing status */
5577: lval=-1;
5578: }else{
5579: errno=0;
5580: lval=strtol(strb,&endptr,10);
5581: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5582: 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);
5583: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
1.136 brouard 5584: return 1;
5585: }
5586: }
5587: if(lval <-1 || lval >1){
1.141 brouard 5588: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5589: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5590: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5591: For example, for multinomial values like 1, 2 and 3,\n \
5592: build V1=0 V2=0 for the reference value (1),\n \
5593: V1=1 V2=0 for (2) \n \
5594: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5595: output of IMaCh is often meaningless.\n \
5596: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5597: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5598: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5599: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5600: For example, for multinomial values like 1, 2 and 3,\n \
5601: build V1=0 V2=0 for the reference value (1),\n \
5602: V1=1 V2=0 for (2) \n \
5603: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5604: output of IMaCh is often meaningless.\n \
5605: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5606: return 1;
5607: }
5608: covar[j][i]=(double)(lval);
5609: strcpy(line,stra);
5610: }
5611: lstra=strlen(stra);
5612:
5613: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5614: stratrunc = &(stra[lstra-9]);
5615: num[i]=atol(stratrunc);
5616: }
5617: else
5618: num[i]=atol(stra);
5619: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5620: 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;}*/
5621:
5622: i=i+1;
5623: } /* End loop reading data */
1.126 brouard 5624:
1.136 brouard 5625: *imax=i-1; /* Number of individuals */
5626: fclose(fic);
5627:
5628: return (0);
1.164 brouard 5629: /* endread: */
1.136 brouard 5630: printf("Exiting readdata: ");
5631: fclose(fic);
5632: return (1);
1.126 brouard 5633:
5634:
5635:
1.136 brouard 5636: }
1.145 brouard 5637: void removespace(char *str) {
5638: char *p1 = str, *p2 = str;
5639: do
5640: while (*p2 == ' ')
5641: p2++;
1.169 brouard 5642: while (*p1++ == *p2++);
1.145 brouard 5643: }
5644:
5645: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 5646: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
5647: * - nagesqr = 1 if age*age in the model, otherwise 0.
5648: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
5649: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 5650: * - cptcovage number of covariates with age*products =2
5651: * - cptcovs number of simple covariates
5652: * - 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
5653: * which is a new column after the 9 (ncovcol) variables.
5654: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
5655: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
5656: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
5657: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
5658: */
1.136 brouard 5659: {
1.145 brouard 5660: int i, j, k, ks;
1.164 brouard 5661: int j1, k1, k2;
1.136 brouard 5662: char modelsav[80];
1.145 brouard 5663: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 5664: char *strpt;
1.136 brouard 5665:
1.145 brouard 5666: /*removespace(model);*/
1.136 brouard 5667: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 5668: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 5669: if (strstr(model,"AGE") !=0){
1.192 brouard 5670: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
5671: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 5672: return 1;
5673: }
1.141 brouard 5674: if (strstr(model,"v") !=0){
5675: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
5676: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
5677: return 1;
5678: }
1.187 brouard 5679: strcpy(modelsav,model);
5680: if ((strpt=strstr(model,"age*age")) !=0){
5681: printf(" strpt=%s, model=%s\n",strpt, model);
5682: if(strpt != model){
5683: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5684: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5685: corresponding column of parameters.\n",model);
5686: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 5687: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 5688: corresponding column of parameters.\n",model); fflush(ficlog);
5689: return 1;
5690: }
5691:
5692: nagesqr=1;
5693: if (strstr(model,"+age*age") !=0)
5694: substrchaine(modelsav, model, "+age*age");
5695: else if (strstr(model,"age*age+") !=0)
5696: substrchaine(modelsav, model, "age*age+");
5697: else
5698: substrchaine(modelsav, model, "age*age");
5699: }else
5700: nagesqr=0;
5701: if (strlen(modelsav) >1){
5702: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
5703: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
5704: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
5705: cptcovt= j+1; /* Number of total covariates in the model, not including
5706: * cst, age and age*age
5707: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
5708: /* including age products which are counted in cptcovage.
5709: * but the covariates which are products must be treated
5710: * separately: ncovn=4- 2=2 (V1+V3). */
5711: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
5712: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
5713:
5714:
5715: /* Design
5716: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
5717: * < ncovcol=8 >
5718: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
5719: * k= 1 2 3 4 5 6 7 8
5720: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
5721: * covar[k,i], value of kth covariate if not including age for individual i:
5722: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
5723: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
5724: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
5725: * Tage[++cptcovage]=k
5726: * if products, new covar are created after ncovcol with k1
5727: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
5728: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
5729: * 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
5730: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
5731: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
5732: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
5733: * < ncovcol=8 >
5734: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
5735: * k= 1 2 3 4 5 6 7 8 9 10 11 12
5736: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
5737: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5738: * p Tprod[1]@2={ 6, 5}
5739: *p Tvard[1][1]@4= {7, 8, 5, 6}
5740: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
5741: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
5742: *How to reorganize?
5743: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
5744: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
5745: * {2, 1, 4, 8, 5, 6, 3, 7}
5746: * Struct []
5747: */
1.145 brouard 5748:
1.187 brouard 5749: /* This loop fills the array Tvar from the string 'model'.*/
5750: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
5751: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
5752: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
5753: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
5754: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
5755: /* k=1 Tvar[1]=2 (from V2) */
5756: /* k=5 Tvar[5] */
5757: /* for (k=1; k<=cptcovn;k++) { */
5758: /* cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]]; */
5759: /* } */
5760: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtab[ij][Tvar[Tage[k]]]]*cov[2]; */
5761: /*
5762: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
5763: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 5764: Tvar[k]=0;
1.187 brouard 5765: cptcovage=0;
5766: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
5767: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
5768: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
5769: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
5770: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
5771: /*scanf("%d",i);*/
5772: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
5773: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
5774: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
5775: /* covar is not filled and then is empty */
5776: cptcovprod--;
5777: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
5778: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
5779: cptcovage++; /* Sums the number of covariates which include age as a product */
5780: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
5781: /*printf("stre=%s ", stre);*/
5782: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
5783: cptcovprod--;
5784: cutl(stre,strb,strc,'V');
5785: Tvar[k]=atoi(stre);
5786: cptcovage++;
5787: Tage[cptcovage]=k;
5788: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
5789: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
5790: cptcovn++;
5791: cptcovprodnoage++;k1++;
5792: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
5793: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
5794: because this model-covariate is a construction we invent a new column
5795: ncovcol + k1
5796: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
5797: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
5798: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
5799: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
5800: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
5801: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
5802: k2=k2+2;
5803: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
5804: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
5805: for (i=1; i<=lastobs;i++){
5806: /* Computes the new covariate which is a product of
5807: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
5808: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
5809: }
5810: } /* End age is not in the model */
5811: } /* End if model includes a product */
5812: else { /* no more sum */
5813: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
5814: /* scanf("%d",i);*/
5815: cutl(strd,strc,strb,'V');
5816: ks++; /**< Number of simple covariates */
1.145 brouard 5817: cptcovn++;
1.187 brouard 5818: Tvar[k]=atoi(strd);
5819: }
5820: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
5821: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
5822: scanf("%d",i);*/
5823: } /* end of loop + on total covariates */
5824: } /* end if strlen(modelsave == 0) age*age might exist */
5825: } /* end if strlen(model == 0) */
1.136 brouard 5826:
5827: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
5828: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
5829:
5830: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
5831: printf("cptcovprod=%d ", cptcovprod);
