Annotation of imach/src/imach.c, revision 1.215
1.215 ! brouard 1: /* $Id: imach.c,v 1.214 2015/12/16 06:57:54 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.215 ! brouard 4: Revision 1.214 2015/12/16 06:57:54 brouard
! 5: Summary: temporary not working
! 6:
1.214 brouard 7: Revision 1.213 2015/12/11 18:22:17 brouard
8: Summary: 0.98r4
9:
1.213 brouard 10: Revision 1.212 2015/11/21 12:47:24 brouard
11: Summary: minor typo
12:
1.212 brouard 13: Revision 1.211 2015/11/21 12:41:11 brouard
14: Summary: 0.98r3 with some graph of projected cross-sectional
15:
16: Author: Nicolas Brouard
17:
1.211 brouard 18: Revision 1.210 2015/11/18 17:41:20 brouard
19: Summary: Start working on projected prevalences
20:
1.210 brouard 21: Revision 1.209 2015/11/17 22:12:03 brouard
22: Summary: Adding ftolpl parameter
23: Author: N Brouard
24:
25: We had difficulties to get smoothed confidence intervals. It was due
26: to the period prevalence which wasn't computed accurately. The inner
27: parameter ftolpl is now an outer parameter of the .imach parameter
28: file after estepm. If ftolpl is small 1.e-4 and estepm too,
29: computation are long.
30:
1.209 brouard 31: Revision 1.208 2015/11/17 14:31:57 brouard
32: Summary: temporary
33:
1.208 brouard 34: Revision 1.207 2015/10/27 17:36:57 brouard
35: *** empty log message ***
36:
1.207 brouard 37: Revision 1.206 2015/10/24 07:14:11 brouard
38: *** empty log message ***
39:
1.206 brouard 40: Revision 1.205 2015/10/23 15:50:53 brouard
41: Summary: 0.98r3 some clarification for graphs on likelihood contributions
42:
1.205 brouard 43: Revision 1.204 2015/10/01 16:20:26 brouard
44: Summary: Some new graphs of contribution to likelihood
45:
1.204 brouard 46: Revision 1.203 2015/09/30 17:45:14 brouard
47: Summary: looking at better estimation of the hessian
48:
49: Also a better criteria for convergence to the period prevalence And
50: therefore adding the number of years needed to converge. (The
51: prevalence in any alive state shold sum to one
52:
1.203 brouard 53: Revision 1.202 2015/09/22 19:45:16 brouard
54: Summary: Adding some overall graph on contribution to likelihood. Might change
55:
1.202 brouard 56: Revision 1.201 2015/09/15 17:34:58 brouard
57: Summary: 0.98r0
58:
59: - Some new graphs like suvival functions
60: - Some bugs fixed like model=1+age+V2.
61:
1.201 brouard 62: Revision 1.200 2015/09/09 16:53:55 brouard
63: Summary: Big bug thanks to Flavia
64:
65: Even model=1+age+V2. did not work anymore
66:
1.200 brouard 67: Revision 1.199 2015/09/07 14:09:23 brouard
68: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
69:
1.199 brouard 70: Revision 1.198 2015/09/03 07:14:39 brouard
71: Summary: 0.98q5 Flavia
72:
1.198 brouard 73: Revision 1.197 2015/09/01 18:24:39 brouard
74: *** empty log message ***
75:
1.197 brouard 76: Revision 1.196 2015/08/18 23:17:52 brouard
77: Summary: 0.98q5
78:
1.196 brouard 79: Revision 1.195 2015/08/18 16:28:39 brouard
80: Summary: Adding a hack for testing purpose
81:
82: After reading the title, ftol and model lines, if the comment line has
83: a q, starting with #q, the answer at the end of the run is quit. It
84: permits to run test files in batch with ctest. The former workaround was
85: $ echo q | imach foo.imach
86:
1.195 brouard 87: Revision 1.194 2015/08/18 13:32:00 brouard
88: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
89:
1.194 brouard 90: Revision 1.193 2015/08/04 07:17:42 brouard
91: Summary: 0.98q4
92:
1.193 brouard 93: Revision 1.192 2015/07/16 16:49:02 brouard
94: Summary: Fixing some outputs
95:
1.192 brouard 96: Revision 1.191 2015/07/14 10:00:33 brouard
97: Summary: Some fixes
98:
1.191 brouard 99: Revision 1.190 2015/05/05 08:51:13 brouard
100: Summary: Adding digits in output parameters (7 digits instead of 6)
101:
102: Fix 1+age+.
103:
1.190 brouard 104: Revision 1.189 2015/04/30 14:45:16 brouard
105: Summary: 0.98q2
106:
1.189 brouard 107: Revision 1.188 2015/04/30 08:27:53 brouard
108: *** empty log message ***
109:
1.188 brouard 110: Revision 1.187 2015/04/29 09:11:15 brouard
111: *** empty log message ***
112:
1.187 brouard 113: Revision 1.186 2015/04/23 12:01:52 brouard
114: Summary: V1*age is working now, version 0.98q1
115:
116: Some codes had been disabled in order to simplify and Vn*age was
117: working in the optimization phase, ie, giving correct MLE parameters,
118: but, as usual, outputs were not correct and program core dumped.
119:
1.186 brouard 120: Revision 1.185 2015/03/11 13:26:42 brouard
121: Summary: Inclusion of compile and links command line for Intel Compiler
122:
1.185 brouard 123: Revision 1.184 2015/03/11 11:52:39 brouard
124: Summary: Back from Windows 8. Intel Compiler
125:
1.184 brouard 126: Revision 1.183 2015/03/10 20:34:32 brouard
127: Summary: 0.98q0, trying with directest, mnbrak fixed
128:
129: We use directest instead of original Powell test; probably no
130: incidence on the results, but better justifications;
131: We fixed Numerical Recipes mnbrak routine which was wrong and gave
132: wrong results.
133:
1.183 brouard 134: Revision 1.182 2015/02/12 08:19:57 brouard
135: Summary: Trying to keep directest which seems simpler and more general
136: Author: Nicolas Brouard
137:
1.182 brouard 138: Revision 1.181 2015/02/11 23:22:24 brouard
139: Summary: Comments on Powell added
140:
141: Author:
142:
1.181 brouard 143: Revision 1.180 2015/02/11 17:33:45 brouard
144: Summary: Finishing move from main to function (hpijx and prevalence_limit)
145:
1.180 brouard 146: Revision 1.179 2015/01/04 09:57:06 brouard
147: Summary: back to OS/X
148:
1.179 brouard 149: Revision 1.178 2015/01/04 09:35:48 brouard
150: *** empty log message ***
151:
1.178 brouard 152: Revision 1.177 2015/01/03 18:40:56 brouard
153: Summary: Still testing ilc32 on OSX
154:
1.177 brouard 155: Revision 1.176 2015/01/03 16:45:04 brouard
156: *** empty log message ***
157:
1.176 brouard 158: Revision 1.175 2015/01/03 16:33:42 brouard
159: *** empty log message ***
160:
1.175 brouard 161: Revision 1.174 2015/01/03 16:15:49 brouard
162: Summary: Still in cross-compilation
163:
1.174 brouard 164: Revision 1.173 2015/01/03 12:06:26 brouard
165: Summary: trying to detect cross-compilation
166:
1.173 brouard 167: Revision 1.172 2014/12/27 12:07:47 brouard
168: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
169:
1.172 brouard 170: Revision 1.171 2014/12/23 13:26:59 brouard
171: Summary: Back from Visual C
172:
173: Still problem with utsname.h on Windows
174:
1.171 brouard 175: Revision 1.170 2014/12/23 11:17:12 brouard
176: Summary: Cleaning some \%% back to %%
177:
178: The escape was mandatory for a specific compiler (which one?), but too many warnings.
179:
1.170 brouard 180: Revision 1.169 2014/12/22 23:08:31 brouard
181: Summary: 0.98p
182:
183: Outputs some informations on compiler used, OS etc. Testing on different platforms.
184:
1.169 brouard 185: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 186: Summary: update
1.169 brouard 187:
1.168 brouard 188: Revision 1.167 2014/12/22 13:50:56 brouard
189: Summary: Testing uname and compiler version and if compiled 32 or 64
190:
191: Testing on Linux 64
192:
1.167 brouard 193: Revision 1.166 2014/12/22 11:40:47 brouard
194: *** empty log message ***
195:
1.166 brouard 196: Revision 1.165 2014/12/16 11:20:36 brouard
197: Summary: After compiling on Visual C
198:
199: * imach.c (Module): Merging 1.61 to 1.162
200:
1.165 brouard 201: Revision 1.164 2014/12/16 10:52:11 brouard
202: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
203:
204: * imach.c (Module): Merging 1.61 to 1.162
205:
1.164 brouard 206: Revision 1.163 2014/12/16 10:30:11 brouard
207: * imach.c (Module): Merging 1.61 to 1.162
208:
1.163 brouard 209: Revision 1.162 2014/09/25 11:43:39 brouard
210: Summary: temporary backup 0.99!
211:
1.162 brouard 212: Revision 1.1 2014/09/16 11:06:58 brouard
213: Summary: With some code (wrong) for nlopt
214:
215: Author:
216:
217: Revision 1.161 2014/09/15 20:41:41 brouard
218: Summary: Problem with macro SQR on Intel compiler
219:
1.161 brouard 220: Revision 1.160 2014/09/02 09:24:05 brouard
221: *** empty log message ***
222:
1.160 brouard 223: Revision 1.159 2014/09/01 10:34:10 brouard
224: Summary: WIN32
225: Author: Brouard
226:
1.159 brouard 227: Revision 1.158 2014/08/27 17:11:51 brouard
228: *** empty log message ***
229:
1.158 brouard 230: Revision 1.157 2014/08/27 16:26:55 brouard
231: Summary: Preparing windows Visual studio version
232: Author: Brouard
233:
234: In order to compile on Visual studio, time.h is now correct and time_t
235: and tm struct should be used. difftime should be used but sometimes I
236: just make the differences in raw time format (time(&now).
237: Trying to suppress #ifdef LINUX
238: Add xdg-open for __linux in order to open default browser.
239:
1.157 brouard 240: Revision 1.156 2014/08/25 20:10:10 brouard
241: *** empty log message ***
242:
1.156 brouard 243: Revision 1.155 2014/08/25 18:32:34 brouard
244: Summary: New compile, minor changes
245: Author: Brouard
246:
1.155 brouard 247: Revision 1.154 2014/06/20 17:32:08 brouard
248: Summary: Outputs now all graphs of convergence to period prevalence
249:
1.154 brouard 250: Revision 1.153 2014/06/20 16:45:46 brouard
251: Summary: If 3 live state, convergence to period prevalence on same graph
252: Author: Brouard
253:
1.153 brouard 254: Revision 1.152 2014/06/18 17:54:09 brouard
255: Summary: open browser, use gnuplot on same dir than imach if not found in the path
256:
1.152 brouard 257: Revision 1.151 2014/06/18 16:43:30 brouard
258: *** empty log message ***
259:
1.151 brouard 260: Revision 1.150 2014/06/18 16:42:35 brouard
261: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
262: Author: brouard
263:
1.150 brouard 264: Revision 1.149 2014/06/18 15:51:14 brouard
265: Summary: Some fixes in parameter files errors
266: Author: Nicolas Brouard
267:
1.149 brouard 268: Revision 1.148 2014/06/17 17:38:48 brouard
269: Summary: Nothing new
270: Author: Brouard
271:
272: Just a new packaging for OS/X version 0.98nS
273:
1.148 brouard 274: Revision 1.147 2014/06/16 10:33:11 brouard
275: *** empty log message ***
276:
1.147 brouard 277: Revision 1.146 2014/06/16 10:20:28 brouard
278: Summary: Merge
279: Author: Brouard
280:
281: Merge, before building revised version.
282:
1.146 brouard 283: Revision 1.145 2014/06/10 21:23:15 brouard
284: Summary: Debugging with valgrind
285: Author: Nicolas Brouard
286:
287: Lot of changes in order to output the results with some covariates
288: After the Edimburgh REVES conference 2014, it seems mandatory to
289: improve the code.
290: No more memory valgrind error but a lot has to be done in order to
291: continue the work of splitting the code into subroutines.
292: Also, decodemodel has been improved. Tricode is still not
293: optimal. nbcode should be improved. Documentation has been added in
294: the source code.
295:
1.144 brouard 296: Revision 1.143 2014/01/26 09:45:38 brouard
297: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
298:
299: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
300: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
301:
1.143 brouard 302: Revision 1.142 2014/01/26 03:57:36 brouard
303: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
304:
305: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
306:
1.142 brouard 307: Revision 1.141 2014/01/26 02:42:01 brouard
308: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
309:
1.141 brouard 310: Revision 1.140 2011/09/02 10:37:54 brouard
311: Summary: times.h is ok with mingw32 now.
312:
1.140 brouard 313: Revision 1.139 2010/06/14 07:50:17 brouard
314: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
315: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
316:
1.139 brouard 317: Revision 1.138 2010/04/30 18:19:40 brouard
318: *** empty log message ***
319:
1.138 brouard 320: Revision 1.137 2010/04/29 18:11:38 brouard
321: (Module): Checking covariates for more complex models
322: than V1+V2. A lot of change to be done. Unstable.
323:
1.137 brouard 324: Revision 1.136 2010/04/26 20:30:53 brouard
325: (Module): merging some libgsl code. Fixing computation
326: of likelione (using inter/intrapolation if mle = 0) in order to
327: get same likelihood as if mle=1.
328: Some cleaning of code and comments added.
329:
1.136 brouard 330: Revision 1.135 2009/10/29 15:33:14 brouard
331: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
332:
1.135 brouard 333: Revision 1.134 2009/10/29 13:18:53 brouard
334: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
335:
1.134 brouard 336: Revision 1.133 2009/07/06 10:21:25 brouard
337: just nforces
338:
1.133 brouard 339: Revision 1.132 2009/07/06 08:22:05 brouard
340: Many tings
341:
1.132 brouard 342: Revision 1.131 2009/06/20 16:22:47 brouard
343: Some dimensions resccaled
344:
1.131 brouard 345: Revision 1.130 2009/05/26 06:44:34 brouard
346: (Module): Max Covariate is now set to 20 instead of 8. A
347: lot of cleaning with variables initialized to 0. Trying to make
348: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
349:
1.130 brouard 350: Revision 1.129 2007/08/31 13:49:27 lievre
351: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
352:
1.129 lievre 353: Revision 1.128 2006/06/30 13:02:05 brouard
354: (Module): Clarifications on computing e.j
355:
1.128 brouard 356: Revision 1.127 2006/04/28 18:11:50 brouard
357: (Module): Yes the sum of survivors was wrong since
358: imach-114 because nhstepm was no more computed in the age
359: loop. Now we define nhstepma in the age loop.
360: (Module): In order to speed up (in case of numerous covariates) we
361: compute health expectancies (without variances) in a first step
362: and then all the health expectancies with variances or standard
363: deviation (needs data from the Hessian matrices) which slows the
364: computation.
365: In the future we should be able to stop the program is only health
366: expectancies and graph are needed without standard deviations.
367:
1.127 brouard 368: Revision 1.126 2006/04/28 17:23:28 brouard
369: (Module): Yes the sum of survivors was wrong since
370: imach-114 because nhstepm was no more computed in the age
371: loop. Now we define nhstepma in the age loop.
372: Version 0.98h
373:
1.126 brouard 374: Revision 1.125 2006/04/04 15:20:31 lievre
375: Errors in calculation of health expectancies. Age was not initialized.
376: Forecasting file added.
377:
378: Revision 1.124 2006/03/22 17:13:53 lievre
379: Parameters are printed with %lf instead of %f (more numbers after the comma).
380: The log-likelihood is printed in the log file
381:
382: Revision 1.123 2006/03/20 10:52:43 brouard
383: * imach.c (Module): <title> changed, corresponds to .htm file
384: name. <head> headers where missing.
385:
386: * imach.c (Module): Weights can have a decimal point as for
387: English (a comma might work with a correct LC_NUMERIC environment,
388: otherwise the weight is truncated).
389: Modification of warning when the covariates values are not 0 or
390: 1.
391: Version 0.98g
392:
393: Revision 1.122 2006/03/20 09:45:41 brouard
394: (Module): Weights can have a decimal point as for
395: English (a comma might work with a correct LC_NUMERIC environment,
396: otherwise the weight is truncated).
397: Modification of warning when the covariates values are not 0 or
398: 1.
399: Version 0.98g
400:
401: Revision 1.121 2006/03/16 17:45:01 lievre
402: * imach.c (Module): Comments concerning covariates added
403:
404: * imach.c (Module): refinements in the computation of lli if
405: status=-2 in order to have more reliable computation if stepm is
406: not 1 month. Version 0.98f
407:
408: Revision 1.120 2006/03/16 15:10:38 lievre
409: (Module): refinements in the computation of lli if
410: status=-2 in order to have more reliable computation if stepm is
411: not 1 month. Version 0.98f
412:
413: Revision 1.119 2006/03/15 17:42:26 brouard
414: (Module): Bug if status = -2, the loglikelihood was
415: computed as likelihood omitting the logarithm. Version O.98e
416:
417: Revision 1.118 2006/03/14 18:20:07 brouard
418: (Module): varevsij Comments added explaining the second
419: table of variances if popbased=1 .
420: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
421: (Module): Function pstamp added
422: (Module): Version 0.98d
423:
424: Revision 1.117 2006/03/14 17:16:22 brouard
425: (Module): varevsij Comments added explaining the second
426: table of variances if popbased=1 .
427: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
428: (Module): Function pstamp added
429: (Module): Version 0.98d
430:
431: Revision 1.116 2006/03/06 10:29:27 brouard
432: (Module): Variance-covariance wrong links and
433: varian-covariance of ej. is needed (Saito).
434:
435: Revision 1.115 2006/02/27 12:17:45 brouard
436: (Module): One freematrix added in mlikeli! 0.98c
437:
438: Revision 1.114 2006/02/26 12:57:58 brouard
439: (Module): Some improvements in processing parameter
440: filename with strsep.
441:
442: Revision 1.113 2006/02/24 14:20:24 brouard
443: (Module): Memory leaks checks with valgrind and:
444: datafile was not closed, some imatrix were not freed and on matrix
445: allocation too.
446:
447: Revision 1.112 2006/01/30 09:55:26 brouard
448: (Module): Back to gnuplot.exe instead of wgnuplot.exe
449:
450: Revision 1.111 2006/01/25 20:38:18 brouard
451: (Module): Lots of cleaning and bugs added (Gompertz)
452: (Module): Comments can be added in data file. Missing date values
453: can be a simple dot '.'.
454:
455: Revision 1.110 2006/01/25 00:51:50 brouard
456: (Module): Lots of cleaning and bugs added (Gompertz)
457:
458: Revision 1.109 2006/01/24 19:37:15 brouard
459: (Module): Comments (lines starting with a #) are allowed in data.
460:
461: Revision 1.108 2006/01/19 18:05:42 lievre
462: Gnuplot problem appeared...
463: To be fixed
464:
465: Revision 1.107 2006/01/19 16:20:37 brouard
466: Test existence of gnuplot in imach path
467:
468: Revision 1.106 2006/01/19 13:24:36 brouard
469: Some cleaning and links added in html output
470:
471: Revision 1.105 2006/01/05 20:23:19 lievre
472: *** empty log message ***
473:
474: Revision 1.104 2005/09/30 16:11:43 lievre
475: (Module): sump fixed, loop imx fixed, and simplifications.
476: (Module): If the status is missing at the last wave but we know
477: that the person is alive, then we can code his/her status as -2
478: (instead of missing=-1 in earlier versions) and his/her
479: contributions to the likelihood is 1 - Prob of dying from last
480: health status (= 1-p13= p11+p12 in the easiest case of somebody in
481: the healthy state at last known wave). Version is 0.98
482:
483: Revision 1.103 2005/09/30 15:54:49 lievre
484: (Module): sump fixed, loop imx fixed, and simplifications.
485:
486: Revision 1.102 2004/09/15 17:31:30 brouard
487: Add the possibility to read data file including tab characters.
488:
489: Revision 1.101 2004/09/15 10:38:38 brouard
490: Fix on curr_time
491:
492: Revision 1.100 2004/07/12 18:29:06 brouard
493: Add version for Mac OS X. Just define UNIX in Makefile
494:
495: Revision 1.99 2004/06/05 08:57:40 brouard
496: *** empty log message ***
497:
498: Revision 1.98 2004/05/16 15:05:56 brouard
499: New version 0.97 . First attempt to estimate force of mortality
500: directly from the data i.e. without the need of knowing the health
501: state at each age, but using a Gompertz model: log u =a + b*age .
502: This is the basic analysis of mortality and should be done before any
503: other analysis, in order to test if the mortality estimated from the
504: cross-longitudinal survey is different from the mortality estimated
505: from other sources like vital statistic data.
506:
507: The same imach parameter file can be used but the option for mle should be -3.
508:
1.133 brouard 509: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 510: former routines in order to include the new code within the former code.
511:
512: The output is very simple: only an estimate of the intercept and of
513: the slope with 95% confident intervals.
514:
515: Current limitations:
516: A) Even if you enter covariates, i.e. with the
517: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
518: B) There is no computation of Life Expectancy nor Life Table.
519:
520: Revision 1.97 2004/02/20 13:25:42 lievre
521: Version 0.96d. Population forecasting command line is (temporarily)
522: suppressed.
523:
524: Revision 1.96 2003/07/15 15:38:55 brouard
525: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
526: rewritten within the same printf. Workaround: many printfs.
527:
528: Revision 1.95 2003/07/08 07:54:34 brouard
529: * imach.c (Repository):
530: (Repository): Using imachwizard code to output a more meaningful covariance
531: matrix (cov(a12,c31) instead of numbers.
532:
533: Revision 1.94 2003/06/27 13:00:02 brouard
534: Just cleaning
535:
536: Revision 1.93 2003/06/25 16:33:55 brouard
537: (Module): On windows (cygwin) function asctime_r doesn't
538: exist so I changed back to asctime which exists.
539: (Module): Version 0.96b
540:
541: Revision 1.92 2003/06/25 16:30:45 brouard
542: (Module): On windows (cygwin) function asctime_r doesn't
543: exist so I changed back to asctime which exists.
544:
545: Revision 1.91 2003/06/25 15:30:29 brouard
546: * imach.c (Repository): Duplicated warning errors corrected.
547: (Repository): Elapsed time after each iteration is now output. It
548: helps to forecast when convergence will be reached. Elapsed time
549: is stamped in powell. We created a new html file for the graphs
550: concerning matrix of covariance. It has extension -cov.htm.
551:
552: Revision 1.90 2003/06/24 12:34:15 brouard
553: (Module): Some bugs corrected for windows. Also, when
554: mle=-1 a template is output in file "or"mypar.txt with the design
555: of the covariance matrix to be input.
556:
557: Revision 1.89 2003/06/24 12:30:52 brouard
558: (Module): Some bugs corrected for windows. Also, when
559: mle=-1 a template is output in file "or"mypar.txt with the design
560: of the covariance matrix to be input.
561:
562: Revision 1.88 2003/06/23 17:54:56 brouard
563: * 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.
564:
565: Revision 1.87 2003/06/18 12:26:01 brouard
566: Version 0.96
567:
568: Revision 1.86 2003/06/17 20:04:08 brouard
569: (Module): Change position of html and gnuplot routines and added
570: routine fileappend.
571:
572: Revision 1.85 2003/06/17 13:12:43 brouard
573: * imach.c (Repository): Check when date of death was earlier that
574: current date of interview. It may happen when the death was just
575: prior to the death. In this case, dh was negative and likelihood
576: was wrong (infinity). We still send an "Error" but patch by
577: assuming that the date of death was just one stepm after the
578: interview.
579: (Repository): Because some people have very long ID (first column)
580: we changed int to long in num[] and we added a new lvector for
581: memory allocation. But we also truncated to 8 characters (left
582: truncation)
583: (Repository): No more line truncation errors.
584:
585: Revision 1.84 2003/06/13 21:44:43 brouard
586: * imach.c (Repository): Replace "freqsummary" at a correct
587: place. It differs from routine "prevalence" which may be called
588: many times. Probs is memory consuming and must be used with
589: parcimony.
590: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
591:
592: Revision 1.83 2003/06/10 13:39:11 lievre
593: *** empty log message ***
594:
595: Revision 1.82 2003/06/05 15:57:20 brouard
596: Add log in imach.c and fullversion number is now printed.
597:
598: */
599: /*
600: Interpolated Markov Chain
601:
602: Short summary of the programme:
603:
604: This program computes Healthy Life Expectancies from
605: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
606: first survey ("cross") where individuals from different ages are
607: interviewed on their health status or degree of disability (in the
608: case of a health survey which is our main interest) -2- at least a
609: second wave of interviews ("longitudinal") which measure each change
610: (if any) in individual health status. Health expectancies are
611: computed from the time spent in each health state according to a
612: model. More health states you consider, more time is necessary to reach the
613: Maximum Likelihood of the parameters involved in the model. The
614: simplest model is the multinomial logistic model where pij is the
615: probability to be observed in state j at the second wave
616: conditional to be observed in state i at the first wave. Therefore
617: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
618: 'age' is age and 'sex' is a covariate. If you want to have a more
619: complex model than "constant and age", you should modify the program
620: where the markup *Covariates have to be included here again* invites
621: you to do it. More covariates you add, slower the
622: convergence.
623:
624: The advantage of this computer programme, compared to a simple
625: multinomial logistic model, is clear when the delay between waves is not
626: identical for each individual. Also, if a individual missed an
627: intermediate interview, the information is lost, but taken into
628: account using an interpolation or extrapolation.
629:
630: hPijx is the probability to be observed in state i at age x+h
631: conditional to the observed state i at age x. The delay 'h' can be
632: split into an exact number (nh*stepm) of unobserved intermediate
633: states. This elementary transition (by month, quarter,
634: semester or year) is modelled as a multinomial logistic. The hPx
635: matrix is simply the matrix product of nh*stepm elementary matrices
636: and the contribution of each individual to the likelihood is simply
637: hPijx.
638:
639: Also this programme outputs the covariance matrix of the parameters but also
640: of the life expectancies. It also computes the period (stable) prevalence.
641:
1.133 brouard 642: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
643: Institut national d'études démographiques, Paris.
1.126 brouard 644: This software have been partly granted by Euro-REVES, a concerted action
645: from the European Union.
646: It is copyrighted identically to a GNU software product, ie programme and
647: software can be distributed freely for non commercial use. Latest version
648: can be accessed at http://euroreves.ined.fr/imach .
649:
650: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
651: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
652:
653: **********************************************************************/
654: /*
655: main
656: read parameterfile
657: read datafile
658: concatwav
659: freqsummary
660: if (mle >= 1)
661: mlikeli
662: print results files
663: if mle==1
664: computes hessian
665: read end of parameter file: agemin, agemax, bage, fage, estepm
666: begin-prev-date,...
667: open gnuplot file
668: open html file
1.145 brouard 669: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
670: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
671: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
672: freexexit2 possible for memory heap.
673:
674: h Pij x | pij_nom ficrestpij
675: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
676: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
677: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
678:
679: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
680: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
681: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
682: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
683: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
684:
1.126 brouard 685: forecasting if prevfcast==1 prevforecast call prevalence()
686: health expectancies
687: Variance-covariance of DFLE
688: prevalence()
689: movingaverage()
690: varevsij()
691: if popbased==1 varevsij(,popbased)
692: total life expectancies
693: Variance of period (stable) prevalence
694: end
695: */
696:
1.187 brouard 697: /* #define DEBUG */
698: /* #define DEBUGBRENT */
1.203 brouard 699: /* #define DEBUGLINMIN */
700: /* #define DEBUGHESS */
701: #define DEBUGHESSIJ
702: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 703: #define POWELL /* Instead of NLOPT */
1.192 brouard 704: #define POWELLF1F3 /* Skip test */
1.186 brouard 705: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
706: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 707:
708: #include <math.h>
709: #include <stdio.h>
710: #include <stdlib.h>
711: #include <string.h>
1.159 brouard 712:
713: #ifdef _WIN32
714: #include <io.h>
1.172 brouard 715: #include <windows.h>
716: #include <tchar.h>
1.159 brouard 717: #else
1.126 brouard 718: #include <unistd.h>
1.159 brouard 719: #endif
1.126 brouard 720:
721: #include <limits.h>
722: #include <sys/types.h>
1.171 brouard 723:
724: #if defined(__GNUC__)
725: #include <sys/utsname.h> /* Doesn't work on Windows */
726: #endif
727:
1.126 brouard 728: #include <sys/stat.h>
729: #include <errno.h>
1.159 brouard 730: /* extern int errno; */
1.126 brouard 731:
1.157 brouard 732: /* #ifdef LINUX */
733: /* #include <time.h> */
734: /* #include "timeval.h" */
735: /* #else */
736: /* #include <sys/time.h> */
737: /* #endif */
738:
1.126 brouard 739: #include <time.h>
740:
1.136 brouard 741: #ifdef GSL
742: #include <gsl/gsl_errno.h>
743: #include <gsl/gsl_multimin.h>
744: #endif
745:
1.167 brouard 746:
1.162 brouard 747: #ifdef NLOPT
748: #include <nlopt.h>
749: typedef struct {
750: double (* function)(double [] );
751: } myfunc_data ;
752: #endif
753:
1.126 brouard 754: /* #include <libintl.h> */
755: /* #define _(String) gettext (String) */
756:
1.141 brouard 757: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 758:
759: #define GNUPLOTPROGRAM "gnuplot"
760: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
761: #define FILENAMELENGTH 132
762:
763: #define GLOCK_ERROR_NOPATH -1 /* empty path */
764: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
765:
1.144 brouard 766: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
767: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 768:
769: #define NINTERVMAX 8
1.144 brouard 770: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
771: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
772: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 773: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.211 brouard 774: /*#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)*/
775: #define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
1.126 brouard 776: #define MAXN 20000
1.144 brouard 777: #define YEARM 12. /**< Number of months per year */
1.126 brouard 778: #define AGESUP 130
779: #define AGEBASE 40
1.194 brouard 780: #define AGEOVERFLOW 1.e20
1.164 brouard 781: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 782: #ifdef _WIN32
783: #define DIRSEPARATOR '\\'
784: #define CHARSEPARATOR "\\"
785: #define ODIRSEPARATOR '/'
786: #else
1.126 brouard 787: #define DIRSEPARATOR '/'
788: #define CHARSEPARATOR "/"
789: #define ODIRSEPARATOR '\\'
790: #endif
791:
1.215 ! brouard 792: /* $Id: imach.c,v 1.214 2015/12/16 06:57:54 brouard Exp $ */
1.126 brouard 793: /* $State: Exp $ */
1.196 brouard 794: #include "version.h"
795: char version[]=__IMACH_VERSION__;
1.204 brouard 796: char copyright[]="October 2015,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015";
1.215 ! brouard 797: char fullversion[]="$Revision: 1.214 $ $Date: 2015/12/16 06:57:54 $";
1.126 brouard 798: char strstart[80];
799: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 800: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 801: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 802: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
803: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
804: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
805: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
806: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
807: int cptcovprodnoage=0; /**< Number of covariate products without age */
808: int cptcoveff=0; /* Total number of covariates to vary for printing results */
809: int cptcov=0; /* Working variable */
1.126 brouard 810: int npar=NPARMAX;
811: int nlstate=2; /* Number of live states */
812: int ndeath=1; /* Number of dead states */
1.130 brouard 813: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 814: int popbased=0;
815:
816: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 817: int maxwav=0; /* Maxim number of waves */
818: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
819: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
820: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 821: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 822: int mle=1, weightopt=0;
1.126 brouard 823: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
824: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
825: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
826: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 827: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 828: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 829: double **matprod2(); /* test */
1.126 brouard 830: double **oldm, **newm, **savm; /* Working pointers to matrices */
831: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 832: /*FILE *fic ; */ /* Used in readdata only */
1.214 brouard 833: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficresphtm, *ficresphtmfr, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 834: FILE *ficlog, *ficrespow;
1.130 brouard 835: int globpr=0; /* Global variable for printing or not */
1.126 brouard 836: double fretone; /* Only one call to likelihood */
1.130 brouard 837: long ipmx=0; /* Number of contributions */
1.126 brouard 838: double sw; /* Sum of weights */
839: char filerespow[FILENAMELENGTH];
840: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
841: FILE *ficresilk;
842: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
843: FILE *ficresprobmorprev;
844: FILE *fichtm, *fichtmcov; /* Html File */
845: FILE *ficreseij;
846: char filerese[FILENAMELENGTH];
847: FILE *ficresstdeij;
848: char fileresstde[FILENAMELENGTH];
849: FILE *ficrescveij;
850: char filerescve[FILENAMELENGTH];
851: FILE *ficresvij;
852: char fileresv[FILENAMELENGTH];
853: FILE *ficresvpl;
854: char fileresvpl[FILENAMELENGTH];
855: char title[MAXLINE];
856: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
857: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
858: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
859: char command[FILENAMELENGTH];
860: int outcmd=0;
861:
862: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 863: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 864: char filelog[FILENAMELENGTH]; /* Log file */
865: char filerest[FILENAMELENGTH];
866: char fileregp[FILENAMELENGTH];
867: char popfile[FILENAMELENGTH];
868:
869: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
870:
1.157 brouard 871: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
872: /* struct timezone tzp; */
873: /* extern int gettimeofday(); */
874: struct tm tml, *gmtime(), *localtime();
875:
876: extern time_t time();
877:
878: struct tm start_time, end_time, curr_time, last_time, forecast_time;
879: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
880: struct tm tm;
881:
1.126 brouard 882: char strcurr[80], strfor[80];
883:
884: char *endptr;
885: long lval;
886: double dval;
887:
888: #define NR_END 1
889: #define FREE_ARG char*
890: #define FTOL 1.0e-10
891:
892: #define NRANSI
893: #define ITMAX 200
894:
895: #define TOL 2.0e-4
896:
897: #define CGOLD 0.3819660
898: #define ZEPS 1.0e-10
899: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
900:
901: #define GOLD 1.618034
902: #define GLIMIT 100.0
903: #define TINY 1.0e-20
904:
905: static double maxarg1,maxarg2;
906: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
907: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
908:
909: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
910: #define rint(a) floor(a+0.5)
1.166 brouard 911: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 912: #define mytinydouble 1.0e-16
1.166 brouard 913: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
914: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
915: /* static double dsqrarg; */
916: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 917: static double sqrarg;
918: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
919: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
920: int agegomp= AGEGOMP;
921:
922: int imx;
923: int stepm=1;
924: /* Stepm, step in month: minimum step interpolation*/
925:
926: int estepm;
927: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
928:
929: int m,nb;
930: long *num;
1.197 brouard 931: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 932: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
933: covariate for which somebody answered excluding
934: undefined. Usually 2: 0 and 1. */
935: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
936: covariate for which somebody answered including
937: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 938: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
939: double **pmmij, ***probs;
940: double *ageexmed,*agecens;
941: double dateintmean=0;
942:
943: double *weight;
944: int **s; /* Status */
1.141 brouard 945: double *agedc;
1.145 brouard 946: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 947: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 948: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 949: double idx;
950: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 951: int *Tage;
1.145 brouard 952: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 953: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 954: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 955: double *lsurv, *lpop, *tpop;
956:
1.143 brouard 957: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
958: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 959:
960: /**************** split *************************/
961: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
962: {
963: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
964: the name of the file (name), its extension only (ext) and its first part of the name (finame)
965: */
966: char *ss; /* pointer */
1.186 brouard 967: int l1=0, l2=0; /* length counters */
1.126 brouard 968:
969: l1 = strlen(path ); /* length of path */
970: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
971: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
972: if ( ss == NULL ) { /* no directory, so determine current directory */
973: strcpy( name, path ); /* we got the fullname name because no directory */
974: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
975: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
976: /* get current working directory */
977: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 978: #ifdef WIN32
979: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
980: #else
981: if (getcwd(dirc, FILENAME_MAX) == NULL) {
982: #endif
1.126 brouard 983: return( GLOCK_ERROR_GETCWD );
984: }
985: /* got dirc from getcwd*/
986: printf(" DIRC = %s \n",dirc);
1.205 brouard 987: } else { /* strip directory from path */
1.126 brouard 988: ss++; /* after this, the filename */
989: l2 = strlen( ss ); /* length of filename */
990: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
991: strcpy( name, ss ); /* save file name */
992: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 993: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 994: printf(" DIRC2 = %s \n",dirc);
995: }
996: /* We add a separator at the end of dirc if not exists */
997: l1 = strlen( dirc ); /* length of directory */
998: if( dirc[l1-1] != DIRSEPARATOR ){
999: dirc[l1] = DIRSEPARATOR;
1000: dirc[l1+1] = 0;
1001: printf(" DIRC3 = %s \n",dirc);
1002: }
1003: ss = strrchr( name, '.' ); /* find last / */
1004: if (ss >0){
1005: ss++;
1006: strcpy(ext,ss); /* save extension */
1007: l1= strlen( name);
1008: l2= strlen(ss)+1;
1009: strncpy( finame, name, l1-l2);
1010: finame[l1-l2]= 0;
1011: }
1012:
1013: return( 0 ); /* we're done */
1014: }
1015:
1016:
1017: /******************************************/
1018:
1019: void replace_back_to_slash(char *s, char*t)
1020: {
1021: int i;
1022: int lg=0;
1023: i=0;
1024: lg=strlen(t);
1025: for(i=0; i<= lg; i++) {
1026: (s[i] = t[i]);
1027: if (t[i]== '\\') s[i]='/';
1028: }
1029: }
1030:
1.132 brouard 1031: char *trimbb(char *out, char *in)
1.137 brouard 1032: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 1033: char *s;
1034: s=out;
1035: while (*in != '\0'){
1.137 brouard 1036: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1037: in++;
1038: }
1039: *out++ = *in++;
1040: }
1041: *out='\0';
1042: return s;
1043: }
1044:
1.187 brouard 1045: /* char *substrchaine(char *out, char *in, char *chain) */
1046: /* { */
1047: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1048: /* char *s, *t; */
1049: /* t=in;s=out; */
1050: /* while ((*in != *chain) && (*in != '\0')){ */
1051: /* *out++ = *in++; */
1052: /* } */
1053:
1054: /* /\* *in matches *chain *\/ */
1055: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1056: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1057: /* } */
1058: /* in--; chain--; */
1059: /* while ( (*in != '\0')){ */
1060: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1061: /* *out++ = *in++; */
1062: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1063: /* } */
1064: /* *out='\0'; */
1065: /* out=s; */
1066: /* return out; */
1067: /* } */
1068: char *substrchaine(char *out, char *in, char *chain)
1069: {
1070: /* Substract chain 'chain' from 'in', return and output 'out' */
1071: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1072:
1073: char *strloc;
1074:
1075: strcpy (out, in);
1076: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1077: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1078: if(strloc != NULL){
1079: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1080: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1081: /* strcpy (strloc, strloc +strlen(chain));*/
1082: }
1083: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1084: return out;
1085: }
1086:
1087:
1.145 brouard 1088: char *cutl(char *blocc, char *alocc, char *in, char occ)
1089: {
1.187 brouard 1090: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1091: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1092: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1093: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1094: */
1.160 brouard 1095: char *s, *t;
1.145 brouard 1096: t=in;s=in;
1097: while ((*in != occ) && (*in != '\0')){
1098: *alocc++ = *in++;
1099: }
1100: if( *in == occ){
1101: *(alocc)='\0';
1102: s=++in;
1103: }
1104:
1105: if (s == t) {/* occ not found */
1106: *(alocc-(in-s))='\0';
1107: in=s;
1108: }
1109: while ( *in != '\0'){
1110: *blocc++ = *in++;
1111: }
1112:
1113: *blocc='\0';
1114: return t;
1115: }
1.137 brouard 1116: char *cutv(char *blocc, char *alocc, char *in, char occ)
1117: {
1.187 brouard 1118: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1119: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1120: gives blocc="abcdef2ghi" and alocc="j".
