Annotation of imach/src/imach.c, revision 1.206
1.206 ! brouard 1: /* $Id: imach.c,v 1.205 2015/10/23 15:50:53 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.206 ! brouard 4: Revision 1.205 2015/10/23 15:50:53 brouard
! 5: Summary: 0.98r3 some clarification for graphs on likelihood contributions
! 6:
1.205 brouard 7: Revision 1.204 2015/10/01 16:20:26 brouard
8: Summary: Some new graphs of contribution to likelihood
9:
1.204 brouard 10: Revision 1.203 2015/09/30 17:45:14 brouard
11: Summary: looking at better estimation of the hessian
12:
13: Also a better criteria for convergence to the period prevalence And
14: therefore adding the number of years needed to converge. (The
15: prevalence in any alive state shold sum to one
16:
1.203 brouard 17: Revision 1.202 2015/09/22 19:45:16 brouard
18: Summary: Adding some overall graph on contribution to likelihood. Might change
19:
1.202 brouard 20: Revision 1.201 2015/09/15 17:34:58 brouard
21: Summary: 0.98r0
22:
23: - Some new graphs like suvival functions
24: - Some bugs fixed like model=1+age+V2.
25:
1.201 brouard 26: Revision 1.200 2015/09/09 16:53:55 brouard
27: Summary: Big bug thanks to Flavia
28:
29: Even model=1+age+V2. did not work anymore
30:
1.200 brouard 31: Revision 1.199 2015/09/07 14:09:23 brouard
32: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
33:
1.199 brouard 34: Revision 1.198 2015/09/03 07:14:39 brouard
35: Summary: 0.98q5 Flavia
36:
1.198 brouard 37: Revision 1.197 2015/09/01 18:24:39 brouard
38: *** empty log message ***
39:
1.197 brouard 40: Revision 1.196 2015/08/18 23:17:52 brouard
41: Summary: 0.98q5
42:
1.196 brouard 43: Revision 1.195 2015/08/18 16:28:39 brouard
44: Summary: Adding a hack for testing purpose
45:
46: After reading the title, ftol and model lines, if the comment line has
47: a q, starting with #q, the answer at the end of the run is quit. It
48: permits to run test files in batch with ctest. The former workaround was
49: $ echo q | imach foo.imach
50:
1.195 brouard 51: Revision 1.194 2015/08/18 13:32:00 brouard
52: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
53:
1.194 brouard 54: Revision 1.193 2015/08/04 07:17:42 brouard
55: Summary: 0.98q4
56:
1.193 brouard 57: Revision 1.192 2015/07/16 16:49:02 brouard
58: Summary: Fixing some outputs
59:
1.192 brouard 60: Revision 1.191 2015/07/14 10:00:33 brouard
61: Summary: Some fixes
62:
1.191 brouard 63: Revision 1.190 2015/05/05 08:51:13 brouard
64: Summary: Adding digits in output parameters (7 digits instead of 6)
65:
66: Fix 1+age+.
67:
1.190 brouard 68: Revision 1.189 2015/04/30 14:45:16 brouard
69: Summary: 0.98q2
70:
1.189 brouard 71: Revision 1.188 2015/04/30 08:27:53 brouard
72: *** empty log message ***
73:
1.188 brouard 74: Revision 1.187 2015/04/29 09:11:15 brouard
75: *** empty log message ***
76:
1.187 brouard 77: Revision 1.186 2015/04/23 12:01:52 brouard
78: Summary: V1*age is working now, version 0.98q1
79:
80: Some codes had been disabled in order to simplify and Vn*age was
81: working in the optimization phase, ie, giving correct MLE parameters,
82: but, as usual, outputs were not correct and program core dumped.
83:
1.186 brouard 84: Revision 1.185 2015/03/11 13:26:42 brouard
85: Summary: Inclusion of compile and links command line for Intel Compiler
86:
1.185 brouard 87: Revision 1.184 2015/03/11 11:52:39 brouard
88: Summary: Back from Windows 8. Intel Compiler
89:
1.184 brouard 90: Revision 1.183 2015/03/10 20:34:32 brouard
91: Summary: 0.98q0, trying with directest, mnbrak fixed
92:
93: We use directest instead of original Powell test; probably no
94: incidence on the results, but better justifications;
95: We fixed Numerical Recipes mnbrak routine which was wrong and gave
96: wrong results.
97:
1.183 brouard 98: Revision 1.182 2015/02/12 08:19:57 brouard
99: Summary: Trying to keep directest which seems simpler and more general
100: Author: Nicolas Brouard
101:
1.182 brouard 102: Revision 1.181 2015/02/11 23:22:24 brouard
103: Summary: Comments on Powell added
104:
105: Author:
106:
1.181 brouard 107: Revision 1.180 2015/02/11 17:33:45 brouard
108: Summary: Finishing move from main to function (hpijx and prevalence_limit)
109:
1.180 brouard 110: Revision 1.179 2015/01/04 09:57:06 brouard
111: Summary: back to OS/X
112:
1.179 brouard 113: Revision 1.178 2015/01/04 09:35:48 brouard
114: *** empty log message ***
115:
1.178 brouard 116: Revision 1.177 2015/01/03 18:40:56 brouard
117: Summary: Still testing ilc32 on OSX
118:
1.177 brouard 119: Revision 1.176 2015/01/03 16:45:04 brouard
120: *** empty log message ***
121:
1.176 brouard 122: Revision 1.175 2015/01/03 16:33:42 brouard
123: *** empty log message ***
124:
1.175 brouard 125: Revision 1.174 2015/01/03 16:15:49 brouard
126: Summary: Still in cross-compilation
127:
1.174 brouard 128: Revision 1.173 2015/01/03 12:06:26 brouard
129: Summary: trying to detect cross-compilation
130:
1.173 brouard 131: Revision 1.172 2014/12/27 12:07:47 brouard
132: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
133:
1.172 brouard 134: Revision 1.171 2014/12/23 13:26:59 brouard
135: Summary: Back from Visual C
136:
137: Still problem with utsname.h on Windows
138:
1.171 brouard 139: Revision 1.170 2014/12/23 11:17:12 brouard
140: Summary: Cleaning some \%% back to %%
141:
142: The escape was mandatory for a specific compiler (which one?), but too many warnings.