5832: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
5833:
5834: scanf("%d ",i);*/
5835:
5836:
1.137 brouard 5837: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 5838: /*endread:*/
1.136 brouard 5839: printf("Exiting decodemodel: ");
5840: return (1);
5841: }
5842:
1.169 brouard 5843: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 5844: {
5845: int i, m;
5846:
5847: for (i=1; i<=imx; i++) {
5848: for(m=2; (m<= maxwav); m++) {
5849: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
5850: anint[m][i]=9999;
5851: s[m][i]=-1;
5852: }
5853: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 5854: *nberr = *nberr + 1;
5855: 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);
5856: 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);
1.136 brouard 5857: s[m][i]=-1;
5858: }
5859: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 5860: (*nberr)++;
1.136 brouard 5861: 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]);
5862: 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]);
5863: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
5864: }
5865: }
5866: }
5867:
5868: for (i=1; i<=imx; i++) {
5869: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
5870: for(m=firstpass; (m<= lastpass); m++){
5871: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
5872: if (s[m][i] >= nlstate+1) {
1.169 brouard 5873: if(agedc[i]>0){
5874: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 5875: agev[m][i]=agedc[i];
5876: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 5877: }else {
1.136 brouard 5878: if ((int)andc[i]!=9999){
5879: nbwarn++;
5880: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
5881: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
5882: agev[m][i]=-1;
5883: }
5884: }
1.169 brouard 5885: } /* agedc > 0 */
1.136 brouard 5886: }
5887: else if(s[m][i] !=9){ /* Standard case, age in fractional
5888: years but with the precision of a month */
5889: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
5890: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
5891: agev[m][i]=1;
5892: else if(agev[m][i] < *agemin){
5893: *agemin=agev[m][i];
5894: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
5895: }
5896: else if(agev[m][i] >*agemax){
5897: *agemax=agev[m][i];
1.156 brouard 5898: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 5899: }
5900: /*agev[m][i]=anint[m][i]-annais[i];*/
5901: /* agev[m][i] = age[i]+2*m;*/
5902: }
5903: else { /* =9 */
5904: agev[m][i]=1;
5905: s[m][i]=-1;
5906: }
5907: }
5908: else /*= 0 Unknown */
5909: agev[m][i]=1;
5910: }
5911:
5912: }
5913: for (i=1; i<=imx; i++) {
5914: for(m=firstpass; (m<=lastpass); m++){
5915: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 5916: (*nberr)++;
1.136 brouard 5917: 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);
5918: 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);
5919: return 1;
5920: }
5921: }
5922: }
5923:
5924: /*for (i=1; i<=imx; i++){
5925: for (m=firstpass; (m<lastpass); m++){
5926: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
5927: }
5928:
5929: }*/
5930:
5931:
1.139 brouard 5932: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
5933: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 5934:
5935: return (0);
1.164 brouard 5936: /* endread:*/
1.136 brouard 5937: printf("Exiting calandcheckages: ");
5938: return (1);
5939: }
5940:
1.172 brouard 5941: #if defined(_MSC_VER)
5942: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5943: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
5944: //#include "stdafx.h"
5945: //#include <stdio.h>
5946: //#include <tchar.h>
5947: //#include <windows.h>
5948: //#include <iostream>
5949: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
5950:
5951: LPFN_ISWOW64PROCESS fnIsWow64Process;
5952:
5953: BOOL IsWow64()
5954: {
5955: BOOL bIsWow64 = FALSE;
5956:
5957: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
5958: // (HANDLE, PBOOL);
5959:
5960: //LPFN_ISWOW64PROCESS fnIsWow64Process;
5961:
5962: HMODULE module = GetModuleHandle(_T("kernel32"));
5963: const char funcName[] = "IsWow64Process";
5964: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
5965: GetProcAddress(module, funcName);
5966:
5967: if (NULL != fnIsWow64Process)
5968: {
5969: if (!fnIsWow64Process(GetCurrentProcess(),
5970: &bIsWow64))
5971: //throw std::exception("Unknown error");
5972: printf("Unknown error\n");
5973: }
5974: return bIsWow64 != FALSE;
5975: }
5976: #endif
1.177 brouard 5977:
1.191 brouard 5978: void syscompilerinfo(int logged)
1.167 brouard 5979: {
5980: /* #include "syscompilerinfo.h"*/
1.185 brouard 5981: /* command line Intel compiler 32bit windows, XP compatible:*/
5982: /* /GS /W3 /Gy
5983: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
5984: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
5985: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 5986: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
5987: */
5988: /* 64 bits */
1.185 brouard 5989: /*
5990: /GS /W3 /Gy
5991: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
5992: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
5993: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
5994: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
5995: /* Optimization are useless and O3 is slower than O2 */
5996: /*
5997: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
5998: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
5999: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6000: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6001: */
1.186 brouard 6002: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6003: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6004: /PDB:"visual studio
6005: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6006: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6007: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6008: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6009: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6010: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6011: uiAccess='false'"
6012: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6013: /NOLOGO /TLBID:1
6014: */
1.177 brouard 6015: #if defined __INTEL_COMPILER
1.178 brouard 6016: #if defined(__GNUC__)
6017: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6018: #endif
1.177 brouard 6019: #elif defined(__GNUC__)
1.179 brouard 6020: #ifndef __APPLE__
1.174 brouard 6021: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6022: #endif
1.177 brouard 6023: struct utsname sysInfo;
1.178 brouard 6024: int cross = CROSS;
6025: if (cross){
6026: printf("Cross-");
1.191 brouard 6027: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6028: }
1.174 brouard 6029: #endif
6030:
1.171 brouard 6031: #include <stdint.h>
1.178 brouard 6032:
1.191 brouard 6033: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6034: #if defined(__clang__)
1.191 brouard 6035: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6036: #endif
6037: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6038: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6039: #endif
6040: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6041: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6042: #endif
6043: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6044: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6045: #endif
6046: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6047: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6048: #endif
6049: #if defined(_MSC_VER)
1.191 brouard 6050: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6051: #endif
6052: #if defined(__PGI)
1.191 brouard 6053: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6054: #endif
6055: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6056: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6057: #endif
1.191 brouard 6058: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6059:
1.167 brouard 6060: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6061: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6062: // Windows (x64 and x86)
1.191 brouard 6063: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6064: #elif __unix__ // all unices, not all compilers
6065: // Unix
1.191 brouard 6066: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6067: #elif __linux__
6068: // linux
1.191 brouard 6069: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6070: #elif __APPLE__
1.174 brouard 6071: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6072: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6073: #endif
6074:
6075: /* __MINGW32__ */
6076: /* __CYGWIN__ */
6077: /* __MINGW64__ */
6078: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6079: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6080: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6081: /* _WIN64 // Defined for applications for Win64. */
6082: /* _M_X64 // Defined for compilations that target x64 processors. */
6083: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6084:
1.167 brouard 6085: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6086: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6087: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6088: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6089: #else
1.191 brouard 6090: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6091: #endif
6092:
1.169 brouard 6093: #if defined(__GNUC__)
6094: # if defined(__GNUC_PATCHLEVEL__)
6095: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6096: + __GNUC_MINOR__ * 100 \
6097: + __GNUC_PATCHLEVEL__)
6098: # else
6099: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6100: + __GNUC_MINOR__ * 100)
6101: # endif
1.174 brouard 6102: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6103: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6104:
6105: if (uname(&sysInfo) != -1) {
6106: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6107: if(logged) fprintf(ficlog,"Running on: %s %s %s %s %s\n ",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.176 brouard 6108: }
6109: else
6110: perror("uname() error");
1.179 brouard 6111: //#ifndef __INTEL_COMPILER
6112: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6113: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6114: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6115: #endif
1.169 brouard 6116: #endif
1.172 brouard 6117:
6118: // void main()
6119: // {
1.169 brouard 6120: #if defined(_MSC_VER)
1.174 brouard 6121: if (IsWow64()){
1.191 brouard 6122: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6123: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6124: }
6125: else{
1.191 brouard 6126: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6127: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6128: }
1.172 brouard 6129: // printf("\nPress Enter to continue...");
6130: // getchar();
6131: // }
6132:
1.169 brouard 6133: #endif