1121: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1122: */
1123: char *s, *t;
1124: t=in;s=in;
1125: while (*in != '\0'){
1126: while( *in == occ){
1127: *blocc++ = *in++;
1128: s=in;
1129: }
1130: *blocc++ = *in++;
1131: }
1132: if (s == t) /* occ not found */
1133: *(blocc-(in-s))='\0';
1134: else
1135: *(blocc-(in-s)-1)='\0';
1136: in=s;
1137: while ( *in != '\0'){
1138: *alocc++ = *in++;
1139: }
1140:
1141: *alocc='\0';
1142: return s;
1143: }
1144:
1.126 brouard 1145: int nbocc(char *s, char occ)
1146: {
1147: int i,j=0;
1148: int lg=20;
1149: i=0;
1150: lg=strlen(s);
1151: for(i=0; i<= lg; i++) {
1152: if (s[i] == occ ) j++;
1153: }
1154: return j;
1155: }
1156:
1.137 brouard 1157: /* void cutv(char *u,char *v, char*t, char occ) */
1158: /* { */
1159: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1160: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1161: /* gives u="abcdef2ghi" and v="j" *\/ */
1162: /* int i,lg,j,p=0; */
1163: /* i=0; */
1164: /* lg=strlen(t); */
1165: /* for(j=0; j<=lg-1; j++) { */
1166: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1167: /* } */
1.126 brouard 1168:
1.137 brouard 1169: /* for(j=0; j<p; j++) { */
1170: /* (u[j] = t[j]); */
1171: /* } */
1172: /* u[p]='\0'; */
1.126 brouard 1173:
1.137 brouard 1174: /* for(j=0; j<= lg; j++) { */
1175: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1176: /* } */
1177: /* } */
1.126 brouard 1178:
1.160 brouard 1179: #ifdef _WIN32
1180: char * strsep(char **pp, const char *delim)
1181: {
1182: char *p, *q;
1183:
1184: if ((p = *pp) == NULL)
1185: return 0;
1186: if ((q = strpbrk (p, delim)) != NULL)
1187: {
1188: *pp = q + 1;
1189: *q = '\0';
1190: }
1191: else
1192: *pp = 0;
1193: return p;
1194: }
1195: #endif
1196:
1.126 brouard 1197: /********************** nrerror ********************/
1198:
1199: void nrerror(char error_text[])
1200: {
1201: fprintf(stderr,"ERREUR ...\n");
1202: fprintf(stderr,"%s\n",error_text);
1203: exit(EXIT_FAILURE);
1204: }
1205: /*********************** vector *******************/
1206: double *vector(int nl, int nh)
1207: {
1208: double *v;
1209: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1210: if (!v) nrerror("allocation failure in vector");
1211: return v-nl+NR_END;
1212: }
1213:
1214: /************************ free vector ******************/
1215: void free_vector(double*v, int nl, int nh)
1216: {
1217: free((FREE_ARG)(v+nl-NR_END));
1218: }
1219:
1220: /************************ivector *******************************/
1221: int *ivector(long nl,long nh)
1222: {
1223: int *v;
1224: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1225: if (!v) nrerror("allocation failure in ivector");
1226: return v-nl+NR_END;
1227: }
1228:
1229: /******************free ivector **************************/
1230: void free_ivector(int *v, long nl, long nh)
1231: {
1232: free((FREE_ARG)(v+nl-NR_END));
1233: }
1234:
1235: /************************lvector *******************************/
1236: long *lvector(long nl,long nh)
1237: {
1238: long *v;
1239: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1240: if (!v) nrerror("allocation failure in ivector");
1241: return v-nl+NR_END;
1242: }
1243:
1244: /******************free lvector **************************/
1245: void free_lvector(long *v, long nl, long nh)
1246: {
1247: free((FREE_ARG)(v+nl-NR_END));
1248: }
1249:
1250: /******************* imatrix *******************************/
1251: int **imatrix(long nrl, long nrh, long ncl, long nch)
1252: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1253: {
1254: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1255: int **m;
1256:
1257: /* allocate pointers to rows */
1258: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1259: if (!m) nrerror("allocation failure 1 in matrix()");
1260: m += NR_END;
1261: m -= nrl;
1262:
1263:
1264: /* allocate rows and set pointers to them */
1265: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1266: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1267: m[nrl] += NR_END;
1268: m[nrl] -= ncl;
1269:
1270: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1271:
1272: /* return pointer to array of pointers to rows */
1273: return m;
1274: }
1275:
1276: /****************** free_imatrix *************************/
1277: void free_imatrix(m,nrl,nrh,ncl,nch)
1278: int **m;
1279: long nch,ncl,nrh,nrl;
1280: /* free an int matrix allocated by imatrix() */
1281: {
1282: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1283: free((FREE_ARG) (m+nrl-NR_END));
1284: }
1285:
1286: /******************* matrix *******************************/
1287: double **matrix(long nrl, long nrh, long ncl, long nch)
1288: {
1289: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1290: double **m;
1291:
1292: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1293: if (!m) nrerror("allocation failure 1 in matrix()");
1294: m += NR_END;
1295: m -= nrl;
1296:
1297: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1298: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1299: m[nrl] += NR_END;
1300: m[nrl] -= ncl;
1301:
1302: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1303: return m;
1.145 brouard 1304: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1305: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1306: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1307: */
1308: }
1309:
1310: /*************************free matrix ************************/
1311: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1312: {
1313: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1314: free((FREE_ARG)(m+nrl-NR_END));
1315: }
1316:
1317: /******************* ma3x *******************************/
1318: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1319: {
1320: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1321: double ***m;
1322:
1323: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1324: if (!m) nrerror("allocation failure 1 in matrix()");
1325: m += NR_END;
1326: m -= nrl;
1327:
1328: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1329: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1330: m[nrl] += NR_END;
1331: m[nrl] -= ncl;
1332:
1333: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1334:
1335: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1336: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1337: m[nrl][ncl] += NR_END;
1338: m[nrl][ncl] -= nll;
1339: for (j=ncl+1; j<=nch; j++)
1340: m[nrl][j]=m[nrl][j-1]+nlay;
1341:
1342: for (i=nrl+1; i<=nrh; i++) {
1343: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1344: for (j=ncl+1; j<=nch; j++)
1345: m[i][j]=m[i][j-1]+nlay;
1346: }
1347: return m;
1348: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1349: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1350: */
1351: }
1352:
1353: /*************************free ma3x ************************/
1354: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1355: {
1356: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1357: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1358: free((FREE_ARG)(m+nrl-NR_END));
1359: }
1360:
1361: /*************** function subdirf ***********/
1362: char *subdirf(char fileres[])
1363: {
1364: /* Caution optionfilefiname is hidden */
1365: strcpy(tmpout,optionfilefiname);
1366: strcat(tmpout,"/"); /* Add to the right */
1367: strcat(tmpout,fileres);
1368: return tmpout;
1369: }
1370:
1371: /*************** function subdirf2 ***********/
1372: char *subdirf2(char fileres[], char *preop)
1373: {
1374:
1375: /* Caution optionfilefiname is hidden */
1376: strcpy(tmpout,optionfilefiname);
1377: strcat(tmpout,"/");
1378: strcat(tmpout,preop);
1379: strcat(tmpout,fileres);
1380: return tmpout;
1381: }
1382:
1383: /*************** function subdirf3 ***********/
1384: char *subdirf3(char fileres[], char *preop, char *preop2)
1385: {
1386:
1387: /* Caution optionfilefiname is hidden */
1388: strcpy(tmpout,optionfilefiname);
1389: strcat(tmpout,"/");
1390: strcat(tmpout,preop);
1391: strcat(tmpout,preop2);
1392: strcat(tmpout,fileres);
1393: return tmpout;
1394: }
1.213 brouard 1395:
1396: /*************** function subdirfext ***********/
1397: char *subdirfext(char fileres[], char *preop, char *postop)
1398: {
1399:
1400: strcpy(tmpout,preop);
1401: strcat(tmpout,fileres);
1402: strcat(tmpout,postop);
1403: return tmpout;
1404: }
1.126 brouard 1405:
1.213 brouard 1406: /*************** function subdirfext3 ***********/
1407: char *subdirfext3(char fileres[], char *preop, char *postop)
1408: {
1409:
1410: /* Caution optionfilefiname is hidden */
1411: strcpy(tmpout,optionfilefiname);
1412: strcat(tmpout,"/");
1413: strcat(tmpout,preop);
1414: strcat(tmpout,fileres);
1415: strcat(tmpout,postop);
1416: return tmpout;
1417: }
1418:
1.162 brouard 1419: char *asc_diff_time(long time_sec, char ascdiff[])
1420: {
1421: long sec_left, days, hours, minutes;
1422: days = (time_sec) / (60*60*24);
1423: sec_left = (time_sec) % (60*60*24);
1424: hours = (sec_left) / (60*60) ;
1425: sec_left = (sec_left) %(60*60);
1426: minutes = (sec_left) /60;
1427: sec_left = (sec_left) % (60);
1428: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1429: return ascdiff;
1430: }
1431:
1.126 brouard 1432: /***************** f1dim *************************/
1433: extern int ncom;
1434: extern double *pcom,*xicom;
1435: extern double (*nrfunc)(double []);
1436:
1437: double f1dim(double x)
1438: {
1439: int j;
1440: double f;
1441: double *xt;
1442:
1443: xt=vector(1,ncom);
1444: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1445: f=(*nrfunc)(xt);
1446: free_vector(xt,1,ncom);
1447: return f;
1448: }
1449:
1450: /*****************brent *************************/
1451: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1452: {
1453: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1454: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1455: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1456: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1457: * returned function value.
1458: */
1.126 brouard 1459: int iter;
1460: double a,b,d,etemp;
1.159 brouard 1461: double fu=0,fv,fw,fx;
1.164 brouard 1462: double ftemp=0.;
1.126 brouard 1463: double p,q,r,tol1,tol2,u,v,w,x,xm;
1464: double e=0.0;
1465:
1466: a=(ax < cx ? ax : cx);
1467: b=(ax > cx ? ax : cx);
1468: x=w=v=bx;
1469: fw=fv=fx=(*f)(x);
1470: for (iter=1;iter<=ITMAX;iter++) {
1471: xm=0.5*(a+b);
1472: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1473: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1474: printf(".");fflush(stdout);
1475: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1476: #ifdef DEBUGBRENT
1.126 brouard 1477: 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);
1478: 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);
1479: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1480: #endif
1481: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1482: *xmin=x;
1483: return fx;
1484: }
1485: ftemp=fu;
1486: if (fabs(e) > tol1) {
1487: r=(x-w)*(fx-fv);
1488: q=(x-v)*(fx-fw);
1489: p=(x-v)*q-(x-w)*r;
1490: q=2.0*(q-r);
1491: if (q > 0.0) p = -p;
1492: q=fabs(q);
1493: etemp=e;
1494: e=d;
1495: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1496: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1497: else {
1498: d=p/q;
1499: u=x+d;
1500: if (u-a < tol2 || b-u < tol2)
1501: d=SIGN(tol1,xm-x);
1502: }
1503: } else {
1504: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1505: }
1506: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1507: fu=(*f)(u);
1508: if (fu <= fx) {
1509: if (u >= x) a=x; else b=x;
1510: SHFT(v,w,x,u)
1.183 brouard 1511: SHFT(fv,fw,fx,fu)
1512: } else {
1513: if (u < x) a=u; else b=u;
1514: if (fu <= fw || w == x) {
1515: v=w;
1516: w=u;
1517: fv=fw;
1518: fw=fu;
1519: } else if (fu <= fv || v == x || v == w) {
1520: v=u;
1521: fv=fu;
1522: }
1523: }
1.126 brouard 1524: }
1525: nrerror("Too many iterations in brent");
1526: *xmin=x;
1527: return fx;
1528: }
1529:
1530: /****************** mnbrak ***********************/
1531:
1532: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1533: double (*func)(double))
1.183 brouard 1534: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1535: the downhill direction (defined by the function as evaluated at the initial points) and returns
1536: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1537: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1538: */
1.126 brouard 1539: double ulim,u,r,q, dum;
1540: double fu;
1.187 brouard 1541:
1542: double scale=10.;
1543: int iterscale=0;
1544:
1545: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1546: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1547:
1548:
1549: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1550: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1551: /* *bx = *ax - (*ax - *bx)/scale; */
1552: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1553: /* } */
1554:
1.126 brouard 1555: if (*fb > *fa) {
1556: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1557: SHFT(dum,*fb,*fa,dum)
1558: }
1.126 brouard 1559: *cx=(*bx)+GOLD*(*bx-*ax);
1560: *fc=(*func)(*cx);
1.183 brouard 1561: #ifdef DEBUG
1562: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1563: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1564: #endif
1565: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1566: r=(*bx-*ax)*(*fb-*fc);
1567: q=(*bx-*cx)*(*fb-*fa);
1568: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1569: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1570: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1571: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1572: fu=(*func)(u);
1.163 brouard 1573: #ifdef DEBUG
1574: /* f(x)=A(x-u)**2+f(u) */
1575: double A, fparabu;
1576: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1577: fparabu= *fa - A*(*ax-u)*(*ax-u);
1578: 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);
1579: 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 1580: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1581: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1582: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1583: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1584: #endif
1.184 brouard 1585: #ifdef MNBRAKORIGINAL
1.183 brouard 1586: #else
1.191 brouard 1587: /* if (fu > *fc) { */
1588: /* #ifdef DEBUG */
1589: /* printf("mnbrak4 fu > fc \n"); */
1590: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1591: /* #endif */
1592: /* /\* 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 *\\/ *\/ */
1593: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1594: /* dum=u; /\* Shifting c and u *\/ */
1595: /* u = *cx; */
1596: /* *cx = dum; */
1597: /* dum = fu; */
1598: /* fu = *fc; */
1599: /* *fc =dum; */
1600: /* } else { /\* end *\/ */
1601: /* #ifdef DEBUG */
1602: /* printf("mnbrak3 fu < fc \n"); */
1603: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1604: /* #endif */
1605: /* dum=u; /\* Shifting c and u *\/ */
1606: /* u = *cx; */
1607: /* *cx = dum; */
1608: /* dum = fu; */
1609: /* fu = *fc; */
1610: /* *fc =dum; */
1611: /* } */
1.183 brouard 1612: #ifdef DEBUG
1.191 brouard 1613: printf("mnbrak34 fu < or >= fc \n");
1614: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1615: #endif
1.191 brouard 1616: dum=u; /* Shifting c and u */
1617: u = *cx;
1618: *cx = dum;
1619: dum = fu;
1620: fu = *fc;
1621: *fc =dum;
1.183 brouard 1622: #endif
1.162 brouard 1623: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1624: #ifdef DEBUG
1625: printf("mnbrak2 u after c but before ulim\n");
1626: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1627: #endif
1.126 brouard 1628: fu=(*func)(u);
1629: if (fu < *fc) {
1.183 brouard 1630: #ifdef DEBUG
1631: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1632: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1633: #endif
1.126 brouard 1634: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1635: SHFT(*fb,*fc,fu,(*func)(u))
1636: }
1.162 brouard 1637: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1638: #ifdef DEBUG
1639: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1640: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1641: #endif
1.126 brouard 1642: u=ulim;
1643: fu=(*func)(u);
1.183 brouard 1644: } else { /* u could be left to b (if r > q parabola has a maximum) */
1645: #ifdef DEBUG
1646: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1647: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1648: #endif
1.126 brouard 1649: u=(*cx)+GOLD*(*cx-*bx);
1650: fu=(*func)(u);
1.183 brouard 1651: } /* end tests */
1.126 brouard 1652: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1653: SHFT(*fa,*fb,*fc,fu)
1654: #ifdef DEBUG
1655: 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);
1656: 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);
1657: #endif
1658: } /* 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 1659: }
1660:
1661: /*************** linmin ************************/
1.162 brouard 1662: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1663: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1664: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1665: the value of func at the returned location p . This is actually all accomplished by calling the
1666: routines mnbrak and brent .*/
1.126 brouard 1667: int ncom;
1668: double *pcom,*xicom;
1669: double (*nrfunc)(double []);
1670:
1671: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1672: {
1673: double brent(double ax, double bx, double cx,
1674: double (*f)(double), double tol, double *xmin);
1675: double f1dim(double x);
1676: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1677: double *fc, double (*func)(double));
1678: int j;
1679: double xx,xmin,bx,ax;
1680: double fx,fb,fa;
1.187 brouard 1681:
1.203 brouard 1682: #ifdef LINMINORIGINAL
1683: #else
1684: double scale=10., axs, xxs; /* Scale added for infinity */
1685: #endif
1686:
1.126 brouard 1687: ncom=n;
1688: pcom=vector(1,n);
1689: xicom=vector(1,n);
1690: nrfunc=func;
1691: for (j=1;j<=n;j++) {
1692: pcom[j]=p[j];
1.202 brouard 1693: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1694: }
1.187 brouard 1695:
1.203 brouard 1696: #ifdef LINMINORIGINAL
1697: xx=1.;
1698: #else
1699: axs=0.0;
1700: xxs=1.;
1701: do{
1702: xx= xxs;
1703: #endif
1.187 brouard 1704: ax=0.;
1705: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1706: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1707: /* 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)) */
1708: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1709: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1710: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1711: /* 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]]*/
1.203 brouard 1712: #ifdef LINMINORIGINAL
1713: #else
1714: if (fx != fx){
1715: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1716: printf("|");
1717: fprintf(ficlog,"|");
1718: #ifdef DEBUGLINMIN
1719: 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);
1720: #endif
1721: }
1722: }while(fx != fx);
1723: #endif
1724:
1.191 brouard 1725: #ifdef DEBUGLINMIN
1726: 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);
1.202 brouard 1727: fprintf(ficlog,"\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);
1.191 brouard 1728: #endif
1.187 brouard 1729: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1730: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1731: /* fmin = f(p[j] + xmin * xi[j]) */
1732: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1733: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1734: #ifdef DEBUG
1735: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1736: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1737: #endif
1.191 brouard 1738: #ifdef DEBUGLINMIN
1739: printf("linmin end ");
1.202 brouard 1740: fprintf(ficlog,"linmin end ");
1.191 brouard 1741: #endif
1.126 brouard 1742: for (j=1;j<=n;j++) {
1.203 brouard 1743: #ifdef LINMINORIGINAL
1744: xi[j] *= xmin;
1745: #else
1746: #ifdef DEBUGLINMIN
1747: if(xxs <1.0)
1748: printf(" before xi[%d]=%12.8f", j,xi[j]);
1749: #endif
1750: xi[j] *= xmin*xxs; /* xi rescaled by xmin and number of loops: if xmin=-1.237 and xi=(1,0,...,0) xi=(-1.237,0,...,0) */
1751: #ifdef DEBUGLINMIN
1752: if(xxs <1.0)
1753: 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 );
1754: #endif
1755: #endif
1.187 brouard 1756: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1757: }
1.191 brouard 1758: #ifdef DEBUGLINMIN
1.203 brouard 1759: printf("\n");
1.191 brouard 1760: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1761: fprintf(ficlog,"Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.191 brouard 1762: for (j=1;j<=n;j++) {
1.202 brouard 1763: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1764: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1765: if(j % ncovmodel == 0){
1.191 brouard 1766: printf("\n");
1.202 brouard 1767: fprintf(ficlog,"\n");
1768: }
1.191 brouard 1769: }
1.203 brouard 1770: #else
1.191 brouard 1771: #endif
1.126 brouard 1772: free_vector(xicom,1,n);
1773: free_vector(pcom,1,n);
1774: }
1775:
1776:
1777: /*************** powell ************************/
1.162 brouard 1778: /*
1779: Minimization of a function func of n variables. Input consists of an initial starting point
1780: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1781: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1782: such that failure to decrease by more than this amount on one iteration signals doneness. On
1783: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1784: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1785: */
1.126 brouard 1786: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1787: double (*func)(double []))
1788: {
1789: void linmin(double p[], double xi[], int n, double *fret,
1790: double (*func)(double []));
1791: int i,ibig,j;
1792: double del,t,*pt,*ptt,*xit;
1.181 brouard 1793: double directest;
1.126 brouard 1794: double fp,fptt;
1795: double *xits;
1796: int niterf, itmp;
1797:
1798: pt=vector(1,n);
1799: ptt=vector(1,n);
1800: xit=vector(1,n);
1801: xits=vector(1,n);
1802: *fret=(*func)(p);
1803: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1804: rcurr_time = time(NULL);
1.126 brouard 1805: for (*iter=1;;++(*iter)) {
1.187 brouard 1806: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1807: ibig=0;
1808: del=0.0;
1.157 brouard 1809: rlast_time=rcurr_time;
1810: /* (void) gettimeofday(&curr_time,&tzp); */
1811: rcurr_time = time(NULL);
1812: curr_time = *localtime(&rcurr_time);
1813: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1814: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1815: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1816: for (i=1;i<=n;i++) {
1.126 brouard 1817: printf(" %d %.12f",i, p[i]);
1818: fprintf(ficlog," %d %.12lf",i, p[i]);
1819: fprintf(ficrespow," %.12lf", p[i]);
1820: }
1821: printf("\n");
1822: fprintf(ficlog,"\n");
1823: fprintf(ficrespow,"\n");fflush(ficrespow);
1824: if(*iter <=3){
1.157 brouard 1825: tml = *localtime(&rcurr_time);
1826: strcpy(strcurr,asctime(&tml));
1827: rforecast_time=rcurr_time;
1.126 brouard 1828: itmp = strlen(strcurr);
1829: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1830: strcurr[itmp-1]='\0';
1.162 brouard 1831: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1832: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1833: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1834: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1835: forecast_time = *localtime(&rforecast_time);
1836: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1837: itmp = strlen(strfor);
1838: if(strfor[itmp-1]=='\n')
1839: strfor[itmp-1]='\0';
1.157 brouard 1840: 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);
1841: 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 1842: }
1843: }
1.187 brouard 1844: for (i=1;i<=n;i++) { /* For each direction i */
1845: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1846: fptt=(*fret);
1847: #ifdef DEBUG
1.203 brouard 1848: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1849: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1850: #endif
1.203 brouard 1851: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1852: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1853: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1854: /* Outputs are fret(new point p) p is updated and xit rescaled */
1855: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1856: /* because that direction will be replaced unless the gain del is small */
1857: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1858: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1859: /* with the new direction. */
1.126 brouard 1860: del=fabs(fptt-(*fret));
1861: ibig=i;
1862: }
1863: #ifdef DEBUG
1864: printf("%d %.12e",i,(*fret));
1865: fprintf(ficlog,"%d %.12e",i,(*fret));
1866: for (j=1;j<=n;j++) {
1867: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1868: printf(" x(%d)=%.12e",j,xit[j]);
1869: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1870: }
1871: for(j=1;j<=n;j++) {
1.162 brouard 1872: printf(" p(%d)=%.12e",j,p[j]);
1873: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1874: }
1875: printf("\n");
1876: fprintf(ficlog,"\n");
1877: #endif
1.187 brouard 1878: } /* end loop on each direction i */
1879: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1880: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1881: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1882: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1883: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1884: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1885: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1886: /* decreased of more than 3.84 */
1887: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1888: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1889: /* By adding 10 parameters more the gain should be 18.31 */
1890:
1891: /* Starting the program with initial values given by a former maximization will simply change */
1892: /* the scales of the directions and the directions, because the are reset to canonical directions */
1893: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1894: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1895: #ifdef DEBUG
1896: int k[2],l;
1897: k[0]=1;
1898: k[1]=-1;
1899: printf("Max: %.12e",(*func)(p));
1900: fprintf(ficlog,"Max: %.12e",(*func)(p));
1901: for (j=1;j<=n;j++) {
1902: printf(" %.12e",p[j]);
1903: fprintf(ficlog," %.12e",p[j]);
1904: }
1905: printf("\n");
1906: fprintf(ficlog,"\n");
1907: for(l=0;l<=1;l++) {
1908: for (j=1;j<=n;j++) {
1909: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1910: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1911: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1912: }
1913: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1914: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1915: }
1916: #endif
1917:
1918:
1919: free_vector(xit,1,n);
1920: free_vector(xits,1,n);
1921: free_vector(ptt,1,n);
1922: free_vector(pt,1,n);
1923: return;
1.192 brouard 1924: } /* enough precision */
1.126 brouard 1925: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1926: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1927: ptt[j]=2.0*p[j]-pt[j];
1928: xit[j]=p[j]-pt[j];
1929: pt[j]=p[j];
1930: }
1.181 brouard 1931: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1932: #ifdef POWELLF1F3
1933: #else
1.161 brouard 1934: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1935: #endif
1.162 brouard 1936: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1937: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1938: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1939: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1940: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1941: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1942: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1943: #ifdef NRCORIGINAL
1944: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1945: #else
1946: 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 1947: t= t- del*SQR(fp-fptt);
1.183 brouard 1948: #endif
1.202 brouard 1949: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1950: #ifdef DEBUG
1.181 brouard 1951: 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);
1952: 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 1953: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1954: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1955: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1956: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1957: 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);
1958: 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);
1959: #endif
1.183 brouard 1960: #ifdef POWELLORIGINAL
1961: if (t < 0.0) { /* Then we use it for new direction */
1962: #else
1.182 brouard 1963: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1964: printf("directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt,del);
1.192 brouard 1965: printf("f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1.202 brouard 1966: fprintf(ficlog,"directest= %.12lf (if <0 we include P0 Pn as new direction), t= %.12lf, f1= %.12lf,f2= %.12lf,f3= %.12lf, del= %.12lf\n",directest, t, fp,(*fret),fptt, del);
1.192 brouard 1967: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1968: }
1.181 brouard 1969: if (directest < 0.0) { /* Then we use it for new direction */
1970: #endif
1.191 brouard 1971: #ifdef DEBUGLINMIN
1972: printf("Before linmin in direction P%d-P0\n",n);
1973: for (j=1;j<=n;j++) {
1.202 brouard 1974: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1975: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1976: if(j % ncovmodel == 0){
1.191 brouard 1977: printf("\n");
1.202 brouard 1978: fprintf(ficlog,"\n");
1979: }
1.191 brouard 1980: }
1981: #endif
1.187 brouard 1982: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1983: #ifdef DEBUGLINMIN
1984: for (j=1;j<=n;j++) {
1985: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1986: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1987: if(j % ncovmodel == 0){
1.191 brouard 1988: printf("\n");
1.202 brouard 1989: fprintf(ficlog,"\n");
1990: }
1.191 brouard 1991: }
1992: #endif
1.126 brouard 1993: for (j=1;j<=n;j++) {
1.181 brouard 1994: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1995: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1996: }
1.181 brouard 1997: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1998: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1999:
1.126 brouard 2000: #ifdef DEBUG
1.164 brouard 2001: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
2002: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 2003: for(j=1;j<=n;j++){
2004: printf(" %.12e",xit[j]);
2005: fprintf(ficlog," %.12e",xit[j]);
2006: }
2007: printf("\n");
2008: fprintf(ficlog,"\n");
2009: #endif
1.192 brouard 2010: } /* end of t or directest negative */
2011: #ifdef POWELLF1F3
2012: #else
1.162 brouard 2013: } /* end if (fptt < fp) */
1.192 brouard 2014: #endif
2015: } /* loop iteration */
1.126 brouard 2016: }
2017:
2018: /**** Prevalence limit (stable or period prevalence) ****************/
2019:
1.203 brouard 2020: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 2021: {
2022: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 2023: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 2024: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
2025: /* Wx is row vector: population in state 1, population in state 2, population dead */
2026: /* or prevalence in state 1, prevalence in state 2, 0 */
2027: /* newm is the matrix after multiplications, its rows are identical at a factor */
2028: /* Initial matrix pimij */
2029: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
2030: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
2031: /* 0, 0 , 1} */
2032: /*
2033: * and after some iteration: */
2034: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
2035: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
2036: /* 0, 0 , 1} */
2037: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
2038: /* {0.51571254859325999, 0.4842874514067399, */
2039: /* 0.51326036147820708, 0.48673963852179264} */
2040: /* If we start from prlim again, prlim tends to a constant matrix */
2041:
1.126 brouard 2042: int i, ii,j,k;
1.209 brouard 2043: double *min, *max, *meandiff, maxmax,sumnew=0.;
1.145 brouard 2044: /* double **matprod2(); */ /* test */
1.131 brouard 2045: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 2046: double **newm;
1.209 brouard 2047: double agefin, delaymax=200. ; /* 100 Max number of years to converge */
1.203 brouard 2048: int ncvloop=0;
1.169 brouard 2049:
1.209 brouard 2050: min=vector(1,nlstate);
2051: max=vector(1,nlstate);
2052: meandiff=vector(1,nlstate);
2053:
1.126 brouard 2054: for (ii=1;ii<=nlstate+ndeath;ii++)
2055: for (j=1;j<=nlstate+ndeath;j++){
2056: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2057: }
1.169 brouard 2058:
2059: cov[1]=1.;
2060:
2061: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2062: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2063: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2064: ncvloop++;
1.126 brouard 2065: newm=savm;
2066: /* Covariates have to be included here again */
1.138 brouard 2067: cov[2]=agefin;
1.187 brouard 2068: if(nagesqr==1)
2069: cov[3]= agefin*agefin;;
1.138 brouard 2070: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2071: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2072: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2073: /* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
1.138 brouard 2074: }
1.186 brouard 2075: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2076: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2077: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2078: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2079: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2080: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2081:
2082: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2083: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2084: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2085: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2086: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2087: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2088:
1.126 brouard 2089: savm=oldm;
2090: oldm=newm;
1.209 brouard 2091:
2092: for(j=1; j<=nlstate; j++){
2093: max[j]=0.;
2094: min[j]=1.;
2095: }
2096: for(i=1;i<=nlstate;i++){
2097: sumnew=0;
2098: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2099: for(j=1; j<=nlstate; j++){
2100: prlim[i][j]= newm[i][j]/(1-sumnew);
2101: max[j]=FMAX(max[j],prlim[i][j]);
2102: min[j]=FMIN(min[j],prlim[i][j]);
2103: }
2104: }
2105:
1.126 brouard 2106: maxmax=0.;
1.209 brouard 2107: for(j=1; j<=nlstate; j++){
2108: meandiff[j]=(max[j]-min[j])/(max[j]+min[j])*2.; /* mean difference for each column */
2109: maxmax=FMAX(maxmax,meandiff[j]);
2110: /* printf(" age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, j, meandiff[j],(int)agefin, j, max[j], j, min[j],maxmax); */
1.169 brouard 2111: } /* j loop */
1.203 brouard 2112: *ncvyear= (int)age- (int)agefin;
1.208 brouard 2113: /* printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2114: if(maxmax < ftolpl){
1.209 brouard 2115: /* printf("maxmax=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, *ncvyear); */
2116: free_vector(min,1,nlstate);
2117: free_vector(max,1,nlstate);
2118: free_vector(meandiff,1,nlstate);
1.126 brouard 2119: return prlim;
2120: }
1.169 brouard 2121: } /* age loop */
1.208 brouard 2122: /* After some age loop it doesn't converge */
1.209 brouard 2123: printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
1.208 brouard 2124: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
1.209 brouard 2125: /* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
2126: free_vector(min,1,nlstate);
2127: free_vector(max,1,nlstate);
2128: free_vector(meandiff,1,nlstate);
1.208 brouard 2129:
1.169 brouard 2130: return prlim; /* should not reach here */
1.126 brouard 2131: }
2132:
2133: /*************** transition probabilities ***************/
2134:
2135: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2136: {
1.138 brouard 2137: /* According to parameters values stored in x and the covariate's values stored in cov,
2138: computes the probability to be observed in state j being in state i by appying the
2139: model to the ncovmodel covariates (including constant and age).