143:
1.170 brouard 144: Revision 1.169 2014/12/22 23:08:31 brouard
145: Summary: 0.98p
146:
147: Outputs some informations on compiler used, OS etc. Testing on different platforms.
148:
1.169 brouard 149: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 150: Summary: update
1.169 brouard 151:
1.168 brouard 152: Revision 1.167 2014/12/22 13:50:56 brouard
153: Summary: Testing uname and compiler version and if compiled 32 or 64
154:
155: Testing on Linux 64
156:
1.167 brouard 157: Revision 1.166 2014/12/22 11:40:47 brouard
158: *** empty log message ***
159:
1.166 brouard 160: Revision 1.165 2014/12/16 11:20:36 brouard
161: Summary: After compiling on Visual C
162:
163: * imach.c (Module): Merging 1.61 to 1.162
164:
1.165 brouard 165: Revision 1.164 2014/12/16 10:52:11 brouard
166: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
167:
168: * imach.c (Module): Merging 1.61 to 1.162
169:
1.164 brouard 170: Revision 1.163 2014/12/16 10:30:11 brouard
171: * imach.c (Module): Merging 1.61 to 1.162
172:
1.163 brouard 173: Revision 1.162 2014/09/25 11:43:39 brouard
174: Summary: temporary backup 0.99!
175:
1.162 brouard 176: Revision 1.1 2014/09/16 11:06:58 brouard
177: Summary: With some code (wrong) for nlopt
178:
179: Author:
180:
181: Revision 1.161 2014/09/15 20:41:41 brouard
182: Summary: Problem with macro SQR on Intel compiler
183:
1.161 brouard 184: Revision 1.160 2014/09/02 09:24:05 brouard
185: *** empty log message ***
186:
1.160 brouard 187: Revision 1.159 2014/09/01 10:34:10 brouard
188: Summary: WIN32
189: Author: Brouard
190:
1.159 brouard 191: Revision 1.158 2014/08/27 17:11:51 brouard
192: *** empty log message ***
193:
1.158 brouard 194: Revision 1.157 2014/08/27 16:26:55 brouard
195: Summary: Preparing windows Visual studio version
196: Author: Brouard
197:
198: In order to compile on Visual studio, time.h is now correct and time_t
199: and tm struct should be used. difftime should be used but sometimes I
200: just make the differences in raw time format (time(&now).
201: Trying to suppress #ifdef LINUX
202: Add xdg-open for __linux in order to open default browser.
203:
1.157 brouard 204: Revision 1.156 2014/08/25 20:10:10 brouard
205: *** empty log message ***
206:
1.156 brouard 207: Revision 1.155 2014/08/25 18:32:34 brouard
208: Summary: New compile, minor changes
209: Author: Brouard
210:
1.155 brouard 211: Revision 1.154 2014/06/20 17:32:08 brouard
212: Summary: Outputs now all graphs of convergence to period prevalence
213:
1.154 brouard 214: Revision 1.153 2014/06/20 16:45:46 brouard
215: Summary: If 3 live state, convergence to period prevalence on same graph
216: Author: Brouard
217:
1.153 brouard 218: Revision 1.152 2014/06/18 17:54:09 brouard
219: Summary: open browser, use gnuplot on same dir than imach if not found in the path
220:
1.152 brouard 221: Revision 1.151 2014/06/18 16:43:30 brouard
222: *** empty log message ***
223:
1.151 brouard 224: Revision 1.150 2014/06/18 16:42:35 brouard
225: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
226: Author: brouard
227:
1.150 brouard 228: Revision 1.149 2014/06/18 15:51:14 brouard
229: Summary: Some fixes in parameter files errors
230: Author: Nicolas Brouard
231:
1.149 brouard 232: Revision 1.148 2014/06/17 17:38:48 brouard
233: Summary: Nothing new
234: Author: Brouard
235:
236: Just a new packaging for OS/X version 0.98nS
237:
1.148 brouard 238: Revision 1.147 2014/06/16 10:33:11 brouard
239: *** empty log message ***
240:
1.147 brouard 241: Revision 1.146 2014/06/16 10:20:28 brouard
242: Summary: Merge
243: Author: Brouard
244:
245: Merge, before building revised version.
246:
1.146 brouard 247: Revision 1.145 2014/06/10 21:23:15 brouard
248: Summary: Debugging with valgrind
249: Author: Nicolas Brouard
250:
251: Lot of changes in order to output the results with some covariates
252: After the Edimburgh REVES conference 2014, it seems mandatory to
253: improve the code.