6134:
1.167 brouard 6135:
6136: }
1.136 brouard 6137:
1.180 brouard 6138: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar){
6139: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6140: int i, j, k, i1 ;
6141: double ftolpl = 1.e-10;
6142: double age, agebase, agelim;
6143:
6144: strcpy(filerespl,"pl");
6145: strcat(filerespl,fileres);
6146: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6147: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6148: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6149: }
6150: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6151: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6152: pstamp(ficrespl);
6153: fprintf(ficrespl,"# Period (stable) prevalence \n");
6154: fprintf(ficrespl,"#Age ");
6155: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6156: fprintf(ficrespl,"\n");
6157:
6158: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6159:
6160: agebase=ageminpar;
6161: agelim=agemaxpar;
6162:
6163: i1=pow(2,cptcoveff);
6164: if (cptcovn < 1){i1=1;}
6165:
6166: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6167: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6168: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6169: k=k+1;
6170: /* to clean */
6171: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtab[cptcod][cptcov]);
6172: fprintf(ficrespl,"\n#******");
6173: printf("\n#******");
6174: fprintf(ficlog,"\n#******");
6175: for(j=1;j<=cptcoveff;j++) {
6176: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6177: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6178: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6179: }
6180: fprintf(ficrespl,"******\n");
6181: printf("******\n");
6182: fprintf(ficlog,"******\n");
6183:
6184: fprintf(ficrespl,"#Age ");
6185: for(j=1;j<=cptcoveff;j++) {
6186: fprintf(ficrespl,"V%d %d",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6187: }
6188: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6189: fprintf(ficrespl,"\n");
6190:
6191: for (age=agebase; age<=agelim; age++){
6192: /* for (age=agebase; age<=agebase; age++){ */
6193: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
6194: fprintf(ficrespl,"%.0f ",age );
6195: for(j=1;j<=cptcoveff;j++)
6196: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6197: for(i=1; i<=nlstate;i++)
6198: fprintf(ficrespl," %.5f", prlim[i][i]);
6199: fprintf(ficrespl,"\n");
6200: } /* Age */
6201: /* was end of cptcod */
6202: } /* cptcov */
1.184 brouard 6203: return 0;
1.180 brouard 6204: }
6205:
6206: int hPijx(double *p, int bage, int fage){
6207: /*------------- h Pij x at various ages ------------*/
6208:
6209: int stepsize;
6210: int agelim;
6211: int hstepm;
6212: int nhstepm;
6213: int h, i, i1, j, k;
6214:
6215: double agedeb;
6216: double ***p3mat;
6217:
6218: strcpy(filerespij,"pij"); strcat(filerespij,fileres);
6219: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6220: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6221: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6222: }
6223: printf("Computing pij: result on file '%s' \n", filerespij);
6224: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6225:
6226: stepsize=(int) (stepm+YEARM-1)/YEARM;
6227: /*if (stepm<=24) stepsize=2;*/
6228:
6229: agelim=AGESUP;
6230: hstepm=stepsize*YEARM; /* Every year of age */
6231: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6232:
6233: /* hstepm=1; aff par mois*/
6234: pstamp(ficrespij);
6235: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6236: i1= pow(2,cptcoveff);
1.183 brouard 6237: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6238: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6239: /* k=k+1; */
6240: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6241: fprintf(ficrespij,"\n#****** ");
6242: for(j=1;j<=cptcoveff;j++)
6243: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
6244: fprintf(ficrespij,"******\n");
6245:
6246: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6247: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6248: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6249:
6250: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6251:
1.183 brouard 6252: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6253: oldm=oldms;savm=savms;
6254: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6255: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6256: for(i=1; i<=nlstate;i++)
6257: for(j=1; j<=nlstate+ndeath;j++)
6258: fprintf(ficrespij," %1d-%1d",i,j);
6259: fprintf(ficrespij,"\n");
6260: for (h=0; h<=nhstepm; h++){
6261: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6262: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6263: for(i=1; i<=nlstate;i++)
6264: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6265: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6266: fprintf(ficrespij,"\n");
6267: }
1.183 brouard 6268: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6269: fprintf(ficrespij,"\n");
6270: }
1.180 brouard 6271: /*}*/
6272: }
1.184 brouard 6273: return 0;
1.180 brouard 6274: }
6275:
6276:
1.136 brouard 6277: /***********************************************/
6278: /**************** Main Program *****************/
6279: /***********************************************/
6280:
6281: int main(int argc, char *argv[])
6282: {
6283: #ifdef GSL
6284: const gsl_multimin_fminimizer_type *T;
6285: size_t iteri = 0, it;
6286: int rval = GSL_CONTINUE;
6287: int status = GSL_SUCCESS;
6288: double ssval;
6289: #endif
6290: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6291: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
6292:
6293: int jj, ll, li, lj, lk;
1.136 brouard 6294: int numlinepar=0; /* Current linenumber of parameter file */
1.197 ! brouard 6295: int num_filled;
1.136 brouard 6296: int itimes;
6297: int NDIM=2;
6298: int vpopbased=0;
6299:
1.164 brouard 6300: char ca[32], cb[32];
1.136 brouard 6301: /* FILE *fichtm; *//* Html File */
6302: /* FILE *ficgp;*/ /*Gnuplot File */
6303: struct stat info;
1.191 brouard 6304: double agedeb=0.;
1.194 brouard 6305:
6306: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6307:
1.165 brouard 6308: double fret;
1.191 brouard 6309: double dum=0.; /* Dummy variable */
1.136 brouard 6310: double ***p3mat;
6311: double ***mobaverage;
1.164 brouard 6312:
6313: char line[MAXLINE];
1.197 ! brouard 6314: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
! 6315:
! 6316: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6317: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6318: char *tok, *val; /* pathtot */
1.136 brouard 6319: int firstobs=1, lastobs=10;
1.195 brouard 6320: int c, h , cpt, c2;
1.191 brouard 6321: int jl=0;
6322: int i1, j1, jk, stepsize=0;
1.194 brouard 6323: int count=0;
6324:
1.164 brouard 6325: int *tab;
1.136 brouard 6326: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6327: int mobilav=0,popforecast=0;
1.191 brouard 6328: int hstepm=0, nhstepm=0;
1.136 brouard 6329: int agemortsup;
6330: float sumlpop=0.;
6331: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6332: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6333:
1.191 brouard 6334: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6335: double ftolpl=FTOL;
6336: double **prlim;
6337: double ***param; /* Matrix of parameters */
6338: double *p;
6339: double **matcov; /* Matrix of covariance */
6340: double ***delti3; /* Scale */
6341: double *delti; /* Scale */
6342: double ***eij, ***vareij;
6343: double **varpl; /* Variances of prevalence limits by age */
6344: double *epj, vepp;
1.164 brouard 6345:
1.136 brouard 6346: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6347: double **ximort;
1.145 brouard 6348: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6349: int *dcwave;
6350:
1.164 brouard 6351: char z[1]="c";
1.136 brouard 6352:
6353: /*char *strt;*/
6354: char strtend[80];
1.126 brouard 6355:
1.164 brouard 6356:
1.126 brouard 6357: /* setlocale (LC_ALL, ""); */
6358: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6359: /* textdomain (PACKAGE); */
6360: /* setlocale (LC_CTYPE, ""); */
6361: /* setlocale (LC_MESSAGES, ""); */
6362:
6363: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6364: rstart_time = time(NULL);
6365: /* (void) gettimeofday(&start_time,&tzp);*/
6366: start_time = *localtime(&rstart_time);
1.126 brouard 6367: curr_time=start_time;
1.157 brouard 6368: /*tml = *localtime(&start_time.tm_sec);*/
6369: /* strcpy(strstart,asctime(&tml)); */
6370: strcpy(strstart,asctime(&start_time));
1.126 brouard 6371:
6372: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6373: /* tp.tm_sec = tp.tm_sec +86400; */
6374: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6375: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6376: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6377: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6378: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6379: /* strt=asctime(&tmg); */
6380: /* printf("Time(after) =%s",strstart); */
6381: /* (void) time (&time_value);
6382: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6383: * tm = *localtime(&time_value);
6384: * strstart=asctime(&tm);
6385: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6386: */
6387:
6388: nberr=0; /* Number of errors and warnings */
6389: nbwarn=0;
1.184 brouard 6390: #ifdef WIN32
6391: _getcwd(pathcd, size);
6392: #else
1.126 brouard 6393: getcwd(pathcd, size);
1.184 brouard 6394: #endif
1.191 brouard 6395: syscompilerinfo(0);
1.196 brouard 6396: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6397: if(argc <=1){
6398: printf("\nEnter the parameter file name: ");
6399: fgets(pathr,FILENAMELENGTH,stdin);
6400: i=strlen(pathr);
6401: if(pathr[i-1]=='\n')
6402: pathr[i-1]='\0';
1.156 brouard 6403: i=strlen(pathr);
6404: if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
6405: pathr[i-1]='\0';
1.126 brouard 6406: for (tok = pathr; tok != NULL; ){
6407: printf("Pathr |%s|\n",pathr);
6408: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6409: printf("val= |%s| pathr=%s\n",val,pathr);
6410: strcpy (pathtot, val);
6411: if(pathr[0] == '\0') break; /* Dirty */
6412: }
6413: }
6414: else{
6415: strcpy(pathtot,argv[1]);
6416: }
6417: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6418: /*cygwin_split_path(pathtot,path,optionfile);
6419: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6420: /* cutv(path,optionfile,pathtot,'\\');*/
6421:
6422: /* Split argv[0], imach program to get pathimach */
6423: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6424: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6425: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6426: /* strcpy(pathimach,argv[0]); */
6427: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6428: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6429: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6430: #ifdef WIN32