2140: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2141: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2142: ncth covariate in the global vector x is given by the formula:
2143: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2144: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2145: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2146: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2147: Outputs ps[i][j] the probability to be observed in j being in j according to
2148: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2149: */
2150: double s1, lnpijopii;
1.126 brouard 2151: /*double t34;*/
1.164 brouard 2152: int i,j, nc, ii, jj;
1.126 brouard 2153:
2154: for(i=1; i<= nlstate; i++){
2155: for(j=1; j<i;j++){
1.138 brouard 2156: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2157: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2158: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2159: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2160: }
1.138 brouard 2161: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2162: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2163: }
2164: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2165: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2166: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2167: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2168: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2169: }
1.138 brouard 2170: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2171: }
2172: }
2173:
2174: for(i=1; i<= nlstate; i++){
2175: s1=0;
1.131 brouard 2176: for(j=1; j<i; j++){
1.138 brouard 2177: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2178: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2179: }
2180: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2181: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2182: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2183: }
1.138 brouard 2184: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2185: ps[i][i]=1./(s1+1.);
1.138 brouard 2186: /* Computing other pijs */
1.126 brouard 2187: for(j=1; j<i; j++)
2188: ps[i][j]= exp(ps[i][j])*ps[i][i];
2189: for(j=i+1; j<=nlstate+ndeath; j++)
2190: ps[i][j]= exp(ps[i][j])*ps[i][i];
2191: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2192: } /* end i */
2193:
2194: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2195: for(jj=1; jj<= nlstate+ndeath; jj++){
2196: ps[ii][jj]=0;
2197: ps[ii][ii]=1;
2198: }
2199: }
2200:
1.145 brouard 2201:
2202: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2203: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2204: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2205: /* } */
2206: /* printf("\n "); */
2207: /* } */
2208: /* printf("\n ");printf("%lf ",cov[2]);*/
2209: /*
1.126 brouard 2210: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2211: goto end;*/
2212: return ps;
2213: }
2214:
2215: /**************** Product of 2 matrices ******************/
2216:
1.145 brouard 2217: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2218: {
2219: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2220: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2221: /* in, b, out are matrice of pointers which should have been initialized
2222: before: only the contents of out is modified. The function returns
2223: a pointer to pointers identical to out */
1.145 brouard 2224: int i, j, k;
1.126 brouard 2225: for(i=nrl; i<= nrh; i++)
1.145 brouard 2226: for(k=ncolol; k<=ncoloh; k++){
2227: out[i][k]=0.;
2228: for(j=ncl; j<=nch; j++)
2229: out[i][k] +=in[i][j]*b[j][k];
2230: }
1.126 brouard 2231: return out;
2232: }
2233:
2234:
2235: /************* Higher Matrix Product ***************/
2236:
2237: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2238: {
2239: /* Computes the transition matrix starting at age 'age' over
2240: 'nhstepm*hstepm*stepm' months (i.e. until
2241: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2242: nhstepm*hstepm matrices.
2243: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2244: (typically every 2 years instead of every month which is too big
2245: for the memory).
2246: Model is determined by parameters x and covariates have to be
2247: included manually here.
2248:
2249: */
2250:
2251: int i, j, d, h, k;
1.131 brouard 2252: double **out, cov[NCOVMAX+1];
1.126 brouard 2253: double **newm;
1.187 brouard 2254: double agexact;
1.214 brouard 2255: double agebegin, ageend;
1.126 brouard 2256:
2257: /* Hstepm could be zero and should return the unit matrix */
2258: for (i=1;i<=nlstate+ndeath;i++)
2259: for (j=1;j<=nlstate+ndeath;j++){
2260: oldm[i][j]=(i==j ? 1.0 : 0.0);
2261: po[i][j][0]=(i==j ? 1.0 : 0.0);
2262: }
2263: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2264: for(h=1; h <=nhstepm; h++){
2265: for(d=1; d <=hstepm; d++){
2266: newm=savm;
2267: /* Covariates have to be included here again */
2268: cov[1]=1.;
1.214 brouard 2269: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM; /* age just before transition */
1.187 brouard 2270: cov[2]=agexact;
2271: if(nagesqr==1)
2272: cov[3]= agexact*agexact;
1.131 brouard 2273: for (k=1; k<=cptcovn;k++)
1.200 brouard 2274: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2275: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2276: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2277: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2278: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2279: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2280: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2281: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2282: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]*nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
1.126 brouard 2283:
2284:
2285: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2286: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2287: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2288: pmij(pmmij,cov,ncovmodel,x,nlstate));
2289: savm=oldm;
2290: oldm=newm;
2291: }
2292: for(i=1; i<=nlstate+ndeath; i++)
2293: for(j=1;j<=nlstate+ndeath;j++) {
2294: po[i][j][h]=newm[i][j];
1.128 brouard 2295: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2296: }
1.128 brouard 2297: /*printf("h=%d ",h);*/
1.126 brouard 2298: } /* end h */
1.128 brouard 2299: /* printf("\n H=%d \n",h); */
1.126 brouard 2300: return po;
2301: }
2302:
1.162 brouard 2303: #ifdef NLOPT
2304: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2305: double fret;
2306: double *xt;
2307: int j;
2308: myfunc_data *d2 = (myfunc_data *) pd;
2309: /* xt = (p1-1); */
2310: xt=vector(1,n);
2311: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2312:
2313: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2314: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2315: printf("Function = %.12lf ",fret);
2316: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2317: printf("\n");
2318: free_vector(xt,1,n);
2319: return fret;
2320: }
2321: #endif
1.126 brouard 2322:
2323: /*************** log-likelihood *************/
2324: double func( double *x)
2325: {
2326: int i, ii, j, k, mi, d, kk;
1.131 brouard 2327: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2328: double **out;
2329: double sw; /* Sum of weights */
2330: double lli; /* Individual log likelihood */
2331: int s1, s2;
2332: double bbh, survp;
2333: long ipmx;
1.187 brouard 2334: double agexact;
1.126 brouard 2335: /*extern weight */
2336: /* We are differentiating ll according to initial status */
2337: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2338: /*for(i=1;i<imx;i++)
2339: printf(" %d\n",s[4][i]);
2340: */
1.162 brouard 2341:
2342: ++countcallfunc;
2343:
1.126 brouard 2344: cov[1]=1.;
2345:
2346: for(k=1; k<=nlstate; k++) ll[k]=0.;
2347:
2348: if(mle==1){
2349: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2350: /* Computes the values of the ncovmodel covariates of the model
2351: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2352: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2353: to be observed in j being in i according to the model.
2354: */
1.145 brouard 2355: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2356: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2357: }
1.137 brouard 2358: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2359: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2360: has been calculated etc */
1.126 brouard 2361: for(mi=1; mi<= wav[i]-1; mi++){
2362: for (ii=1;ii<=nlstate+ndeath;ii++)
2363: for (j=1;j<=nlstate+ndeath;j++){
2364: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2365: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2366: }
2367: for(d=0; d<dh[mi][i]; d++){
2368: newm=savm;
1.187 brouard 2369: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2370: cov[2]=agexact;
2371: if(nagesqr==1)
2372: cov[3]= agexact*agexact;
1.126 brouard 2373: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2374: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2375: }
2376: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2377: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2378: savm=oldm;
2379: oldm=newm;
2380: } /* end mult */
2381:
2382: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2383: /* But now since version 0.9 we anticipate for bias at large stepm.
2384: * If stepm is larger than one month (smallest stepm) and if the exact delay
2385: * (in months) between two waves is not a multiple of stepm, we rounded to
2386: * the nearest (and in case of equal distance, to the lowest) interval but now
2387: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2388: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2389: * probability in order to take into account the bias as a fraction of the way
2390: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2391: * -stepm/2 to stepm/2 .
2392: * For stepm=1 the results are the same as for previous versions of Imach.
2393: * For stepm > 1 the results are less biased than in previous versions.
2394: */
2395: s1=s[mw[mi][i]][i];
2396: s2=s[mw[mi+1][i]][i];
2397: bbh=(double)bh[mi][i]/(double)stepm;
2398: /* bias bh is positive if real duration
2399: * is higher than the multiple of stepm and negative otherwise.
2400: */
2401: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2402: if( s2 > nlstate){
2403: /* i.e. if s2 is a death state and if the date of death is known
2404: then the contribution to the likelihood is the probability to
2405: die between last step unit time and current step unit time,
2406: which is also equal to probability to die before dh
2407: minus probability to die before dh-stepm .
2408: In version up to 0.92 likelihood was computed
2409: as if date of death was unknown. Death was treated as any other
2410: health state: the date of the interview describes the actual state
2411: and not the date of a change in health state. The former idea was
2412: to consider that at each interview the state was recorded
2413: (healthy, disable or death) and IMaCh was corrected; but when we
2414: introduced the exact date of death then we should have modified
2415: the contribution of an exact death to the likelihood. This new
2416: contribution is smaller and very dependent of the step unit
2417: stepm. It is no more the probability to die between last interview
2418: and month of death but the probability to survive from last
2419: interview up to one month before death multiplied by the
2420: probability to die within a month. Thanks to Chris
2421: Jackson for correcting this bug. Former versions increased
2422: mortality artificially. The bad side is that we add another loop
2423: which slows down the processing. The difference can be up to 10%
2424: lower mortality.
2425: */
1.183 brouard 2426: /* If, at the beginning of the maximization mostly, the
2427: cumulative probability or probability to be dead is
2428: constant (ie = 1) over time d, the difference is equal to
2429: 0. out[s1][3] = savm[s1][3]: probability, being at state
2430: s1 at precedent wave, to be dead a month before current
2431: wave is equal to probability, being at state s1 at
2432: precedent wave, to be dead at mont of the current
2433: wave. Then the observed probability (that this person died)
2434: is null according to current estimated parameter. In fact,
2435: it should be very low but not zero otherwise the log go to
2436: infinity.
2437: */
2438: /* #ifdef INFINITYORIGINAL */
2439: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2440: /* #else */
2441: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2442: /* lli=log(mytinydouble); */
2443: /* else */
2444: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2445: /* #endif */
2446: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2447:
2448: } else if (s2==-2) {
2449: for (j=1,survp=0. ; j<=nlstate; j++)
2450: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2451: /*survp += out[s1][j]; */
2452: lli= log(survp);
2453: }
2454:
2455: else if (s2==-4) {
2456: for (j=3,survp=0. ; j<=nlstate; j++)
2457: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2458: lli= log(survp);
2459: }
2460:
2461: else if (s2==-5) {
2462: for (j=1,survp=0. ; j<=2; j++)
2463: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2464: lli= log(survp);
2465: }
2466:
2467: else{
2468: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2469: /* 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 */
2470: }
2471: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2472: /*if(lli ==000.0)*/
2473: /*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); */
2474: ipmx +=1;
2475: sw += weight[i];
2476: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2477: /* if (lli < log(mytinydouble)){ */
2478: /* 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); */
2479: /* 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]); */
2480: /* } */
1.126 brouard 2481: } /* end of wave */
2482: } /* end of individual */
2483: } else if(mle==2){
2484: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2485: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2486: for(mi=1; mi<= wav[i]-1; mi++){
2487: for (ii=1;ii<=nlstate+ndeath;ii++)
2488: for (j=1;j<=nlstate+ndeath;j++){
2489: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2490: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2491: }
2492: for(d=0; d<=dh[mi][i]; d++){
2493: newm=savm;
1.187 brouard 2494: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2495: cov[2]=agexact;
2496: if(nagesqr==1)
2497: cov[3]= agexact*agexact;
1.126 brouard 2498: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2499: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2500: }
2501: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2502: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2503: savm=oldm;
2504: oldm=newm;
2505: } /* end mult */
2506:
2507: s1=s[mw[mi][i]][i];
2508: s2=s[mw[mi+1][i]][i];
2509: bbh=(double)bh[mi][i]/(double)stepm;
2510: 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 */
2511: ipmx +=1;
2512: sw += weight[i];
2513: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2514: } /* end of wave */
2515: } /* end of individual */
2516: } else if(mle==3){ /* exponential inter-extrapolation */
2517: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2518: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2519: for(mi=1; mi<= wav[i]-1; mi++){
2520: for (ii=1;ii<=nlstate+ndeath;ii++)
2521: for (j=1;j<=nlstate+ndeath;j++){
2522: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2523: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2524: }
2525: for(d=0; d<dh[mi][i]; d++){
2526: newm=savm;
1.187 brouard 2527: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2528: cov[2]=agexact;
2529: if(nagesqr==1)
2530: cov[3]= agexact*agexact;
1.126 brouard 2531: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2532: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2533: }
2534: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2535: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2536: savm=oldm;
2537: oldm=newm;
2538: } /* end mult */
2539:
2540: s1=s[mw[mi][i]][i];
2541: s2=s[mw[mi+1][i]][i];
2542: bbh=(double)bh[mi][i]/(double)stepm;
2543: 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 */
2544: ipmx +=1;
2545: sw += weight[i];
2546: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2547: } /* end of wave */
2548: } /* end of individual */
2549: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2550: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2551: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2552: for(mi=1; mi<= wav[i]-1; mi++){
2553: for (ii=1;ii<=nlstate+ndeath;ii++)
2554: for (j=1;j<=nlstate+ndeath;j++){
2555: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2556: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2557: }
2558: for(d=0; d<dh[mi][i]; d++){
2559: newm=savm;
1.187 brouard 2560: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2561: cov[2]=agexact;
2562: if(nagesqr==1)
2563: cov[3]= agexact*agexact;
1.126 brouard 2564: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2565: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2566: }
2567:
2568: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2569: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2570: savm=oldm;
2571: oldm=newm;
2572: } /* end mult */
2573:
2574: s1=s[mw[mi][i]][i];
2575: s2=s[mw[mi+1][i]][i];
2576: if( s2 > nlstate){
2577: lli=log(out[s1][s2] - savm[s1][s2]);
2578: }else{
2579: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2580: }
2581: ipmx +=1;
2582: sw += weight[i];
2583: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2584: /* 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]); */
2585: } /* end of wave */
2586: } /* end of individual */
2587: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2588: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2589: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2590: for(mi=1; mi<= wav[i]-1; mi++){
2591: for (ii=1;ii<=nlstate+ndeath;ii++)
2592: for (j=1;j<=nlstate+ndeath;j++){
2593: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2594: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2595: }
2596: for(d=0; d<dh[mi][i]; d++){
2597: newm=savm;
1.187 brouard 2598: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2599: cov[2]=agexact;
2600: if(nagesqr==1)
2601: cov[3]= agexact*agexact;
1.126 brouard 2602: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2603: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2604: }
2605:
2606: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2607: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2608: savm=oldm;
2609: oldm=newm;
2610: } /* end mult */
2611:
2612: s1=s[mw[mi][i]][i];
2613: s2=s[mw[mi+1][i]][i];
2614: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2615: ipmx +=1;
2616: sw += weight[i];
2617: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2618: /*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]);*/
2619: } /* end of wave */
2620: } /* end of individual */
2621: } /* End of if */
2622: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2623: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2624: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2625: return -l;
2626: }
2627:
2628: /*************** log-likelihood *************/
2629: double funcone( double *x)
2630: {
2631: /* Same as likeli but slower because of a lot of printf and if */
2632: int i, ii, j, k, mi, d, kk;
1.131 brouard 2633: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2634: double **out;
2635: double lli; /* Individual log likelihood */
2636: double llt;
2637: int s1, s2;
2638: double bbh, survp;
1.187 brouard 2639: double agexact;
1.214 brouard 2640: double agebegin, ageend;
1.126 brouard 2641: /*extern weight */
2642: /* We are differentiating ll according to initial status */
2643: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2644: /*for(i=1;i<imx;i++)
2645: printf(" %d\n",s[4][i]);
2646: */
2647: cov[1]=1.;
2648:
2649: for(k=1; k<=nlstate; k++) ll[k]=0.;
2650:
2651: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2652: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2653: for(mi=1; mi<= wav[i]-1; mi++){
2654: for (ii=1;ii<=nlstate+ndeath;ii++)
2655: for (j=1;j<=nlstate+ndeath;j++){
2656: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2657: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2658: }
1.214 brouard 2659:
2660: agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
2661: ageend=agev[mw[mi][i]][i] + (dh[mi][i])*stepm/YEARM; /* Age at end of effective wave and at the end of transition */
2662: for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
2663: /*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
2664: and mw[mi+1][i]. dh depends on stepm.*/
1.126 brouard 2665: newm=savm;
1.187 brouard 2666: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2667: cov[2]=agexact;
2668: if(nagesqr==1)
2669: cov[3]= agexact*agexact;
1.126 brouard 2670: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2671: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2672: }
1.187 brouard 2673:
1.145 brouard 2674: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2675: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2676: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2677: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2678: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2679: savm=oldm;
2680: oldm=newm;
2681: } /* end mult */
2682:
2683: s1=s[mw[mi][i]][i];
2684: s2=s[mw[mi+1][i]][i];
2685: bbh=(double)bh[mi][i]/(double)stepm;
2686: /* bias is positive if real duration
2687: * is higher than the multiple of stepm and negative otherwise.
2688: */
2689: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2690: lli=log(out[s1][s2] - savm[s1][s2]);
2691: } else if (s2==-2) {
2692: for (j=1,survp=0. ; j<=nlstate; j++)
2693: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2694: lli= log(survp);
2695: }else if (mle==1){
2696: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2697: } else if(mle==2){
2698: 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 */
2699: } else if(mle==3){ /* exponential inter-extrapolation */
2700: 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 */
2701: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2702: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2703: } else{ /* mle=0 back to 1 */
2704: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2705: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2706: } /* End of if */
2707: ipmx +=1;
2708: sw += weight[i];
2709: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2710: /*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 2711: if(globpr){
1.214 brouard 2712: fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2713: %11.6f %11.6f %11.6f ", \
1.214 brouard 2714: num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2715: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2716: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2717: llt +=ll[k]*gipmx/gsw;
2718: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2719: }
2720: fprintf(ficresilk," %10.6f\n", -llt);
2721: }
2722: } /* end of wave */
2723: } /* end of individual */
2724: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2725: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2726: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2727: if(globpr==0){ /* First time we count the contributions and weights */
2728: gipmx=ipmx;
2729: gsw=sw;
2730: }
2731: return -l;
2732: }
2733:
2734:
2735: /*************** function likelione ***********/
2736: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2737: {
2738: /* This routine should help understanding what is done with
2739: the selection of individuals/waves and
2740: to check the exact contribution to the likelihood.
2741: Plotting could be done.
2742: */
2743: int k;
2744:
2745: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2746: strcpy(fileresilk,"ILK_");
1.202 brouard 2747: strcat(fileresilk,fileresu);
1.126 brouard 2748: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2749: printf("Problem with resultfile: %s\n", fileresilk);
2750: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2751: }
1.214 brouard 2752: fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
2753: fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2754: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2755: for(k=1; k<=nlstate; k++)
2756: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2757: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2758: }
2759:
2760: *fretone=(*funcone)(p);
2761: if(*globpri !=0){
2762: fclose(ficresilk);
1.205 brouard 2763: if (mle ==0)
2764: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2765: else if(mle >=1)
2766: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2767: fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.207 brouard 2768:
1.208 brouard 2769:
2770: for (k=1; k<= nlstate ; k++) {
1.211 brouard 2771: fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.208 brouard 2772: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
2773: }
1.207 brouard 2774: fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
1.204 brouard 2775: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2776: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2777: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 brouard 2778: fflush(fichtm);
1.205 brouard 2779: }
1.126 brouard 2780: return;
2781: }
2782:
2783:
2784: /*********** Maximum Likelihood Estimation ***************/
2785:
2786: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2787: {
1.165 brouard 2788: int i,j, iter=0;
1.126 brouard 2789: double **xi;
2790: double fret;
2791: double fretone; /* Only one call to likelihood */
2792: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2793:
2794: #ifdef NLOPT
2795: int creturn;
2796: nlopt_opt opt;
2797: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2798: double *lb;
2799: double minf; /* the minimum objective value, upon return */
2800: double * p1; /* Shifted parameters from 0 instead of 1 */
2801: myfunc_data dinst, *d = &dinst;
2802: #endif
2803:
2804:
1.126 brouard 2805: xi=matrix(1,npar,1,npar);
2806: for (i=1;i<=npar;i++)
2807: for (j=1;j<=npar;j++)
2808: xi[i][j]=(i==j ? 1.0 : 0.0);
2809: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2810: strcpy(filerespow,"POW_");
1.126 brouard 2811: strcat(filerespow,fileres);
2812: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2813: printf("Problem with resultfile: %s\n", filerespow);
2814: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2815: }
2816: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2817: for (i=1;i<=nlstate;i++)
2818: for(j=1;j<=nlstate+ndeath;j++)
2819: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2820: fprintf(ficrespow,"\n");
1.162 brouard 2821: #ifdef POWELL
1.126 brouard 2822: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2823: #endif
1.126 brouard 2824:
1.162 brouard 2825: #ifdef NLOPT
2826: #ifdef NEWUOA
2827: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2828: #else
2829: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2830: #endif
2831: lb=vector(0,npar-1);
2832: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2833: nlopt_set_lower_bounds(opt, lb);
2834: nlopt_set_initial_step1(opt, 0.1);
2835:
2836: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2837: d->function = func;
2838: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2839: nlopt_set_min_objective(opt, myfunc, d);
2840: nlopt_set_xtol_rel(opt, ftol);
2841: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2842: printf("nlopt failed! %d\n",creturn);
2843: }
2844: else {
2845: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2846: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2847: iter=1; /* not equal */
2848: }
2849: nlopt_destroy(opt);
2850: #endif
1.126 brouard 2851: free_matrix(xi,1,npar,1,npar);
2852: fclose(ficrespow);
1.203 brouard 2853: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2854: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2855: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2856:
2857: }
2858:
2859: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2860: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2861: {
2862: double **a,**y,*x,pd;
1.203 brouard 2863: /* double **hess; */
1.164 brouard 2864: int i, j;
1.126 brouard 2865: int *indx;
2866:
2867: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2868: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2869: void lubksb(double **a, int npar, int *indx, double b[]) ;
2870: void ludcmp(double **a, int npar, int *indx, double *d) ;
2871: double gompertz(double p[]);
1.203 brouard 2872: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2873:
2874: printf("\nCalculation of the hessian matrix. Wait...\n");
2875: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2876: for (i=1;i<=npar;i++){
1.203 brouard 2877: printf("%d-",i);fflush(stdout);
2878: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2879:
2880: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2881:
2882: /* printf(" %f ",p[i]);
2883: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2884: }
2885:
2886: for (i=1;i<=npar;i++) {
2887: for (j=1;j<=npar;j++) {
2888: if (j>i) {
1.203 brouard 2889: printf(".%d-%d",i,j);fflush(stdout);
2890: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2891: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2892:
2893: hess[j][i]=hess[i][j];
2894: /*printf(" %lf ",hess[i][j]);*/
2895: }
2896: }
2897: }
2898: printf("\n");
2899: fprintf(ficlog,"\n");
2900:
2901: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2902: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2903:
2904: a=matrix(1,npar,1,npar);
2905: y=matrix(1,npar,1,npar);
2906: x=vector(1,npar);
2907: indx=ivector(1,npar);
2908: for (i=1;i<=npar;i++)
2909: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2910: ludcmp(a,npar,indx,&pd);
2911:
2912: for (j=1;j<=npar;j++) {
2913: for (i=1;i<=npar;i++) x[i]=0;
2914: x[j]=1;
2915: lubksb(a,npar,indx,x);
2916: for (i=1;i<=npar;i++){
2917: matcov[i][j]=x[i];
2918: }
2919: }
2920:
2921: printf("\n#Hessian matrix#\n");
2922: fprintf(ficlog,"\n#Hessian matrix#\n");
2923: for (i=1;i<=npar;i++) {
2924: for (j=1;j<=npar;j++) {
1.203 brouard 2925: printf("%.6e ",hess[i][j]);
2926: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2927: }
2928: printf("\n");
2929: fprintf(ficlog,"\n");
2930: }
2931:
1.203 brouard 2932: /* printf("\n#Covariance matrix#\n"); */
2933: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2934: /* for (i=1;i<=npar;i++) { */
2935: /* for (j=1;j<=npar;j++) { */
2936: /* printf("%.6e ",matcov[i][j]); */
2937: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2938: /* } */
2939: /* printf("\n"); */
2940: /* fprintf(ficlog,"\n"); */
2941: /* } */
2942:
1.126 brouard 2943: /* Recompute Inverse */
1.203 brouard 2944: /* for (i=1;i<=npar;i++) */
2945: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2946: /* ludcmp(a,npar,indx,&pd); */
2947:
2948: /* printf("\n#Hessian matrix recomputed#\n"); */
2949:
2950: /* for (j=1;j<=npar;j++) { */
2951: /* for (i=1;i<=npar;i++) x[i]=0; */
2952: /* x[j]=1; */
2953: /* lubksb(a,npar,indx,x); */
2954: /* for (i=1;i<=npar;i++){ */
2955: /* y[i][j]=x[i]; */
2956: /* printf("%.3e ",y[i][j]); */
2957: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2958: /* } */
2959: /* printf("\n"); */
2960: /* fprintf(ficlog,"\n"); */
2961: /* } */
2962:
2963: /* Verifying the inverse matrix */
2964: #ifdef DEBUGHESS
2965: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2966:
1.203 brouard 2967: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2968: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2969:
2970: for (j=1;j<=npar;j++) {
2971: for (i=1;i<=npar;i++){
1.203 brouard 2972: printf("%.2f ",y[i][j]);
2973: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2974: }
2975: printf("\n");
2976: fprintf(ficlog,"\n");
2977: }
1.203 brouard 2978: #endif
1.126 brouard 2979:
2980: free_matrix(a,1,npar,1,npar);
2981: free_matrix(y,1,npar,1,npar);
2982: free_vector(x,1,npar);
2983: free_ivector(indx,1,npar);
1.203 brouard 2984: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2985:
2986:
2987: }
2988:
2989: /*************** hessian matrix ****************/
2990: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2991: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2992: int i;
2993: int l=1, lmax=20;
1.203 brouard 2994: double k1,k2, res, fx;
1.132 brouard 2995: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2996: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2997: int k=0,kmax=10;
2998: double l1;
2999:
3000: fx=func(x);
3001: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 3002: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 3003: l1=pow(10,l);
3004: delts=delt;
3005: for(k=1 ; k <kmax; k=k+1){
3006: delt = delta*(l1*k);
3007: p2[theta]=x[theta] +delt;
1.145 brouard 3008: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 3009: p2[theta]=x[theta]-delt;
3010: k2=func(p2)-fx;
3011: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 3012: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 3013:
1.203 brouard 3014: #ifdef DEBUGHESSII
1.126 brouard 3015: 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);
3016: 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);
3017: #endif
3018: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
3019: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
3020: k=kmax;
3021: }
3022: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 3023: k=kmax; l=lmax*10;
1.126 brouard 3024: }
3025: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
3026: delts=delt;
3027: }
1.203 brouard 3028: } /* End loop k */
1.126 brouard 3029: }
3030: delti[theta]=delts;
3031: return res;
3032:
3033: }
3034:
1.203 brouard 3035: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 3036: {
3037: int i;
1.164 brouard 3038: int l=1, lmax=20;
1.126 brouard 3039: double k1,k2,k3,k4,res,fx;
1.132 brouard 3040: double p2[MAXPARM+1];
1.203 brouard 3041: int k, kmax=1;
3042: double v1, v2, cv12, lc1, lc2;
1.208 brouard 3043:
3044: int firstime=0;
1.203 brouard 3045:
1.126 brouard 3046: fx=func(x);
1.203 brouard 3047: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 3048: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 3049: p2[thetai]=x[thetai]+delti[thetai]*k;
3050: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3051: k1=func(p2)-fx;
3052:
1.203 brouard 3053: p2[thetai]=x[thetai]+delti[thetai]*k;
3054: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3055: k2=func(p2)-fx;
3056:
1.203 brouard 3057: p2[thetai]=x[thetai]-delti[thetai]*k;
3058: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 3059: k3=func(p2)-fx;
3060:
1.203 brouard 3061: p2[thetai]=x[thetai]-delti[thetai]*k;
3062: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 3063: k4=func(p2)-fx;
1.203 brouard 3064: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
3065: if(k1*k2*k3*k4 <0.){
1.208 brouard 3066: firstime=1;
1.203 brouard 3067: kmax=kmax+10;
1.208 brouard 3068: }
3069: if(kmax >=10 || firstime ==1){
1.203 brouard 3070: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3071: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
3072: 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);
3073: 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);
3074: }
3075: #ifdef DEBUGHESSIJ
3076: v1=hess[thetai][thetai];
3077: v2=hess[thetaj][thetaj];
3078: cv12=res;
3079: /* Computing eigen value of Hessian matrix */
3080: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3081: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
3082: if ((lc2 <0) || (lc1 <0) ){
3083: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3084: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
3085: 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);
3086: 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);
3087: }
1.126 brouard 3088: #endif
3089: }
3090: return res;
3091: }
3092:
1.203 brouard 3093: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3094: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3095: /* { */
3096: /* int i; */
3097: /* int l=1, lmax=20; */
3098: /* double k1,k2,k3,k4,res,fx; */
3099: /* double p2[MAXPARM+1]; */
3100: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3101: /* int k=0,kmax=10; */
3102: /* double l1; */
3103:
3104: /* fx=func(x); */
3105: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3106: /* l1=pow(10,l); */
3107: /* delts=delt; */
3108: /* for(k=1 ; k <kmax; k=k+1){ */
3109: /* delt = delti*(l1*k); */
3110: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3111: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3112: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3113: /* k1=func(p2)-fx; */
3114:
3115: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3116: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3117: /* k2=func(p2)-fx; */
3118:
3119: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3120: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3121: /* k3=func(p2)-fx; */
3122:
3123: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3124: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3125: /* k4=func(p2)-fx; */
3126: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3127: /* #ifdef DEBUGHESSIJ */
3128: /* 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); */
3129: /* 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); */
3130: /* #endif */
3131: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3132: /* k=kmax; */
3133: /* } */
3134: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3135: /* k=kmax; l=lmax*10; */
3136: /* } */
3137: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3138: /* delts=delt; */
3139: /* } */
3140: /* } /\* End loop k *\/ */
3141: /* } */
3142: /* delti[theta]=delts; */
3143: /* return res; */
3144: /* } */
3145:
3146:
1.126 brouard 3147: /************** Inverse of matrix **************/
3148: void ludcmp(double **a, int n, int *indx, double *d)
3149: {
3150: int i,imax,j,k;
3151: double big,dum,sum,temp;
3152: double *vv;
3153:
3154: vv=vector(1,n);
3155: *d=1.0;
3156: for (i=1;i<=n;i++) {
3157: big=0.0;
3158: for (j=1;j<=n;j++)
3159: if ((temp=fabs(a[i][j])) > big) big=temp;
3160: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3161: vv[i]=1.0/big;
3162: }
3163: for (j=1;j<=n;j++) {
3164: for (i=1;i<j;i++) {
3165: sum=a[i][j];
3166: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3167: a[i][j]=sum;
3168: }
3169: big=0.0;
3170: for (i=j;i<=n;i++) {
3171: sum=a[i][j];
3172: for (k=1;k<j;k++)
3173: sum -= a[i][k]*a[k][j];
3174: a[i][j]=sum;
3175: if ( (dum=vv[i]*fabs(sum)) >= big) {
3176: big=dum;
3177: imax=i;
3178: }
3179: }
3180: if (j != imax) {
3181: for (k=1;k<=n;k++) {
3182: dum=a[imax][k];
3183: a[imax][k]=a[j][k];
3184: a[j][k]=dum;
3185: }
3186: *d = -(*d);
3187: vv[imax]=vv[j];
3188: }
3189: indx[j]=imax;
3190: if (a[j][j] == 0.0) a[j][j]=TINY;
3191: if (j != n) {
3192: dum=1.0/(a[j][j]);
3193: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3194: }
3195: }
3196: free_vector(vv,1,n); /* Doesn't work */
3197: ;
3198: }
3199:
3200: void lubksb(double **a, int n, int *indx, double b[])
3201: {
3202: int i,ii=0,ip,j;
3203: double sum;
3204:
3205: for (i=1;i<=n;i++) {
3206: ip=indx[i];
3207: sum=b[ip];
3208: b[ip]=b[i];
3209: if (ii)
3210: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3211: else if (sum) ii=i;
3212: b[i]=sum;
3213: }
3214: for (i=n;i>=1;i--) {
3215: sum=b[i];
3216: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3217: b[i]=sum/a[i][i];
3218: }
3219: }
3220:
3221: void pstamp(FILE *fichier)
3222: {
1.196 brouard 3223: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3224: }
3225:
3226: /************ Frequencies ********************/
1.214 brouard 3227: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, \
3228: int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[],\
3229: int firstpass, int lastpass, int stepm, int weightopt, char model[])
1.126 brouard 3230: { /* Some frequencies */
3231:
1.164 brouard 3232: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3233: int mi; /* Effective wave */
1.126 brouard 3234: int first;
3235: double ***freq; /* Frequencies */
3236: double *pp, **prop;
3237: double pos,posprop, k2, dateintsum=0,k2cpt=0;
1.214 brouard 3238: char fileresp[FILENAMELENGTH], fileresphtm[FILENAMELENGTH], fileresphtmfr[FILENAMELENGTH];
3239: double agebegin, ageend;
3240:
1.126 brouard 3241: pp=vector(1,nlstate);
3242: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3243: strcpy(fileresp,"P_");
3244: strcat(fileresp,fileresu);
1.213 brouard 3245: /*strcat(fileresphtm,fileresu);*/
1.126 brouard 3246: if((ficresp=fopen(fileresp,"w"))==NULL) {
3247: printf("Problem with prevalence resultfile: %s\n", fileresp);
3248: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3249: exit(0);
3250: }
1.214 brouard 3251:
1.213 brouard 3252: strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
3253: if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
3254: printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3255: fprintf(ficlog,"Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
3256: fflush(ficlog);
3257: exit(70);
3258: }
1.214 brouard 3259: else{
3260: fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3261: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3262: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3263: fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3264: }
3265: fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);
3266:
3267: strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
3268: if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
3269: printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3270: fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
3271: fflush(ficlog);
3272: exit(70);
3273: }
3274: else{
3275: fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
3276: <hr size=\"2\" color=\"#EC5E5E\"> \n\
3277: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
3278: fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
3279: }
3280: fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);
3281:
1.126 brouard 3282: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3283: j1=0;
3284:
3285: j=cptcoveff;
3286: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3287:
3288: first=1;
3289:
1.214 brouard 3290: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){ /* Loop on covariates combination */
1.126 brouard 3291: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3292: scanf("%d", i);*/
3293: for (i=-5; i<=nlstate+ndeath; i++)
3294: for (jk=-5; jk<=nlstate+ndeath; jk++)
3295: for(m=iagemin; m <= iagemax+3; m++)
3296: freq[i][jk][m]=0;
1.143 brouard 3297:
3298: for (i=1; i<=nlstate; i++)
3299: for(m=iagemin; m <= iagemax+3; m++)
3300: prop[i][m]=0;
1.126 brouard 3301:
3302: dateintsum=0;
3303: k2cpt=0;
1.214 brouard 3304: for (i=1; i<=imx; i++) { /* For each individual i */
1.126 brouard 3305: bool=1;
1.210 brouard 3306: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
1.144 brouard 3307: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3308: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3309: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3310: bool=0;
1.198 brouard 3311: /* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
3312: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3313: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3314: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3315: }
1.210 brouard 3316: } /* cptcovn > 0 */
1.214 brouard 3317:
1.126 brouard 3318: if (bool==1){
1.214 brouard 3319: /* for(m=firstpass; m<=lastpass; m++){ */
3320: for(mi=1; mi<wav[i];mi++){
3321: m=mw[mi][i];
3322: /* dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective (mi) waves m=mw[mi][i]
3323: and mw[mi+1][i]. dh depends on stepm. */
3324: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3325: ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /* Age at end of wave and transition */
3326: if(m >=firstpass && m <=lastpass){
3327: k2=anint[m][i]+(mint[m][i]/12.);
3328: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3329: if(agev[m][i]==0) agev[m][i]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
3330: if(agev[m][i]==1) agev[m][i]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
3331: if (s[m][i]>0 && s[m][i]<=nlstate) /* If status at wave m is known and a live state */
3332: prop[s[m][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
1.126 brouard 3333: if (m<lastpass) {
1.214 brouard 3334: /* if(s[m][i]==4 && s[m+1][i]==4) */
3335: /* printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i]); */
3336: if(s[m][i]==-1)
3337: printf(" num=%ld m=%d, i=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[i], m, i,s[m][i],s[m+1][i], (int)agev[m][i],agebegin, ageend, (int)((agebegin+ageend)/2.));
3338: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i]; /* At age of beginning of transition, where status is known */
3339: /* freq[s[m][i]][s[m+1][i]][(int)((agebegin+ageend)/2.)] += weight[i]; */
3340: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i]; /* Total is in iagemax+3 *//* At age of beginning of transition, where status is known */
1.126 brouard 3341: }
1.214 brouard 3342: }
3343: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3)) && (anint[m][i]!=9999) && (mint[m][i]!=99)) {
3344: dateintsum=dateintsum+k2;
3345: k2cpt++;
3346: /* printf("i=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",i, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
3347: }
3348: /*}*/
1.210 brouard 3349: } /* end m */
3350: } /* end bool */
3351: } /* end i = 1 to imx */
1.126 brouard 3352:
3353: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3354: pstamp(ficresp);
3355: if (cptcovn>0) {
3356: fprintf(ficresp, "\n#********** Variable ");
1.214 brouard 3357: fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
3358: fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
1.213 brouard 3359: for (z1=1; z1<=cptcoveff; z1++){
3360: fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
3361: fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3362: fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.213 brouard 3363: }
3364: fprintf(ficresp, "**********\n#");
1.214 brouard 3365: fprintf(ficresphtm, "**********</h3>\n");
3366: fprintf(ficresphtmfr, "**********</h3>\n");
1.143 brouard 3367: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3368: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.214 brouard 3369: fprintf(ficlog, "**********\n");
1.126 brouard 3370: }
1.214 brouard 3371: fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
1.213 brouard 3372: for(i=1; i<=nlstate;i++) {
1.126 brouard 3373: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
1.213 brouard 3374: fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
3375: }
1.126 brouard 3376: fprintf(ficresp, "\n");
1.213 brouard 3377: fprintf(ficresphtm, "\n");
1.126 brouard 3378:
1.214 brouard 3379: /* Header of frequency table by age */
3380: fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
3381: fprintf(ficresphtmfr,"<th>Age</th> ");
3382: for(jk=-1; jk <=nlstate+ndeath; jk++){
3383: for(m=-1; m <=nlstate+ndeath; m++){
3384: if(jk!=0 && m!=0)
3385: fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
3386: }
3387: }
3388: fprintf(ficresphtmfr, "\n");
3389:
3390: /* For each age */
1.126 brouard 3391: for(i=iagemin; i <= iagemax+3; i++){
1.213 brouard 3392: fprintf(ficresphtm,"<tr>");
1.214 brouard 3393: if(i==iagemax+1){
3394: fprintf(ficlog,"1");
3395: fprintf(ficresphtmfr,"<tr><th>0</th> ");
3396: }else if(i==iagemax+2){
3397: fprintf(ficlog,"0");
3398: fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
3399: }else if(i==iagemax+3){
1.126 brouard 3400: fprintf(ficlog,"Total");
1.214 brouard 3401: fprintf(ficresphtmfr,"<tr><th>Total</th> ");
1.126 brouard 3402: }else{
3403: if(first==1){
3404: first=0;
3405: printf("See log file for details...\n");
3406: }
1.214 brouard 3407: fprintf(ficresphtmfr,"<tr><th>%d</th> ",i);
1.126 brouard 3408: fprintf(ficlog,"Age %d", i);
3409: }
3410: for(jk=1; jk <=nlstate ; jk++){
3411: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3412: pp[jk] += freq[jk][m][i];
3413: }
3414: for(jk=1; jk <=nlstate ; jk++){
3415: for(m=-1, pos=0; m <=0 ; m++)
3416: pos += freq[jk][m][i];
3417: if(pp[jk]>=1.e-10){
3418: if(first==1){
1.132 brouard 3419: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3420: }
3421: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3422: }else{
3423: if(first==1)
3424: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3425: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3426: }
3427: }
3428:
3429: for(jk=1; jk <=nlstate ; jk++){
3430: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3431: pp[jk] += freq[jk][m][i];
3432: }
3433: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3434: pos += pp[jk];
3435: posprop += prop[jk][i];
3436: }
3437: for(jk=1; jk <=nlstate ; jk++){
3438: if(pos>=1.e-5){
3439: if(first==1)
3440: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3441: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3442: }else{
3443: if(first==1)
3444: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3445: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3446: }
3447: if( i <= iagemax){
3448: if(pos>=1.e-5){
3449: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.213 brouard 3450: fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",i,prop[jk][i]/posprop, prop[jk][i],posprop);
1.126 brouard 3451: /*probs[i][jk][j1]= pp[jk]/pos;*/
3452: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3453: }
1.213 brouard 3454: else{
1.126 brouard 3455: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
1.213 brouard 3456: fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",i, prop[jk][i],posprop);
3457: }
1.126 brouard 3458: }
3459: }
3460:
1.214 brouard 3461: for(jk=-1; jk <=nlstate+ndeath; jk++){
3462: for(m=-1; m <=nlstate+ndeath; m++){
3463: if(freq[jk][m][i] !=0 ) { /* minimizing output */
3464: if(first==1){
3465: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3466: }
1.126 brouard 3467: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3468: }
1.214 brouard 3469: if(jk!=0 && m!=0)
3470: fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][i]);
3471: }
3472: }
3473: fprintf(ficresphtmfr,"</tr>\n ");
1.213 brouard 3474: if(i <= iagemax){
1.126 brouard 3475: fprintf(ficresp,"\n");
1.213 brouard 3476: fprintf(ficresphtm,"</tr>\n");
3477: }
1.126 brouard 3478: if(first==1)
3479: printf("Others in log...\n");
3480: fprintf(ficlog,"\n");
1.210 brouard 3481: } /* end loop i */
1.213 brouard 3482: fprintf(ficresphtm,"</table>\n");
1.214 brouard 3483: fprintf(ficresphtmfr,"</table>\n");
1.145 brouard 3484: /*}*/
1.210 brouard 3485: } /* end j1 */
1.126 brouard 3486: dateintmean=dateintsum/k2cpt;
3487:
3488: fclose(ficresp);
1.213 brouard 3489: fclose(ficresphtm);
1.214 brouard 3490: fclose(ficresphtmfr);
1.126 brouard 3491: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3492: free_vector(pp,1,nlstate);
3493: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3494: /* End of Freq */
3495: }
3496:
3497: /************ Prevalence ********************/
3498: 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)
3499: {
3500: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3501: in each health status at the date of interview (if between dateprev1 and dateprev2).