254: No more memory valgrind error but a lot has to be done in order to
255: continue the work of splitting the code into subroutines.
256: Also, decodemodel has been improved. Tricode is still not
257: optimal. nbcode should be improved. Documentation has been added in
258: the source code.
259:
1.144 brouard 260: Revision 1.143 2014/01/26 09:45:38 brouard
261: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
262:
263: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
264: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
265:
1.143 brouard 266: Revision 1.142 2014/01/26 03:57:36 brouard
267: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
268:
269: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
270:
1.142 brouard 271: Revision 1.141 2014/01/26 02:42:01 brouard
272: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
273:
1.141 brouard 274: Revision 1.140 2011/09/02 10:37:54 brouard
275: Summary: times.h is ok with mingw32 now.
276:
1.140 brouard 277: Revision 1.139 2010/06/14 07:50:17 brouard
278: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
279: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
280:
1.139 brouard 281: Revision 1.138 2010/04/30 18:19:40 brouard
282: *** empty log message ***
283:
1.138 brouard 284: Revision 1.137 2010/04/29 18:11:38 brouard
285: (Module): Checking covariates for more complex models
286: than V1+V2. A lot of change to be done. Unstable.
287:
1.137 brouard 288: Revision 1.136 2010/04/26 20:30:53 brouard
289: (Module): merging some libgsl code. Fixing computation
290: of likelione (using inter/intrapolation if mle = 0) in order to
291: get same likelihood as if mle=1.
292: Some cleaning of code and comments added.
293:
1.136 brouard 294: Revision 1.135 2009/10/29 15:33:14 brouard
295: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
296:
1.135 brouard 297: Revision 1.134 2009/10/29 13:18:53 brouard
298: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
299:
1.134 brouard 300: Revision 1.133 2009/07/06 10:21:25 brouard
301: just nforces
302:
1.133 brouard 303: Revision 1.132 2009/07/06 08:22:05 brouard
304: Many tings
305:
1.132 brouard 306: Revision 1.131 2009/06/20 16:22:47 brouard
307: Some dimensions resccaled
308:
1.131 brouard 309: Revision 1.130 2009/05/26 06:44:34 brouard
310: (Module): Max Covariate is now set to 20 instead of 8. A
311: lot of cleaning with variables initialized to 0. Trying to make
312: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
313:
1.130 brouard 314: Revision 1.129 2007/08/31 13:49:27 lievre
315: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
316:
1.129 lievre 317: Revision 1.128 2006/06/30 13:02:05 brouard
318: (Module): Clarifications on computing e.j
319:
1.128 brouard 320: Revision 1.127 2006/04/28 18:11:50 brouard
321: (Module): Yes the sum of survivors was wrong since
322: imach-114 because nhstepm was no more computed in the age
323: loop. Now we define nhstepma in the age loop.
324: (Module): In order to speed up (in case of numerous covariates) we
325: compute health expectancies (without variances) in a first step
326: and then all the health expectancies with variances or standard
327: deviation (needs data from the Hessian matrices) which slows the
328: computation.
329: In the future we should be able to stop the program is only health
330: expectancies and graph are needed without standard deviations.
331:
1.127 brouard 332: Revision 1.126 2006/04/28 17:23:28 brouard
333: (Module): Yes the sum of survivors was wrong since
334: imach-114 because nhstepm was no more computed in the age
335: loop. Now we define nhstepma in the age loop.
336: Version 0.98h
337:
1.126 brouard 338: Revision 1.125 2006/04/04 15:20:31 lievre
339: Errors in calculation of health expectancies. Age was not initialized.
340: Forecasting file added.
341:
342: Revision 1.124 2006/03/22 17:13:53 lievre
343: Parameters are printed with %lf instead of %f (more numbers after the comma).
344: The log-likelihood is printed in the log file
345:
346: Revision 1.123 2006/03/20 10:52:43 brouard
347: * imach.c (Module): <title> changed, corresponds to .htm file
348: name. <head> headers where missing.
349:
350: * imach.c (Module): Weights can have a decimal point as for
351: English (a comma might work with a correct LC_NUMERIC environment,
352: otherwise the weight is truncated).
353: Modification of warning when the covariates values are not 0 or
354: 1.
355: Version 0.98g
356:
357: Revision 1.122 2006/03/20 09:45:41 brouard
358: (Module): Weights can have a decimal point as for
359: English (a comma might work with a correct LC_NUMERIC environment,
360: otherwise the weight is truncated).
361: Modification of warning when the covariates values are not 0 or
362: 1.
363: Version 0.98g
364:
365: Revision 1.121 2006/03/16 17:45:01 lievre
366: * imach.c (Module): Comments concerning covariates added
367:
368: * imach.c (Module): refinements in the computation of lli if
369: status=-2 in order to have more reliable computation if stepm is
370: not 1 month. Version 0.98f
371:
372: Revision 1.120 2006/03/16 15:10:38 lievre
373: (Module): refinements in the computation of lli if
374: status=-2 in order to have more reliable computation if stepm is
375: not 1 month. Version 0.98f
376:
377: Revision 1.119 2006/03/15 17:42:26 brouard
378: (Module): Bug if status = -2, the loglikelihood was
379: computed as likelihood omitting the logarithm. Version O.98e
380:
381: Revision 1.118 2006/03/14 18:20:07 brouard
382: (Module): varevsij Comments added explaining the second
383: table of variances if popbased=1 .