6431: _chdir(path); /* Can be a relative path */
6432: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6433: #else
1.126 brouard 6434: chdir(path); /* Can be a relative path */
1.184 brouard 6435: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6436: #endif
6437: printf("Current directory %s!\n",pathcd);
1.126 brouard 6438: strcpy(command,"mkdir ");
6439: strcat(command,optionfilefiname);
6440: if((outcmd=system(command)) != 0){
1.169 brouard 6441: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6442: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6443: /* fclose(ficlog); */
6444: /* exit(1); */
6445: }
6446: /* if((imk=mkdir(optionfilefiname))<0){ */
6447: /* perror("mkdir"); */
6448: /* } */
6449:
6450: /*-------- arguments in the command line --------*/
6451:
1.186 brouard 6452: /* Main Log file */
1.126 brouard 6453: strcat(filelog, optionfilefiname);
6454: strcat(filelog,".log"); /* */
6455: if((ficlog=fopen(filelog,"w"))==NULL) {
6456: printf("Problem with logfile %s\n",filelog);
6457: goto end;
6458: }
6459: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 ! brouard 6460: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6461: fprintf(ficlog,"\nEnter the parameter file name: \n");
6462: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6463: path=%s \n\
6464: optionfile=%s\n\
6465: optionfilext=%s\n\
1.156 brouard 6466: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6467:
1.197 ! brouard 6468: syscompilerinfo(1);
1.167 brouard 6469:
1.126 brouard 6470: printf("Local time (at start):%s",strstart);
6471: fprintf(ficlog,"Local time (at start): %s",strstart);
6472: fflush(ficlog);
6473: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6474: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6475:
6476: /* */
6477: strcpy(fileres,"r");
6478: strcat(fileres, optionfilefiname);
6479: strcat(fileres,".txt"); /* Other files have txt extension */
6480:
1.186 brouard 6481: /* Main ---------arguments file --------*/
1.126 brouard 6482:
6483: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6484: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6485: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6486: fflush(ficlog);
1.149 brouard 6487: /* goto end; */
6488: exit(70);
1.126 brouard 6489: }
6490:
6491:
6492:
6493: strcpy(filereso,"o");
6494: strcat(filereso,fileres);
6495: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6496: printf("Problem with Output resultfile: %s\n", filereso);
6497: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6498: fflush(ficlog);
6499: goto end;
6500: }
6501:
6502: /* Reads comments: lines beginning with '#' */
6503: numlinepar=0;
1.197 ! brouard 6504:
! 6505: /* First parameter line */
! 6506: while(fgets(line, MAXLINE, ficpar)) {
! 6507: /* If line starts with a # it is a comment */
! 6508: if (line[0] == '#') {
! 6509: numlinepar++;
! 6510: fputs(line,stdout);
! 6511: fputs(line,ficparo);
! 6512: fputs(line,ficlog);
! 6513: continue;
! 6514: }else
! 6515: break;
! 6516: }
! 6517: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
! 6518: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
! 6519: if (num_filled != 5) {
! 6520: printf("Should be 5 parameters\n");
! 6521: }
1.126 brouard 6522: numlinepar++;
1.197 ! brouard 6523: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
! 6524: }
! 6525: /* Second parameter line */
! 6526: while(fgets(line, MAXLINE, ficpar)) {
! 6527: /* If line starts with a # it is a comment */
! 6528: if (line[0] == '#') {
! 6529: numlinepar++;
! 6530: fputs(line,stdout);
! 6531: fputs(line,ficparo);
! 6532: fputs(line,ficlog);
! 6533: continue;
! 6534: }else
! 6535: break;
! 6536: }
! 6537: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
! 6538: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
! 6539: if (num_filled != 8) {
! 6540: printf("Not 8\n");
! 6541: }
! 6542: printf("ftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt);
1.126 brouard 6543: }
6544:
1.197 ! brouard 6545: /* Third parameter line */
! 6546: while(fgets(line, MAXLINE, ficpar)) {
! 6547: /* If line starts with a # it is a comment */
! 6548: if (line[0] == '#') {
! 6549: numlinepar++;
! 6550: fputs(line,stdout);
! 6551: fputs(line,ficparo);
! 6552: fputs(line,ficlog);
! 6553: continue;
! 6554: }else
! 6555: break;
! 6556: }
! 6557: if((num_filled=sscanf(line,"model=1+age%[^.\n]\n", model)) !=EOF){
! 6558: if (num_filled != 1) {
! 6559: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
! 6560: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
! 6561: model[0]='\0';
! 6562: goto end;
! 6563: }
! 6564: else{
! 6565: if (model[0]=='+'){
! 6566: for(i=1; i<=strlen(model);i++)
! 6567: modeltemp[i-1]=model[i];
! 6568: }
! 6569: strcpy(model,modeltemp);
! 6570: }
! 6571: printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout);
! 6572: }
! 6573: /* 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); */
! 6574: /* numlinepar=numlinepar+3; /\* In general *\/ */
! 6575: /* 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); */
1.187 brouard 6576: if(model[strlen(model)-1]=='.') /* Suppressing leading dot in the model */
6577: model[strlen(model)-1]='\0';
1.197 ! brouard 6578: 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);
! 6579: 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);
1.126 brouard 6580: fflush(ficlog);
1.190 brouard 6581: /* if(model[0]=='#'|| model[0]== '\0'){ */
6582: if(model[0]=='#'){
1.187 brouard 6583: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6584: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6585: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6586: if(mle != -1){
6587: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6588: exit(1);
6589: }
6590: }
1.126 brouard 6591: while((c=getc(ficpar))=='#' && c!= EOF){
6592: ungetc(c,ficpar);
6593: fgets(line, MAXLINE, ficpar);
6594: numlinepar++;
1.195 brouard 6595: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6596: z[0]=line[1];
6597: }
6598: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6599: fputs(line, stdout);
6600: //puts(line);
1.126 brouard 6601: fputs(line,ficparo);
6602: fputs(line,ficlog);
6603: }
6604: ungetc(c,ficpar);
6605:
6606:
1.145 brouard 6607: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6608: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6609: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6610: v1+v2*age+v2*v3 makes cptcovn = 3
6611: */
6612: if (strlen(model)>1)
1.187 brouard 6613: 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*/
1.145 brouard 6614: else
1.187 brouard 6615: ncovmodel=2; /* Constant and age */
1.133 brouard 6616: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
6617: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 6618: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
6619: 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);
6620: 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);
6621: fflush(stdout);
6622: fclose (ficlog);
6623: goto end;
6624: }
1.126 brouard 6625: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6626: delti=delti3[1][1];
6627: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
6628: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
6629: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 6630: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
6631: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6632: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
6633: fclose (ficparo);
6634: fclose (ficlog);
6635: goto end;
6636: exit(0);
6637: }
1.186 brouard 6638: else if(mle==-3) { /* Main Wizard */
1.126 brouard 6639: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 6640: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
6641: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 6642: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6643: matcov=matrix(1,npar,1,npar);
6644: }
6645: else{
1.145 brouard 6646: /* Read guessed parameters */
1.126 brouard 6647: /* Reads comments: lines beginning with '#' */
6648: while((c=getc(ficpar))=='#' && c!= EOF){
6649: ungetc(c,ficpar);
6650: fgets(line, MAXLINE, ficpar);
6651: numlinepar++;
1.141 brouard 6652: fputs(line,stdout);
1.126 brouard 6653: fputs(line,ficparo);
6654: fputs(line,ficlog);
6655: }
6656: ungetc(c,ficpar);
6657:
6658: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
6659: for(i=1; i <=nlstate; i++){
6660: j=0;
6661: for(jj=1; jj <=nlstate+ndeath; jj++){
6662: if(jj==i) continue;
6663: j++;
6664: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 6665: if ((i1 != i) || (j1 != jj)){
1.126 brouard 6666: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
6667: It might be a problem of design; if ncovcol and the model are correct\n \
6668: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
6669: exit(1);
6670: }
6671: fprintf(ficparo,"%1d%1d",i1,j1);
6672: if(mle==1)
1.193 brouard 6673: printf("%1d%1d",i,jj);
6674: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 6675: for(k=1; k<=ncovmodel;k++){
6676: fscanf(ficpar," %lf",¶m[i][j][k]);
6677: if(mle==1){
6678: printf(" %lf",param[i][j][k]);
6679: fprintf(ficlog," %lf",param[i][j][k]);
6680: }
6681: else
6682: fprintf(ficlog," %lf",param[i][j][k]);
6683: fprintf(ficparo," %lf",param[i][j][k]);
6684: }
6685: fscanf(ficpar,"\n");
6686: numlinepar++;
6687: if(mle==1)
6688: printf("\n");
6689: fprintf(ficlog,"\n");
6690: fprintf(ficparo,"\n");
6691: }
6692: }
6693: fflush(ficlog);
6694:
1.145 brouard 6695: /* Reads scales values */
1.126 brouard 6696: p=param[1][1];
6697:
6698: /* Reads comments: lines beginning with '#' */
6699: while((c=getc(ficpar))=='#' && c!= EOF){
6700: ungetc(c,ficpar);
6701: fgets(line, MAXLINE, ficpar);
6702: numlinepar++;
1.141 brouard 6703: fputs(line,stdout);
1.126 brouard 6704: fputs(line,ficparo);
6705: fputs(line,ficlog);
6706: }
6707: ungetc(c,ficpar);
6708:
6709: for(i=1; i <=nlstate; i++){
6710: for(j=1; j <=nlstate+ndeath-1; j++){
6711: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 6712: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 6713: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
6714: exit(1);
6715: }
6716: printf("%1d%1d",i,j);
6717: fprintf(ficparo,"%1d%1d",i1,j1);
6718: fprintf(ficlog,"%1d%1d",i1,j1);
6719: for(k=1; k<=ncovmodel;k++){
6720: fscanf(ficpar,"%le",&delti3[i][j][k]);
6721: printf(" %le",delti3[i][j][k]);
6722: fprintf(ficparo," %le",delti3[i][j][k]);
6723: fprintf(ficlog," %le",delti3[i][j][k]);
6724: }
6725: fscanf(ficpar,"\n");
6726: numlinepar++;
6727: printf("\n");
6728: fprintf(ficparo,"\n");
6729: fprintf(ficlog,"\n");
6730: }
6731: }
6732: fflush(ficlog);
6733:
1.145 brouard 6734: /* Reads covariance matrix */
1.126 brouard 6735: delti=delti3[1][1];
6736:
6737:
6738: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
6739:
6740: /* Reads comments: lines beginning with '#' */
6741: while((c=getc(ficpar))=='#' && c!= EOF){