3502: We still use firstpass and lastpass as another selection.
3503: */
3504:
1.164 brouard 3505: int i, m, jk, j1, bool, z1,j;
1.214 brouard 3506: int mi; /* Effective wave */
3507: int iage;
3508: double agebegin, ageend;
1.164 brouard 3509:
3510: double **prop;
3511: double posprop;
1.126 brouard 3512: double y2; /* in fractional years */
3513: int iagemin, iagemax;
1.145 brouard 3514: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3515:
3516: iagemin= (int) agemin;
3517: iagemax= (int) agemax;
3518: /*pp=vector(1,nlstate);*/
3519: prop=matrix(1,nlstate,iagemin,iagemax+3);
3520: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3521: j1=0;
3522:
1.145 brouard 3523: /*j=cptcoveff;*/
1.126 brouard 3524: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3525:
1.145 brouard 3526: first=1;
3527: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
1.214 brouard 3528: for (i=1; i<=nlstate; i++)
3529: for(iage=iagemin; iage <= iagemax+3; iage++)
3530: prop[i][iage]=0.0;
3531:
3532: for (i=1; i<=imx; i++) { /* Each individual */
3533: bool=1;
3534: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3535: for (z1=1; z1<=cptcoveff; z1++)
3536: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
3537: bool=0;
3538: }
3539: if (bool==1) {
3540: /* for(m=firstpass; m<=lastpass; m++){/\* Other selection (we can limit to certain interviews*\/ */
3541: for(mi=1; mi<wav[i];mi++){
3542: m=mw[mi][i];
3543: agebegin=agev[m][i]; /* Age at beginning of wave before transition*/
3544: /* ageend=agev[m][i]+(dh[m][i])*stepm/YEARM; /\* Age at end of wave and transition *\/ */
3545: if(m >=firstpass && m <=lastpass){
1.126 brouard 3546: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3547: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3548: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3549: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3550: 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);
1.214 brouard 3551: if (s[m][i]>0 && s[m][i]<=nlstate) {
1.126 brouard 3552: /*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]]);*/
1.214 brouard 3553: prop[s[m][i]][(int)agev[m][i]] += weight[i];/* At age of beginning of transition, where status is known */
3554: prop[s[m][i]][iagemax+3] += weight[i];
3555: } /* end valid statuses */
3556: } /* end selection of dates */
1.126 brouard 3557: } /* end selection of waves */
1.214 brouard 3558: } /* end effective waves */
3559: } /* end bool */
3560: }
3561: for(i=iagemin; i <= iagemax+3; i++){
3562: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3563: posprop += prop[jk][i];
3564: }
3565:
3566: for(jk=1; jk <=nlstate ; jk++){
3567: if( i <= iagemax){
3568: if(posprop>=1.e-5){
3569: probs[i][jk][j1]= prop[jk][i]/posprop;
3570: } else{
3571: if(first==1){
3572: first=0;
3573: 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]);
1.145 brouard 3574: }
1.214 brouard 3575: }
3576: }
3577: }/* end jk */
3578: }/* end i */
1.145 brouard 3579: /*} *//* end i1 */
3580: } /* end j1 */
1.126 brouard 3581:
3582: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3583: /*free_vector(pp,1,nlstate);*/
3584: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3585: } /* End of prevalence */
3586:
3587: /************* Waves Concatenation ***************/
3588:
3589: 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)
3590: {
3591: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3592: Death is a valid wave (if date is known).
3593: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3594: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3595: and mw[mi+1][i]. dh depends on stepm.
3596: */
3597:
3598: int i, mi, m;
3599: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3600: double sum=0., jmean=0.;*/
1.214 brouard 3601: int first, firstwo;
1.126 brouard 3602: int j, k=0,jk, ju, jl;
3603: double sum=0.;
3604: first=0;
1.214 brouard 3605: firstwo=0;
1.164 brouard 3606: jmin=100000;
1.126 brouard 3607: jmax=-1;
3608: jmean=0.;
1.214 brouard 3609: for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
1.126 brouard 3610: mi=0;
3611: m=firstpass;
1.214 brouard 3612: while(s[m][i] <= nlstate){ /* a live state */
1.126 brouard 3613: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3614: mw[++mi][i]=m;
3615: if(m >=lastpass)
3616: break;
3617: else
3618: m++;
3619: }/* end while */
1.214 brouard 3620: if (s[m][i] > nlstate){ /* In a death state */
1.126 brouard 3621: mi++; /* Death is another wave */
3622: /* if(mi==0) never been interviewed correctly before death */
3623: /* Only death is a correct wave */
3624: mw[mi][i]=m;
1.214 brouard 3625: }else if (andc[i] != 9999) { /* A death occured after lastpass */
3626: m++;
3627: mi++;
3628: s[m][i]=nlstate+1; /* We are setting the status to the last of non live state */
3629: mw[mi][i]=m;
3630: nbwarn++;
3631: if(firstwo==0){
3632: printf("Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\nOthers in log file only\n",num[i],i,lastpass,nlstate+1, m);
3633: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
3634: firstwo=1;
3635: }
3636: if(firstwo==1){
3637: fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred after last wave %d. Since 0.98r4 we considered a status %d at wave %d\n",num[i],i,lastpass,nlstate+1, m);
3638: }
1.126 brouard 3639: }
3640: wav[i]=mi;
3641: if(mi==0){
3642: nbwarn++;
3643: if(first==0){
3644: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3645: first=1;
3646: }
3647: if(first==1){
3648: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3649: }
3650: } /* end mi==0 */
3651: } /* End individuals */
1.214 brouard 3652: /* wav and mw are no more changed */
1.126 brouard 3653:
1.214 brouard 3654:
1.126 brouard 3655: for(i=1; i<=imx; i++){
3656: for(mi=1; mi<wav[i];mi++){
3657: if (stepm <=0)
3658: dh[mi][i]=1;
3659: else{
3660: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3661: if (agedc[i] < 2*AGESUP) {
3662: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3663: if(j==0) j=1; /* Survives at least one month after exam */
3664: else if(j<0){
3665: nberr++;
3666: 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]);
3667: j=1; /* Temporary Dangerous patch */
3668: 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);
3669: 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]);
3670: 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);
3671: }
3672: k=k+1;
3673: if (j >= jmax){
3674: jmax=j;
3675: ijmax=i;
3676: }
3677: if (j <= jmin){
3678: jmin=j;
3679: ijmin=i;
3680: }
3681: sum=sum+j;
3682: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3683: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3684: }
3685: }
3686: else{
3687: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3688: /* 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]); */
3689:
3690: k=k+1;
3691: if (j >= jmax) {
3692: jmax=j;
3693: ijmax=i;
3694: }
3695: else if (j <= jmin){
3696: jmin=j;
3697: ijmin=i;
3698: }
3699: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3700: /*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]);*/
3701: if(j<0){
3702: nberr++;
3703: 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]);
3704: 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]);
3705: }
3706: sum=sum+j;
3707: }
3708: jk= j/stepm;
3709: jl= j -jk*stepm;
3710: ju= j -(jk+1)*stepm;
3711: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3712: if(jl==0){
3713: dh[mi][i]=jk;
3714: bh[mi][i]=0;
3715: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3716: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3717: dh[mi][i]=jk+1;
3718: bh[mi][i]=ju;
3719: }
3720: }else{
3721: if(jl <= -ju){
3722: dh[mi][i]=jk;
3723: bh[mi][i]=jl; /* bias is positive if real duration
3724: * is higher than the multiple of stepm and negative otherwise.
3725: */
3726: }
3727: else{
3728: dh[mi][i]=jk+1;
3729: bh[mi][i]=ju;
3730: }
3731: if(dh[mi][i]==0){
3732: dh[mi][i]=1; /* At least one step */
3733: bh[mi][i]=ju; /* At least one step */
3734: /* 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);*/
3735: }
3736: } /* end if mle */
3737: }
3738: } /* end wave */
3739: }
3740: jmean=sum/k;
3741: 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 3742: 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 3743: }
3744:
3745: /*********** Tricode ****************************/
1.145 brouard 3746: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3747: {
1.144 brouard 3748: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3749: /* 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 3750: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3751: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3752: * nbcode[Tvar[j]][1]=
1.144 brouard 3753: */
1.130 brouard 3754:
1.145 brouard 3755: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3756: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3757: int cptcode=0; /* Modality max of covariates j */
3758: int modmincovj=0; /* Modality min of covariates j */
3759:
3760:
1.126 brouard 3761: cptcoveff=0;
3762:
1.144 brouard 3763: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3764:
1.145 brouard 3765: /* Loop on covariates without age and products */
1.186 brouard 3766: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3767: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3768: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3769: modality of this covariate Vj*/
1.145 brouard 3770: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3771: * If product of Vn*Vm, still boolean *:
3772: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3773: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3774: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3775: modality of the nth covariate of individual i. */
1.145 brouard 3776: if (ij > modmaxcovj)
3777: modmaxcovj=ij;
3778: else if (ij < modmincovj)
3779: modmincovj=ij;
3780: if ((ij < -1) && (ij > NCOVMAX)){
3781: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3782: exit(1);
3783: }else
1.136 brouard 3784: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3785: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3786: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3787: /* getting the maximum value of the modality of the covariate
3788: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3789: female is 1, then modmaxcovj=1.*/
1.192 brouard 3790: } /* end for loop on individuals i */
1.145 brouard 3791: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3792: 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 3793: cptcode=modmaxcovj;
1.137 brouard 3794: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3795: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3796: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3797: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3798: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3799: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3800: if( k != -1){
3801: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3802: covariate for which somebody answered excluding
3803: undefined. Usually 2: 0 and 1. */
3804: }
3805: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3806: covariate for which somebody answered including
3807: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3808: }
3809: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3810: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3811: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3812:
1.136 brouard 3813: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3814: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3815: 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 3816: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3817: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3818: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3819: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3820: nbcode[Tvar[j]][ij]=k;
3821: nbcode[Tvar[j]][1]=0;
3822: nbcode[Tvar[j]][2]=1;
3823: nbcode[Tvar[j]][3]=2;
1.197 brouard 3824: To be continued (not working yet).
1.145 brouard 3825: */
1.197 brouard 3826: ij=0; /* ij is similar to i but can jump over null modalities */
3827: 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*/
3828: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3829: break;
3830: }
3831: ij++;
1.197 brouard 3832: 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 3833: cptcode = ij; /* New max modality for covar j */
3834: } /* end of loop on modality i=-1 to 1 or more */
3835:
3836: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3837: /* /\*recode from 0 *\/ */
3838: /* k is a modality. If we have model=V1+V1*sex */
3839: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3840: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3841: /* } */
3842: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3843: /* if (ij > ncodemax[j]) { */
3844: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3845: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3846: /* break; */
3847: /* } */
3848: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3849: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3850:
1.145 brouard 3851: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3852:
1.187 brouard 3853: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3854: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3855: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3856: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3857: }
1.126 brouard 3858:
1.192 brouard 3859: ij=0;
1.145 brouard 3860: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3861: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3862: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3863: ij++;
1.145 brouard 3864: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3865: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3866: }else{
3867: /* Tvaraff[ij]=0; */
3868: }
1.126 brouard 3869: }
1.192 brouard 3870: /* ij--; */
1.144 brouard 3871: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3872:
1.126 brouard 3873: }
3874:
1.145 brouard 3875:
1.126 brouard 3876: /*********** Health Expectancies ****************/
3877:
1.127 brouard 3878: 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 3879:
3880: {
3881: /* Health expectancies, no variances */
1.164 brouard 3882: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3883: int nhstepma, nstepma; /* Decreasing with age */
3884: double age, agelim, hf;
3885: double ***p3mat;
3886: double eip;
3887:
3888: pstamp(ficreseij);
3889: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3890: fprintf(ficreseij,"# Age");
3891: for(i=1; i<=nlstate;i++){
3892: for(j=1; j<=nlstate;j++){
3893: fprintf(ficreseij," e%1d%1d ",i,j);
3894: }
3895: fprintf(ficreseij," e%1d. ",i);
3896: }
3897: fprintf(ficreseij,"\n");
3898:
3899:
3900: if(estepm < stepm){
3901: printf ("Problem %d lower than %d\n",estepm, stepm);
3902: }
3903: else hstepm=estepm;
3904: /* We compute the life expectancy from trapezoids spaced every estepm months
3905: * This is mainly to measure the difference between two models: for example
3906: * if stepm=24 months pijx are given only every 2 years and by summing them
3907: * we are calculating an estimate of the Life Expectancy assuming a linear
3908: * progression in between and thus overestimating or underestimating according
3909: * to the curvature of the survival function. If, for the same date, we
3910: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3911: * to compare the new estimate of Life expectancy with the same linear
3912: * hypothesis. A more precise result, taking into account a more precise
3913: * curvature will be obtained if estepm is as small as stepm. */
3914:
3915: /* For example we decided to compute the life expectancy with the smallest unit */
3916: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3917: nhstepm is the number of hstepm from age to agelim
3918: nstepm is the number of stepm from age to agelin.
3919: Look at hpijx to understand the reason of that which relies in memory size
3920: and note for a fixed period like estepm months */
3921: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3922: survival function given by stepm (the optimization length). Unfortunately it
3923: means that if the survival funtion is printed only each two years of age and if
3924: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3925: results. So we changed our mind and took the option of the best precision.
3926: */
3927: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3928:
3929: agelim=AGESUP;
3930: /* If stepm=6 months */
3931: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3932: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3933:
3934: /* nhstepm age range expressed in number of stepm */
3935: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3936: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3937: /* if (stepm >= YEARM) hstepm=1;*/
3938: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3939: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3940:
3941: for (age=bage; age<=fage; age ++){
3942: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3943: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3944: /* if (stepm >= YEARM) hstepm=1;*/
3945: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3946:
3947: /* If stepm=6 months */
3948: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3949: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3950:
3951: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3952:
3953: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3954:
3955: printf("%d|",(int)age);fflush(stdout);
3956: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3957:
3958: /* Computing expectancies */
3959: for(i=1; i<=nlstate;i++)
3960: for(j=1; j<=nlstate;j++)
3961: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3962: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3963:
3964: /* 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]);*/
3965:
3966: }
3967:
3968: fprintf(ficreseij,"%3.0f",age );
3969: for(i=1; i<=nlstate;i++){
3970: eip=0;
3971: for(j=1; j<=nlstate;j++){
3972: eip +=eij[i][j][(int)age];
3973: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3974: }
3975: fprintf(ficreseij,"%9.4f", eip );
3976: }
3977: fprintf(ficreseij,"\n");
3978:
3979: }
3980: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3981: printf("\n");
3982: fprintf(ficlog,"\n");
3983:
3984: }
3985:
1.127 brouard 3986: 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 3987:
3988: {
3989: /* Covariances of health expectancies eij and of total life expectancies according
3990: to initial status i, ei. .
3991: */
3992: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3993: int nhstepma, nstepma; /* Decreasing with age */
3994: double age, agelim, hf;
3995: double ***p3matp, ***p3matm, ***varhe;
3996: double **dnewm,**doldm;
3997: double *xp, *xm;
3998: double **gp, **gm;
3999: double ***gradg, ***trgradg;
4000: int theta;
4001:
4002: double eip, vip;
4003:
4004: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
4005: xp=vector(1,npar);
4006: xm=vector(1,npar);
4007: dnewm=matrix(1,nlstate*nlstate,1,npar);
4008: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
4009:
4010: pstamp(ficresstdeij);
4011: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
4012: fprintf(ficresstdeij,"# Age");
4013: for(i=1; i<=nlstate;i++){
4014: for(j=1; j<=nlstate;j++)
4015: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
4016: fprintf(ficresstdeij," e%1d. ",i);
4017: }
4018: fprintf(ficresstdeij,"\n");
4019:
4020: pstamp(ficrescveij);
4021: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
4022: fprintf(ficrescveij,"# Age");
4023: for(i=1; i<=nlstate;i++)
4024: for(j=1; j<=nlstate;j++){
4025: cptj= (j-1)*nlstate+i;
4026: for(i2=1; i2<=nlstate;i2++)
4027: for(j2=1; j2<=nlstate;j2++){
4028: cptj2= (j2-1)*nlstate+i2;
4029: if(cptj2 <= cptj)
4030: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
4031: }
4032: }
4033: fprintf(ficrescveij,"\n");
4034:
4035: if(estepm < stepm){
4036: printf ("Problem %d lower than %d\n",estepm, stepm);
4037: }
4038: else hstepm=estepm;
4039: /* We compute the life expectancy from trapezoids spaced every estepm months
4040: * This is mainly to measure the difference between two models: for example
4041: * if stepm=24 months pijx are given only every 2 years and by summing them
4042: * we are calculating an estimate of the Life Expectancy assuming a linear
4043: * progression in between and thus overestimating or underestimating according
4044: * to the curvature of the survival function. If, for the same date, we
4045: * estimate the model with stepm=1 month, we can keep estepm to 24 months
4046: * to compare the new estimate of Life expectancy with the same linear
4047: * hypothesis. A more precise result, taking into account a more precise
4048: * curvature will be obtained if estepm is as small as stepm. */
4049:
4050: /* For example we decided to compute the life expectancy with the smallest unit */
4051: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4052: nhstepm is the number of hstepm from age to agelim
4053: nstepm is the number of stepm from age to agelin.
4054: Look at hpijx to understand the reason of that which relies in memory size
4055: and note for a fixed period like estepm months */
4056: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4057: survival function given by stepm (the optimization length). Unfortunately it
4058: means that if the survival funtion is printed only each two years of age and if
4059: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4060: results. So we changed our mind and took the option of the best precision.
4061: */
4062: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4063:
4064: /* If stepm=6 months */
4065: /* nhstepm age range expressed in number of stepm */
4066: agelim=AGESUP;
4067: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
4068: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4069: /* if (stepm >= YEARM) hstepm=1;*/
4070: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4071:
4072: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4073: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4074: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
4075: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
4076: gp=matrix(0,nhstepm,1,nlstate*nlstate);
4077: gm=matrix(0,nhstepm,1,nlstate*nlstate);
4078:
4079: for (age=bage; age<=fage; age ++){
4080: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
4081: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
4082: /* if (stepm >= YEARM) hstepm=1;*/
4083: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
4084:
4085: /* If stepm=6 months */
4086: /* Computed by stepm unit matrices, product of hstepma matrices, stored
4087: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
4088:
4089: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4090:
4091: /* Computing Variances of health expectancies */
4092: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
4093: decrease memory allocation */
4094: for(theta=1; theta <=npar; theta++){
4095: for(i=1; i<=npar; i++){
4096: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4097: xm[i] = x[i] - (i==theta ?delti[theta]:0);
4098: }
4099: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
4100: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
4101:
4102: for(j=1; j<= nlstate; j++){
4103: for(i=1; i<=nlstate; i++){
4104: for(h=0; h<=nhstepm-1; h++){
4105: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
4106: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
4107: }
4108: }
4109: }
4110:
4111: for(ij=1; ij<= nlstate*nlstate; ij++)
4112: for(h=0; h<=nhstepm-1; h++){
4113: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
4114: }
4115: }/* End theta */
4116:
4117:
4118: for(h=0; h<=nhstepm-1; h++)
4119: for(j=1; j<=nlstate*nlstate;j++)
4120: for(theta=1; theta <=npar; theta++)
4121: trgradg[h][j][theta]=gradg[h][theta][j];
4122:
4123:
4124: for(ij=1;ij<=nlstate*nlstate;ij++)
4125: for(ji=1;ji<=nlstate*nlstate;ji++)
4126: varhe[ij][ji][(int)age] =0.;
4127:
4128: printf("%d|",(int)age);fflush(stdout);
4129: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
4130: for(h=0;h<=nhstepm-1;h++){
4131: for(k=0;k<=nhstepm-1;k++){
4132: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
4133: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
4134: for(ij=1;ij<=nlstate*nlstate;ij++)
4135: for(ji=1;ji<=nlstate*nlstate;ji++)
4136: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
4137: }
4138: }
4139:
4140: /* Computing expectancies */
4141: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
4142: for(i=1; i<=nlstate;i++)
4143: for(j=1; j<=nlstate;j++)
4144: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
4145: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
4146:
4147: /* 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]);*/
4148:
4149: }
4150:
4151: fprintf(ficresstdeij,"%3.0f",age );
4152: for(i=1; i<=nlstate;i++){
4153: eip=0.;
4154: vip=0.;
4155: for(j=1; j<=nlstate;j++){
4156: eip += eij[i][j][(int)age];
4157: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
4158: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
4159: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
4160: }
4161: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
4162: }
4163: fprintf(ficresstdeij,"\n");
4164:
4165: fprintf(ficrescveij,"%3.0f",age );
4166: for(i=1; i<=nlstate;i++)
4167: for(j=1; j<=nlstate;j++){
4168: cptj= (j-1)*nlstate+i;
4169: for(i2=1; i2<=nlstate;i2++)
4170: for(j2=1; j2<=nlstate;j2++){
4171: cptj2= (j2-1)*nlstate+i2;
4172: if(cptj2 <= cptj)
4173: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
4174: }
4175: }
4176: fprintf(ficrescveij,"\n");
4177:
4178: }
4179: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
4180: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
4181: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
4182: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
4183: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4184: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4185: printf("\n");
4186: fprintf(ficlog,"\n");
4187:
4188: free_vector(xm,1,npar);
4189: free_vector(xp,1,npar);
4190: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
4191: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
4192: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
4193: }
4194:
4195: /************ Variance ******************/
1.209 brouard 4196: 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 *ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 4197: {
4198: /* Variance of health expectancies */
4199: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
4200: /* double **newm;*/
1.169 brouard 4201: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
4202:
4203: int movingaverage();
1.126 brouard 4204: double **dnewm,**doldm;
4205: double **dnewmp,**doldmp;
4206: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4207: int k;
1.126 brouard 4208: double *xp;
4209: double **gp, **gm; /* for var eij */
4210: double ***gradg, ***trgradg; /*for var eij */
4211: double **gradgp, **trgradgp; /* for var p point j */
4212: double *gpp, *gmp; /* for var p point j */
4213: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4214: double ***p3mat;
4215: double age,agelim, hf;
4216: double ***mobaverage;
4217: int theta;
4218: char digit[4];
4219: char digitp[25];
4220:
4221: char fileresprobmorprev[FILENAMELENGTH];
4222:
4223: if(popbased==1){
4224: if(mobilav!=0)
1.201 brouard 4225: strcpy(digitp,"-POPULBASED-MOBILAV_");
4226: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4227: }
4228: else
1.201 brouard 4229: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4230:
4231: if (mobilav!=0) {
4232: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4233: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4234: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4235: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4236: }
4237: }
4238:
1.201 brouard 4239: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4240: sprintf(digit,"%-d",ij);
4241: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4242: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4243: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4244: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4245: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4246: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4247: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4248: }
4249: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4250: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4251: pstamp(ficresprobmorprev);
4252: 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);
4253: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4254: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4255: fprintf(ficresprobmorprev," p.%-d SE",j);
4256: for(i=1; i<=nlstate;i++)
4257: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4258: }
4259: fprintf(ficresprobmorprev,"\n");
1.208 brouard 4260:
1.126 brouard 4261: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4262: fprintf(ficgp,"\nunset title \n");
4263: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4264: 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");
4265: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4266: /* } */
4267: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4268: pstamp(ficresvij);
4269: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4270: if(popbased==1)
1.128 brouard 4271: 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 4272: else
4273: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4274: fprintf(ficresvij,"# Age");
4275: for(i=1; i<=nlstate;i++)
4276: for(j=1; j<=nlstate;j++)
4277: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4278: fprintf(ficresvij,"\n");
4279:
4280: xp=vector(1,npar);
4281: dnewm=matrix(1,nlstate,1,npar);
4282: doldm=matrix(1,nlstate,1,nlstate);
4283: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4284: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4285:
4286: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4287: gpp=vector(nlstate+1,nlstate+ndeath);
4288: gmp=vector(nlstate+1,nlstate+ndeath);
4289: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4290:
4291: if(estepm < stepm){
4292: printf ("Problem %d lower than %d\n",estepm, stepm);
4293: }
4294: else hstepm=estepm;
4295: /* For example we decided to compute the life expectancy with the smallest unit */
4296: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4297: nhstepm is the number of hstepm from age to agelim
1.208 brouard 4298: nstepm is the number of stepm from age to agelim.
1.209 brouard 4299: Look at function hpijx to understand why because of memory size limitations,
1.208 brouard 4300: we decided (b) to get a life expectancy respecting the most precise curvature of the
1.126 brouard 4301: survival function given by stepm (the optimization length). Unfortunately it
4302: means that if the survival funtion is printed every two years of age and if
4303: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4304: results. So we changed our mind and took the option of the best precision.