384: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
385: (Module): Function pstamp added
386: (Module): Version 0.98d
387:
388: Revision 1.117 2006/03/14 17:16:22 brouard
389: (Module): varevsij Comments added explaining the second
390: table of variances if popbased=1 .
391: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
392: (Module): Function pstamp added
393: (Module): Version 0.98d
394:
395: Revision 1.116 2006/03/06 10:29:27 brouard
396: (Module): Variance-covariance wrong links and
397: varian-covariance of ej. is needed (Saito).
398:
399: Revision 1.115 2006/02/27 12:17:45 brouard
400: (Module): One freematrix added in mlikeli! 0.98c
401:
402: Revision 1.114 2006/02/26 12:57:58 brouard
403: (Module): Some improvements in processing parameter
404: filename with strsep.
405:
406: Revision 1.113 2006/02/24 14:20:24 brouard
407: (Module): Memory leaks checks with valgrind and:
408: datafile was not closed, some imatrix were not freed and on matrix
409: allocation too.
410:
411: Revision 1.112 2006/01/30 09:55:26 brouard
412: (Module): Back to gnuplot.exe instead of wgnuplot.exe
413:
414: Revision 1.111 2006/01/25 20:38:18 brouard
415: (Module): Lots of cleaning and bugs added (Gompertz)
416: (Module): Comments can be added in data file. Missing date values
417: can be a simple dot '.'.
418:
419: Revision 1.110 2006/01/25 00:51:50 brouard
420: (Module): Lots of cleaning and bugs added (Gompertz)
421:
422: Revision 1.109 2006/01/24 19:37:15 brouard
423: (Module): Comments (lines starting with a #) are allowed in data.
424:
425: Revision 1.108 2006/01/19 18:05:42 lievre
426: Gnuplot problem appeared...
427: To be fixed
428:
429: Revision 1.107 2006/01/19 16:20:37 brouard
430: Test existence of gnuplot in imach path
431:
432: Revision 1.106 2006/01/19 13:24:36 brouard
433: Some cleaning and links added in html output
434:
435: Revision 1.105 2006/01/05 20:23:19 lievre
436: *** empty log message ***
437:
438: Revision 1.104 2005/09/30 16:11:43 lievre
439: (Module): sump fixed, loop imx fixed, and simplifications.
440: (Module): If the status is missing at the last wave but we know
441: that the person is alive, then we can code his/her status as -2
442: (instead of missing=-1 in earlier versions) and his/her
443: contributions to the likelihood is 1 - Prob of dying from last
444: health status (= 1-p13= p11+p12 in the easiest case of somebody in
445: the healthy state at last known wave). Version is 0.98
446:
447: Revision 1.103 2005/09/30 15:54:49 lievre
448: (Module): sump fixed, loop imx fixed, and simplifications.
449:
450: Revision 1.102 2004/09/15 17:31:30 brouard
451: Add the possibility to read data file including tab characters.
452:
453: Revision 1.101 2004/09/15 10:38:38 brouard
454: Fix on curr_time
455:
456: Revision 1.100 2004/07/12 18:29:06 brouard
457: Add version for Mac OS X. Just define UNIX in Makefile
458:
459: Revision 1.99 2004/06/05 08:57:40 brouard
460: *** empty log message ***
461:
462: Revision 1.98 2004/05/16 15:05:56 brouard
463: New version 0.97 . First attempt to estimate force of mortality
464: directly from the data i.e. without the need of knowing the health
465: state at each age, but using a Gompertz model: log u =a + b*age .
466: This is the basic analysis of mortality and should be done before any
467: other analysis, in order to test if the mortality estimated from the
468: cross-longitudinal survey is different from the mortality estimated
469: from other sources like vital statistic data.
470:
471: The same imach parameter file can be used but the option for mle should be -3.
472:
1.133 brouard 473: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 474: former routines in order to include the new code within the former code.
475:
476: The output is very simple: only an estimate of the intercept and of
477: the slope with 95% confident intervals.
478:
479: Current limitations:
480: A) Even if you enter covariates, i.e. with the
481: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
482: B) There is no computation of Life Expectancy nor Life Table.
483:
484: Revision 1.97 2004/02/20 13:25:42 lievre
485: Version 0.96d. Population forecasting command line is (temporarily)
486: suppressed.
487:
488: Revision 1.96 2003/07/15 15:38:55 brouard
489: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
490: rewritten within the same printf. Workaround: many printfs.
491:
492: Revision 1.95 2003/07/08 07:54:34 brouard
493: * imach.c (Repository):
494: (Repository): Using imachwizard code to output a more meaningful covariance
495: matrix (cov(a12,c31) instead of numbers.
496:
497: Revision 1.94 2003/06/27 13:00:02 brouard
498: Just cleaning
499:
500: Revision 1.93 2003/06/25 16:33:55 brouard
501: (Module): On windows (cygwin) function asctime_r doesn't
502: exist so I changed back to asctime which exists.
503: (Module): Version 0.96b
504:
505: Revision 1.92 2003/06/25 16:30:45 brouard
506: (Module): On windows (cygwin) function asctime_r doesn't
507: exist so I changed back to asctime which exists.