6742: ungetc(c,ficpar);
6743: fgets(line, MAXLINE, ficpar);
6744: numlinepar++;
1.141 brouard 6745: fputs(line,stdout);
1.126 brouard 6746: fputs(line,ficparo);
6747: fputs(line,ficlog);
6748: }
6749: ungetc(c,ficpar);
6750:
6751: matcov=matrix(1,npar,1,npar);
1.131 brouard 6752: for(i=1; i <=npar; i++)
6753: for(j=1; j <=npar; j++) matcov[i][j]=0.;
6754:
1.194 brouard 6755: /* Scans npar lines */
1.126 brouard 6756: for(i=1; i <=npar; i++){
1.194 brouard 6757: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
6758: if(count != 3){
6759: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6760: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6761: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6762: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
6763: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
6764: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
6765: exit(1);
6766: }else
1.126 brouard 6767: if(mle==1)
1.194 brouard 6768: printf("%1d%1d%1d",i1,j1,jk);
6769: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
6770: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 6771: for(j=1; j <=i; j++){
6772: fscanf(ficpar," %le",&matcov[i][j]);
6773: if(mle==1){
6774: printf(" %.5le",matcov[i][j]);
6775: }
6776: fprintf(ficlog," %.5le",matcov[i][j]);
6777: fprintf(ficparo," %.5le",matcov[i][j]);
6778: }
6779: fscanf(ficpar,"\n");
6780: numlinepar++;
6781: if(mle==1)
6782: printf("\n");
6783: fprintf(ficlog,"\n");
6784: fprintf(ficparo,"\n");
6785: }
1.194 brouard 6786: /* End of read covariance matrix npar lines */
1.126 brouard 6787: for(i=1; i <=npar; i++)
6788: for(j=i+1;j<=npar;j++)
6789: matcov[i][j]=matcov[j][i];
6790:
6791: if(mle==1)
6792: printf("\n");
6793: fprintf(ficlog,"\n");
6794:
6795: fflush(ficlog);
6796:
6797: /*-------- Rewriting parameter file ----------*/
6798: strcpy(rfileres,"r"); /* "Rparameterfile */
6799: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
6800: strcat(rfileres,"."); /* */
6801: strcat(rfileres,optionfilext); /* Other files have txt extension */
6802: if((ficres =fopen(rfileres,"w"))==NULL) {
6803: printf("Problem writing new parameter file: %s\n", fileres);goto end;
6804: fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
6805: }
6806: fprintf(ficres,"#%s\n",version);
6807: } /* End of mle != -3 */
6808:
1.186 brouard 6809: /* Main data
6810: */
1.126 brouard 6811: n= lastobs;
6812: num=lvector(1,n);
6813: moisnais=vector(1,n);
6814: annais=vector(1,n);
6815: moisdc=vector(1,n);
6816: andc=vector(1,n);
6817: agedc=vector(1,n);
6818: cod=ivector(1,n);
6819: weight=vector(1,n);
6820: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
6821: mint=matrix(1,maxwav,1,n);
6822: anint=matrix(1,maxwav,1,n);
1.131 brouard 6823: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 6824: tab=ivector(1,NCOVMAX);
1.144 brouard 6825: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 6826: ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.126 brouard 6827:
1.136 brouard 6828: /* Reads data from file datafile */
6829: if (readdata(datafile, firstobs, lastobs, &imx)==1)
6830: goto end;
6831:
6832: /* Calculation of the number of parameters from char model */
1.137 brouard 6833: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
6834: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
6835: k=3 V4 Tvar[k=3]= 4 (from V4)
6836: k=2 V1 Tvar[k=2]= 1 (from V1)
6837: k=1 Tvar[1]=2 (from V2)
6838: */
6839: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
6840: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
6841: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
6842: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
6843: */
6844: /* For model-covariate k tells which data-covariate to use but
6845: because this model-covariate is a construction we invent a new column
6846: ncovcol + k1
6847: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
6848: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 6849: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 6850: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
6851: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
6852: */
1.145 brouard 6853: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
6854: Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
1.141 brouard 6855: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
6856: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 6857: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 6858: 4 covariates (3 plus signs)
6859: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
6860: */
1.136 brouard 6861:
1.186 brouard 6862: /* Main decodemodel */
6863:
1.187 brouard 6864:
1.136 brouard 6865: if(decodemodel(model, lastobs) == 1)
6866: goto end;
6867:
1.137 brouard 6868: if((double)(lastobs-imx)/(double)imx > 1.10){
6869: nbwarn++;
6870: 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);
6871: 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);
6872: }
1.136 brouard 6873: /* if(mle==1){*/
1.137 brouard 6874: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
6875: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 6876: }
6877:
6878: /*-calculation of age at interview from date of interview and age at death -*/
6879: agev=matrix(1,maxwav,1,imx);
6880:
6881: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
6882: goto end;
6883:
1.126 brouard 6884:
1.136 brouard 6885: agegomp=(int)agemin;
6886: free_vector(moisnais,1,n);
6887: free_vector(annais,1,n);
1.126 brouard 6888: /* free_matrix(mint,1,maxwav,1,n);
6889: free_matrix(anint,1,maxwav,1,n);*/
6890: free_vector(moisdc,1,n);
6891: free_vector(andc,1,n);
1.145 brouard 6892: /* */
6893:
1.126 brouard 6894: wav=ivector(1,imx);
6895: dh=imatrix(1,lastpass-firstpass+1,1,imx);
6896: bh=imatrix(1,lastpass-firstpass+1,1,imx);
6897: mw=imatrix(1,lastpass-firstpass+1,1,imx);
6898:
6899: /* Concatenates waves */
6900: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 6901: /* */
6902:
1.126 brouard 6903: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
6904:
6905: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
6906: ncodemax[1]=1;
1.145 brouard 6907: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 6908: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 6909: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 6910: /* Nbcode gives the value of the lth modality of jth covariate, in
6911: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
6912: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 6913:
6914: codtab=imatrix(1,100,1,10); /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
6915: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtab[100][10]);*/
1.186 brouard 6916: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 6917: h=0;
6918:
6919:
6920: /*if (cptcovn > 0) */
1.126 brouard 6921:
1.145 brouard 6922:
1.126 brouard 6923: m=pow(2,cptcoveff);
6924:
1.144 brouard 6925: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 6926: * For k=4 covariates, h goes from 1 to 2**k
6927: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
6928: * h\k 1 2 3 4
1.143 brouard 6929: *______________________________
6930: * 1 i=1 1 i=1 1 i=1 1 i=1 1
6931: * 2 2 1 1 1
6932: * 3 i=2 1 2 1 1
6933: * 4 2 2 1 1
6934: * 5 i=3 1 i=2 1 2 1
6935: * 6 2 1 2 1
6936: * 7 i=4 1 2 2 1
6937: * 8 2 2 2 1
1.197 ! brouard 6938: * 9 i=5 1 i=3 1 i=2 1 2
! 6939: * 10 2 1 1 2
! 6940: * 11 i=6 1 2 1 2
! 6941: * 12 2 2 1 2
! 6942: * 13 i=7 1 i=4 1 2 2
! 6943: * 14 2 1 2 2
! 6944: * 15 i=8 1 2 2 2
! 6945: * 16 2 2 2 2
1.143 brouard 6946: */
1.197 ! brouard 6947: for(h=1; h <=100 ;h++){
! 6948: /* printf("h=%2d ", h); */
! 6949: for(k=1; k <=10; k++){
! 6950: /* printf("k=%d %d ",k,codtabm(h,k)); */
! 6951: codtab[h][k]=codtabm(h,k);
! 6952: }
! 6953: /* printf("\n"); */
! 6954: }
! 6955: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
! 6956: /* 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 *\/ */
! 6957: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
! 6958: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
! 6959: /* h++; */
! 6960: /* if (h>m) */
! 6961: /* h=1; */
! 6962: /* codtab[h][k]=j; */
! 6963: /* /\* codtab[12][3]=1; *\/ */
! 6964: /* /\*codtab[h][Tvar[k]]=j;*\/ */
! 6965: /* /\* 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]]); *\/ */
! 6966: /* } */
! 6967: /* } */
! 6968: /* } */
! 6969: /* } */
1.126 brouard 6970: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
6971: codtab[1][2]=1;codtab[2][2]=2; */
1.197 ! brouard 6972: /* for(i=1; i <=m ;i++){ */
! 6973: /* for(k=1; k <=cptcovn; k++){ */
! 6974: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
! 6975: /* } */
! 6976: /* printf("\n"); */
! 6977: /* } */
! 6978: /* scanf("%d",i);*/
1.145 brouard 6979:
6980: free_ivector(Ndum,-1,NCOVMAX);
6981:
6982:
1.126 brouard 6983:
1.186 brouard 6984: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 6985: strcpy(optionfilegnuplot,optionfilefiname);
6986: if(mle==-3)
6987: strcat(optionfilegnuplot,"-mort");
6988: strcat(optionfilegnuplot,".gp");
6989:
6990: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
6991: printf("Problem with file %s",optionfilegnuplot);
6992: }
6993: else{
6994: fprintf(ficgp,"\n# %s\n", version);
6995: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 6996: //fprintf(ficgp,"set missing 'NaNq'\n");
6997: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 6998: }
6999: /* fclose(ficgp);*/
1.186 brouard 7000:
7001:
7002: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7003:
7004: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7005: if(mle==-3)
7006: strcat(optionfilehtm,"-mort");
7007: strcat(optionfilehtm,".htm");
7008: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7009: printf("Problem with %s \n",optionfilehtm);
7010: exit(0);
1.126 brouard 7011: }
7012:
7013: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7014: strcat(optionfilehtmcov,"-cov.htm");
7015: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7016: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7017: }
7018: else{
7019: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7020: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7021: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
7022: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7023: }
7024:
7025: fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7026: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7027: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
7028: \n\
7029: <hr size=\"2\" color=\"#EC5E5E\">\
7030: <ul><li><h4>Parameter files</h4>\n\
7031: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7032: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7033: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7034: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7035: - Date and time at start: %s</ul>\n",\