4305: */
4306: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4307: agelim = AGESUP;
4308: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4309: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4310: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4311: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4312: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4313: gp=matrix(0,nhstepm,1,nlstate);
4314: gm=matrix(0,nhstepm,1,nlstate);
4315:
4316:
4317: for(theta=1; theta <=npar; theta++){
4318: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4319: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4320: }
1.209 brouard 4321:
4322: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4323:
4324: if (popbased==1) {
4325: if(mobilav ==0){
4326: for(i=1; i<=nlstate;i++)
4327: prlim[i][i]=probs[(int)age][i][ij];
4328: }else{ /* mobilav */
4329: for(i=1; i<=nlstate;i++)
4330: prlim[i][i]=mobaverage[(int)age][i][ij];
4331: }
4332: }
4333:
1.209 brouard 4334: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
1.126 brouard 4335: for(j=1; j<= nlstate; j++){
4336: for(h=0; h<=nhstepm; h++){
4337: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4338: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4339: }
4340: }
1.209 brouard 4341: /* Next for computing probability of death (h=1 means
1.126 brouard 4342: computed over hstepm matrices product = hstepm*stepm months)
4343: as a weighted average of prlim.
4344: */
4345: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4346: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4347: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4348: }
4349: /* end probability of death */
4350:
4351: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4352: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4353:
4354: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);
1.126 brouard 4355:
4356: if (popbased==1) {
4357: if(mobilav ==0){
4358: for(i=1; i<=nlstate;i++)
4359: prlim[i][i]=probs[(int)age][i][ij];
4360: }else{ /* mobilav */
4361: for(i=1; i<=nlstate;i++)
4362: prlim[i][i]=mobaverage[(int)age][i][ij];
4363: }
4364: }
4365:
1.209 brouard 4366: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
4367:
1.128 brouard 4368: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4369: for(h=0; h<=nhstepm; h++){
4370: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4371: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4372: }
4373: }
4374: /* This for computing probability of death (h=1 means
4375: computed over hstepm matrices product = hstepm*stepm months)
4376: as a weighted average of prlim.
4377: */
4378: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4379: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4380: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4381: }
4382: /* end probability of death */
4383:
4384: for(j=1; j<= nlstate; j++) /* vareij */
4385: for(h=0; h<=nhstepm; h++){
4386: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4387: }
4388:
4389: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4390: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4391: }
4392:
4393: } /* End theta */
4394:
4395: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4396:
4397: for(h=0; h<=nhstepm; h++) /* veij */
4398: for(j=1; j<=nlstate;j++)
4399: for(theta=1; theta <=npar; theta++)
4400: trgradg[h][j][theta]=gradg[h][theta][j];
4401:
4402: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4403: for(theta=1; theta <=npar; theta++)
4404: trgradgp[j][theta]=gradgp[theta][j];
4405:
4406:
4407: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4408: for(i=1;i<=nlstate;i++)
4409: for(j=1;j<=nlstate;j++)
4410: vareij[i][j][(int)age] =0.;
4411:
4412: for(h=0;h<=nhstepm;h++){
4413: for(k=0;k<=nhstepm;k++){
4414: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4415: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4416: for(i=1;i<=nlstate;i++)
4417: for(j=1;j<=nlstate;j++)
4418: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4419: }
4420: }
4421:
4422: /* pptj */
4423: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4424: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4425: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4426: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4427: varppt[j][i]=doldmp[j][i];
4428: /* end ppptj */
4429: /* x centered again */
1.209 brouard 4430:
4431: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);
1.126 brouard 4432:
4433: if (popbased==1) {
4434: if(mobilav ==0){
4435: for(i=1; i<=nlstate;i++)
4436: prlim[i][i]=probs[(int)age][i][ij];
4437: }else{ /* mobilav */
4438: for(i=1; i<=nlstate;i++)
4439: prlim[i][i]=mobaverage[(int)age][i][ij];
4440: }
4441: }
4442:
4443: /* This for computing probability of death (h=1 means
4444: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4445: as a weighted average of prlim.
4446: */
1.209 brouard 4447: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.126 brouard 4448: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4449: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4450: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4451: }
4452: /* end probability of death */
4453:
4454: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4455: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4456: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4457: for(i=1; i<=nlstate;i++){
4458: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4459: }
4460: }
4461: fprintf(ficresprobmorprev,"\n");
4462:
4463: fprintf(ficresvij,"%.0f ",age );
4464: for(i=1; i<=nlstate;i++)
4465: for(j=1; j<=nlstate;j++){
4466: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4467: }
4468: fprintf(ficresvij,"\n");
4469: free_matrix(gp,0,nhstepm,1,nlstate);
4470: free_matrix(gm,0,nhstepm,1,nlstate);
4471: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4472: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4473: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4474: } /* End age */
4475: free_vector(gpp,nlstate+1,nlstate+ndeath);
4476: free_vector(gmp,nlstate+1,nlstate+ndeath);
4477: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4478: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4479: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4480: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4481: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4482: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4483: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4484: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4485: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4486: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4487: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4488: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4489: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4490: fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
1.201 brouard 4491: fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.svg\"> <br>\n", estepm,subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.199 brouard 4492: /* 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.svg\"> <br>\n", stepm,YEARM,digitp,digit);
1.126 brouard 4493: */
1.199 brouard 4494: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4495: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4496:
4497: free_vector(xp,1,npar);
4498: free_matrix(doldm,1,nlstate,1,nlstate);
4499: free_matrix(dnewm,1,nlstate,1,npar);
4500: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4501: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4502: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4503: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4504: fclose(ficresprobmorprev);
4505: fflush(ficgp);
4506: fflush(fichtm);
4507: } /* end varevsij */
4508:
4509: /************ Variance of prevlim ******************/
1.209 brouard 4510: 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 *ncvyearp, int ij, char strstart[])
1.126 brouard 4511: {
1.205 brouard 4512: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4513: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4514:
1.126 brouard 4515: double **dnewm,**doldm;
4516: int i, j, nhstepm, hstepm;
4517: double *xp;
4518: double *gp, *gm;
4519: double **gradg, **trgradg;
1.208 brouard 4520: double **mgm, **mgp;
1.126 brouard 4521: double age,agelim;
4522: int theta;
4523:
4524: pstamp(ficresvpl);
4525: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4526: fprintf(ficresvpl,"# Age");
4527: for(i=1; i<=nlstate;i++)
4528: fprintf(ficresvpl," %1d-%1d",i,i);
4529: fprintf(ficresvpl,"\n");
4530:
4531: xp=vector(1,npar);
4532: dnewm=matrix(1,nlstate,1,npar);
4533: doldm=matrix(1,nlstate,1,nlstate);
4534:
4535: hstepm=1*YEARM; /* Every year of age */
4536: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4537: agelim = AGESUP;
4538: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4539: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4540: if (stepm >= YEARM) hstepm=1;
4541: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4542: gradg=matrix(1,npar,1,nlstate);
1.208 brouard 4543: mgp=matrix(1,npar,1,nlstate);
4544: mgm=matrix(1,npar,1,nlstate);
1.126 brouard 4545: gp=vector(1,nlstate);
4546: gm=vector(1,nlstate);
4547:
4548: for(theta=1; theta <=npar; theta++){
4549: for(i=1; i<=npar; i++){ /* Computes gradient */
4550: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4551: }
1.209 brouard 4552: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4553: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4554: else
4555: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4556: for(i=1;i<=nlstate;i++){
1.126 brouard 4557: gp[i] = prlim[i][i];
1.208 brouard 4558: mgp[theta][i] = prlim[i][i];
4559: }
1.126 brouard 4560: for(i=1; i<=npar; i++) /* Computes gradient */
4561: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.209 brouard 4562: if((int)age==79 ||(int)age== 80 ||(int)age== 81 )
4563: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
4564: else
4565: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);
1.208 brouard 4566: for(i=1;i<=nlstate;i++){
1.126 brouard 4567: gm[i] = prlim[i][i];
1.208 brouard 4568: mgm[theta][i] = prlim[i][i];
4569: }
1.126 brouard 4570: for(i=1;i<=nlstate;i++)
4571: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
1.209 brouard 4572: /* gradg[theta][2]= -gradg[theta][1]; */ /* For testing if nlstate=2 */
1.126 brouard 4573: } /* End theta */
4574:
4575: trgradg =matrix(1,nlstate,1,npar);
4576:
4577: for(j=1; j<=nlstate;j++)
4578: for(theta=1; theta <=npar; theta++)
4579: trgradg[j][theta]=gradg[theta][j];
1.209 brouard 4580: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4581: /* printf("\nmgm mgp %d ",(int)age); */
4582: /* for(j=1; j<=nlstate;j++){ */
4583: /* printf(" %d ",j); */
4584: /* for(theta=1; theta <=npar; theta++) */
4585: /* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
4586: /* printf("\n "); */
4587: /* } */
4588: /* } */
4589: /* if((int)age==79 ||(int)age== 80 ||(int)age== 81 ){ */
4590: /* printf("\n gradg %d ",(int)age); */
4591: /* for(j=1; j<=nlstate;j++){ */
4592: /* printf("%d ",j); */
4593: /* for(theta=1; theta <=npar; theta++) */
4594: /* printf("%d %lf ",theta,gradg[theta][j]); */
4595: /* printf("\n "); */
4596: /* } */
4597: /* } */
1.126 brouard 4598:
4599: for(i=1;i<=nlstate;i++)
4600: varpl[i][(int)age] =0.;
1.209 brouard 4601: if((int)age==79 ||(int)age== 80 ||(int)age== 81){
1.205 brouard 4602: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4603: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4604: }else{
1.126 brouard 4605: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4606: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4607: }
1.126 brouard 4608: for(i=1;i<=nlstate;i++)
4609: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4610:
4611: fprintf(ficresvpl,"%.0f ",age );
4612: for(i=1; i<=nlstate;i++)
4613: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4614: fprintf(ficresvpl,"\n");
4615: free_vector(gp,1,nlstate);
4616: free_vector(gm,1,nlstate);
1.208 brouard 4617: free_matrix(mgm,1,npar,1,nlstate);
4618: free_matrix(mgp,1,npar,1,nlstate);
1.126 brouard 4619: free_matrix(gradg,1,npar,1,nlstate);
4620: free_matrix(trgradg,1,nlstate,1,npar);
4621: } /* End age */
4622:
4623: free_vector(xp,1,npar);
4624: free_matrix(doldm,1,nlstate,1,npar);
4625: free_matrix(dnewm,1,nlstate,1,nlstate);
4626:
4627: }
4628:
4629: /************ Variance of one-step probabilities ******************/
4630: 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[])
4631: {
1.164 brouard 4632: int i, j=0, k1, l1, tj;
1.126 brouard 4633: int k2, l2, j1, z1;
1.164 brouard 4634: int k=0, l;
1.145 brouard 4635: int first=1, first1, first2;
1.126 brouard 4636: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4637: double **dnewm,**doldm;
4638: double *xp;
4639: double *gp, *gm;
4640: double **gradg, **trgradg;
4641: double **mu;
1.164 brouard 4642: double age, cov[NCOVMAX+1];
1.126 brouard 4643: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4644: int theta;
4645: char fileresprob[FILENAMELENGTH];
4646: char fileresprobcov[FILENAMELENGTH];
4647: char fileresprobcor[FILENAMELENGTH];
4648: double ***varpij;
4649:
1.201 brouard 4650: strcpy(fileresprob,"PROB_");
1.126 brouard 4651: strcat(fileresprob,fileres);
4652: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4653: printf("Problem with resultfile: %s\n", fileresprob);
4654: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4655: }
1.201 brouard 4656: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4657: strcat(fileresprobcov,fileresu);
1.126 brouard 4658: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4659: printf("Problem with resultfile: %s\n", fileresprobcov);
4660: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4661: }
1.201 brouard 4662: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4663: strcat(fileresprobcor,fileresu);
1.126 brouard 4664: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4665: printf("Problem with resultfile: %s\n", fileresprobcor);
4666: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4667: }
4668: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4669: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4670: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4671: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4672: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4673: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4674: pstamp(ficresprob);
4675: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4676: fprintf(ficresprob,"# Age");
4677: pstamp(ficresprobcov);
4678: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4679: fprintf(ficresprobcov,"# Age");
4680: pstamp(ficresprobcor);
4681: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4682: fprintf(ficresprobcor,"# Age");
4683:
4684:
4685: for(i=1; i<=nlstate;i++)
4686: for(j=1; j<=(nlstate+ndeath);j++){
4687: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4688: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4689: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4690: }
4691: /* fprintf(ficresprob,"\n");
4692: fprintf(ficresprobcov,"\n");
4693: fprintf(ficresprobcor,"\n");
4694: */
1.131 brouard 4695: xp=vector(1,npar);
1.126 brouard 4696: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4697: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4698: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4699: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4700: first=1;
4701: fprintf(ficgp,"\n# Routine varprob");
4702: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4703: fprintf(fichtm,"\n");
4704:
1.200 brouard 4705: fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);
1.197 brouard 4706: 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);
4707: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4708: and drawn. It helps understanding how is the covariance between two incidences.\
4709: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4710: 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. \
4711: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4712: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4713: standard deviations wide on each axis. <br>\
4714: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4715: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4716: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4717:
4718: cov[1]=1;
1.145 brouard 4719: /* tj=cptcoveff; */
4720: tj = (int) pow(2,cptcoveff);
1.126 brouard 4721: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4722: j1=0;
1.145 brouard 4723: for(j1=1; j1<=tj;j1++){
4724: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4725: /*j1++;*/
1.126 brouard 4726: if (cptcovn>0) {
4727: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4728: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4729: fprintf(ficresprob, "**********\n#\n");
4730: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4731: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4732: fprintf(ficresprobcov, "**********\n#\n");
4733:
4734: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4735: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4736: fprintf(ficgp, "**********\n#\n");
4737:
4738:
4739: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4740: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4741: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4742:
4743: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4744: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4745: fprintf(ficresprobcor, "**********\n#");
4746: }
4747:
1.145 brouard 4748: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4749: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4750: gp=vector(1,(nlstate)*(nlstate+ndeath));
4751: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4752: for (age=bage; age<=fage; age ++){
4753: cov[2]=age;
1.187 brouard 4754: if(nagesqr==1)
4755: cov[3]= age*age;
1.126 brouard 4756: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4757: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4758: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4759: * 1 1 1 1 1
4760: * 2 2 1 1 1
4761: * 3 1 2 1 1
4762: */
4763: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4764: }
1.186 brouard 4765: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4766: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4767: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4768: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4769:
4770:
4771: for(theta=1; theta <=npar; theta++){
4772: for(i=1; i<=npar; i++)
4773: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4774:
4775: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4776:
4777: k=0;
4778: for(i=1; i<= (nlstate); i++){
4779: for(j=1; j<=(nlstate+ndeath);j++){
4780: k=k+1;
4781: gp[k]=pmmij[i][j];
4782: }
4783: }
4784:
4785: for(i=1; i<=npar; i++)
4786: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4787:
4788: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4789: k=0;
4790: for(i=1; i<=(nlstate); i++){
4791: for(j=1; j<=(nlstate+ndeath);j++){
4792: k=k+1;
4793: gm[k]=pmmij[i][j];
4794: }
4795: }
4796:
4797: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4798: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4799: }
4800:
4801: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4802: for(theta=1; theta <=npar; theta++)
4803: trgradg[j][theta]=gradg[theta][j];
4804:
4805: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4806: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4807:
4808: pmij(pmmij,cov,ncovmodel,x,nlstate);
4809:
4810: k=0;
4811: for(i=1; i<=(nlstate); i++){
4812: for(j=1; j<=(nlstate+ndeath);j++){
4813: k=k+1;
4814: mu[k][(int) age]=pmmij[i][j];
4815: }
4816: }
4817: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4818: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4819: varpij[i][j][(int)age] = doldm[i][j];
4820:
4821: /*printf("\n%d ",(int)age);
4822: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4823: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4824: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4825: }*/
4826:
4827: fprintf(ficresprob,"\n%d ",(int)age);
4828: fprintf(ficresprobcov,"\n%d ",(int)age);
4829: fprintf(ficresprobcor,"\n%d ",(int)age);
4830:
4831: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4832: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4833: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4834: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4835: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4836: }
4837: i=0;
4838: for (k=1; k<=(nlstate);k++){
4839: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4840: i++;
1.126 brouard 4841: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4842: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4843: for (j=1; j<=i;j++){
1.145 brouard 4844: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4845: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4846: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4847: }
4848: }
4849: }/* end of loop for state */
4850: } /* end of loop for age */
1.145 brouard 4851: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4852: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4853: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4854: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4855:
1.126 brouard 4856: /* Confidence intervalle of pij */
4857: /*
1.131 brouard 4858: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4859: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4860: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4861: 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);
4862: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4863: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4864: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4865: */
4866:
4867: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4868: first1=1;first2=2;
1.126 brouard 4869: for (k2=1; k2<=(nlstate);k2++){
4870: for (l2=1; l2<=(nlstate+ndeath);l2++){
4871: if(l2==k2) continue;
4872: j=(k2-1)*(nlstate+ndeath)+l2;
4873: for (k1=1; k1<=(nlstate);k1++){
4874: for (l1=1; l1<=(nlstate+ndeath);l1++){
4875: if(l1==k1) continue;
4876: i=(k1-1)*(nlstate+ndeath)+l1;
4877: if(i<=j) continue;
4878: for (age=bage; age<=fage; age ++){
4879: if ((int)age %5==0){
4880: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4881: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4882: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4883: mu1=mu[i][(int) age]/stepm*YEARM ;
4884: mu2=mu[j][(int) age]/stepm*YEARM;
4885: c12=cv12/sqrt(v1*v2);
4886: /* Computing eigen value of matrix of covariance */
4887: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4888: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4889: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4890: if(first2==1){
4891: first1=0;
4892: 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);
4893: }
4894: 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);
4895: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4896: /* lc2=fabs(lc2); */
1.135 brouard 4897: }
4898:
1.126 brouard 4899: /* Eigen vectors */
4900: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4901: /*v21=sqrt(1.-v11*v11); *//* error */
4902: v21=(lc1-v1)/cv12*v11;
4903: v12=-v21;
4904: v22=v11;
4905: tnalp=v21/v11;
4906: if(first1==1){
4907: first1=0;
4908: 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);
4909: }
4910: 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);
4911: /*printf(fignu*/
4912: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4913: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4914: if(first==1){
4915: first=0;
1.200 brouard 4916: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4917: fprintf(ficgp,"\nset parametric;unset label");
4918: 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);
1.199 brouard 4919: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4920: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4921: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4922: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4923: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4924: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4925: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4926: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4927: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4928: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4929: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4930: 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",\
4931: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4932: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4933: }else{
4934: first=0;
4935: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4936: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4937: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4938: 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",\
4939: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4940: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4941: }/* if first */
4942: } /* age mod 5 */
4943: } /* end loop age */
1.201 brouard 4944: fprintf(ficgp,"\nset out;\nset out \"%s_%d%1d%1d-%1d%1d.svg\";replot;set out;",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4945: first=1;
4946: } /*l12 */
4947: } /* k12 */
4948: } /*l1 */
4949: }/* k1 */
1.169 brouard 4950: /* } */ /* loop covariates */
1.126 brouard 4951: }
4952: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4953: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4954: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4955: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4956: free_vector(xp,1,npar);
4957: fclose(ficresprob);
4958: fclose(ficresprobcov);
4959: fclose(ficresprobcor);
4960: fflush(ficgp);
4961: fflush(fichtmcov);
4962: }
4963:
4964:
4965: /******************* Printing html file ***********/
1.201 brouard 4966: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4967: int lastpass, int stepm, int weightopt, char model[],\
4968: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
1.211 brouard 4969: int popforecast, int prevfcast, int estepm , \
1.213 brouard 4970: double jprev1, double mprev1,double anprev1, double dateprev1, \
4971: double jprev2, double mprev2,double anprev2, double dateprev2){
1.126 brouard 4972: int jj1, k1, i1, cpt;
4973:
4974: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4975: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4976: </ul>");
1.214 brouard 4977: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
4978: fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
4979: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
4980: fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
1.213 brouard 4981: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
4982: fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4983: fprintf(fichtm,"\
4984: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4985: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4986: fprintf(fichtm,"\
4987: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4988: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4989: fprintf(fichtm,"\
1.211 brouard 4990: - (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . 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 4991: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4992: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.211 brouard 4993: if(prevfcast==1){
4994: fprintf(fichtm,"\
4995: - Prevalence projections by age and states: \
1.201 brouard 4996: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.211 brouard 4997: }
1.126 brouard 4998:
4999: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
5000:
1.145 brouard 5001: m=pow(2,cptcoveff);
1.126 brouard 5002: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5003:
5004: jj1=0;
5005: for(k1=1; k1<=m;k1++){
1.192 brouard 5006: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5007: jj1++;
5008: if (cptcovn > 0) {
5009: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 5010: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 5011: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
5012: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 5013: }
1.126 brouard 5014: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5015: }
1.201 brouard 5016: /* aij, bij */
1.211 brouard 5017: fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \
5018: <img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5019: /* Pij */
1.211 brouard 5020: fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \
1.201 brouard 5021: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 5022: /* Quasi-incidences */
1.211 brouard 5023: fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
1.201 brouard 5024: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
1.211 brouard 5025: incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
5026: divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
1.201 brouard 5027: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
5028: /* Survival functions (period) in state j */
5029: for(cpt=1; cpt<=nlstate;cpt++){
5030: fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \
5031: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
5032: }
5033: /* State specific survival functions (period) */
5034: for(cpt=1; cpt<=nlstate;cpt++){
1.208 brouard 5035: fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
1.201 brouard 5036: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
5037: <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);
5038: }
5039: /* Period (stable) prevalence in each health state */
5040: for(cpt=1; cpt<=nlstate;cpt++){
5041: fprintf(fichtm,"<br>\n- 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.svg\">%s%d_%d.svg</a><br> \
5042: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
5043: }
1.211 brouard 5044: if(prevfcast==1){
5045: /* Projection of prevalence up to period (stable) prevalence in each health state */
5046: for(cpt=1; cpt<=nlstate;cpt++){
1.214 brouard 5047: fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up 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.svg\">%s%d_%d.svg</a><br> \
1.213 brouard 5048: <img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);
1.211 brouard 5049: }
5050: }
5051:
1.126 brouard 5052: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 5053: 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) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \
1.201 brouard 5054: <img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);
1.126 brouard 5055: }
1.192 brouard 5056: /* } /\* end i1 *\/ */
1.126 brouard 5057: }/* End k1 */
5058: fprintf(fichtm,"</ul>");
5059:
5060: fprintf(fichtm,"\
5061: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 5062: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 5063: - 95%% confidence intervals and Wald tests of the estimated parameters are in the log file if optimization has been done (mle != 0).<br> \
1.197 brouard 5064: But because parameters are usually highly correlated (a higher incidence of disability \
5065: and a higher incidence of recovery can give very close observed transition) it might \
5066: be very useful to look not only at linear confidence intervals estimated from the \
5067: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
5068: (parameters) of the logistic regression, it might be more meaningful to visualize the \
5069: covariance matrix of the one-step probabilities. \
5070: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 5071:
1.193 brouard 5072: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5073: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 5074: fprintf(fichtm,"\
5075: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5076: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 5077:
5078: fprintf(fichtm,"\
5079: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 5080: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 5081: fprintf(fichtm,"\
5082: - 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): \
5083: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5084: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 5085: fprintf(fichtm,"\
5086: - (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): \
5087: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 5088: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 5089: fprintf(fichtm,"\
1.128 brouard 5090: - 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",
1.201 brouard 5091: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 5092: fprintf(fichtm,"\
1.128 brouard 5093: - 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",
1.201 brouard 5094: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 5095: fprintf(fichtm,"\
5096: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 5097: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 5098:
5099: /* if(popforecast==1) fprintf(fichtm,"\n */
5100: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
5101: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
5102: /* <br>",fileres,fileres,fileres,fileres); */
5103: /* else */
5104: /* 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); */
5105: fflush(fichtm);
5106: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
5107:
1.145 brouard 5108: m=pow(2,cptcoveff);
1.126 brouard 5109: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
5110:
5111: jj1=0;
5112: for(k1=1; k1<=m;k1++){
1.192 brouard 5113: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 5114: jj1++;
5115: if (cptcovn > 0) {
5116: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
5117: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 5118: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 5119: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
5120: }
5121: for(cpt=1; cpt<=nlstate;cpt++) {
5122: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 5123: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
5124: <img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);
1.126 brouard 5125: }
5126: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 5127: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
5128: true period expectancies (those weighted with period prevalences are also\
5129: drawn in addition to the population based expectancies computed using\
1.205 brouard 5130: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
5131: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 5132: /* } /\* end i1 *\/ */
1.126 brouard 5133: }/* End k1 */
5134: fprintf(fichtm,"</ul>");
5135: fflush(fichtm);
5136: }
5137:
5138: /******************* Gnuplot file **************/
1.211 brouard 5139: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, char pathc[], double p[]){
1.126 brouard 5140:
5141: char dirfileres[132],optfileres[132];
1.164 brouard 5142: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.211 brouard 5143: int lv=0, vlv=0, kl=0;
1.130 brouard 5144: int ng=0;
1.201 brouard 5145: int vpopbased;
1.126 brouard 5146: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
5147: /* printf("Problem with file %s",optionfilegnuplot); */
5148: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
5149: /* } */
5150:
5151: /*#ifdef windows */
5152: fprintf(ficgp,"cd \"%s\" \n",pathc);
5153: /*#endif */
5154: m=pow(2,cptcoveff);
5155:
1.202 brouard 5156: /* Contribution to likelihood */
5157: /* Plot the probability implied in the likelihood */
5158: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
5159: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
5160: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 5161: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 5162: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 5163: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
5164: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
5165: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 5166: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5167: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):6 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 5168: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.214 brouard 5169: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$13):5 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 5170: for (i=1; i<= nlstate ; i ++) {
5171: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 5172: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
1.214 brouard 5173: fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 5174: for (j=2; j<= nlstate+ndeath ; j ++) {
1.214 brouard 5175: fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($12/4.):6 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 5176: }
5177: fprintf(ficgp,";\nset out; unset ylabel;\n");
5178: }
5179: /* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
5180: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
5181: /* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
1.203 brouard 5182: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 5183: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
5184:
1.126 brouard 5185: strcpy(dirfileres,optionfilefiname);
5186: strcpy(optfileres,"vpl");
5187: /* 1eme*/
1.211 brouard 5188: for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
5189: for (k1=1; k1<= m ; k1 ++) { /* For each combination of covariate */
5190: /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
5191: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");
5192: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5193: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5194: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5195: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5196: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5197: vlv= nbcode[Tvaraff[lv]][lv];
5198: fprintf(ficgp," V%d=%d ",k,vlv);
5199: }
5200: fprintf(ficgp,"\n#\n");
5201:
1.201 brouard 5202: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
5203: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 5204: fprintf(ficgp,"set xlabel \"Age\" \n\
5205: set ylabel \"Probability\" \n\
1.199 brouard 5206: set ter svg size 640, 480\n\
1.201 brouard 5207: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5208:
5209: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5210: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5211: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5212: }
1.201 brouard 5213: fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5214: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5215: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5216: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5217: }
1.201 brouard 5218: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 5219: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 5220: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
5221: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 5222: }
1.201 brouard 5223: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
5224: fprintf(ficgp,"\nset out \n");
5225: } /* k1 */
5226: } /* cpt */
1.126 brouard 5227: /*2 eme*/
5228: for (k1=1; k1<= m ; k1 ++) {
1.211 brouard 5229: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
5230: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5231: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5232: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5233: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5234: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5235: vlv= nbcode[Tvaraff[lv]][lv];
5236: fprintf(ficgp," V%d=%d ",k,vlv);
5237: }
5238: fprintf(ficgp,"\n#\n");
5239:
1.201 brouard 5240: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
5241: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
5242: if(vpopbased==0)
5243: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
5244: else
5245: fprintf(ficgp,"\nreplot ");
5246: for (i=1; i<= nlstate+1 ; i ++) {
5247: k=2*i;
5248: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
5249: for (j=1; j<= nlstate+1 ; j ++) {
5250: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5251: else fprintf(ficgp," %%*lf (%%*lf)");
5252: }
5253: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
5254: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
5255: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5256: for (j=1; j<= nlstate+1 ; j ++) {
5257: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5258: else fprintf(ficgp," %%*lf (%%*lf)");
5259: }
5260: fprintf(ficgp,"\" t\"\" w l lt 0,");
5261: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
5262: for (j=1; j<= nlstate+1 ; j ++) {
5263: if (j==i) fprintf(ficgp," %%lf (%%lf)");
5264: else fprintf(ficgp," %%*lf (%%*lf)");
5265: }
5266: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
5267: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
5268: } /* state */
5269: } /* vpopbased */
5270: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
5271: } /* k1 */
1.211 brouard 5272:
5273:
1.126 brouard 5274: /*3eme*/
5275: for (k1=1; k1<= m ; k1 ++) {
5276: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.211 brouard 5277: fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
5278: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5279: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5280: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5281: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5282: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5283: vlv= nbcode[Tvaraff[lv]][lv];
5284: fprintf(ficgp," V%d=%d ",k,vlv);
5285: }
5286: fprintf(ficgp,"\n#\n");
5287:
1.126 brouard 5288: /* k=2+nlstate*(2*cpt-2); */
5289: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5290: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5291: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5292: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5293: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5294: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5295: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5296: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5297: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5298: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5299:
5300: */
5301: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5302: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);
1.126 brouard 5303: /* 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);*/
5304:
5305: }
1.201 brouard 5306: fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);
1.126 brouard 5307: }
5308: }
5309:
1.201 brouard 5310: /* Survival functions (period) from state i in state j by initial state i */
5311: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5312: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5313: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
5314: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5315: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5316: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5317: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5318: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5319: vlv= nbcode[Tvaraff[lv]][lv];
5320: fprintf(ficgp," V%d=%d ",k,vlv);
5321: }
5322: fprintf(ficgp,"\n#\n");
5323:
1.201 brouard 5324: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5325: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5326: set ter svg size 640, 480\n\
5327: unset log y\n\
5328: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5329: k=3;
1.201 brouard 5330: for (i=1; i<= nlstate ; i ++){
5331: if(i==1)
5332: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5333: else
5334: fprintf(ficgp,", '' ");
5335: l=(nlstate+ndeath)*(i-1)+1;
5336: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5337: for (j=2; j<= nlstate+ndeath ; j ++)
5338: fprintf(ficgp,"+$%d",k+l+j-1);
5339: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5340: } /* nlstate */
5341: fprintf(ficgp,"\nset out\n");
5342: } /* end cpt state*/
5343: } /* end covariate */
5344:
5345: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5346: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5347: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5348: fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
1.211 brouard 5349: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5350: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5351: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5352: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5353: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5354: vlv= nbcode[Tvaraff[lv]][lv];
5355: fprintf(ficgp," V%d=%d ",k,vlv);
5356: }
5357: fprintf(ficgp,"\n#\n");
5358:
1.201 brouard 5359: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5360: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5361: set ter svg size 640, 480\n\
5362: unset log y\n\
5363: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5364: k=3;
1.201 brouard 5365: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5366: if(j==1)
5367: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5368: else
5369: fprintf(ficgp,", '' ");
5370: l=(nlstate+ndeath)*(cpt-1) +j;
5371: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5372: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5373: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5374: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5375: } /* nlstate */
5376: fprintf(ficgp,", '' ");
5377: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5378: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5379: l=(nlstate+ndeath)*(cpt-1) +j;
5380: if(j < nlstate)
5381: fprintf(ficgp,"$%d +",k+l);
5382: else
5383: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5384: }
5385: fprintf(ficgp,"\nset out\n");
5386: } /* end cpt state*/
5387: } /* end covariate */
5388:
1.202 brouard 5389: /* CV preval stable (period) for each covariate */
1.211 brouard 5390: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
1.153 brouard 5391: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.211 brouard 5392: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
5393: for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
5394: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
5395: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5396: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5397: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5398: vlv= nbcode[Tvaraff[lv]][lv];
5399: fprintf(ficgp," V%d=%d ",k,vlv);
5400: }
5401: fprintf(ficgp,"\n#\n");
5402:
1.201 brouard 5403: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5404: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5405: set ter svg size 640, 480\n\
1.126 brouard 5406: unset log y\n\
1.153 brouard 5407: plot [%.f:%.f] ", ageminpar, agemaxpar);
1.211 brouard 5408: k=3; /* Offset */
1.153 brouard 5409: for (i=1; i<= nlstate ; i ++){
5410: if(i==1)
1.201 brouard 5411: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5412: else
5413: fprintf(ficgp,", '' ");
1.154 brouard 5414: l=(nlstate+ndeath)*(i-1)+1;
5415: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5416: for (j=2; j<= nlstate ; j ++)
5417: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5418: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5419: } /* nlstate */
1.201 brouard 5420: fprintf(ficgp,"\nset out\n");
1.153 brouard 5421: } /* end cpt state*/
5422: } /* end covariate */
1.201 brouard 5423:
1.211 brouard 5424: if(prevfcast==1){
5425: /* Projection from cross-sectional to stable (period) for each covariate */
5426:
5427: for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2**k), if any covariate is present */
5428: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5429: fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
5430: for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
5431: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5432: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5433: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5434: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5435: vlv= nbcode[Tvaraff[lv]][lv];
5436: fprintf(ficgp," V%d=%d ",k,vlv);
5437: }
5438: fprintf(ficgp,"\n#\n");
5439:
5440: fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
5441: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);
5442: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
5443: set ter svg size 640, 480\n\
5444: unset log y\n\
5445: plot [%.f:%.f] ", ageminpar, agemaxpar);
5446: for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
5447: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5448: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5449: /*# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5450: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5451: if(i==1){
5452: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
5453: }else{
5454: fprintf(ficgp,",\\\n '' ");
5455: }
5456: if(cptcoveff ==0){ /* No covariate */
5457: fprintf(ficgp," u 2:("); /* Age is in 2 */
5458: /*# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4*/
5459: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 */
5460: if(i==nlstate+1)
5461: fprintf(ficgp," $%d/(1.-$%d)) t 'p.%d' with line ", \
5462: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,cpt );
5463: else
5464: fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
5465: 2+(cpt-1)*(nlstate+1)+1+(i-1), 2+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5466: }else{
5467: fprintf(ficgp,"u 6:(("); /* Age is in 6 */
5468: /*# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3*/
5469: /*# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 */
5470: kl=0;
5471: for (k=1; k<=cptcoveff; k++){ /* For each covariate */
5472: lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
5473: /* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
5474: /* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
5475: /* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
5476: vlv= nbcode[Tvaraff[lv]][lv];
5477: kl++;
5478: /* kl=6+(cpt-1)*(nlstate+1)+1+(i-1); /\* 6+(1-1)*(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 *\/ */
5479: /*6+(cpt-1)*(nlstate+1)+1+(i-1)+(nlstate+1)*nlstate; 6+(1-1)*(2+1)+1+(1-1) +(2+1)*2=13 */
5480: /*6+1+(i-1)+(nlstate+1)*nlstate; 6+1+(1-1) +(2+1)*2=13 */
5481: /* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
5482: if(k==cptcoveff)
5483: if(i==nlstate+1)
5484: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5485: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,cpt );
5486: else
5487: fprintf(ficgp,"$%d==%d && $%d==%d)? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv], \
5488: 6+(cpt-1)*(nlstate+1)+1+(i-1), 6+1+(i-1)+(nlstate+1)*nlstate,i,cpt );
5489: else{
5490: fprintf(ficgp,"$%d==%d && $%d==%d && ",kl, k,kl+1,nbcode[Tvaraff[lv]][lv]);
5491: kl++;
5492: }
5493: } /* end covariate */
5494: } /* end if covariate */
5495: } /* nlstate */
5496: fprintf(ficgp,"\nset out\n");
5497: } /* end cpt state*/
5498: } /* end covariate */
5499: } /* End if prevfcast */
5500:
5501:
1.126 brouard 5502: /* proba elementaires */
1.187 brouard 5503: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5504: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5505: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5506: for(k=1; k <=(nlstate+ndeath); k++){
5507: if (k != i) {
1.187 brouard 5508: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5509: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5510: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5511: jk++;
5512: }
1.187 brouard 5513: fprintf(ficgp,"\n");
1.126 brouard 5514: }
5515: }
5516: }
1.187 brouard 5517: fprintf(ficgp,"##############\n#\n");
5518:
1.145 brouard 5519: /*goto avoid;*/
1.200 brouard 5520: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5521: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5522: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5523: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5524: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5525: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5526: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5527: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5528: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5529: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5530: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5531: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5532: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5533: fprintf(ficgp,"#\n");
1.201 brouard 5534: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5535: fprintf(ficgp,"# ng=%d\n",ng);
5536: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5537: for(jk=1; jk <=m; jk++) {
1.187 brouard 5538: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5539: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5540: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5541: if (ng==1){
5542: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5543: fprintf(ficgp,"\nunset log y");
5544: }else if (ng==2){
5545: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5546: fprintf(ficgp,"\nset log y");
5547: }else if (ng==3){
1.126 brouard 5548: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5549: fprintf(ficgp,"\nset log y");
5550: }else
5551: fprintf(ficgp,"\nunset title ");
5552: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5553: i=1;
5554: for(k2=1; k2<=nlstate; k2++) {
5555: k3=i;
5556: for(k=1; k<=(nlstate+ndeath); k++) {
5557: if (k != k2){
1.201 brouard 5558: switch( ng) {
5559: case 1:
1.187 brouard 5560: if(nagesqr==0)
1.201 brouard 5561: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5562: else /* nagesqr =1 */
1.201 brouard 5563: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5564: break;
5565: case 2: /* ng=2 */
1.187 brouard 5566: if(nagesqr==0)
5567: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5568: else /* nagesqr =1 */
1.201 brouard 5569: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5570: break;
5571: case 3:
5572: if(nagesqr==0)
5573: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5574: else /* nagesqr =1 */
5575: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5576: break;
5577: }
1.141 brouard 5578: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5579: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5580: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5581: if(ij <=cptcovage) { /* Bug valgrind */
5582: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5583: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5584: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5585: ij++;
5586: }
1.186 brouard 5587: }
5588: else
1.198 brouard 5589: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5590: }
1.201 brouard 5591: if(ng != 1){
5592: fprintf(ficgp,")/(1");
1.126 brouard 5593:
1.201 brouard 5594: for(k1=1; k1 <=nlstate; k1++){
5595: if(nagesqr==0)
5596: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5597: else /* nagesqr =1 */
5598: 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);
5599:
5600: ij=1;
5601: for(j=3; j <=ncovmodel-nagesqr; j++){
5602: if(ij <=cptcovage) { /* Bug valgrind */
5603: if((j-2)==Tage[ij]) { /* Bug valgrind */
5604: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5605: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5606: ij++;
5607: }
1.197 brouard 5608: }
1.201 brouard 5609: else
5610: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5611: }
1.201 brouard 5612: fprintf(ficgp,")");
1.126 brouard 5613: }
5614: fprintf(ficgp,")");
1.201 brouard 5615: if(ng ==2)
5616: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5617: else /* ng= 3 */
5618: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5619: }else{ /* end ng <> 1 */
5620: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5621: }
5622: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5623: i=i+ncovmodel;
5624: }
5625: } /* end k */
5626: } /* end k2 */
1.201 brouard 5627: fprintf(ficgp,"\n set out\n");
1.126 brouard 5628: } /* end jk */
5629: } /* end ng */
1.164 brouard 5630: /* avoid: */
1.126 brouard 5631: fflush(ficgp);
5632: } /* end gnuplot */
5633:
5634:
5635: /*************** Moving average **************/
5636: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5637:
5638: int i, cpt, cptcod;
5639: int modcovmax =1;
5640: int mobilavrange, mob;
5641: double age;
5642:
5643: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5644: a covariate has 2 modalities */
5645: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5646:
5647: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5648: if(mobilav==1) mobilavrange=5; /* default */
5649: else mobilavrange=mobilav;
5650: for (age=bage; age<=fage; age++)
5651: for (i=1; i<=nlstate;i++)
5652: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5653: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5654: /* We keep the original values on the extreme ages bage, fage and for
5655: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5656: we use a 5 terms etc. until the borders are no more concerned.