508:
509: Revision 1.91 2003/06/25 15:30:29 brouard
510: * imach.c (Repository): Duplicated warning errors corrected.
511: (Repository): Elapsed time after each iteration is now output. It
512: helps to forecast when convergence will be reached. Elapsed time
513: is stamped in powell. We created a new html file for the graphs
514: concerning matrix of covariance. It has extension -cov.htm.
515:
516: Revision 1.90 2003/06/24 12:34:15 brouard
517: (Module): Some bugs corrected for windows. Also, when
518: mle=-1 a template is output in file "or"mypar.txt with the design
519: of the covariance matrix to be input.
520:
521: Revision 1.89 2003/06/24 12:30:52 brouard
522: (Module): Some bugs corrected for windows. Also, when
523: mle=-1 a template is output in file "or"mypar.txt with the design
524: of the covariance matrix to be input.
525:
526: Revision 1.88 2003/06/23 17:54:56 brouard
527: * 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.
528:
529: Revision 1.87 2003/06/18 12:26:01 brouard
530: Version 0.96
531:
532: Revision 1.86 2003/06/17 20:04:08 brouard
533: (Module): Change position of html and gnuplot routines and added
534: routine fileappend.
535:
536: Revision 1.85 2003/06/17 13:12:43 brouard
537: * imach.c (Repository): Check when date of death was earlier that
538: current date of interview. It may happen when the death was just
539: prior to the death. In this case, dh was negative and likelihood
540: was wrong (infinity). We still send an "Error" but patch by
541: assuming that the date of death was just one stepm after the
542: interview.
543: (Repository): Because some people have very long ID (first column)
544: we changed int to long in num[] and we added a new lvector for
545: memory allocation. But we also truncated to 8 characters (left
546: truncation)
547: (Repository): No more line truncation errors.
548:
549: Revision 1.84 2003/06/13 21:44:43 brouard
550: * imach.c (Repository): Replace "freqsummary" at a correct
551: place. It differs from routine "prevalence" which may be called
552: many times. Probs is memory consuming and must be used with
553: parcimony.
554: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
555:
556: Revision 1.83 2003/06/10 13:39:11 lievre
557: *** empty log message ***
558:
559: Revision 1.82 2003/06/05 15:57:20 brouard
560: Add log in imach.c and fullversion number is now printed.
561:
562: */
563: /*
564: Interpolated Markov Chain
565:
566: Short summary of the programme:
567:
568: This program computes Healthy Life Expectancies from
569: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
570: first survey ("cross") where individuals from different ages are
571: interviewed on their health status or degree of disability (in the
572: case of a health survey which is our main interest) -2- at least a
573: second wave of interviews ("longitudinal") which measure each change
574: (if any) in individual health status. Health expectancies are
575: computed from the time spent in each health state according to a
576: model. More health states you consider, more time is necessary to reach the
577: Maximum Likelihood of the parameters involved in the model. The
578: simplest model is the multinomial logistic model where pij is the
579: probability to be observed in state j at the second wave
580: conditional to be observed in state i at the first wave. Therefore
581: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
582: 'age' is age and 'sex' is a covariate. If you want to have a more
583: complex model than "constant and age", you should modify the program
584: where the markup *Covariates have to be included here again* invites
585: you to do it. More covariates you add, slower the
586: convergence.
587:
588: The advantage of this computer programme, compared to a simple
589: multinomial logistic model, is clear when the delay between waves is not
590: identical for each individual. Also, if a individual missed an
591: intermediate interview, the information is lost, but taken into
592: account using an interpolation or extrapolation.
593:
594: hPijx is the probability to be observed in state i at age x+h
595: conditional to the observed state i at age x. The delay 'h' can be
596: split into an exact number (nh*stepm) of unobserved intermediate
597: states. This elementary transition (by month, quarter,
598: semester or year) is modelled as a multinomial logistic. The hPx
599: matrix is simply the matrix product of nh*stepm elementary matrices
600: and the contribution of each individual to the likelihood is simply
601: hPijx.
602:
603: Also this programme outputs the covariance matrix of the parameters but also
604: of the life expectancies. It also computes the period (stable) prevalence.
605:
1.133 brouard 606: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
607: Institut national d'études démographiques, Paris.
1.126 brouard 608: This software have been partly granted by Euro-REVES, a concerted action
609: from the European Union.
610: It is copyrighted identically to a GNU software product, ie programme and
611: software can be distributed freely for non commercial use. Latest version
612: can be accessed at http://euroreves.ined.fr/imach .
613:
614: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
615: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
616:
617: **********************************************************************/
618: /*
619: main
620: read parameterfile
621: read datafile
622: concatwav
623: freqsummary
624: if (mle >= 1)
625: mlikeli
626: print results files
627: if mle==1
628: computes hessian
629: read end of parameter file: agemin, agemax, bage, fage, estepm
630: begin-prev-date,...
631: open gnuplot file
632: open html file
1.145 brouard 633: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
634: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
635: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
636: freexexit2 possible for memory heap.