7036: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7037: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7038: fileres,fileres,\
7039: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7040: fflush(fichtm);
7041:
7042: strcpy(pathr,path);
7043: strcat(pathr,optionfilefiname);
1.184 brouard 7044: #ifdef WIN32
7045: _chdir(optionfilefiname); /* Move to directory named optionfile */
7046: #else
1.126 brouard 7047: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7048: #endif
7049:
1.126 brouard 7050:
7051: /* Calculates basic frequencies. Computes observed prevalence at single age
7052: and prints on file fileres'p'. */
7053: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7054:
7055: fprintf(fichtm,"\n");
7056: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7057: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7058: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7059: imx,agemin,agemax,jmin,jmax,jmean);
7060: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7061: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7062: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7063: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7064: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7065:
7066:
7067: /* For Powell, parameters are in a vector p[] starting at p[1]
7068: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7069: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7070:
7071: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7072: /* For mortality only */
1.126 brouard 7073: if (mle==-3){
1.136 brouard 7074: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7075: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7076: cens=ivector(1,n);
7077: ageexmed=vector(1,n);
7078: agecens=vector(1,n);
7079: dcwave=ivector(1,n);
7080:
7081: for (i=1; i<=imx; i++){
7082: dcwave[i]=-1;
7083: for (m=firstpass; m<=lastpass; m++)
7084: if (s[m][i]>nlstate) {
7085: dcwave[i]=m;
7086: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7087: break;
7088: }
7089: }
7090:
7091: for (i=1; i<=imx; i++) {
7092: if (wav[i]>0){
7093: ageexmed[i]=agev[mw[1][i]][i];
7094: j=wav[i];
7095: agecens[i]=1.;
7096:
7097: if (ageexmed[i]> 1 && wav[i] > 0){
7098: agecens[i]=agev[mw[j][i]][i];
7099: cens[i]= 1;
7100: }else if (ageexmed[i]< 1)
7101: cens[i]= -1;
7102: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7103: cens[i]=0 ;
7104: }
7105: else cens[i]=-1;
7106: }
7107:
7108: for (i=1;i<=NDIM;i++) {
7109: for (j=1;j<=NDIM;j++)
7110: ximort[i][j]=(i == j ? 1.0 : 0.0);
7111: }
7112:
1.145 brouard 7113: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7114: /*printf("%lf %lf", p[1], p[2]);*/
7115:
7116:
1.136 brouard 7117: #ifdef GSL
7118: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7119: #else
1.126 brouard 7120: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7121: #endif
1.126 brouard 7122: strcpy(filerespow,"pow-mort");
7123: strcat(filerespow,fileres);
7124: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7125: printf("Problem with resultfile: %s\n", filerespow);
7126: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7127: }
1.136 brouard 7128: #ifdef GSL
7129: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7130: #else
1.126 brouard 7131: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7132: #endif
1.126 brouard 7133: /* for (i=1;i<=nlstate;i++)
7134: for(j=1;j<=nlstate+ndeath;j++)
7135: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7136: */
7137: fprintf(ficrespow,"\n");
1.136 brouard 7138: #ifdef GSL
7139: /* gsl starts here */
7140: T = gsl_multimin_fminimizer_nmsimplex;
7141: gsl_multimin_fminimizer *sfm = NULL;
7142: gsl_vector *ss, *x;
7143: gsl_multimin_function minex_func;
7144:
7145: /* Initial vertex size vector */
7146: ss = gsl_vector_alloc (NDIM);
7147:
7148: if (ss == NULL){
7149: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7150: }
7151: /* Set all step sizes to 1 */
7152: gsl_vector_set_all (ss, 0.001);
7153:
7154: /* Starting point */
1.126 brouard 7155:
1.136 brouard 7156: x = gsl_vector_alloc (NDIM);
7157:
7158: if (x == NULL){
7159: gsl_vector_free(ss);
7160: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7161: }
7162:
7163: /* Initialize method and iterate */
7164: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7165: /* gsl_vector_set(x, 0, 0.0268); */
7166: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7167: gsl_vector_set(x, 0, p[1]);
7168: gsl_vector_set(x, 1, p[2]);
7169:
7170: minex_func.f = &gompertz_f;
7171: minex_func.n = NDIM;
7172: minex_func.params = (void *)&p; /* ??? */
7173:
7174: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7175: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7176:
7177: printf("Iterations beginning .....\n\n");
7178: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7179:
7180: iteri=0;
7181: while (rval == GSL_CONTINUE){
7182: iteri++;
7183: status = gsl_multimin_fminimizer_iterate(sfm);
7184:
7185: if (status) printf("error: %s\n", gsl_strerror (status));
7186: fflush(0);
7187:
7188: if (status)
7189: break;
7190:
7191: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7192: ssval = gsl_multimin_fminimizer_size (sfm);
7193:
7194: if (rval == GSL_SUCCESS)
7195: printf ("converged to a local maximum at\n");
7196:
7197: printf("%5d ", iteri);
7198: for (it = 0; it < NDIM; it++){
7199: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7200: }
7201: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7202: }
7203:
7204: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7205:
7206: gsl_vector_free(x); /* initial values */
7207: gsl_vector_free(ss); /* inital step size */
7208: for (it=0; it<NDIM; it++){
7209: p[it+1]=gsl_vector_get(sfm->x,it);
7210: fprintf(ficrespow," %.12lf", p[it]);
7211: }
7212: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7213: #endif
7214: #ifdef POWELL
7215: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7216: #endif
1.126 brouard 7217: fclose(ficrespow);
7218:
7219: hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
7220:
7221: for(i=1; i <=NDIM; i++)
7222: for(j=i+1;j<=NDIM;j++)
7223: matcov[i][j]=matcov[j][i];
7224:
7225: printf("\nCovariance matrix\n ");
7226: for(i=1; i <=NDIM; i++) {
7227: for(j=1;j<=NDIM;j++){
7228: printf("%f ",matcov[i][j]);
7229: }
7230: printf("\n ");
7231: }
7232:
7233: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7234: for (i=1;i<=NDIM;i++) {
1.126 brouard 7235: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7236: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7237: }
1.126 brouard 7238: lsurv=vector(1,AGESUP);
7239: lpop=vector(1,AGESUP);
7240: tpop=vector(1,AGESUP);
7241: lsurv[agegomp]=100000;
7242:
7243: for (k=agegomp;k<=AGESUP;k++) {
7244: agemortsup=k;
7245: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7246: }
7247:
7248: for (k=agegomp;k<agemortsup;k++)
7249: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7250:
7251: for (k=agegomp;k<agemortsup;k++){
7252: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7253: sumlpop=sumlpop+lpop[k];
7254: }
7255:
7256: tpop[agegomp]=sumlpop;
7257: for (k=agegomp;k<(agemortsup-3);k++){
7258: /* tpop[k+1]=2;*/
7259: tpop[k+1]=tpop[k]-lpop[k];
7260: }
7261:
7262:
7263: printf("\nAge lx qx dx Lx Tx e(x)\n");
7264: for (k=agegomp;k<(agemortsup-2);k++)
7265: 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]);
7266:
7267:
7268: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7269: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7270: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7271: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7272: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7273: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7274: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7275: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7276: }else
7277: printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7278: printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
7279: stepm, weightopt,\
7280: model,imx,p,matcov,agemortsup);
7281:
7282: free_vector(lsurv,1,AGESUP);
7283: free_vector(lpop,1,AGESUP);
7284: free_vector(tpop,1,AGESUP);
1.136 brouard 7285: #ifdef GSL
7286: free_ivector(cens,1,n);
7287: free_vector(agecens,1,n);
7288: free_ivector(dcwave,1,n);
7289: free_matrix(ximort,1,NDIM,1,NDIM);
7290: #endif
1.186 brouard 7291: } /* Endof if mle==-3 mortality only */
7292: /* Standard maximisation */
1.126 brouard 7293: else{ /* For mle >=1 */
1.132 brouard 7294: globpr=0;/* debug */
1.186 brouard 7295: /* Computes likelihood for initial parameters */
1.132 brouard 7296: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7297: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7298: for (k=1; k<=npar;k++)
7299: printf(" %d %8.5f",k,p[k]);
7300: printf("\n");
1.186 brouard 7301: globpr=1; /* again, to print the contributions */
1.126 brouard 7302: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7303: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7304: for (k=1; k<=npar;k++)
7305: printf(" %d %8.5f",k,p[k]);
7306: printf("\n");
1.186 brouard 7307: if(mle>=1){ /* Could be 1 or 2, Real Maximisation */
1.126 brouard 7308: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7309: }
7310:
7311: /*--------- results files --------------*/
1.192 brouard 7312: 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);
1.126 brouard 7313:
7314:
7315: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7316: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7317: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7318: for(i=1,jk=1; i <=nlstate; i++){
7319: for(k=1; k <=(nlstate+ndeath); k++){
7320: if (k != i) {
7321: printf("%d%d ",i,k);
7322: fprintf(ficlog,"%d%d ",i,k);
7323: fprintf(ficres,"%1d%1d ",i,k);
7324: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7325: printf("%12.7f ",p[jk]);
7326: fprintf(ficlog,"%12.7f ",p[jk]);
7327: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7328: jk++;
7329: }
7330: printf("\n");
7331: fprintf(ficlog,"\n");
7332: fprintf(ficres,"\n");
7333: }
7334: }
7335: }
7336: if(mle!=0){
7337: /* Computing hessian and covariance matrix */
7338: ftolhess=ftol; /* Usually correct */
7339: hesscov(matcov, p, npar, delti, ftolhess, func);
7340: }
1.197 ! brouard 7341: printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
! 7342: fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
1.193 brouard 7343: for(i=1,jk=1; i <=nlstate; i++){
7344: for(k=1; k <=(nlstate+ndeath); k++){
7345: if (k != i) {
7346: printf("%d%d ",i,k);
7347: fprintf(ficlog,"%d%d ",i,k);
7348: for(j=1; j <=ncovmodel; j++){
1.197 ! brouard 7349: printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
! 7350: fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96*sqrt(matcov[jk][jk]),p[jk]+1.96*sqrt(matcov[jk][jk]));
1.193 brouard 7351: jk++;
7352: }
7353: printf("\n");
7354: fprintf(ficlog,"\n");
7355: }
7356: }
7357: }
7358:
1.126 brouard 7359: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7360: printf("# Scales (for hessian or gradient estimation)\n");
7361: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7362: for(i=1,jk=1; i <=nlstate; i++){
7363: for(j=1; j <=nlstate+ndeath; j++){
7364: if (j!=i) {
7365: fprintf(ficres,"%1d%1d",i,j);
7366: printf("%1d%1d",i,j);
7367: fprintf(ficlog,"%1d%1d",i,j);
7368: for(k=1; k<=ncovmodel;k++){
7369: printf(" %.5e",delti[jk]);
7370: fprintf(ficlog," %.5e",delti[jk]);
7371: fprintf(ficres," %.5e",delti[jk]);
7372: jk++;
7373: }
7374: printf("\n");
7375: fprintf(ficlog,"\n");
7376: fprintf(ficres,"\n");
7377: }
7378: }
7379: }
7380:
7381: 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");
7382: if(mle>=1)
7383: 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");
7384: 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");
7385: /* # 121 Var(a12)\n\ */
7386: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7387: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7388: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7389: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7390: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7391: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7392: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7393:
7394:
7395: /* Just to have a covariance matrix which will be more understandable
7396: even is we still don't want to manage dictionary of variables
7397: */
7398: for(itimes=1;itimes<=2;itimes++){
7399: jj=0;
7400: for(i=1; i <=nlstate; i++){
7401: for(j=1; j <=nlstate+ndeath; j++){
7402: if(j==i) continue;
7403: for(k=1; k<=ncovmodel;k++){
7404: jj++;
7405: ca[0]= k+'a'-1;ca[1]='\0';
7406: if(itimes==1){
7407: if(mle>=1)
7408: printf("#%1d%1d%d",i,j,k);
7409: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7410: fprintf(ficres,"#%1d%1d%d",i,j,k);
7411: }else{
7412: if(mle>=1)
7413: printf("%1d%1d%d",i,j,k);
7414: fprintf(ficlog,"%1d%1d%d",i,j,k);
7415: fprintf(ficres,"%1d%1d%d",i,j,k);
7416: }
7417: ll=0;
7418: for(li=1;li <=nlstate; li++){
7419: for(lj=1;lj <=nlstate+ndeath; lj++){
7420: if(lj==li) continue;
7421: for(lk=1;lk<=ncovmodel;lk++){
7422: ll++;
7423: if(ll<=jj){
7424: cb[0]= lk +'a'-1;cb[1]='\0';
7425: if(ll<jj){
7426: if(itimes==1){
7427: if(mle>=1)
7428: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7429: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7430: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7431: }else{
7432: if(mle>=1)
7433: printf(" %.5e",matcov[jj][ll]);
7434: fprintf(ficlog," %.5e",matcov[jj][ll]);
7435: fprintf(ficres," %.5e",matcov[jj][ll]);
7436: }
7437: }else{
7438: if(itimes==1){
7439: if(mle>=1)
7440: printf(" Var(%s%1d%1d)",ca,i,j);
7441: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7442: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7443: }else{
7444: if(mle>=1)
7445: printf(" %.5e",matcov[jj][ll]);
7446: fprintf(ficlog," %.5e",matcov[jj][ll]);
7447: fprintf(ficres," %.5e",matcov[jj][ll]);
7448: }
7449: }
7450: }
7451: } /* end lk */
7452: } /* end lj */
7453: } /* end li */
7454: if(mle>=1)
7455: printf("\n");
7456: fprintf(ficlog,"\n");
7457: fprintf(ficres,"\n");
7458: numlinepar++;
7459: } /* end k*/
7460: } /*end j */
7461: } /* end i */
7462: } /* end itimes */
7463:
7464: fflush(ficlog);
7465: fflush(ficres);
7466:
7467: while((c=getc(ficpar))=='#' && c!= EOF){
7468: ungetc(c,ficpar);
7469: fgets(line, MAXLINE, ficpar);
1.141 brouard 7470: fputs(line,stdout);
1.126 brouard 7471: fputs(line,ficparo);
7472: }
7473: ungetc(c,ficpar);
7474:
7475: estepm=0;
7476: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7477: if (estepm==0 || estepm < stepm) estepm=stepm;
7478: if (fage <= 2) {
7479: bage = ageminpar;
7480: fage = agemaxpar;
7481: }
7482:
7483: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7484: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7485: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7486:
7487: /* Other stuffs, more or less useful */
1.126 brouard 7488: while((c=getc(ficpar))=='#' && c!= EOF){
7489: ungetc(c,ficpar);
7490: fgets(line, MAXLINE, ficpar);
1.141 brouard 7491: fputs(line,stdout);
1.126 brouard 7492: fputs(line,ficparo);
7493: }
7494: ungetc(c,ficpar);
7495:
7496: 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);
7497: 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);
7498: 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);
7499: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7500: 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);
7501:
7502: while((c=getc(ficpar))=='#' && c!= EOF){
7503: ungetc(c,ficpar);
7504: fgets(line, MAXLINE, ficpar);
1.141 brouard 7505: fputs(line,stdout);
1.126 brouard 7506: fputs(line,ficparo);
7507: }
7508: ungetc(c,ficpar);
7509:
7510:
7511: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7512: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7513:
7514: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7515: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7516: fprintf(ficparo,"pop_based=%d\n",popbased);
7517: fprintf(ficres,"pop_based=%d\n",popbased);
7518:
7519: while((c=getc(ficpar))=='#' && c!= EOF){
7520: ungetc(c,ficpar);
7521: fgets(line, MAXLINE, ficpar);
1.141 brouard 7522: fputs(line,stdout);
1.126 brouard 7523: fputs(line,ficparo);
7524: }
7525: ungetc(c,ficpar);
7526:
7527: 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);
7528: 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);
7529: 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);
7530: 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);
7531: 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);
7532: /* day and month of proj2 are not used but only year anproj2.*/
7533:
7534:
7535:
1.145 brouard 7536: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7537: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7538:
7539: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7540: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7541: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7542: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7543: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7544: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7545: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7546: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7547: }else
7548: printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7549:
7550: printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
7551: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7552: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7553:
7554: /*------------ free_vector -------------*/
7555: /* chdir(path); */
7556:
7557: free_ivector(wav,1,imx);
7558: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7559: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7560: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7561: free_lvector(num,1,n);
7562: free_vector(agedc,1,n);
7563: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7564: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7565: fclose(ficparo);
7566: fclose(ficres);
7567:
7568:
1.186 brouard 7569: /* Other results (useful)*/
7570:
7571:
1.126 brouard 7572: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7573: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7574: prlim=matrix(1,nlstate,1,nlstate);
7575: prevalence_limit(p, prlim, ageminpar, agemaxpar);
1.126 brouard 7576: fclose(ficrespl);
7577:
1.145 brouard 7578: #ifdef FREEEXIT2
7579: #include "freeexit2.h"
7580: #endif
7581:
1.126 brouard 7582: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7583: /*#include "hpijx.h"*/
7584: hPijx(p, bage, fage);
1.145 brouard 7585: fclose(ficrespij);
1.126 brouard 7586:
1.145 brouard 7587: /*-------------- Variance of one-step probabilities---*/
7588: k=1;
1.126 brouard 7589: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7590:
7591:
7592: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7593: for(i=1;i<=AGESUP;i++)
7594: for(j=1;j<=NCOVMAX;j++)
7595: for(k=1;k<=NCOVMAX;k++)
7596: probs[i][j][k]=0.;
7597:
7598: /*---------- Forecasting ------------------*/
7599: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
7600: if(prevfcast==1){
7601: /* if(stepm ==1){*/
7602: prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
7603: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
7604: /* } */
7605: /* else{ */
7606: /* erreur=108; */
7607: /* 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); */
7608: /* 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); */
7609: /* } */
7610: }
1.186 brouard 7611:
7612: /* ------ Other prevalence ratios------------ */
1.126 brouard 7613:
1.127 brouard 7614: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
7615:
7616: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
7617: /* 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",\
7618: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
7619: */
1.126 brouard 7620:
1.127 brouard 7621: if (mobilav!=0) {
7622: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7623: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
7624: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
7625: printf(" Error in movingaverage mobilav=%d\n",mobilav);
7626: }
1.126 brouard 7627: }
7628:
7629:
1.127 brouard 7630: /*---------- Health expectancies, no variances ------------*/
7631:
1.126 brouard 7632: strcpy(filerese,"e");
7633: strcat(filerese,fileres);
7634: if((ficreseij=fopen(filerese,"w"))==NULL) {
7635: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7636: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
7637: }
7638: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
7639: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 7640: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7641: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7642:
7643: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 7644: fprintf(ficreseij,"\n#****** ");
7645: for(j=1;j<=cptcoveff;j++) {
7646: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7647: }
7648: fprintf(ficreseij,"******\n");
7649:
7650: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7651: oldm=oldms;savm=savms;
7652: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
7653:
7654: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7655: /*}*/
1.127 brouard 7656: }
7657: fclose(ficreseij);
7658:
7659:
7660: /*---------- Health expectancies and variances ------------*/
7661:
7662:
7663: strcpy(filerest,"t");
7664: strcat(filerest,fileres);
7665: if((ficrest=fopen(filerest,"w"))==NULL) {
7666: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
7667: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
7668: }
7669: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7670: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
7671:
1.126 brouard 7672:
7673: strcpy(fileresstde,"stde");