5657: */
5658: for (mob=3;mob <=mobilavrange;mob=mob+2){
5659: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5660: for (i=1; i<=nlstate;i++){
5661: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5662: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5663: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5664: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5665: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5666: }
5667: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5668: }
5669: }
5670: }/* end age */
5671: }/* end mob */
5672: }else return -1;
5673: return 0;
5674: }/* End movingaverage */
5675:
5676:
5677: /************** Forecasting ******************/
1.169 brouard 5678: 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 5679: /* proj1, year, month, day of starting projection
5680: agemin, agemax range of age
5681: dateprev1 dateprev2 range of dates during which prevalence is computed
5682: anproj2 year of en of projection (same day and month as proj1).
5683: */
1.164 brouard 5684: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5685: double agec; /* generic age */
5686: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5687: double *popeffectif,*popcount;
5688: double ***p3mat;
5689: double ***mobaverage;
5690: char fileresf[FILENAMELENGTH];
5691:
5692: agelim=AGESUP;
1.211 brouard 5693: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
5694: in each health status at the date of interview (if between dateprev1 and dateprev2).
5695: We still use firstpass and lastpass as another selection.
5696: */
1.214 brouard 5697: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
5698: /* firstpass, lastpass, stepm, weightopt, model); */
1.126 brouard 5699: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5700:
1.201 brouard 5701: strcpy(fileresf,"F_");
5702: strcat(fileresf,fileresu);
1.126 brouard 5703: if((ficresf=fopen(fileresf,"w"))==NULL) {
5704: printf("Problem with forecast resultfile: %s\n", fileresf);
5705: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5706: }
1.215 ! brouard 5707: printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);
! 5708: fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);
1.126 brouard 5709:
5710: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5711:
5712: if (mobilav!=0) {
5713: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5714: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5715: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5716: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5717: }
5718: }
5719:
5720: stepsize=(int) (stepm+YEARM-1)/YEARM;
5721: if (stepm<=12) stepsize=1;
5722: if(estepm < stepm){
5723: printf ("Problem %d lower than %d\n",estepm, stepm);
5724: }
5725: else hstepm=estepm;
5726:
5727: hstepm=hstepm/stepm;
5728: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5729: fractional in yp1 */
5730: anprojmean=yp;
5731: yp2=modf((yp1*12),&yp);
5732: mprojmean=yp;
5733: yp1=modf((yp2*30.5),&yp);
5734: jprojmean=yp;
5735: if(jprojmean==0) jprojmean=1;
5736: if(mprojmean==0) jprojmean=1;
5737:
5738: i1=cptcoveff;
5739: if (cptcovn < 1){i1=1;}
5740:
5741: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5742:
5743: fprintf(ficresf,"#****** Routine prevforecast **\n");
5744:
5745: /* if (h==(int)(YEARM*yearp)){ */
5746: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5747: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5748: k=k+1;
1.211 brouard 5749: fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
1.126 brouard 5750: for(j=1;j<=cptcoveff;j++) {
1.211 brouard 5751: fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5752: }
1.211 brouard 5753: fprintf(ficresf," yearproj age");
1.126 brouard 5754: for(j=1; j<=nlstate+ndeath;j++){
5755: for(i=1; i<=nlstate;i++)
5756: fprintf(ficresf," p%d%d",i,j);
5757: fprintf(ficresf," p.%d",j);
5758: }
5759: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5760: fprintf(ficresf,"\n");
5761: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5762:
5763: for (agec=fage; agec>=(ageminpar-1); agec--){
5764: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5765: nhstepm = nhstepm/hstepm;
5766: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5767: oldm=oldms;savm=savms;
5768: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5769:
5770: for (h=0; h<=nhstepm; h++){
5771: if (h*hstepm/YEARM*stepm ==yearp) {
5772: fprintf(ficresf,"\n");
5773: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5774: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5775: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5776: }
5777: for(j=1; j<=nlstate+ndeath;j++) {
5778: ppij=0.;
5779: for(i=1; i<=nlstate;i++) {
5780: if (mobilav==1)
5781: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5782: else {
5783: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5784: }
5785: if (h*hstepm/YEARM*stepm== yearp) {
5786: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5787: }
5788: } /* end i */
5789: if (h*hstepm/YEARM*stepm==yearp) {
5790: fprintf(ficresf," %.3f", ppij);
5791: }
5792: }/* end j */
5793: } /* end h */
5794: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5795: } /* end agec */
5796: } /* end yearp */
5797: } /* end cptcod */
5798: } /* end cptcov */
5799:
5800: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5801:
5802: fclose(ficresf);
1.215 ! brouard 5803: printf("End of Computing forecasting \n");
! 5804: fprintf(ficlog,"End of Computing forecasting\n");
! 5805:
1.126 brouard 5806: }
5807:
5808: /************** Forecasting *****not tested NB*************/
1.169 brouard 5809: 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 5810:
5811: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5812: int *popage;
5813: double calagedatem, agelim, kk1, kk2;
5814: double *popeffectif,*popcount;
5815: double ***p3mat,***tabpop,***tabpopprev;
5816: double ***mobaverage;
5817: char filerespop[FILENAMELENGTH];
5818:
5819: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5820: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5821: agelim=AGESUP;
5822: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5823:
5824: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5825:
5826:
1.201 brouard 5827: strcpy(filerespop,"POP_");
5828: strcat(filerespop,fileresu);
1.126 brouard 5829: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5830: printf("Problem with forecast resultfile: %s\n", filerespop);
5831: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5832: }
5833: printf("Computing forecasting: result on file '%s' \n", filerespop);
5834: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5835:
5836: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5837:
5838: if (mobilav!=0) {
5839: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5840: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5841: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5842: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5843: }
5844: }
5845:
5846: stepsize=(int) (stepm+YEARM-1)/YEARM;
5847: if (stepm<=12) stepsize=1;
5848:
5849: agelim=AGESUP;
5850:
5851: hstepm=1;
5852: hstepm=hstepm/stepm;
5853:
5854: if (popforecast==1) {
5855: if((ficpop=fopen(popfile,"r"))==NULL) {
5856: printf("Problem with population file : %s\n",popfile);exit(0);
5857: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5858: }
5859: popage=ivector(0,AGESUP);
5860: popeffectif=vector(0,AGESUP);
5861: popcount=vector(0,AGESUP);
5862:
5863: i=1;
5864: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5865:
5866: imx=i;
5867: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5868: }
5869:
5870: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5871: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5872: k=k+1;
5873: fprintf(ficrespop,"\n#******");
5874: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5875: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5876: }
5877: fprintf(ficrespop,"******\n");
5878: fprintf(ficrespop,"# Age");
5879: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5880: if (popforecast==1) fprintf(ficrespop," [Population]");
5881:
5882: for (cpt=0; cpt<=0;cpt++) {
5883: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5884:
5885: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5886: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5887: nhstepm = nhstepm/hstepm;
5888:
5889: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5890: oldm=oldms;savm=savms;
5891: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5892:
5893: for (h=0; h<=nhstepm; h++){
5894: if (h==(int) (calagedatem+YEARM*cpt)) {
5895: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5896: }
5897: for(j=1; j<=nlstate+ndeath;j++) {
5898: kk1=0.;kk2=0;
5899: for(i=1; i<=nlstate;i++) {
5900: if (mobilav==1)
5901: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5902: else {
5903: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5904: }
5905: }
5906: if (h==(int)(calagedatem+12*cpt)){
5907: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5908: /*fprintf(ficrespop," %.3f", kk1);
5909: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5910: }
5911: }
5912: for(i=1; i<=nlstate;i++){
5913: kk1=0.;
5914: for(j=1; j<=nlstate;j++){
5915: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5916: }
5917: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5918: }
5919:
5920: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5921: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5922: }
5923: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5924: }
5925: }
5926:
5927: /******/
5928:
5929: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5930: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5931: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5932: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5933: nhstepm = nhstepm/hstepm;
5934:
5935: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5936: oldm=oldms;savm=savms;
5937: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5938: for (h=0; h<=nhstepm; h++){
5939: if (h==(int) (calagedatem+YEARM*cpt)) {
5940: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5941: }
5942: for(j=1; j<=nlstate+ndeath;j++) {
5943: kk1=0.;kk2=0;
5944: for(i=1; i<=nlstate;i++) {
5945: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5946: }
5947: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5948: }
5949: }
5950: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5951: }
5952: }
5953: }
5954: }
5955:
5956: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5957:
5958: if (popforecast==1) {
5959: free_ivector(popage,0,AGESUP);
5960: free_vector(popeffectif,0,AGESUP);
5961: free_vector(popcount,0,AGESUP);
5962: }
5963: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5964: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5965: fclose(ficrespop);
5966: } /* End of popforecast */
5967:
5968: int fileappend(FILE *fichier, char *optionfich)
5969: {
5970: if((fichier=fopen(optionfich,"a"))==NULL) {
5971: printf("Problem with file: %s\n", optionfich);
5972: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5973: return (0);
5974: }
5975: fflush(fichier);
5976: return (1);
5977: }
5978:
5979:
5980: /**************** function prwizard **********************/
5981: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5982: {
5983:
5984: /* Wizard to print covariance matrix template */
5985:
1.164 brouard 5986: char ca[32], cb[32];
5987: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5988: int numlinepar;
5989:
5990: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5991: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5992: for(i=1; i <=nlstate; i++){
5993: jj=0;
5994: for(j=1; j <=nlstate+ndeath; j++){
5995: if(j==i) continue;
5996: jj++;
5997: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5998: printf("%1d%1d",i,j);
5999: fprintf(ficparo,"%1d%1d",i,j);
6000: for(k=1; k<=ncovmodel;k++){
6001: /* printf(" %lf",param[i][j][k]); */
6002: /* fprintf(ficparo," %lf",param[i][j][k]); */
6003: printf(" 0.");
6004: fprintf(ficparo," 0.");
6005: }
6006: printf("\n");
6007: fprintf(ficparo,"\n");
6008: }
6009: }
6010: printf("# Scales (for hessian or gradient estimation)\n");
6011: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
6012: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
6013: for(i=1; i <=nlstate; i++){
6014: jj=0;
6015: for(j=1; j <=nlstate+ndeath; j++){
6016: if(j==i) continue;
6017: jj++;
6018: fprintf(ficparo,"%1d%1d",i,j);
6019: printf("%1d%1d",i,j);
6020: fflush(stdout);
6021: for(k=1; k<=ncovmodel;k++){
6022: /* printf(" %le",delti3[i][j][k]); */
6023: /* fprintf(ficparo," %le",delti3[i][j][k]); */
6024: printf(" 0.");
6025: fprintf(ficparo," 0.");
6026: }
6027: numlinepar++;
6028: printf("\n");
6029: fprintf(ficparo,"\n");
6030: }
6031: }
6032: printf("# Covariance matrix\n");
6033: /* # 121 Var(a12)\n\ */
6034: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6035: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
6036: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
6037: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
6038: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
6039: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
6040: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6041: fflush(stdout);
6042: fprintf(ficparo,"# Covariance matrix\n");
6043: /* # 121 Var(a12)\n\ */
6044: /* # 122 Cov(b12,a12) Var(b12)\n\ */
6045: /* # ...\n\ */
6046: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
6047:
6048: for(itimes=1;itimes<=2;itimes++){
6049: jj=0;
6050: for(i=1; i <=nlstate; i++){
6051: for(j=1; j <=nlstate+ndeath; j++){
6052: if(j==i) continue;
6053: for(k=1; k<=ncovmodel;k++){
6054: jj++;
6055: ca[0]= k+'a'-1;ca[1]='\0';
6056: if(itimes==1){
6057: printf("#%1d%1d%d",i,j,k);
6058: fprintf(ficparo,"#%1d%1d%d",i,j,k);
6059: }else{
6060: printf("%1d%1d%d",i,j,k);
6061: fprintf(ficparo,"%1d%1d%d",i,j,k);
6062: /* printf(" %.5le",matcov[i][j]); */
6063: }
6064: ll=0;
6065: for(li=1;li <=nlstate; li++){
6066: for(lj=1;lj <=nlstate+ndeath; lj++){
6067: if(lj==li) continue;
6068: for(lk=1;lk<=ncovmodel;lk++){
6069: ll++;
6070: if(ll<=jj){
6071: cb[0]= lk +'a'-1;cb[1]='\0';
6072: if(ll<jj){
6073: if(itimes==1){
6074: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6075: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
6076: }else{
6077: printf(" 0.");
6078: fprintf(ficparo," 0.");
6079: }
6080: }else{
6081: if(itimes==1){
6082: printf(" Var(%s%1d%1d)",ca,i,j);
6083: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
6084: }else{
6085: printf(" 0.");
6086: fprintf(ficparo," 0.");
6087: }
6088: }
6089: }
6090: } /* end lk */
6091: } /* end lj */
6092: } /* end li */
6093: printf("\n");
6094: fprintf(ficparo,"\n");
6095: numlinepar++;
6096: } /* end k*/
6097: } /*end j */
6098: } /* end i */
6099: } /* end itimes */
6100:
6101: } /* end of prwizard */
6102: /******************* Gompertz Likelihood ******************************/
6103: double gompertz(double x[])
6104: {
6105: double A,B,L=0.0,sump=0.,num=0.;
6106: int i,n=0; /* n is the size of the sample */
6107:
6108: for (i=0;i<=imx-1 ; i++) {
6109: sump=sump+weight[i];
6110: /* sump=sump+1;*/
6111: num=num+1;
6112: }
6113:
6114:
6115: /* for (i=0; i<=imx; i++)
6116: 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]);*/
6117:
6118: for (i=1;i<=imx ; i++)
6119: {
6120: if (cens[i] == 1 && wav[i]>1)
6121: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
6122:
6123: if (cens[i] == 0 && wav[i]>1)
6124: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
6125: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
6126:
6127: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6128: if (wav[i] > 1 ) { /* ??? */
6129: L=L+A*weight[i];
6130: /* 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]);*/
6131: }
6132: }
6133:
6134: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6135:
6136: return -2*L*num/sump;
6137: }
6138:
1.136 brouard 6139: #ifdef GSL
6140: /******************* Gompertz_f Likelihood ******************************/
6141: double gompertz_f(const gsl_vector *v, void *params)
6142: {
6143: double A,B,LL=0.0,sump=0.,num=0.;
6144: double *x= (double *) v->data;
6145: int i,n=0; /* n is the size of the sample */
6146:
6147: for (i=0;i<=imx-1 ; i++) {
6148: sump=sump+weight[i];
6149: /* sump=sump+1;*/
6150: num=num+1;
6151: }
6152:
6153:
6154: /* for (i=0; i<=imx; i++)
6155: 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]);*/
6156: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
6157: for (i=1;i<=imx ; i++)
6158: {
6159: if (cens[i] == 1 && wav[i]>1)
6160: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
6161:
6162: if (cens[i] == 0 && wav[i]>1)
6163: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
6164: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
6165:
6166: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
6167: if (wav[i] > 1 ) { /* ??? */
6168: LL=LL+A*weight[i];
6169: /* 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]);*/
6170: }
6171: }
6172:
6173: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
6174: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
6175:
6176: return -2*LL*num/sump;
6177: }
6178: #endif
6179:
1.126 brouard 6180: /******************* Printing html file ***********/
1.201 brouard 6181: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 6182: int lastpass, int stepm, int weightopt, char model[],\
6183: int imx, double p[],double **matcov,double agemortsup){
6184: int i,k;
6185:
6186: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
6187: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
6188: for (i=1;i<=2;i++)
6189: 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]));
1.199 brouard 6190: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 6191: fprintf(fichtm,"</ul>");
6192:
6193: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
6194:
6195: 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>");
6196:
6197: for (k=agegomp;k<(agemortsup-2);k++)
6198: 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]);
6199:
6200:
6201: fflush(fichtm);
6202: }
6203:
6204: /******************* Gnuplot file **************/
1.201 brouard 6205: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 6206:
6207: char dirfileres[132],optfileres[132];
1.164 brouard 6208:
1.126 brouard 6209: int ng;
6210:
6211:
6212: /*#ifdef windows */
6213: fprintf(ficgp,"cd \"%s\" \n",pathc);
6214: /*#endif */
6215:
6216:
6217: strcpy(dirfileres,optionfilefiname);
6218: strcpy(optfileres,"vpl");
1.199 brouard 6219: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 6220: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 6221: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 6222: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 6223: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
6224:
6225: }
6226:
1.136 brouard 6227: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
6228: {
1.126 brouard 6229:
1.136 brouard 6230: /*-------- data file ----------*/
6231: FILE *fic;
6232: char dummy[]=" ";
1.164 brouard 6233: int i=0, j=0, n=0;
1.136 brouard 6234: int linei, month, year,iout;
6235: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 6236: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 6237: char *stratrunc;
6238: int lstra;
1.126 brouard 6239:
6240:
1.136 brouard 6241: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 6242: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
6243: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 6244: }
1.126 brouard 6245:
1.136 brouard 6246: i=1;
6247: linei=0;
6248: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
6249: linei=linei+1;
6250: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
6251: if(line[j] == '\t')
6252: line[j] = ' ';
6253: }
6254: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
6255: ;
6256: };
6257: line[j+1]=0; /* Trims blanks at end of line */
6258: if(line[0]=='#'){
6259: fprintf(ficlog,"Comment line\n%s\n",line);
6260: printf("Comment line\n%s\n",line);
6261: continue;
6262: }
6263: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 6264: strcpy(line, linetmp);
1.136 brouard 6265:
1.126 brouard 6266:
1.136 brouard 6267: for (j=maxwav;j>=1;j--){
1.137 brouard 6268: cutv(stra, strb, line, ' ');
1.136 brouard 6269: if(strb[0]=='.') { /* Missing status */
6270: lval=-1;
6271: }else{
6272: errno=0;
6273: lval=strtol(strb,&endptr,10);
6274: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
6275: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6276: 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);
6277: 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 6278: return 1;
6279: }
6280: }
6281: s[j][i]=lval;
6282:
6283: strcpy(line,stra);
6284: cutv(stra, strb,line,' ');
1.169 brouard 6285: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6286: }
1.169 brouard 6287: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6288: month=99;
6289: year=9999;
6290: }else{
1.141 brouard 6291: 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);
6292: 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 6293: return 1;
6294: }
6295: anint[j][i]= (double) year;
6296: mint[j][i]= (double)month;
6297: strcpy(line,stra);
6298: } /* ENd Waves */
6299:
6300: cutv(stra, strb,line,' ');
1.169 brouard 6301: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6302: }
1.169 brouard 6303: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 6304: month=99;
6305: year=9999;
6306: }else{
1.141 brouard 6307: 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);
6308: 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 6309: return 1;
6310: }
6311: andc[i]=(double) year;
6312: moisdc[i]=(double) month;
6313: strcpy(line,stra);
6314:
6315: cutv(stra, strb,line,' ');
1.169 brouard 6316: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 6317: }
1.169 brouard 6318: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 6319: month=99;
6320: year=9999;
6321: }else{
1.141 brouard 6322: 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);
6323: 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 6324: return 1;
6325: }
6326: if (year==9999) {
1.141 brouard 6327: 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);
6328: 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 6329: return 1;
1.126 brouard 6330:
1.136 brouard 6331: }
6332: annais[i]=(double)(year);
6333: moisnais[i]=(double)(month);
6334: strcpy(line,stra);
6335:
6336: cutv(stra, strb,line,' ');
6337: errno=0;
6338: dval=strtod(strb,&endptr);
6339: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6340: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
6341: 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 6342: fflush(ficlog);
6343: return 1;
6344: }
6345: weight[i]=dval;
6346: strcpy(line,stra);
6347:
6348: for (j=ncovcol;j>=1;j--){
6349: cutv(stra, strb,line,' ');
6350: if(strb[0]=='.') { /* Missing status */
6351: lval=-1;
6352: }else{
6353: errno=0;
6354: lval=strtol(strb,&endptr,10);
6355: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 6356: 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);
6357: 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 6358: return 1;
6359: }
6360: }
6361: if(lval <-1 || lval >1){
1.141 brouard 6362: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6363: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6364: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6365: For example, for multinomial values like 1, 2 and 3,\n \
6366: build V1=0 V2=0 for the reference value (1),\n \
6367: V1=1 V2=0 for (2) \n \
6368: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6369: output of IMaCh is often meaningless.\n \
6370: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 6371: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 6372: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
6373: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
6374: For example, for multinomial values like 1, 2 and 3,\n \
6375: build V1=0 V2=0 for the reference value (1),\n \
6376: V1=1 V2=0 for (2) \n \
6377: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
6378: output of IMaCh is often meaningless.\n \
6379: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
6380: return 1;
6381: }
6382: covar[j][i]=(double)(lval);
6383: strcpy(line,stra);
6384: }
6385: lstra=strlen(stra);
6386:
6387: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
6388: stratrunc = &(stra[lstra-9]);
6389: num[i]=atol(stratrunc);
6390: }
6391: else
6392: num[i]=atol(stra);
6393: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
6394: 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;}*/
6395:
6396: i=i+1;
6397: } /* End loop reading data */
1.126 brouard 6398:
1.136 brouard 6399: *imax=i-1; /* Number of individuals */
6400: fclose(fic);
6401:
6402: return (0);
1.164 brouard 6403: /* endread: */
1.136 brouard 6404: printf("Exiting readdata: ");
6405: fclose(fic);
6406: return (1);
1.126 brouard 6407:
6408:
6409:
1.136 brouard 6410: }
1.145 brouard 6411: void removespace(char *str) {
6412: char *p1 = str, *p2 = str;
6413: do
6414: while (*p2 == ' ')
6415: p2++;
1.169 brouard 6416: while (*p1++ == *p2++);
1.145 brouard 6417: }
6418:
6419: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6420: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6421: * - nagesqr = 1 if age*age in the model, otherwise 0.
6422: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6423: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6424: * - cptcovage number of covariates with age*products =2
6425: * - cptcovs number of simple covariates
6426: * - 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
6427: * which is a new column after the 9 (ncovcol) variables.
6428: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6429: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6430: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6431: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6432: */
1.136 brouard 6433: {
1.145 brouard 6434: int i, j, k, ks;
1.164 brouard 6435: int j1, k1, k2;
1.136 brouard 6436: char modelsav[80];
1.145 brouard 6437: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6438: char *strpt;
1.136 brouard 6439:
1.145 brouard 6440: /*removespace(model);*/
1.136 brouard 6441: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6442: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6443: if (strstr(model,"AGE") !=0){
1.192 brouard 6444: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6445: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6446: return 1;
6447: }
1.141 brouard 6448: if (strstr(model,"v") !=0){
6449: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6450: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6451: return 1;
6452: }
1.187 brouard 6453: strcpy(modelsav,model);
6454: if ((strpt=strstr(model,"age*age")) !=0){
6455: printf(" strpt=%s, model=%s\n",strpt, model);
6456: if(strpt != model){
6457: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6458: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6459: corresponding column of parameters.\n",model);
6460: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6461: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6462: corresponding column of parameters.\n",model); fflush(ficlog);
6463: return 1;
6464: }
6465:
6466: nagesqr=1;
6467: if (strstr(model,"+age*age") !=0)
6468: substrchaine(modelsav, model, "+age*age");
6469: else if (strstr(model,"age*age+") !=0)
6470: substrchaine(modelsav, model, "age*age+");
6471: else
6472: substrchaine(modelsav, model, "age*age");
6473: }else
6474: nagesqr=0;
6475: if (strlen(modelsav) >1){
6476: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6477: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6478: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6479: cptcovt= j+1; /* Number of total covariates in the model, not including
6480: * cst, age and age*age
6481: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6482: /* including age products which are counted in cptcovage.
6483: * but the covariates which are products must be treated
6484: * separately: ncovn=4- 2=2 (V1+V3). */
6485: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6486: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6487:
6488:
6489: /* Design
6490: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6491: * < ncovcol=8 >
6492: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6493: * k= 1 2 3 4 5 6 7 8
6494: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6495: * covar[k,i], value of kth covariate if not including age for individual i:
6496: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6497: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6498: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6499: * Tage[++cptcovage]=k
6500: * if products, new covar are created after ncovcol with k1
6501: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6502: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6503: * 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
6504: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6505: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6506: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6507: * < ncovcol=8 >
6508: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6509: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6510: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6511: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6512: * p Tprod[1]@2={ 6, 5}
6513: *p Tvard[1][1]@4= {7, 8, 5, 6}
6514: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6515: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6516: *How to reorganize?