637:
638: h Pij x | pij_nom ficrestpij
639: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
640: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
641: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
642:
643: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
644: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
645: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
646: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
647: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
648:
1.126 brouard 649: forecasting if prevfcast==1 prevforecast call prevalence()
650: health expectancies
651: Variance-covariance of DFLE
652: prevalence()
653: movingaverage()
654: varevsij()
655: if popbased==1 varevsij(,popbased)
656: total life expectancies
657: Variance of period (stable) prevalence
658: end
659: */
660:
1.187 brouard 661: /* #define DEBUG */
662: /* #define DEBUGBRENT */
1.203 brouard 663: /* #define DEBUGLINMIN */
664: /* #define DEBUGHESS */
665: #define DEBUGHESSIJ
666: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 667: #define POWELL /* Instead of NLOPT */
1.192 brouard 668: #define POWELLF1F3 /* Skip test */
1.186 brouard 669: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
670: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 671:
672: #include <math.h>
673: #include <stdio.h>
674: #include <stdlib.h>
675: #include <string.h>
1.159 brouard 676:
677: #ifdef _WIN32
678: #include <io.h>
1.172 brouard 679: #include <windows.h>
680: #include <tchar.h>
1.159 brouard 681: #else
1.126 brouard 682: #include <unistd.h>
1.159 brouard 683: #endif
1.126 brouard 684:
685: #include <limits.h>
686: #include <sys/types.h>
1.171 brouard 687:
688: #if defined(__GNUC__)
689: #include <sys/utsname.h> /* Doesn't work on Windows */
690: #endif
691:
1.126 brouard 692: #include <sys/stat.h>
693: #include <errno.h>
1.159 brouard 694: /* extern int errno; */
1.126 brouard 695:
1.157 brouard 696: /* #ifdef LINUX */
697: /* #include <time.h> */
698: /* #include "timeval.h" */
699: /* #else */
700: /* #include <sys/time.h> */
701: /* #endif */
702:
1.126 brouard 703: #include <time.h>
704:
1.136 brouard 705: #ifdef GSL
706: #include <gsl/gsl_errno.h>
707: #include <gsl/gsl_multimin.h>
708: #endif
709:
1.167 brouard 710:
1.162 brouard 711: #ifdef NLOPT
712: #include <nlopt.h>
713: typedef struct {
714: double (* function)(double [] );
715: } myfunc_data ;
716: #endif
717:
1.126 brouard 718: /* #include <libintl.h> */
719: /* #define _(String) gettext (String) */
720:
1.141 brouard 721: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 722:
723: #define GNUPLOTPROGRAM "gnuplot"
724: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
725: #define FILENAMELENGTH 132
726:
727: #define GLOCK_ERROR_NOPATH -1 /* empty path */
728: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
729:
1.144 brouard 730: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
731: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 732:
733: #define NINTERVMAX 8
1.144 brouard 734: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
735: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
736: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 737: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 738: #define MAXN 20000
1.144 brouard 739: #define YEARM 12. /**< Number of months per year */
1.126 brouard 740: #define AGESUP 130
741: #define AGEBASE 40
1.194 brouard 742: #define AGEOVERFLOW 1.e20
1.164 brouard 743: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 744: #ifdef _WIN32
745: #define DIRSEPARATOR '\\'
746: #define CHARSEPARATOR "\\"
747: #define ODIRSEPARATOR '/'
748: #else
1.126 brouard 749: #define DIRSEPARATOR '/'
750: #define CHARSEPARATOR "/"
751: #define ODIRSEPARATOR '\\'
752: #endif
753:
1.206 ! brouard 754: /* $Id: imach.c,v 1.205 2015/10/23 15:50:53 brouard Exp $ */
1.126 brouard 755: /* $State: Exp $ */
1.196 brouard 756: #include "version.h"
757: char version[]=__IMACH_VERSION__;
1.204 brouard 758: 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";
1.206 ! brouard 759: char fullversion[]="$Revision: 1.205 $ $Date: 2015/10/23 15:50:53 $";
1.126 brouard 760: char strstart[80];
761: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 762: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 763: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 764: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
765: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
766: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
767: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
768: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
769: int cptcovprodnoage=0; /**< Number of covariate products without age */
770: int cptcoveff=0; /* Total number of covariates to vary for printing results */
771: int cptcov=0; /* Working variable */
1.126 brouard 772: int npar=NPARMAX;
773: int nlstate=2; /* Number of live states */
774: int ndeath=1; /* Number of dead states */
1.130 brouard 775: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 776: int popbased=0;
777:
778: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 779: int maxwav=0; /* Maxim number of waves */
780: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
781: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
782: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 783: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 784: int mle=1, weightopt=0;
1.126 brouard 785: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
786: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
787: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
788: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 789: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 790: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 791: double **matprod2(); /* test */
1.126 brouard 792: double **oldm, **newm, **savm; /* Working pointers to matrices */
793: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 794: /*FILE *fic ; */ /* Used in readdata only */
795: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 796: FILE *ficlog, *ficrespow;