7674: strcat(fileresstde,fileres);
7675: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
7676: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7677: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
7678: }
7679: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7680: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
7681:
7682: strcpy(filerescve,"cve");
7683: strcat(filerescve,fileres);
7684: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
7685: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7686: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
7687: }
7688: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7689: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
7690:
7691: strcpy(fileresv,"v");
7692: strcat(fileresv,fileres);
7693: if((ficresvij=fopen(fileresv,"w"))==NULL) {
7694: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
7695: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
7696: }
7697: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7698: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
7699:
1.145 brouard 7700: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7701: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7702:
7703: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7704: fprintf(ficrest,"\n#****** ");
1.126 brouard 7705: for(j=1;j<=cptcoveff;j++)
7706: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7707: fprintf(ficrest,"******\n");
7708:
7709: fprintf(ficresstdeij,"\n#****** ");
7710: fprintf(ficrescveij,"\n#****** ");
7711: for(j=1;j<=cptcoveff;j++) {
7712: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7713: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7714: }
7715: fprintf(ficresstdeij,"******\n");
7716: fprintf(ficrescveij,"******\n");
7717:
7718: fprintf(ficresvij,"\n#****** ");
7719: for(j=1;j<=cptcoveff;j++)
7720: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7721: fprintf(ficresvij,"******\n");
7722:
7723: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7724: oldm=oldms;savm=savms;
1.127 brouard 7725: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 7726: /*
7727: */
7728: /* goto endfree; */
1.126 brouard 7729:
7730: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
7731: pstamp(ficrest);
1.145 brouard 7732:
7733:
1.128 brouard 7734: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.145 brouard 7735: oldm=oldms;savm=savms; /* Segmentation fault */
1.161 brouard 7736: cptcod= 0; /* To be deleted */
7737: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.145 brouard 7738: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 7739: if(vpopbased==1)
7740: 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);
7741: else
7742: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
7743: fprintf(ficrest,"# Age e.. (std) ");
7744: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
7745: fprintf(ficrest,"\n");
1.126 brouard 7746:
1.128 brouard 7747: epj=vector(1,nlstate+1);
7748: for(age=bage; age <=fage ;age++){
7749: prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
7750: if (vpopbased==1) {
7751: if(mobilav ==0){
7752: for(i=1; i<=nlstate;i++)
7753: prlim[i][i]=probs[(int)age][i][k];
7754: }else{ /* mobilav */
7755: for(i=1; i<=nlstate;i++)
7756: prlim[i][i]=mobaverage[(int)age][i][k];
7757: }
1.126 brouard 7758: }
7759:
1.128 brouard 7760: fprintf(ficrest," %4.0f",age);
7761: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
7762: for(i=1, epj[j]=0.;i <=nlstate;i++) {
7763: epj[j] += prlim[i][i]*eij[i][j][(int)age];
7764: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
7765: }
7766: epj[nlstate+1] +=epj[j];
1.126 brouard 7767: }
7768:
1.128 brouard 7769: for(i=1, vepp=0.;i <=nlstate;i++)
7770: for(j=1;j <=nlstate;j++)
7771: vepp += vareij[i][j][(int)age];
7772: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
7773: for(j=1;j <=nlstate;j++){
7774: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
7775: }
7776: fprintf(ficrest,"\n");
1.126 brouard 7777: }
7778: }
7779: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7780: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
7781: free_vector(epj,1,nlstate+1);
1.145 brouard 7782: /*}*/
1.126 brouard 7783: }
7784: free_vector(weight,1,n);
1.145 brouard 7785: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 7786: free_imatrix(s,1,maxwav+1,1,n);
7787: free_matrix(anint,1,maxwav,1,n);
7788: free_matrix(mint,1,maxwav,1,n);
7789: free_ivector(cod,1,n);
7790: free_ivector(tab,1,NCOVMAX);
7791: fclose(ficresstdeij);
7792: fclose(ficrescveij);
7793: fclose(ficresvij);
7794: fclose(ficrest);
7795: fclose(ficpar);
7796:
7797: /*------- Variance of period (stable) prevalence------*/
7798:
7799: strcpy(fileresvpl,"vpl");
7800: strcat(fileresvpl,fileres);
7801: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
7802: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
7803: exit(0);
7804: }
7805: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
7806:
1.145 brouard 7807: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
7808: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
7809:
7810: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7811: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 7812: for(j=1;j<=cptcoveff;j++)
7813: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
7814: fprintf(ficresvpl,"******\n");
7815:
7816: varpl=matrix(1,nlstate,(int) bage, (int) fage);
7817: oldm=oldms;savm=savms;
7818: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
7819: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 7820: /*}*/
1.126 brouard 7821: }
7822:
7823: fclose(ficresvpl);
7824:
7825: /*---------- End : free ----------------*/
7826: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
7827: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7828: } /* mle==-3 arrives here for freeing */
1.164 brouard 7829: /* endfree:*/
1.141 brouard 7830: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 7831: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
7832: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
7833: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
7834: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
7835: free_matrix(covar,0,NCOVMAX,1,n);
7836: free_matrix(matcov,1,npar,1,npar);
7837: /*free_vector(delti,1,npar);*/
7838: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7839: free_matrix(agev,1,maxwav,1,imx);
7840: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7841:
1.145 brouard 7842: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 7843: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 7844: free_ivector(Tvar,1,NCOVMAX);
7845: free_ivector(Tprod,1,NCOVMAX);
7846: free_ivector(Tvaraff,1,NCOVMAX);
7847: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 7848:
7849: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
7850: free_imatrix(codtab,1,100,1,10);
7851: fflush(fichtm);
7852: fflush(ficgp);
7853:
7854:
7855: if((nberr >0) || (nbwarn>0)){
7856: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
7857: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
7858: }else{
7859: printf("End of Imach\n");
7860: fprintf(ficlog,"End of Imach\n");
7861: }
7862: printf("See log file on %s\n",filelog);
7863: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 7864: /*(void) gettimeofday(&end_time,&tzp);*/
7865: rend_time = time(NULL);
7866: end_time = *localtime(&rend_time);
7867: /* tml = *localtime(&end_time.tm_sec); */
7868: strcpy(strtend,asctime(&end_time));
1.126 brouard 7869: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
7870: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 7871: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 7872:
1.157 brouard 7873: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
7874: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
7875: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 7876: /* printf("Total time was %d uSec.\n", total_usecs);*/
7877: /* if(fileappend(fichtm,optionfilehtm)){ */
7878: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7879: fclose(fichtm);
7880: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
7881: fclose(fichtmcov);
7882: fclose(ficgp);
7883: fclose(ficlog);
7884: /*------ End -----------*/
7885:
7886:
7887: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 7888: #ifdef WIN32
7889: if (_chdir(pathcd) != 0)
7890: printf("Can't move to directory %s!\n",path);
7891: if(_getcwd(pathcd,MAXLINE) > 0)
7892: #else
1.126 brouard 7893: if(chdir(pathcd) != 0)
1.184 brouard 7894: printf("Can't move to directory %s!\n", path);
7895: if (getcwd(pathcd, MAXLINE) > 0)
7896: #endif
1.126 brouard 7897: printf("Current directory %s!\n",pathcd);
7898: /*strcat(plotcmd,CHARSEPARATOR);*/
7899: sprintf(plotcmd,"gnuplot");
1.157 brouard 7900: #ifdef _WIN32
1.126 brouard 7901: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
7902: #endif
7903: if(!stat(plotcmd,&info)){
1.158 brouard 7904: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7905: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 7906: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 7907: }else
7908: strcpy(pplotcmd,plotcmd);
1.157 brouard 7909: #ifdef __unix
1.126 brouard 7910: strcpy(plotcmd,GNUPLOTPROGRAM);
7911: if(!stat(plotcmd,&info)){
1.158 brouard 7912: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7913: }else
7914: strcpy(pplotcmd,plotcmd);
7915: #endif
7916: }else
7917: strcpy(pplotcmd,plotcmd);
7918:
7919: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 7920: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 7921:
7922: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 7923: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 7924: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 7925: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 7926: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 7927: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 7928: }
1.158 brouard 7929: printf(" Successful, please wait...");
1.126 brouard 7930: while (z[0] != 'q') {
7931: /* chdir(path); */
1.154 brouard 7932: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 7933: scanf("%s",z);
7934: /* if (z[0] == 'c') system("./imach"); */
7935: if (z[0] == 'e') {
1.158 brouard 7936: #ifdef __APPLE__
1.152 brouard 7937: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 7938: #elif __linux
7939: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 7940: #else
1.152 brouard 7941: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 7942: #endif
7943: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
7944: system(pplotcmd);
1.126 brouard 7945: }
7946: else if (z[0] == 'g') system(plotcmd);
7947: else if (z[0] == 'q') exit(0);
7948: }
7949: end:
7950: while (z[0] != 'q') {
1.195 brouard 7951: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 7952: scanf("%s",z);
7953: }
7954: }
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