6517: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6518: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6519: * {2, 1, 4, 8, 5, 6, 3, 7}
6520: * Struct []
6521: */
1.145 brouard 6522:
1.187 brouard 6523: /* This loop fills the array Tvar from the string 'model'.*/
6524: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6525: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6526: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6527: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6528: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6529: /* k=1 Tvar[1]=2 (from V2) */
6530: /* k=5 Tvar[5] */
6531: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6532: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6533: /* } */
1.198 brouard 6534: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6535: /*
6536: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6537: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6538: Tvar[k]=0;
1.187 brouard 6539: cptcovage=0;
6540: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6541: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6542: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6543: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6544: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6545: /*scanf("%d",i);*/
6546: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6547: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6548: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6549: /* covar is not filled and then is empty */
6550: cptcovprod--;
6551: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6552: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6553: cptcovage++; /* Sums the number of covariates which include age as a product */
6554: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6555: /*printf("stre=%s ", stre);*/
6556: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6557: cptcovprod--;
6558: cutl(stre,strb,strc,'V');
6559: Tvar[k]=atoi(stre);
6560: cptcovage++;
6561: Tage[cptcovage]=k;
6562: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6563: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6564: cptcovn++;
6565: cptcovprodnoage++;k1++;
6566: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6567: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6568: because this model-covariate is a construction we invent a new column
6569: ncovcol + k1
6570: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6571: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6572: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6573: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6574: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6575: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6576: k2=k2+2;
6577: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6578: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6579: for (i=1; i<=lastobs;i++){
6580: /* Computes the new covariate which is a product of
6581: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6582: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6583: }
6584: } /* End age is not in the model */
6585: } /* End if model includes a product */
6586: else { /* no more sum */
6587: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6588: /* scanf("%d",i);*/
6589: cutl(strd,strc,strb,'V');
6590: ks++; /**< Number of simple covariates */
1.145 brouard 6591: cptcovn++;
1.187 brouard 6592: Tvar[k]=atoi(strd);
6593: }
6594: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6595: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6596: scanf("%d",i);*/
6597: } /* end of loop + on total covariates */
6598: } /* end if strlen(modelsave == 0) age*age might exist */
6599: } /* end if strlen(model == 0) */
1.136 brouard 6600:
6601: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6602: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6603:
6604: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6605: printf("cptcovprod=%d ", cptcovprod);
6606: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6607:
6608: scanf("%d ",i);*/
6609:
6610:
1.137 brouard 6611: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6612: /*endread:*/
1.136 brouard 6613: printf("Exiting decodemodel: ");
6614: return (1);
6615: }
6616:
1.169 brouard 6617: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6618: {
6619: int i, m;
6620:
6621: for (i=1; i<=imx; i++) {
6622: for(m=2; (m<= maxwav); m++) {
6623: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6624: anint[m][i]=9999;
6625: s[m][i]=-1;
6626: }
6627: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6628: *nberr = *nberr + 1;
6629: 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);
6630: 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 6631: s[m][i]=-1;
6632: }
6633: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6634: (*nberr)++;
1.136 brouard 6635: 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]);
6636: 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]);
6637: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6638: }
6639: }
6640: }
6641:
6642: for (i=1; i<=imx; i++) {
6643: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6644: for(m=firstpass; (m<= lastpass); m++){
1.214 brouard 6645: if(s[m][i] >0 || s[m][i]==-1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){ /* What if s[m][i]=-1 */
1.136 brouard 6646: if (s[m][i] >= nlstate+1) {
1.169 brouard 6647: if(agedc[i]>0){
6648: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6649: agev[m][i]=agedc[i];
1.214 brouard 6650: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6651: }else {
1.136 brouard 6652: if ((int)andc[i]!=9999){
6653: nbwarn++;
6654: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6655: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6656: agev[m][i]=-1;
6657: }
6658: }
1.169 brouard 6659: } /* agedc > 0 */
1.214 brouard 6660: } /* end if */
1.136 brouard 6661: else if(s[m][i] !=9){ /* Standard case, age in fractional
6662: years but with the precision of a month */
6663: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6664: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6665: agev[m][i]=1;
6666: else if(agev[m][i] < *agemin){
6667: *agemin=agev[m][i];
6668: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6669: }
6670: else if(agev[m][i] >*agemax){
6671: *agemax=agev[m][i];
1.156 brouard 6672: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6673: }
6674: /*agev[m][i]=anint[m][i]-annais[i];*/
6675: /* agev[m][i] = age[i]+2*m;*/
1.214 brouard 6676: } /* en if 9*/
1.136 brouard 6677: else { /* =9 */
1.214 brouard 6678: /* printf("Debug num[%d]=%ld s[%d][%d]=%d\n",i,num[i], m,i, s[m][i]); */
1.136 brouard 6679: agev[m][i]=1;
6680: s[m][i]=-1;
6681: }
6682: }
1.214 brouard 6683: else if(s[m][i]==0) /*= 0 Unknown */
1.136 brouard 6684: agev[m][i]=1;
1.214 brouard 6685: else{
6686: printf("Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
6687: fprintf(ficlog, "Warning, num[%d]=%ld, s[%d][%d]=%d\n", i, num[i], m, i,s[m][i]);
6688: agev[m][i]=0;
6689: }
6690: } /* End for lastpass */
6691: }
1.136 brouard 6692:
6693: for (i=1; i<=imx; i++) {
6694: for(m=firstpass; (m<=lastpass); m++){
6695: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6696: (*nberr)++;
1.136 brouard 6697: 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);
6698: 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);
6699: return 1;
6700: }
6701: }
6702: }
6703:
6704: /*for (i=1; i<=imx; i++){
6705: for (m=firstpass; (m<lastpass); m++){
6706: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6707: }
6708:
6709: }*/
6710:
6711:
1.139 brouard 6712: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6713: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6714:
6715: return (0);
1.164 brouard 6716: /* endread:*/
1.136 brouard 6717: printf("Exiting calandcheckages: ");
6718: return (1);
6719: }
6720:
1.172 brouard 6721: #if defined(_MSC_VER)
6722: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6723: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6724: //#include "stdafx.h"
6725: //#include <stdio.h>
6726: //#include <tchar.h>
6727: //#include <windows.h>
6728: //#include <iostream>
6729: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6730:
6731: LPFN_ISWOW64PROCESS fnIsWow64Process;
6732:
6733: BOOL IsWow64()
6734: {
6735: BOOL bIsWow64 = FALSE;
6736:
6737: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6738: // (HANDLE, PBOOL);
6739:
6740: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6741:
6742: HMODULE module = GetModuleHandle(_T("kernel32"));
6743: const char funcName[] = "IsWow64Process";
6744: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6745: GetProcAddress(module, funcName);
6746:
6747: if (NULL != fnIsWow64Process)
6748: {
6749: if (!fnIsWow64Process(GetCurrentProcess(),
6750: &bIsWow64))
6751: //throw std::exception("Unknown error");
6752: printf("Unknown error\n");
6753: }
6754: return bIsWow64 != FALSE;
6755: }
6756: #endif
1.177 brouard 6757:
1.191 brouard 6758: void syscompilerinfo(int logged)
1.167 brouard 6759: {
6760: /* #include "syscompilerinfo.h"*/
1.185 brouard 6761: /* command line Intel compiler 32bit windows, XP compatible:*/
6762: /* /GS /W3 /Gy
6763: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6764: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6765: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6766: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6767: */
6768: /* 64 bits */
1.185 brouard 6769: /*
6770: /GS /W3 /Gy
6771: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6772: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6773: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6774: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6775: /* Optimization are useless and O3 is slower than O2 */
6776: /*
6777: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6778: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6779: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6780: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6781: */
1.186 brouard 6782: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6783: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6784: /PDB:"visual studio
6785: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6786: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6787: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6788: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6789: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6790: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6791: uiAccess='false'"
6792: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6793: /NOLOGO /TLBID:1
6794: */
1.177 brouard 6795: #if defined __INTEL_COMPILER
1.178 brouard 6796: #if defined(__GNUC__)
6797: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6798: #endif
1.177 brouard 6799: #elif defined(__GNUC__)
1.179 brouard 6800: #ifndef __APPLE__
1.174 brouard 6801: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6802: #endif
1.177 brouard 6803: struct utsname sysInfo;
1.178 brouard 6804: int cross = CROSS;
6805: if (cross){
6806: printf("Cross-");
1.191 brouard 6807: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6808: }
1.174 brouard 6809: #endif
6810:
1.171 brouard 6811: #include <stdint.h>
1.178 brouard 6812:
1.191 brouard 6813: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6814: #if defined(__clang__)
1.191 brouard 6815: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6816: #endif
6817: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6818: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6819: #endif
6820: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6821: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6822: #endif
6823: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6824: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6825: #endif
6826: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6827: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6828: #endif
6829: #if defined(_MSC_VER)
1.191 brouard 6830: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6831: #endif
6832: #if defined(__PGI)
1.191 brouard 6833: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6834: #endif
6835: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6836: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6837: #endif
1.191 brouard 6838: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6839:
1.167 brouard 6840: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6841: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6842: // Windows (x64 and x86)
1.191 brouard 6843: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6844: #elif __unix__ // all unices, not all compilers
6845: // Unix
1.191 brouard 6846: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6847: #elif __linux__
6848: // linux
1.191 brouard 6849: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6850: #elif __APPLE__
1.174 brouard 6851: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6852: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6853: #endif
6854:
6855: /* __MINGW32__ */
6856: /* __CYGWIN__ */
6857: /* __MINGW64__ */
6858: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6859: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6860: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6861: /* _WIN64 // Defined for applications for Win64. */
6862: /* _M_X64 // Defined for compilations that target x64 processors. */
6863: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6864:
1.167 brouard 6865: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6866: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6867: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6868: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6869: #else
1.191 brouard 6870: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6871: #endif
6872:
1.169 brouard 6873: #if defined(__GNUC__)
6874: # if defined(__GNUC_PATCHLEVEL__)
6875: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6876: + __GNUC_MINOR__ * 100 \
6877: + __GNUC_PATCHLEVEL__)
6878: # else
6879: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6880: + __GNUC_MINOR__ * 100)
6881: # endif
1.174 brouard 6882: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6883: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6884:
6885: if (uname(&sysInfo) != -1) {
6886: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6887: 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 6888: }
6889: else
6890: perror("uname() error");
1.179 brouard 6891: //#ifndef __INTEL_COMPILER
6892: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6893: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6894: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6895: #endif
1.169 brouard 6896: #endif
1.172 brouard 6897:
6898: // void main()
6899: // {
1.169 brouard 6900: #if defined(_MSC_VER)
1.174 brouard 6901: if (IsWow64()){
1.191 brouard 6902: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6903: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6904: }
6905: else{
1.191 brouard 6906: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6907: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6908: }
1.172 brouard 6909: // printf("\nPress Enter to continue...");
6910: // getchar();
6911: // }
6912:
1.169 brouard 6913: #endif
6914:
1.167 brouard 6915:
6916: }
1.136 brouard 6917:
1.209 brouard 6918: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyearp){
1.180 brouard 6919: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6920: int i, j, k, i1 ;
1.202 brouard 6921: /* double ftolpl = 1.e-10; */
1.180 brouard 6922: double age, agebase, agelim;
1.203 brouard 6923: double tot;
1.180 brouard 6924:
1.202 brouard 6925: strcpy(filerespl,"PL_");
6926: strcat(filerespl,fileresu);
6927: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6928: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6929: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6930: }
6931: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6932: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6933: pstamp(ficrespl);
1.203 brouard 6934: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6935: fprintf(ficrespl,"#Age ");
6936: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6937: fprintf(ficrespl,"\n");
1.180 brouard 6938:
6939: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6940:
6941: agebase=ageminpar;
6942: agelim=agemaxpar;
6943:
6944: i1=pow(2,cptcoveff);
6945: if (cptcovn < 1){i1=1;}
6946:
6947: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6948: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6949: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6950: k=k+1;
6951: /* to clean */
1.198 brouard 6952: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6953: fprintf(ficrespl,"#******");
6954: printf("#******");
6955: fprintf(ficlog,"#******");
1.180 brouard 6956: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6957: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6958: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6959: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6960: }
6961: fprintf(ficrespl,"******\n");
6962: printf("******\n");
6963: fprintf(ficlog,"******\n");
6964:
6965: fprintf(ficrespl,"#Age ");
6966: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6967: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6968: }
1.203 brouard 6969: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6970: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6971:
6972: for (age=agebase; age<=agelim; age++){
6973: /* for (age=agebase; age<=agebase; age++){ */
1.209 brouard 6974: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);
1.180 brouard 6975: fprintf(ficrespl,"%.0f ",age );
6976: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6977: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6978: tot=0.;
6979: for(i=1; i<=nlstate;i++){
6980: tot += prlim[i][i];
1.180 brouard 6981: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6982: }
1.209 brouard 6983: fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
1.180 brouard 6984: } /* Age */
6985: /* was end of cptcod */
6986: } /* cptcov */
1.184 brouard 6987: return 0;
1.180 brouard 6988: }
6989:
6990: int hPijx(double *p, int bage, int fage){
6991: /*------------- h Pij x at various ages ------------*/
6992:
6993: int stepsize;
6994: int agelim;
6995: int hstepm;
6996: int nhstepm;
6997: int h, i, i1, j, k;
6998:
6999: double agedeb;
7000: double ***p3mat;
7001:
1.201 brouard 7002: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 7003: if((ficrespij=fopen(filerespij,"w"))==NULL) {
7004: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
7005: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
7006: }
7007: printf("Computing pij: result on file '%s' \n", filerespij);
7008: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
7009:
7010: stepsize=(int) (stepm+YEARM-1)/YEARM;
7011: /*if (stepm<=24) stepsize=2;*/
7012:
7013: agelim=AGESUP;
7014: hstepm=stepsize*YEARM; /* Every year of age */
7015: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
7016:
7017: /* hstepm=1; aff par mois*/
7018: pstamp(ficrespij);
7019: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
7020: i1= pow(2,cptcoveff);
1.183 brouard 7021: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
7022: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
7023: /* k=k+1; */
7024: for (k=1; k <= (int) pow(2,cptcoveff); k++){
7025: fprintf(ficrespij,"\n#****** ");
7026: for(j=1;j<=cptcoveff;j++)
1.198 brouard 7027: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 7028: fprintf(ficrespij,"******\n");
7029:
7030: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
7031: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
7032: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
7033:
7034: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 7035:
1.183 brouard 7036: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7037: oldm=oldms;savm=savms;
7038: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
7039: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
7040: for(i=1; i<=nlstate;i++)
7041: for(j=1; j<=nlstate+ndeath;j++)
7042: fprintf(ficrespij," %1d-%1d",i,j);
7043: fprintf(ficrespij,"\n");
7044: for (h=0; h<=nhstepm; h++){
7045: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
7046: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 7047: for(i=1; i<=nlstate;i++)
7048: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 7049: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 7050: fprintf(ficrespij,"\n");
7051: }
1.183 brouard 7052: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
7053: fprintf(ficrespij,"\n");
7054: }
1.180 brouard 7055: /*}*/
7056: }
1.184 brouard 7057: return 0;
1.180 brouard 7058: }
7059:
7060:
1.136 brouard 7061: /***********************************************/
7062: /**************** Main Program *****************/
7063: /***********************************************/
7064:
7065: int main(int argc, char *argv[])
7066: {
7067: #ifdef GSL
7068: const gsl_multimin_fminimizer_type *T;
7069: size_t iteri = 0, it;
7070: int rval = GSL_CONTINUE;
7071: int status = GSL_SUCCESS;
7072: double ssval;
7073: #endif
7074: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 7075: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.209 brouard 7076: int ncvyear=0; /* Number of years needed for the period prevalence to converge */
1.164 brouard 7077: int jj, ll, li, lj, lk;
1.136 brouard 7078: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 7079: int num_filled;
1.136 brouard 7080: int itimes;
7081: int NDIM=2;
7082: int vpopbased=0;
7083:
1.164 brouard 7084: char ca[32], cb[32];
1.136 brouard 7085: /* FILE *fichtm; *//* Html File */
7086: /* FILE *ficgp;*/ /*Gnuplot File */
7087: struct stat info;
1.191 brouard 7088: double agedeb=0.;
1.194 brouard 7089:
7090: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 7091:
1.165 brouard 7092: double fret;
1.191 brouard 7093: double dum=0.; /* Dummy variable */
1.136 brouard 7094: double ***p3mat;
7095: double ***mobaverage;
1.164 brouard 7096:
7097: char line[MAXLINE];
1.197 brouard 7098: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
7099:
7100: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 7101: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 7102: char *tok, *val; /* pathtot */
1.136 brouard 7103: int firstobs=1, lastobs=10;
1.195 brouard 7104: int c, h , cpt, c2;
1.191 brouard 7105: int jl=0;
7106: int i1, j1, jk, stepsize=0;
1.194 brouard 7107: int count=0;
7108:
1.164 brouard 7109: int *tab;
1.136 brouard 7110: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
7111: int mobilav=0,popforecast=0;
1.191 brouard 7112: int hstepm=0, nhstepm=0;
1.136 brouard 7113: int agemortsup;
7114: float sumlpop=0.;
7115: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
7116: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
7117:
1.191 brouard 7118: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 7119: double ftolpl=FTOL;
7120: double **prlim;
7121: double ***param; /* Matrix of parameters */
7122: double *p;
7123: double **matcov; /* Matrix of covariance */
1.203 brouard 7124: double **hess; /* Hessian matrix */
1.136 brouard 7125: double ***delti3; /* Scale */
7126: double *delti; /* Scale */
7127: double ***eij, ***vareij;
7128: double **varpl; /* Variances of prevalence limits by age */
7129: double *epj, vepp;
1.164 brouard 7130:
1.136 brouard 7131: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
7132: double **ximort;
1.145 brouard 7133: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 7134: int *dcwave;
7135:
1.164 brouard 7136: char z[1]="c";
1.136 brouard 7137:
7138: /*char *strt;*/
7139: char strtend[80];
1.126 brouard 7140:
1.164 brouard 7141:
1.126 brouard 7142: /* setlocale (LC_ALL, ""); */
7143: /* bindtextdomain (PACKAGE, LOCALEDIR); */
7144: /* textdomain (PACKAGE); */
7145: /* setlocale (LC_CTYPE, ""); */
7146: /* setlocale (LC_MESSAGES, ""); */
7147:
7148: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 7149: rstart_time = time(NULL);
7150: /* (void) gettimeofday(&start_time,&tzp);*/
7151: start_time = *localtime(&rstart_time);
1.126 brouard 7152: curr_time=start_time;
1.157 brouard 7153: /*tml = *localtime(&start_time.tm_sec);*/
7154: /* strcpy(strstart,asctime(&tml)); */
7155: strcpy(strstart,asctime(&start_time));
1.126 brouard 7156:
7157: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 7158: /* tp.tm_sec = tp.tm_sec +86400; */
7159: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 7160: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
7161: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
7162: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 7163: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 7164: /* strt=asctime(&tmg); */
7165: /* printf("Time(after) =%s",strstart); */
7166: /* (void) time (&time_value);
7167: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
7168: * tm = *localtime(&time_value);
7169: * strstart=asctime(&tm);
7170: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
7171: */
7172:
7173: nberr=0; /* Number of errors and warnings */
7174: nbwarn=0;
1.184 brouard 7175: #ifdef WIN32
7176: _getcwd(pathcd, size);
7177: #else
1.126 brouard 7178: getcwd(pathcd, size);
1.184 brouard 7179: #endif
1.191 brouard 7180: syscompilerinfo(0);
1.196 brouard 7181: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 7182: if(argc <=1){
7183: printf("\nEnter the parameter file name: ");
1.205 brouard 7184: if(!fgets(pathr,FILENAMELENGTH,stdin)){
7185: printf("ERROR Empty parameter file name\n");
7186: goto end;
7187: }
1.126 brouard 7188: i=strlen(pathr);
7189: if(pathr[i-1]=='\n')
7190: pathr[i-1]='\0';
1.156 brouard 7191: i=strlen(pathr);
1.205 brouard 7192: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 7193: pathr[i-1]='\0';
1.205 brouard 7194: }
7195: i=strlen(pathr);
7196: if( i==0 ){
7197: printf("ERROR Empty parameter file name\n");
7198: goto end;
7199: }
7200: for (tok = pathr; tok != NULL; ){
1.126 brouard 7201: printf("Pathr |%s|\n",pathr);
7202: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
7203: printf("val= |%s| pathr=%s\n",val,pathr);
7204: strcpy (pathtot, val);
7205: if(pathr[0] == '\0') break; /* Dirty */
7206: }
7207: }
7208: else{
7209: strcpy(pathtot,argv[1]);
7210: }
7211: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
7212: /*cygwin_split_path(pathtot,path,optionfile);
7213: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
7214: /* cutv(path,optionfile,pathtot,'\\');*/
7215:
7216: /* Split argv[0], imach program to get pathimach */
7217: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
7218: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7219: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
7220: /* strcpy(pathimach,argv[0]); */
7221: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
7222: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
7223: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 7224: #ifdef WIN32
7225: _chdir(path); /* Can be a relative path */
7226: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
7227: #else
1.126 brouard 7228: chdir(path); /* Can be a relative path */
1.184 brouard 7229: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
7230: #endif
7231: printf("Current directory %s!\n",pathcd);
1.126 brouard 7232: strcpy(command,"mkdir ");
7233: strcat(command,optionfilefiname);
7234: if((outcmd=system(command)) != 0){
1.169 brouard 7235: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 7236: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
7237: /* fclose(ficlog); */
7238: /* exit(1); */
7239: }
7240: /* if((imk=mkdir(optionfilefiname))<0){ */
7241: /* perror("mkdir"); */
7242: /* } */
7243:
7244: /*-------- arguments in the command line --------*/
7245:
1.186 brouard 7246: /* Main Log file */
1.126 brouard 7247: strcat(filelog, optionfilefiname);
7248: strcat(filelog,".log"); /* */
7249: if((ficlog=fopen(filelog,"w"))==NULL) {
7250: printf("Problem with logfile %s\n",filelog);
7251: goto end;
7252: }
7253: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 7254: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 7255: fprintf(ficlog,"\nEnter the parameter file name: \n");
7256: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
7257: path=%s \n\
7258: optionfile=%s\n\
7259: optionfilext=%s\n\
1.156 brouard 7260: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 7261:
1.197 brouard 7262: syscompilerinfo(1);
1.167 brouard 7263:
1.126 brouard 7264: printf("Local time (at start):%s",strstart);
7265: fprintf(ficlog,"Local time (at start): %s",strstart);
7266: fflush(ficlog);
7267: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 7268: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 7269:
7270: /* */
7271: strcpy(fileres,"r");
7272: strcat(fileres, optionfilefiname);
1.201 brouard 7273: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 7274: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 7275: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 7276:
1.186 brouard 7277: /* Main ---------arguments file --------*/
1.126 brouard 7278:
7279: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 7280: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
7281: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 7282: fflush(ficlog);
1.149 brouard 7283: /* goto end; */
7284: exit(70);
1.126 brouard 7285: }
7286:
7287:
7288:
7289: strcpy(filereso,"o");
1.201 brouard 7290: strcat(filereso,fileresu);
1.126 brouard 7291: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
7292: printf("Problem with Output resultfile: %s\n", filereso);
7293: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
7294: fflush(ficlog);
7295: goto end;
7296: }
7297:
7298: /* Reads comments: lines beginning with '#' */
7299: numlinepar=0;
1.197 brouard 7300:
7301: /* First parameter line */
7302: while(fgets(line, MAXLINE, ficpar)) {
7303: /* If line starts with a # it is a comment */
7304: if (line[0] == '#') {
7305: numlinepar++;
7306: fputs(line,stdout);
7307: fputs(line,ficparo);
7308: fputs(line,ficlog);
7309: continue;
7310: }else
7311: break;
7312: }
7313: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
7314: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
7315: if (num_filled != 5) {
7316: printf("Should be 5 parameters\n");
7317: }
1.126 brouard 7318: numlinepar++;
1.197 brouard 7319: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
7320: }
7321: /* Second parameter line */
7322: while(fgets(line, MAXLINE, ficpar)) {
7323: /* If line starts with a # it is a comment */
7324: if (line[0] == '#') {
7325: numlinepar++;
7326: fputs(line,stdout);
7327: fputs(line,ficparo);
7328: fputs(line,ficlog);
7329: continue;
7330: }else
7331: break;
7332: }
7333: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
7334: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
7335: if (num_filled != 8) {
1.209 brouard 7336: printf("Not 8 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
7337: printf("but line=%s\n",line);
1.197 brouard 7338: }
7339: 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 7340: }
1.203 brouard 7341: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
1.209 brouard 7342: /*ftolpl=6.e-4; *//* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 7343: /* Third parameter line */
7344: while(fgets(line, MAXLINE, ficpar)) {
7345: /* If line starts with a # it is a comment */
7346: if (line[0] == '#') {
7347: numlinepar++;
7348: fputs(line,stdout);
7349: fputs(line,ficparo);
7350: fputs(line,ficlog);
7351: continue;
7352: }else
7353: break;
7354: }
1.201 brouard 7355: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
7356: if (num_filled == 0)
7357: model[0]='\0';
7358: else if (num_filled != 1){
1.197 brouard 7359: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7360: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
7361: model[0]='\0';
7362: goto end;
7363: }
7364: else{
7365: if (model[0]=='+'){
7366: for(i=1; i<=strlen(model);i++)
7367: modeltemp[i-1]=model[i];
1.201 brouard 7368: strcpy(model,modeltemp);
1.197 brouard 7369: }
7370: }
1.199 brouard 7371: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 7372: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 7373: }
7374: /* 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); */
7375: /* numlinepar=numlinepar+3; /\* In general *\/ */
7376: /* 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); */
1.203 brouard 7377: 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);
7378: 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 7379: fflush(ficlog);
1.190 brouard 7380: /* if(model[0]=='#'|| model[0]== '\0'){ */
7381: if(model[0]=='#'){
1.187 brouard 7382: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
7383: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
7384: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
7385: if(mle != -1){
7386: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
7387: exit(1);
7388: }
7389: }
1.126 brouard 7390: while((c=getc(ficpar))=='#' && c!= EOF){
7391: ungetc(c,ficpar);
7392: fgets(line, MAXLINE, ficpar);
7393: numlinepar++;
1.195 brouard 7394: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
7395: z[0]=line[1];
7396: }
7397: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 7398: fputs(line, stdout);
7399: //puts(line);
1.126 brouard 7400: fputs(line,ficparo);
7401: fputs(line,ficlog);
7402: }
7403: ungetc(c,ficpar);
7404:
7405:
1.145 brouard 7406: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 7407: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7408: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7409: v1+v2*age+v2*v3 makes cptcovn = 3
7410: */
7411: if (strlen(model)>1)
1.187 brouard 7412: 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 7413: else
1.187 brouard 7414: ncovmodel=2; /* Constant and age */
1.133 brouard 7415: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7416: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7417: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7418: 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);
7419: 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);
7420: fflush(stdout);
7421: fclose (ficlog);
7422: goto end;
7423: }
1.126 brouard 7424: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7425: delti=delti3[1][1];
7426: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7427: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7428: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7429: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7430: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7431: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7432: fclose (ficparo);
7433: fclose (ficlog);
7434: goto end;
7435: exit(0);
7436: }
1.186 brouard 7437: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7438: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7439: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7440: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7441: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7442: matcov=matrix(1,npar,1,npar);
1.203 brouard 7443: hess=matrix(1,npar,1,npar);
1.126 brouard 7444: }
7445: else{
1.145 brouard 7446: /* Read guessed parameters */
1.126 brouard 7447: /* Reads comments: lines beginning with '#' */
7448: while((c=getc(ficpar))=='#' && c!= EOF){
7449: ungetc(c,ficpar);
7450: fgets(line, MAXLINE, ficpar);
7451: numlinepar++;
1.141 brouard 7452: fputs(line,stdout);
1.126 brouard 7453: fputs(line,ficparo);
7454: fputs(line,ficlog);
7455: }
7456: ungetc(c,ficpar);
7457:
7458: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7459: for(i=1; i <=nlstate; i++){
7460: j=0;
7461: for(jj=1; jj <=nlstate+ndeath; jj++){
7462: if(jj==i) continue;
7463: j++;
7464: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7465: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7466: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7467: It might be a problem of design; if ncovcol and the model are correct\n \
7468: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7469: exit(1);
7470: }
7471: fprintf(ficparo,"%1d%1d",i1,j1);
7472: if(mle==1)
1.193 brouard 7473: printf("%1d%1d",i,jj);
7474: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7475: for(k=1; k<=ncovmodel;k++){
7476: fscanf(ficpar," %lf",¶m[i][j][k]);
7477: if(mle==1){
7478: printf(" %lf",param[i][j][k]);
7479: fprintf(ficlog," %lf",param[i][j][k]);
7480: }
7481: else
7482: fprintf(ficlog," %lf",param[i][j][k]);
7483: fprintf(ficparo," %lf",param[i][j][k]);
7484: }
7485: fscanf(ficpar,"\n");
7486: numlinepar++;
7487: if(mle==1)
7488: printf("\n");
7489: fprintf(ficlog,"\n");
7490: fprintf(ficparo,"\n");
7491: }
7492: }
7493: fflush(ficlog);
7494:
1.145 brouard 7495: /* Reads scales values */
1.126 brouard 7496: p=param[1][1];
7497:
7498: /* Reads comments: lines beginning with '#' */
7499: while((c=getc(ficpar))=='#' && c!= EOF){
7500: ungetc(c,ficpar);
7501: fgets(line, MAXLINE, ficpar);
7502: numlinepar++;
1.141 brouard 7503: fputs(line,stdout);
1.126 brouard 7504: fputs(line,ficparo);
7505: fputs(line,ficlog);
7506: }
7507: ungetc(c,ficpar);
7508:
7509: for(i=1; i <=nlstate; i++){
7510: for(j=1; j <=nlstate+ndeath-1; j++){
7511: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7512: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7513: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7514: exit(1);
7515: }
7516: printf("%1d%1d",i,j);
7517: fprintf(ficparo,"%1d%1d",i1,j1);
7518: fprintf(ficlog,"%1d%1d",i1,j1);
7519: for(k=1; k<=ncovmodel;k++){
7520: fscanf(ficpar,"%le",&delti3[i][j][k]);
7521: printf(" %le",delti3[i][j][k]);
7522: fprintf(ficparo," %le",delti3[i][j][k]);
7523: fprintf(ficlog," %le",delti3[i][j][k]);
7524: }
7525: fscanf(ficpar,"\n");
7526: numlinepar++;
7527: printf("\n");
7528: fprintf(ficparo,"\n");
7529: fprintf(ficlog,"\n");
7530: }
7531: }
7532: fflush(ficlog);
7533:
1.145 brouard 7534: /* Reads covariance matrix */
1.126 brouard 7535: delti=delti3[1][1];
7536:
7537:
7538: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7539:
7540: /* Reads comments: lines beginning with '#' */
7541: while((c=getc(ficpar))=='#' && c!= EOF){
7542: ungetc(c,ficpar);
7543: fgets(line, MAXLINE, ficpar);
7544: numlinepar++;
1.141 brouard 7545: fputs(line,stdout);
1.126 brouard 7546: fputs(line,ficparo);
7547: fputs(line,ficlog);
7548: }
7549: ungetc(c,ficpar);
7550:
7551: matcov=matrix(1,npar,1,npar);
1.203 brouard 7552: hess=matrix(1,npar,1,npar);
1.131 brouard 7553: for(i=1; i <=npar; i++)
7554: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7555:
1.194 brouard 7556: /* Scans npar lines */
1.126 brouard 7557: for(i=1; i <=npar; i++){
1.194 brouard 7558: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7559: if(count != 3){
7560: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7561: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7562: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7563: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7564: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7565: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7566: exit(1);
7567: }else
1.126 brouard 7568: if(mle==1)
1.194 brouard 7569: printf("%1d%1d%1d",i1,j1,jk);
7570: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7571: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7572: for(j=1; j <=i; j++){
7573: fscanf(ficpar," %le",&matcov[i][j]);
7574: if(mle==1){
7575: printf(" %.5le",matcov[i][j]);
7576: }
7577: fprintf(ficlog," %.5le",matcov[i][j]);
7578: fprintf(ficparo," %.5le",matcov[i][j]);
7579: }
7580: fscanf(ficpar,"\n");
7581: numlinepar++;
7582: if(mle==1)
7583: printf("\n");
7584: fprintf(ficlog,"\n");
7585: fprintf(ficparo,"\n");
7586: }
1.194 brouard 7587: /* End of read covariance matrix npar lines */
1.126 brouard 7588: for(i=1; i <=npar; i++)
7589: for(j=i+1;j<=npar;j++)
7590: matcov[i][j]=matcov[j][i];
7591:
7592: if(mle==1)
7593: printf("\n");
7594: fprintf(ficlog,"\n");
7595:
7596: fflush(ficlog);
7597:
7598: /*-------- Rewriting parameter file ----------*/
7599: strcpy(rfileres,"r"); /* "Rparameterfile */
7600: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7601: strcat(rfileres,"."); /* */
7602: strcat(rfileres,optionfilext); /* Other files have txt extension */
7603: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7604: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7605: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7606: }
7607: fprintf(ficres,"#%s\n",version);
7608: } /* End of mle != -3 */
7609:
1.186 brouard 7610: /* Main data
7611: */
1.126 brouard 7612: n= lastobs;
7613: num=lvector(1,n);
7614: moisnais=vector(1,n);
7615: annais=vector(1,n);
7616: moisdc=vector(1,n);
7617: andc=vector(1,n);
7618: agedc=vector(1,n);
7619: cod=ivector(1,n);
7620: weight=vector(1,n);
7621: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7622: mint=matrix(1,maxwav,1,n);
7623: anint=matrix(1,maxwav,1,n);
1.131 brouard 7624: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7625: tab=ivector(1,NCOVMAX);
1.144 brouard 7626: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7627: 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 7628:
1.136 brouard 7629: /* Reads data from file datafile */
7630: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7631: goto end;
7632:
7633: /* Calculation of the number of parameters from char model */
1.137 brouard 7634: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7635: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7636: k=3 V4 Tvar[k=3]= 4 (from V4)
7637: k=2 V1 Tvar[k=2]= 1 (from V1)
7638: k=1 Tvar[1]=2 (from V2)
7639: */
7640: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7641: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7642: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7643: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7644: */
7645: /* For model-covariate k tells which data-covariate to use but
7646: because this model-covariate is a construction we invent a new column
7647: ncovcol + k1
7648: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7649: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7650: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7651: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7652: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7653: */
1.145 brouard 7654: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7655: 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 7656: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7657: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7658: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7659: 4 covariates (3 plus signs)
7660: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7661: */
1.136 brouard 7662:
1.186 brouard 7663: /* Main decodemodel */
7664:
1.187 brouard 7665:
1.136 brouard 7666: if(decodemodel(model, lastobs) == 1)
7667: goto end;
7668:
1.137 brouard 7669: if((double)(lastobs-imx)/(double)imx > 1.10){
7670: nbwarn++;
7671: 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);
7672: 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);
7673: }
1.136 brouard 7674: /* if(mle==1){*/
1.137 brouard 7675: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7676: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7677: }
7678:
7679: /*-calculation of age at interview from date of interview and age at death -*/
7680: agev=matrix(1,maxwav,1,imx);
7681:
7682: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7683: goto end;
7684:
1.126 brouard 7685:
1.136 brouard 7686: agegomp=(int)agemin;
7687: free_vector(moisnais,1,n);
7688: free_vector(annais,1,n);
1.126 brouard 7689: /* free_matrix(mint,1,maxwav,1,n);
7690: free_matrix(anint,1,maxwav,1,n);*/
1.215 ! brouard 7691: /* free_vector(moisdc,1,n); */
! 7692: /* free_vector(andc,1,n); */
1.145 brouard 7693: /* */
7694:
1.126 brouard 7695: wav=ivector(1,imx);
1.214 brouard 7696: /* dh=imatrix(1,lastpass-firstpass+1,1,imx); */
7697: /* bh=imatrix(1,lastpass-firstpass+1,1,imx); */
7698: /* mw=imatrix(1,lastpass-firstpass+1,1,imx); */
7699: dh=imatrix(1,lastpass-firstpass+2,1,imx); /* We are adding a wave if status is unknown at last wave but death occurs after last wave.*/
7700: bh=imatrix(1,lastpass-firstpass+2,1,imx);
7701: mw=imatrix(1,lastpass-firstpass+2,1,imx);
1.126 brouard 7702:
7703: /* Concatenates waves */
1.214 brouard 7704: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
7705: Death is a valid wave (if date is known).
7706: mw[mi][i] is the number of (mi=1 to wav[i]) effective wave out of mi of individual i
7707: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
7708: and mw[mi+1][i]. dh depends on stepm.
7709: */
7710:
1.126 brouard 7711: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7712: /* */
7713:
1.215 ! brouard 7714: free_vector(moisdc,1,n);
! 7715: free_vector(andc,1,n);
! 7716:
1.126 brouard 7717: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7718:
7719: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7720: ncodemax[1]=1;
1.145 brouard 7721: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7722: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7723: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.211 brouard 7724: /* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
1.186 brouard 7725: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
1.211 brouard 7726: /* 1 to ncodemax[j] which is the maximum value of this jth covariate */
1.145 brouard 7727:
1.200 brouard 7728: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7729: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7730: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.211 brouard 7731: /* nbcode[Tvaraff[j]][codtabm(h,j)]) : if there are only 2 modalities for a covariate j,
7732: * codtabm(h,j) gives its value classified at position h and nbcode gives how it is coded
7733: * (currently 0 or 1) in the data.
7734: * In a loop on h=1 to 2**k, and a loop on j (=1 to k), we get the value of
7735: * corresponding modality (h,j).
7736: */
7737:
1.145 brouard 7738: h=0;
7739:
7740:
7741: /*if (cptcovn > 0) */
1.126 brouard 7742:
1.145 brouard 7743:
1.126 brouard 7744: m=pow(2,cptcoveff);
7745:
1.144 brouard 7746: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.211 brouard 7747: * For k=4 covariates, h goes from 1 to m=2**k
7748: * codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
7749: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.186 brouard 7750: * h\k 1 2 3 4
1.143 brouard 7751: *______________________________
7752: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7753: * 2 2 1 1 1
7754: * 3 i=2 1 2 1 1
7755: * 4 2 2 1 1
7756: * 5 i=3 1 i=2 1 2 1
7757: * 6 2 1 2 1
7758: * 7 i=4 1 2 2 1
7759: * 8 2 2 2 1
1.197 brouard 7760: * 9 i=5 1 i=3 1 i=2 1 2
7761: * 10 2 1 1 2
7762: * 11 i=6 1 2 1 2
7763: * 12 2 2 1 2
7764: * 13 i=7 1 i=4 1 2 2
7765: * 14 2 1 2 2
7766: * 15 i=8 1 2 2 2
7767: * 16 2 2 2 2
1.143 brouard 7768: */
1.212 brouard 7769: /* How to do the opposite? From combination h (=1 to 2**k) how to get the value on the covariates? */
1.211 brouard 7770: /* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
7771: * and the value of each covariate?
7772: * V1=1, V2=1, V3=2, V4=1 ?
7773: * h-1=4 and 4 is 0100 or reverse 0010, and +1 is 1121 ok.
7774: * h=6, 6-1=5, 5 is 0101, 1010, 2121, V1=2nd, V2=1st, V3=2nd, V4=1st.
7775: * In order to get the real value in the data, we use nbcode
7776: * nbcode[Tvar[3][2nd]]=1 and nbcode[Tvar[4][1]]=0
7777: * We are keeping this crazy system in order to be able (in the future?)
7778: * to have more than 2 values (0 or 1) for a covariate.
7779: * #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
7780: * h=6, k=2? h-1=5=0101, reverse 1010, +1=2121, k=2nd position: value is 1: codtabm(6,2)=1
7781: * bbbbbbbb
7782: * 76543210
7783: * h-1 00000101 (6-1=5)
7784: *(h-1)>>(k-1)= 00000001 >> (2-1) = 1 right shift
7785: * &
7786: * 1 00000001 (1)
7787: * 00000001 = 1 & ((h-1) >> (k-1))
7788: * +1= 00000010 =2
7789: *
7790: * h=14, k=3 => h'=h-1=13, k'=k-1=2
7791: * h' 1101 =2^3+2^2+0x2^1+2^0
7792: * >>k' 11
7793: * & 00000001
7794: * = 00000001
7795: * +1 = 00000010=2 = codtabm(14,3)
7796: * Reverse h=6 and m=16?