1.130 brouard 797: int globpr=0; /* Global variable for printing or not */
1.126 brouard 798: double fretone; /* Only one call to likelihood */
1.130 brouard 799: long ipmx=0; /* Number of contributions */
1.126 brouard 800: double sw; /* Sum of weights */
801: char filerespow[FILENAMELENGTH];
802: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
803: FILE *ficresilk;
804: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
805: FILE *ficresprobmorprev;
806: FILE *fichtm, *fichtmcov; /* Html File */
807: FILE *ficreseij;
808: char filerese[FILENAMELENGTH];
809: FILE *ficresstdeij;
810: char fileresstde[FILENAMELENGTH];
811: FILE *ficrescveij;
812: char filerescve[FILENAMELENGTH];
813: FILE *ficresvij;
814: char fileresv[FILENAMELENGTH];
815: FILE *ficresvpl;
816: char fileresvpl[FILENAMELENGTH];
817: char title[MAXLINE];
818: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
819: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
820: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
821: char command[FILENAMELENGTH];
822: int outcmd=0;
823:
824: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 825: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 826: char filelog[FILENAMELENGTH]; /* Log file */
827: char filerest[FILENAMELENGTH];
828: char fileregp[FILENAMELENGTH];
829: char popfile[FILENAMELENGTH];
830:
831: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
832:
1.157 brouard 833: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
834: /* struct timezone tzp; */
835: /* extern int gettimeofday(); */
836: struct tm tml, *gmtime(), *localtime();
837:
838: extern time_t time();
839:
840: struct tm start_time, end_time, curr_time, last_time, forecast_time;
841: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
842: struct tm tm;
843:
1.126 brouard 844: char strcurr[80], strfor[80];
845:
846: char *endptr;
847: long lval;
848: double dval;
849:
850: #define NR_END 1
851: #define FREE_ARG char*
852: #define FTOL 1.0e-10
853:
854: #define NRANSI
855: #define ITMAX 200
856:
857: #define TOL 2.0e-4
858:
859: #define CGOLD 0.3819660
860: #define ZEPS 1.0e-10
861: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
862:
863: #define GOLD 1.618034
864: #define GLIMIT 100.0
865: #define TINY 1.0e-20
866:
867: static double maxarg1,maxarg2;
868: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
869: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
870:
871: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
872: #define rint(a) floor(a+0.5)
1.166 brouard 873: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 874: #define mytinydouble 1.0e-16
1.166 brouard 875: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
876: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
877: /* static double dsqrarg; */
878: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 879: static double sqrarg;
880: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
881: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
882: int agegomp= AGEGOMP;
883:
884: int imx;
885: int stepm=1;
886: /* Stepm, step in month: minimum step interpolation*/
887:
888: int estepm;
889: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
890:
891: int m,nb;
892: long *num;
1.197 brouard 893: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 894: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
895: covariate for which somebody answered excluding
896: undefined. Usually 2: 0 and 1. */
897: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
898: covariate for which somebody answered including
899: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 900: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
901: double **pmmij, ***probs;
902: double *ageexmed,*agecens;
903: double dateintmean=0;
904:
905: double *weight;
906: int **s; /* Status */
1.141 brouard 907: double *agedc;
1.145 brouard 908: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 909: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 910: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 911: double idx;
912: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 913: int *Tage;
1.145 brouard 914: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 915: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 916: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 917: double *lsurv, *lpop, *tpop;
918:
1.143 brouard 919: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
920: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 921:
922: /**************** split *************************/
923: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
924: {
925: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
926: the name of the file (name), its extension only (ext) and its first part of the name (finame)
927: */
928: char *ss; /* pointer */
1.186 brouard 929: int l1=0, l2=0; /* length counters */
1.126 brouard 930:
931: l1 = strlen(path ); /* length of path */
932: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
933: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
934: if ( ss == NULL ) { /* no directory, so determine current directory */
935: strcpy( name, path ); /* we got the fullname name because no directory */
936: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
937: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
938: /* get current working directory */
939: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 940: #ifdef WIN32
941: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
942: #else
943: if (getcwd(dirc, FILENAME_MAX) == NULL) {
944: #endif
1.126 brouard 945: return( GLOCK_ERROR_GETCWD );
946: }
947: /* got dirc from getcwd*/
948: printf(" DIRC = %s \n",dirc);
1.205 brouard 949: } else { /* strip directory from path */
1.126 brouard 950: ss++; /* after this, the filename */
951: l2 = strlen( ss ); /* length of filename */
952: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
953: strcpy( name, ss ); /* save file name */
954: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 955: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 956: printf(" DIRC2 = %s \n",dirc);