7797: * cptcoveff=log(16)/log(2)=4 covariate: 6-1=5=0101 reversed=1010 +1=2121 =>V1=2, V2=1, V3=2, V4=1.
7798: * for (j=1 to cptcoveff) Vj=decodtabm(j,h,cptcoveff)
7799: * decodtabm(h,j,cptcoveff)= (((h-1) >> (j-1)) & 1) +1
7800: * decodtabm(h,j,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (j-1)) & 1) +1 : -1)
7801: * V3=decodtabm(14,3,2**4)=2
7802: * h'=13 1101 =2^3+2^2+0x2^1+2^0
7803: *(h-1) >> (j-1) 0011 =13 >> 2
7804: * &1 000000001
7805: * = 000000001
7806: * +1= 000000010 =2
7807: * 2211
7808: * V1=1+1, V2=0+1, V3=1+1, V4=1+1
7809: * V3=2
7810: */
7811:
1.202 brouard 7812: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7813: /* /\* printf("h=%2d ", h); *\/ */
7814: /* /\* for(k=1; k <=10; k++){ *\/ */
7815: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7816: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7817: /* /\* } *\/ */
7818: /* /\* printf("\n"); *\/ */
7819: /* } */
1.197 brouard 7820: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7821: /* 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 *\/ */
7822: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7823: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7824: /* h++; */
7825: /* if (h>m) */
7826: /* h=1; */
7827: /* codtab[h][k]=j; */
7828: /* /\* codtab[12][3]=1; *\/ */
7829: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7830: /* /\* 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]]); *\/ */
7831: /* } */
7832: /* } */
7833: /* } */
7834: /* } */
1.126 brouard 7835: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7836: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7837: /* for(i=1; i <=m ;i++){ */
7838: /* for(k=1; k <=cptcovn; k++){ */
7839: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7840: /* } */
7841: /* printf("\n"); */
7842: /* } */
7843: /* scanf("%d",i);*/
1.145 brouard 7844:
7845: free_ivector(Ndum,-1,NCOVMAX);
7846:
7847:
1.126 brouard 7848:
1.186 brouard 7849: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7850: strcpy(optionfilegnuplot,optionfilefiname);
7851: if(mle==-3)
1.201 brouard 7852: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7853: strcat(optionfilegnuplot,".gp");
7854:
7855: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7856: printf("Problem with file %s",optionfilegnuplot);
7857: }
7858: else{
1.204 brouard 7859: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7860: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7861: //fprintf(ficgp,"set missing 'NaNq'\n");
7862: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7863: }
7864: /* fclose(ficgp);*/
1.186 brouard 7865:
7866:
7867: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7868:
7869: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7870: if(mle==-3)
1.201 brouard 7871: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7872: strcat(optionfilehtm,".htm");
7873: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7874: printf("Problem with %s \n",optionfilehtm);
7875: exit(0);
1.126 brouard 7876: }
7877:
7878: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7879: strcat(optionfilehtmcov,"-cov.htm");
7880: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7881: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7882: }
7883: else{
7884: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7885: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7886: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7887: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7888: }
7889:
1.213 brouard 7890: fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
1.204 brouard 7891: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7892: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7893: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7894: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7895: \n\
7896: <hr size=\"2\" color=\"#EC5E5E\">\
7897: <ul><li><h4>Parameter files</h4>\n\
7898: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7899: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7900: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7901: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7902: - Date and time at start: %s</ul>\n",\
7903: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7904: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7905: fileres,fileres,\
7906: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7907: fflush(fichtm);
7908:
7909: strcpy(pathr,path);
7910: strcat(pathr,optionfilefiname);
1.184 brouard 7911: #ifdef WIN32
7912: _chdir(optionfilefiname); /* Move to directory named optionfile */
7913: #else
1.126 brouard 7914: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7915: #endif
7916:
1.126 brouard 7917:
7918: /* Calculates basic frequencies. Computes observed prevalence at single age
7919: and prints on file fileres'p'. */
1.214 brouard 7920: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\
7921: firstpass, lastpass, stepm, weightopt, model);
1.126 brouard 7922:
7923: fprintf(fichtm,"\n");
7924: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7925: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7926: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7927: imx,agemin,agemax,jmin,jmax,jmean);
7928: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7929: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7930: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7931: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7932: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7933:
7934:
7935: /* For Powell, parameters are in a vector p[] starting at p[1]
7936: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7937: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7938:
7939: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7940: /* For mortality only */
1.126 brouard 7941: if (mle==-3){
1.136 brouard 7942: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7943: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7944: cens=ivector(1,n);
7945: ageexmed=vector(1,n);
7946: agecens=vector(1,n);
7947: dcwave=ivector(1,n);
7948:
7949: for (i=1; i<=imx; i++){
7950: dcwave[i]=-1;
7951: for (m=firstpass; m<=lastpass; m++)
7952: if (s[m][i]>nlstate) {
7953: dcwave[i]=m;
7954: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7955: break;
7956: }
7957: }
7958:
7959: for (i=1; i<=imx; i++) {
7960: if (wav[i]>0){
7961: ageexmed[i]=agev[mw[1][i]][i];
7962: j=wav[i];
7963: agecens[i]=1.;
7964:
7965: if (ageexmed[i]> 1 && wav[i] > 0){
7966: agecens[i]=agev[mw[j][i]][i];
7967: cens[i]= 1;
7968: }else if (ageexmed[i]< 1)
7969: cens[i]= -1;
7970: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7971: cens[i]=0 ;
7972: }
7973: else cens[i]=-1;
7974: }
7975:
7976: for (i=1;i<=NDIM;i++) {
7977: for (j=1;j<=NDIM;j++)
7978: ximort[i][j]=(i == j ? 1.0 : 0.0);
7979: }
7980:
1.145 brouard 7981: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7982: /*printf("%lf %lf", p[1], p[2]);*/
7983:
7984:
1.136 brouard 7985: #ifdef GSL
7986: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7987: #else
1.126 brouard 7988: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7989: #endif
1.201 brouard 7990: strcpy(filerespow,"POW-MORT_");
7991: strcat(filerespow,fileresu);
1.126 brouard 7992: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7993: printf("Problem with resultfile: %s\n", filerespow);
7994: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7995: }
1.136 brouard 7996: #ifdef GSL
7997: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7998: #else
1.126 brouard 7999: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 8000: #endif
1.126 brouard 8001: /* for (i=1;i<=nlstate;i++)
8002: for(j=1;j<=nlstate+ndeath;j++)
8003: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
8004: */
8005: fprintf(ficrespow,"\n");
1.136 brouard 8006: #ifdef GSL
8007: /* gsl starts here */
8008: T = gsl_multimin_fminimizer_nmsimplex;
8009: gsl_multimin_fminimizer *sfm = NULL;
8010: gsl_vector *ss, *x;
8011: gsl_multimin_function minex_func;
8012:
8013: /* Initial vertex size vector */
8014: ss = gsl_vector_alloc (NDIM);
8015:
8016: if (ss == NULL){
8017: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
8018: }
8019: /* Set all step sizes to 1 */
8020: gsl_vector_set_all (ss, 0.001);
8021:
8022: /* Starting point */
1.126 brouard 8023:
1.136 brouard 8024: x = gsl_vector_alloc (NDIM);
8025:
8026: if (x == NULL){
8027: gsl_vector_free(ss);
8028: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
8029: }
8030:
8031: /* Initialize method and iterate */
8032: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 8033: /* gsl_vector_set(x, 0, 0.0268); */
8034: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 8035: gsl_vector_set(x, 0, p[1]);
8036: gsl_vector_set(x, 1, p[2]);
8037:
8038: minex_func.f = &gompertz_f;
8039: minex_func.n = NDIM;
8040: minex_func.params = (void *)&p; /* ??? */
8041:
8042: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
8043: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
8044:
8045: printf("Iterations beginning .....\n\n");
8046: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
8047:
8048: iteri=0;
8049: while (rval == GSL_CONTINUE){
8050: iteri++;
8051: status = gsl_multimin_fminimizer_iterate(sfm);
8052:
8053: if (status) printf("error: %s\n", gsl_strerror (status));
8054: fflush(0);
8055:
8056: if (status)
8057: break;
8058:
8059: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
8060: ssval = gsl_multimin_fminimizer_size (sfm);
8061:
8062: if (rval == GSL_SUCCESS)
8063: printf ("converged to a local maximum at\n");
8064:
8065: printf("%5d ", iteri);
8066: for (it = 0; it < NDIM; it++){
8067: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
8068: }
8069: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
8070: }
8071:
8072: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
8073:
8074: gsl_vector_free(x); /* initial values */
8075: gsl_vector_free(ss); /* inital step size */
8076: for (it=0; it<NDIM; it++){
8077: p[it+1]=gsl_vector_get(sfm->x,it);
8078: fprintf(ficrespow," %.12lf", p[it]);
8079: }
8080: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
8081: #endif
8082: #ifdef POWELL
8083: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
8084: #endif
1.126 brouard 8085: fclose(ficrespow);
8086:
1.203 brouard 8087: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 8088:
8089: for(i=1; i <=NDIM; i++)
8090: for(j=i+1;j<=NDIM;j++)
8091: matcov[i][j]=matcov[j][i];
8092:
8093: printf("\nCovariance matrix\n ");
1.203 brouard 8094: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 8095: for(i=1; i <=NDIM; i++) {
8096: for(j=1;j<=NDIM;j++){
8097: printf("%f ",matcov[i][j]);
1.203 brouard 8098: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 8099: }
1.203 brouard 8100: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 8101: }
8102:
8103: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 8104: for (i=1;i<=NDIM;i++) {
1.126 brouard 8105: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 8106: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
8107: }
1.126 brouard 8108: lsurv=vector(1,AGESUP);
8109: lpop=vector(1,AGESUP);
8110: tpop=vector(1,AGESUP);
8111: lsurv[agegomp]=100000;
8112:
8113: for (k=agegomp;k<=AGESUP;k++) {
8114: agemortsup=k;
8115: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
8116: }
8117:
8118: for (k=agegomp;k<agemortsup;k++)
8119: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
8120:
8121: for (k=agegomp;k<agemortsup;k++){
8122: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
8123: sumlpop=sumlpop+lpop[k];
8124: }
8125:
8126: tpop[agegomp]=sumlpop;
8127: for (k=agegomp;k<(agemortsup-3);k++){
8128: /* tpop[k+1]=2;*/
8129: tpop[k+1]=tpop[k]-lpop[k];
8130: }
8131:
8132:
8133: printf("\nAge lx qx dx Lx Tx e(x)\n");
8134: for (k=agegomp;k<(agemortsup-2);k++)
8135: 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]);
8136:
8137:
8138: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8139: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
8140: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8141: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8142: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8143: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8144: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8145: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8146: }else
1.201 brouard 8147: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
8148: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 8149: stepm, weightopt,\
8150: model,imx,p,matcov,agemortsup);
8151:
8152: free_vector(lsurv,1,AGESUP);
8153: free_vector(lpop,1,AGESUP);
8154: free_vector(tpop,1,AGESUP);
1.136 brouard 8155: #ifdef GSL
8156: free_ivector(cens,1,n);
8157: free_vector(agecens,1,n);
8158: free_ivector(dcwave,1,n);
8159: free_matrix(ximort,1,NDIM,1,NDIM);
8160: #endif
1.186 brouard 8161: } /* Endof if mle==-3 mortality only */
1.205 brouard 8162: /* Standard */
8163: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
8164: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8165: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 8166: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 8167: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8168: for (k=1; k<=npar;k++)
8169: printf(" %d %8.5f",k,p[k]);
8170: printf("\n");
1.205 brouard 8171: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
8172: /* mlikeli uses func not funcone */
8173: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
8174: }
8175: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
8176: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
8177: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
8178: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8179: }
8180: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 8181: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
8182: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
8183: for (k=1; k<=npar;k++)
8184: printf(" %d %8.5f",k,p[k]);
8185: printf("\n");
8186:
8187: /*--------- results files --------------*/
1.192 brouard 8188: 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 8189:
8190:
8191: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8192: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8193: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
8194: for(i=1,jk=1; i <=nlstate; i++){
8195: for(k=1; k <=(nlstate+ndeath); k++){
8196: if (k != i) {
8197: printf("%d%d ",i,k);
8198: fprintf(ficlog,"%d%d ",i,k);
8199: fprintf(ficres,"%1d%1d ",i,k);
8200: for(j=1; j <=ncovmodel; j++){
1.190 brouard 8201: printf("%12.7f ",p[jk]);
8202: fprintf(ficlog,"%12.7f ",p[jk]);
8203: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 8204: jk++;
8205: }
8206: printf("\n");
8207: fprintf(ficlog,"\n");
8208: fprintf(ficres,"\n");
8209: }
8210: }
8211: }
1.203 brouard 8212: if(mle != 0){
8213: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 8214: ftolhess=ftol; /* Usually correct */
1.203 brouard 8215: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
8216: 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");
8217: 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");
8218: for(i=1,jk=1; i <=nlstate; i++){
8219: for(k=1; k <=(nlstate+ndeath); k++){
8220: if (k != i) {
8221: printf("%d%d ",i,k);
8222: fprintf(ficlog,"%d%d ",i,k);
8223: for(j=1; j <=ncovmodel; j++){
8224: 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]));
8225: 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]));
8226: jk++;
8227: }
8228: printf("\n");
8229: fprintf(ficlog,"\n");
1.193 brouard 8230: }
8231: }
8232: }
1.203 brouard 8233: } /* end of hesscov and Wald tests */
1.193 brouard 8234:
1.203 brouard 8235: /* */
1.126 brouard 8236: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
8237: printf("# Scales (for hessian or gradient estimation)\n");
8238: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
8239: for(i=1,jk=1; i <=nlstate; i++){
8240: for(j=1; j <=nlstate+ndeath; j++){
8241: if (j!=i) {
8242: fprintf(ficres,"%1d%1d",i,j);
8243: printf("%1d%1d",i,j);
8244: fprintf(ficlog,"%1d%1d",i,j);
8245: for(k=1; k<=ncovmodel;k++){
8246: printf(" %.5e",delti[jk]);
8247: fprintf(ficlog," %.5e",delti[jk]);
8248: fprintf(ficres," %.5e",delti[jk]);
8249: jk++;
8250: }
8251: printf("\n");
8252: fprintf(ficlog,"\n");
8253: fprintf(ficres,"\n");
8254: }
8255: }
8256: }
8257:
8258: 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");
1.203 brouard 8259: if(mle >= 1) /* To big for the screen */
1.126 brouard 8260: 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");
8261: 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");
8262: /* # 121 Var(a12)\n\ */
8263: /* # 122 Cov(b12,a12) Var(b12)\n\ */
8264: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
8265: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
8266: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
8267: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
8268: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
8269: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
8270:
8271:
8272: /* Just to have a covariance matrix which will be more understandable
8273: even is we still don't want to manage dictionary of variables
8274: */
8275: for(itimes=1;itimes<=2;itimes++){
8276: jj=0;
8277: for(i=1; i <=nlstate; i++){
8278: for(j=1; j <=nlstate+ndeath; j++){
8279: if(j==i) continue;
8280: for(k=1; k<=ncovmodel;k++){
8281: jj++;
8282: ca[0]= k+'a'-1;ca[1]='\0';
8283: if(itimes==1){
8284: if(mle>=1)
8285: printf("#%1d%1d%d",i,j,k);
8286: fprintf(ficlog,"#%1d%1d%d",i,j,k);
8287: fprintf(ficres,"#%1d%1d%d",i,j,k);
8288: }else{
8289: if(mle>=1)
8290: printf("%1d%1d%d",i,j,k);
8291: fprintf(ficlog,"%1d%1d%d",i,j,k);
8292: fprintf(ficres,"%1d%1d%d",i,j,k);
8293: }
8294: ll=0;
8295: for(li=1;li <=nlstate; li++){
8296: for(lj=1;lj <=nlstate+ndeath; lj++){
8297: if(lj==li) continue;
8298: for(lk=1;lk<=ncovmodel;lk++){
8299: ll++;
8300: if(ll<=jj){
8301: cb[0]= lk +'a'-1;cb[1]='\0';
8302: if(ll<jj){
8303: if(itimes==1){
8304: if(mle>=1)
8305: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8306: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8307: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
8308: }else{
8309: if(mle>=1)
8310: printf(" %.5e",matcov[jj][ll]);
8311: fprintf(ficlog," %.5e",matcov[jj][ll]);
8312: fprintf(ficres," %.5e",matcov[jj][ll]);
8313: }
8314: }else{
8315: if(itimes==1){
8316: if(mle>=1)
8317: printf(" Var(%s%1d%1d)",ca,i,j);
8318: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
8319: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
8320: }else{
8321: if(mle>=1)
1.203 brouard 8322: printf(" %.7e",matcov[jj][ll]);
8323: fprintf(ficlog," %.7e",matcov[jj][ll]);
8324: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 8325: }
8326: }
8327: }
8328: } /* end lk */
8329: } /* end lj */
8330: } /* end li */
8331: if(mle>=1)
8332: printf("\n");
8333: fprintf(ficlog,"\n");
8334: fprintf(ficres,"\n");
8335: numlinepar++;
8336: } /* end k*/
8337: } /*end j */
8338: } /* end i */
8339: } /* end itimes */
8340:
8341: fflush(ficlog);
8342: fflush(ficres);
1.209 brouard 8343: while(fgets(line, MAXLINE, ficpar)) {
8344: /* If line starts with a # it is a comment */
8345: if (line[0] == '#') {
8346: numlinepar++;
1.141 brouard 8347: fputs(line,stdout);
1.126 brouard 8348: fputs(line,ficparo);
1.209 brouard 8349: fputs(line,ficlog);
8350: continue;
8351: }else
8352: break;
8353: }
8354:
8355: /* while((c=getc(ficpar))=='#' && c!= EOF){ */
8356: /* ungetc(c,ficpar); */
8357: /* fgets(line, MAXLINE, ficpar); */
8358: /* fputs(line,stdout); */
8359: /* fputs(line,ficparo); */
8360: /* } */
8361: /* ungetc(c,ficpar); */
1.126 brouard 8362:
8363: estepm=0;
1.209 brouard 8364: if((num_filled=sscanf(line,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm, &ftolpl)) !=EOF){
8365:
8366: if (num_filled != 6) {
8367: printf("Not 6 parameters in line, for example:agemin=60 agemax=95 bage=55 fage=95 estepm=24 ftolpl=6e-4\n");
8368: printf("but line=%s\n",line);
8369: goto end;
8370: }
8371: printf("agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%lf\n",ageminpar,agemaxpar, bage, fage, estepm, ftolpl);
8372: }
8373: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
8374: /*ftolpl=6.e-4;*/ /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
8375:
8376: /* fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d ftolpl=%\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm); */
1.126 brouard 8377: if (estepm==0 || estepm < stepm) estepm=stepm;
8378: if (fage <= 2) {
8379: bage = ageminpar;
8380: fage = agemaxpar;
8381: }
8382:
8383: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
1.211 brouard 8384: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
8385: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);
1.186 brouard 8386:
8387: /* Other stuffs, more or less useful */
1.126 brouard 8388: while((c=getc(ficpar))=='#' && c!= EOF){
8389: ungetc(c,ficpar);
8390: fgets(line, MAXLINE, ficpar);
1.141 brouard 8391: fputs(line,stdout);
1.126 brouard 8392: fputs(line,ficparo);
8393: }
8394: ungetc(c,ficpar);
8395:
8396: 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);
8397: 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);
8398: 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);
8399: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
8400: 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);
8401:
8402: while((c=getc(ficpar))=='#' && c!= EOF){
8403: ungetc(c,ficpar);
8404: fgets(line, MAXLINE, ficpar);
1.141 brouard 8405: fputs(line,stdout);
1.126 brouard 8406: fputs(line,ficparo);
8407: }
8408: ungetc(c,ficpar);
8409:
8410:
8411: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
8412: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
8413:
8414: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 8415: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 8416: fprintf(ficparo,"pop_based=%d\n",popbased);
8417: fprintf(ficres,"pop_based=%d\n",popbased);
8418:
8419: while((c=getc(ficpar))=='#' && c!= EOF){
8420: ungetc(c,ficpar);
8421: fgets(line, MAXLINE, ficpar);
1.141 brouard 8422: fputs(line,stdout);
1.126 brouard 8423: fputs(line,ficparo);
8424: }
8425: ungetc(c,ficpar);
8426:
8427: 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);
8428: 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);
8429: 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);
8430: 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);
8431: 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);
8432: /* day and month of proj2 are not used but only year anproj2.*/
8433:
8434:
8435:
1.145 brouard 8436: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
8437: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 8438:
8439: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 8440: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
8441: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8442: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8443: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8444: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
8445: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
8446: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
8447: }else
1.211 brouard 8448: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, pathc,p);
1.126 brouard 8449:
1.201 brouard 8450: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.211 brouard 8451: model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,estepm, \
1.213 brouard 8452: jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);
1.126 brouard 8453:
8454: /*------------ free_vector -------------*/
8455: /* chdir(path); */
8456:
1.215 ! brouard 8457: /* free_ivector(wav,1,imx); */ /* Moved after last prevalence call */
! 8458: /* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
! 8459: /* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
! 8460: /* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
1.126 brouard 8461: free_lvector(num,1,n);
8462: free_vector(agedc,1,n);
8463: /*free_matrix(covar,0,NCOVMAX,1,n);*/
8464: /*free_matrix(covar,1,NCOVMAX,1,n);*/
8465: fclose(ficparo);
8466: fclose(ficres);
8467:
8468:
1.186 brouard 8469: /* Other results (useful)*/
8470:
8471:
1.126 brouard 8472: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 8473: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
8474: prlim=matrix(1,nlstate,1,nlstate);
1.209 brouard 8475: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
1.126 brouard 8476: fclose(ficrespl);
8477:
1.145 brouard 8478: #ifdef FREEEXIT2
8479: #include "freeexit2.h"
8480: #endif
8481:
1.126 brouard 8482: /*------------- h Pij x at various ages ------------*/
1.180 brouard 8483: /*#include "hpijx.h"*/
8484: hPijx(p, bage, fage);
1.145 brouard 8485: fclose(ficrespij);
1.126 brouard 8486:
1.145 brouard 8487: /*-------------- Variance of one-step probabilities---*/
8488: k=1;
1.126 brouard 8489: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
8490:
8491:
8492: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8493: for(i=1;i<=AGESUP;i++)
8494: for(j=1;j<=NCOVMAX;j++)
8495: for(k=1;k<=NCOVMAX;k++)
8496: probs[i][j][k]=0.;
8497:
8498: /*---------- Forecasting ------------------*/
8499: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8500: if(prevfcast==1){
8501: /* if(stepm ==1){*/
1.201 brouard 8502: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8503: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8504: /* } */
8505: /* else{ */
8506: /* erreur=108; */
8507: /* 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); */
8508: /* 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); */
8509: /* } */
8510: }
1.186 brouard 8511:
8512: /* ------ Other prevalence ratios------------ */
1.126 brouard 8513:
1.127 brouard 8514: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8515:
8516: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8517: /* 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",\
8518: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8519: */
1.215 ! brouard 8520: free_ivector(wav,1,imx);
! 8521: free_imatrix(dh,1,lastpass-firstpass+2,1,imx);
! 8522: free_imatrix(bh,1,lastpass-firstpass+2,1,imx);
! 8523: free_imatrix(mw,1,lastpass-firstpass+2,1,imx);
! 8524:
1.126 brouard 8525:
1.127 brouard 8526: if (mobilav!=0) {
8527: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8528: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8529: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8530: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8531: }
1.126 brouard 8532: }
8533:
8534:
1.127 brouard 8535: /*---------- Health expectancies, no variances ------------*/
8536:
1.201 brouard 8537: strcpy(filerese,"E_");
8538: strcat(filerese,fileresu);
1.126 brouard 8539: if((ficreseij=fopen(filerese,"w"))==NULL) {
8540: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8541: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8542: }
1.208 brouard 8543: printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
8544: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);
1.145 brouard 8545: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8546: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8547:
8548: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8549: fprintf(ficreseij,"\n#****** ");
8550: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8551: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8552: }
8553: fprintf(ficreseij,"******\n");
8554:
8555: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8556: oldm=oldms;savm=savms;
8557: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8558:
8559: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8560: /*}*/
1.127 brouard 8561: }
8562: fclose(ficreseij);
1.208 brouard 8563: printf("done evsij\n");fflush(stdout);
8564: fprintf(ficlog,"done evsij\n");fflush(ficlog);
1.127 brouard 8565:
8566: /*---------- Health expectancies and variances ------------*/
8567:
8568:
1.201 brouard 8569: strcpy(filerest,"T_");
8570: strcat(filerest,fileresu);
1.127 brouard 8571: if((ficrest=fopen(filerest,"w"))==NULL) {
8572: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8573: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8574: }
1.208 brouard 8575: printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
8576: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);
1.127 brouard 8577:
1.126 brouard 8578:
1.201 brouard 8579: strcpy(fileresstde,"STDE_");
8580: strcat(fileresstde,fileresu);
1.126 brouard 8581: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8582: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8583: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8584: }
1.208 brouard 8585: printf(" Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8586: fprintf(ficlog," Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
1.126 brouard 8587:
1.201 brouard 8588: strcpy(filerescve,"CVE_");
8589: strcat(filerescve,fileresu);
1.126 brouard 8590: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8591: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8592: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8593: }
1.208 brouard 8594: printf(" Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8595: fprintf(ficlog," Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
1.126 brouard 8596:
1.201 brouard 8597: strcpy(fileresv,"V_");
8598: strcat(fileresv,fileresu);
1.126 brouard 8599: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8600: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8601: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8602: }
1.208 brouard 8603: printf(" Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(stdout);
8604: fprintf(ficlog," Computing Variance-covariance of DFLEs: file '%s' ... ", fileresv);fflush(ficlog);
1.126 brouard 8605:
1.145 brouard 8606: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8607: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8608:
8609: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.208 brouard 8610: fprintf(ficrest,"\n#****** ");
8611: for(j=1;j<=cptcoveff;j++)
8612: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8613: fprintf(ficrest,"******\n");
8614:
8615: fprintf(ficresstdeij,"\n#****** ");
8616: fprintf(ficrescveij,"\n#****** ");
8617: for(j=1;j<=cptcoveff;j++) {
8618: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8619: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8620: }
8621: fprintf(ficresstdeij,"******\n");
8622: fprintf(ficrescveij,"******\n");
8623:
8624: fprintf(ficresvij,"\n#****** ");
8625: for(j=1;j<=cptcoveff;j++)
8626: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8627: fprintf(ficresvij,"******\n");
8628:
8629: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8630: oldm=oldms;savm=savms;
8631: printf(" cvevsij %d, ",k);
8632: fprintf(ficlog, " cvevsij %d, ",k);
8633: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
8634: printf(" end cvevsij \n ");
8635: fprintf(ficlog, " end cvevsij \n ");
8636:
8637: /*
8638: */
8639: /* goto endfree; */
8640:
8641: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8642: pstamp(ficrest);
8643:
8644:
8645: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
8646: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
8647: cptcod= 0; /* To be deleted */
8648: printf("varevsij %d \n",vpopbased);
8649: fprintf(ficlog, "varevsij %d \n",vpopbased);
1.209 brouard 8650: varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
1.208 brouard 8651: 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 ");
8652: if(vpopbased==1)
8653: 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);
8654: else
8655: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
8656: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
8657: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8658: fprintf(ficrest,"\n");
8659: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
8660: epj=vector(1,nlstate+1);
8661: printf("Computing age specific period (stable) prevalences in each health state \n");
8662: fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
8663: for(age=bage; age <=fage ;age++){
1.209 brouard 8664: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /*ZZ Is it the correct prevalim */
1.208 brouard 8665: if (vpopbased==1) {
8666: if(mobilav ==0){
8667: for(i=1; i<=nlstate;i++)
8668: prlim[i][i]=probs[(int)age][i][k];
8669: }else{ /* mobilav */
8670: for(i=1; i<=nlstate;i++)
8671: prlim[i][i]=mobaverage[(int)age][i][k];
1.126 brouard 8672: }
1.208 brouard 8673: }
8674:
8675: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
8676: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
8677: /* printf(" age %4.0f ",age); */
8678: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8679: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8680: epj[j] += prlim[i][i]*eij[i][j][(int)age];
8681: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8682: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.126 brouard 8683: }
1.208 brouard 8684: epj[nlstate+1] +=epj[j];
8685: }
8686: /* printf(" age %4.0f \n",age); */
8687:
8688: for(i=1, vepp=0.;i <=nlstate;i++)
8689: for(j=1;j <=nlstate;j++)
8690: vepp += vareij[i][j][(int)age];
8691: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8692: for(j=1;j <=nlstate;j++){
8693: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
1.126 brouard 8694: }
1.208 brouard 8695: fprintf(ficrest,"\n");
1.126 brouard 8696: }
1.208 brouard 8697: } /* End vpopbased */
8698: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8699: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8700: free_vector(epj,1,nlstate+1);
8701: printf("done \n");fflush(stdout);
8702: fprintf(ficlog,"done\n");fflush(ficlog);
8703:
1.145 brouard 8704: /*}*/
1.208 brouard 8705: } /* End k */
1.126 brouard 8706: free_vector(weight,1,n);
1.145 brouard 8707: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8708: free_imatrix(s,1,maxwav+1,1,n);
8709: free_matrix(anint,1,maxwav,1,n);
8710: free_matrix(mint,1,maxwav,1,n);
8711: free_ivector(cod,1,n);
8712: free_ivector(tab,1,NCOVMAX);
8713: fclose(ficresstdeij);
8714: fclose(ficrescveij);
8715: fclose(ficresvij);
8716: fclose(ficrest);
1.208 brouard 8717: printf("done Health expectancies\n");fflush(stdout);
8718: fprintf(ficlog,"done Health expectancies\n");fflush(ficlog);
1.126 brouard 8719: fclose(ficpar);
8720:
8721: /*------- Variance of period (stable) prevalence------*/
8722:
1.201 brouard 8723: strcpy(fileresvpl,"VPL_");
8724: strcat(fileresvpl,fileresu);
1.126 brouard 8725: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8726: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8727: exit(0);
8728: }
1.208 brouard 8729: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
8730: fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);
1.126 brouard 8731:
1.145 brouard 8732: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8733: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8734:
8735: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8736: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8737: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8738: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8739: fprintf(ficresvpl,"******\n");
8740:
8741: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8742: oldm=oldms;savm=savms;
1.209 brouard 8743: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);
1.126 brouard 8744: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8745: /*}*/
1.126 brouard 8746: }
8747:
8748: fclose(ficresvpl);
1.208 brouard 8749: printf("done variance-covariance of period prevalence\n");fflush(stdout);
8750: fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);
1.126 brouard 8751:
8752: /*---------- End : free ----------------*/
8753: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8754: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8755: } /* mle==-3 arrives here for freeing */
1.164 brouard 8756: /* endfree:*/
1.141 brouard 8757: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8758: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8759: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8760: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8761: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8762: free_matrix(covar,0,NCOVMAX,1,n);
8763: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8764: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8765: /*free_vector(delti,1,npar);*/
8766: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8767: free_matrix(agev,1,maxwav,1,imx);
8768: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8769:
1.145 brouard 8770: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8771: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8772: free_ivector(Tvar,1,NCOVMAX);
8773: free_ivector(Tprod,1,NCOVMAX);
8774: free_ivector(Tvaraff,1,NCOVMAX);
8775: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8776:
8777: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8778: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8779: fflush(fichtm);
8780: fflush(ficgp);
8781:
8782:
8783: if((nberr >0) || (nbwarn>0)){
8784: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8785: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8786: }else{
8787: printf("End of Imach\n");
8788: fprintf(ficlog,"End of Imach\n");
8789: }
8790: printf("See log file on %s\n",filelog);
8791: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8792: /*(void) gettimeofday(&end_time,&tzp);*/
8793: rend_time = time(NULL);
8794: end_time = *localtime(&rend_time);
8795: /* tml = *localtime(&end_time.tm_sec); */
8796: strcpy(strtend,asctime(&end_time));
1.126 brouard 8797: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8798: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8799: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8800:
1.157 brouard 8801: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8802: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8803: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8804: /* printf("Total time was %d uSec.\n", total_usecs);*/
8805: /* if(fileappend(fichtm,optionfilehtm)){ */
8806: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8807: fclose(fichtm);
8808: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8809: fclose(fichtmcov);
8810: fclose(ficgp);
8811: fclose(ficlog);
8812: /*------ End -----------*/
8813:
8814:
8815: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8816: #ifdef WIN32
8817: if (_chdir(pathcd) != 0)
8818: printf("Can't move to directory %s!\n",path);
8819: if(_getcwd(pathcd,MAXLINE) > 0)
8820: #else
1.126 brouard 8821: if(chdir(pathcd) != 0)
1.184 brouard 8822: printf("Can't move to directory %s!\n", path);
8823: if (getcwd(pathcd, MAXLINE) > 0)
8824: #endif
1.126 brouard 8825: printf("Current directory %s!\n",pathcd);
8826: /*strcat(plotcmd,CHARSEPARATOR);*/
8827: sprintf(plotcmd,"gnuplot");
1.157 brouard 8828: #ifdef _WIN32
1.126 brouard 8829: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8830: #endif
8831: if(!stat(plotcmd,&info)){
1.158 brouard 8832: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8833: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8834: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8835: }else
8836: strcpy(pplotcmd,plotcmd);
1.157 brouard 8837: #ifdef __unix
1.126 brouard 8838: strcpy(plotcmd,GNUPLOTPROGRAM);
8839: if(!stat(plotcmd,&info)){
1.158 brouard 8840: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8841: }else
8842: strcpy(pplotcmd,plotcmd);
8843: #endif
8844: }else
8845: strcpy(pplotcmd,plotcmd);
8846:
8847: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8848: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8849:
8850: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8851: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8852: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8853: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8854: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8855: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8856: }
1.158 brouard 8857: printf(" Successful, please wait...");
1.126 brouard 8858: while (z[0] != 'q') {
8859: /* chdir(path); */
1.154 brouard 8860: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8861: scanf("%s",z);
8862: /* if (z[0] == 'c') system("./imach"); */
8863: if (z[0] == 'e') {
1.158 brouard 8864: #ifdef __APPLE__
1.152 brouard 8865: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8866: #elif __linux
8867: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8868: #else
1.152 brouard 8869: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8870: #endif
8871: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8872: system(pplotcmd);
1.126 brouard 8873: }
8874: else if (z[0] == 'g') system(plotcmd);
8875: else if (z[0] == 'q') exit(0);
8876: }
8877: end:
8878: while (z[0] != 'q') {
1.195 brouard 8879: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8880: scanf("%s",z);
8881: }
8882: }
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