957: }
958: /* We add a separator at the end of dirc if not exists */
959: l1 = strlen( dirc ); /* length of directory */
960: if( dirc[l1-1] != DIRSEPARATOR ){
961: dirc[l1] = DIRSEPARATOR;
962: dirc[l1+1] = 0;
963: printf(" DIRC3 = %s \n",dirc);
964: }
965: ss = strrchr( name, '.' ); /* find last / */
966: if (ss >0){
967: ss++;
968: strcpy(ext,ss); /* save extension */
969: l1= strlen( name);
970: l2= strlen(ss)+1;
971: strncpy( finame, name, l1-l2);
972: finame[l1-l2]= 0;
973: }
974:
975: return( 0 ); /* we're done */
976: }
977:
978:
979: /******************************************/
980:
981: void replace_back_to_slash(char *s, char*t)
982: {
983: int i;
984: int lg=0;
985: i=0;
986: lg=strlen(t);
987: for(i=0; i<= lg; i++) {
988: (s[i] = t[i]);
989: if (t[i]== '\\') s[i]='/';
990: }
991: }
992:
1.132 brouard 993: char *trimbb(char *out, char *in)
1.137 brouard 994: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 995: char *s;
996: s=out;
997: while (*in != '\0'){
1.137 brouard 998: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 999: in++;
1000: }
1001: *out++ = *in++;
1002: }
1003: *out='\0';
1004: return s;
1005: }
1006:
1.187 brouard 1007: /* char *substrchaine(char *out, char *in, char *chain) */
1008: /* { */
1009: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1010: /* char *s, *t; */
1011: /* t=in;s=out; */
1012: /* while ((*in != *chain) && (*in != '\0')){ */
1013: /* *out++ = *in++; */
1014: /* } */
1015:
1016: /* /\* *in matches *chain *\/ */
1017: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1018: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1019: /* } */
1020: /* in--; chain--; */
1021: /* while ( (*in != '\0')){ */
1022: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1023: /* *out++ = *in++; */
1024: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1025: /* } */
1026: /* *out='\0'; */
1027: /* out=s; */
1028: /* return out; */
1029: /* } */
1030: char *substrchaine(char *out, char *in, char *chain)
1031: {
1032: /* Substract chain 'chain' from 'in', return and output 'out' */
1033: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1034:
1035: char *strloc;
1036:
1037: strcpy (out, in);
1038: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1039: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1040: if(strloc != NULL){
1041: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1042: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1043: /* strcpy (strloc, strloc +strlen(chain));*/
1044: }
1045: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1046: return out;
1047: }
1048:
1049:
1.145 brouard 1050: char *cutl(char *blocc, char *alocc, char *in, char occ)
1051: {
1.187 brouard 1052: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1053: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1054: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1055: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1056: */
1.160 brouard 1057: char *s, *t;
1.145 brouard 1058: t=in;s=in;
1059: while ((*in != occ) && (*in != '\0')){
1060: *alocc++ = *in++;
1061: }
1062: if( *in == occ){
1063: *(alocc)='\0';
1064: s=++in;
1065: }
1066:
1067: if (s == t) {/* occ not found */
1068: *(alocc-(in-s))='\0';
1069: in=s;
1070: }
1071: while ( *in != '\0'){
1072: *blocc++ = *in++;
1073: }
1074:
1075: *blocc='\0';
1076: return t;
1077: }
1.137 brouard 1078: char *cutv(char *blocc, char *alocc, char *in, char occ)
1079: {
1.187 brouard 1080: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1081: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1082: gives blocc="abcdef2ghi" and alocc="j".
1083: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1084: */
1085: char *s, *t;
1086: t=in;s=in;
1087: while (*in != '\0'){
1088: while( *in == occ){
1089: *blocc++ = *in++;
1090: s=in;
1091: }
1092: *blocc++ = *in++;
1093: }
1094: if (s == t) /* occ not found */
1095: *(blocc-(in-s))='\0';
1096: else
1097: *(blocc-(in-s)-1)='\0';
1098: in=s;
1099: while ( *in != '\0'){
1100: *alocc++ = *in++;
1101: }
1102:
1103: *alocc='\0';
1104: return s;
1105: }
1106:
1.126 brouard 1107: int nbocc(char *s, char occ)
1108: {
1109: int i,j=0;
1110: int lg=20;
1111: i=0;
1112: lg=strlen(s);
1113: for(i=0; i<= lg; i++) {
1114: if (s[i] == occ ) j++;
1115: }
1116: return j;
1117: }
1118:
1.137 brouard 1119: /* void cutv(char *u,char *v, char*t, char occ) */
1120: /* { */
1121: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1122: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1123: /* gives u="abcdef2ghi" and v="j" *\/ */
1124: /* int i,lg,j,p=0; */
1125: /* i=0; */
1126: /* lg=strlen(t); */
1127: /* for(j=0; j<=lg-1; j++) { */
1128: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1129: /* } */
1.126 brouard 1130:
1.137 brouard 1131: /* for(j=0; j<p; j++) { */
1132: /* (u[j] = t[j]); */
1133: /* } */
1134: /* u[p]='\0'; */
1.126 brouard 1135:
1.137 brouard 1136: /* for(j=0; j<= lg; j++) { */
1137: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1138: /* } */
1139: /* } */
1.126 brouard 1140:
1.160 brouard 1141: #ifdef _WIN32
1142: char * strsep(char **pp, const char *delim)
1143: {
1144: char *p, *q;
1145:
1146: if ((p = *pp) == NULL)
1147: return 0;
1148: if ((q = strpbrk (p, delim)) != NULL)
1149: {
1150: *pp = q + 1;
1151: *q = '\0';
1152: }
1153: else
1154: *pp = 0;
1155: return p;
1156: }
1157: #endif
1158:
1.126 brouard 1159: /********************** nrerror ********************/
1160:
1161: void nrerror(char error_text[])
1162: {
1163: fprintf(stderr,"ERREUR ...\n");
1164: fprintf(stderr,"%s\n",error_text);
1165: exit(EXIT_FAILURE);
1166: }
1167: /*********************** vector *******************/
1168: double *vector(int nl, int nh)
1169: {
1170: double *v;
1171: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1172: if (!v) nrerror("allocation failure in vector");
1173: return v-nl+NR_END;
1174: }
1175:
1176: /************************ free vector ******************/
1177: void free_vector(double*v, int nl, int nh)
1178: {
1179: free((FREE_ARG)(v+nl-NR_END));
1180: }
1181:
1182: /************************ivector *******************************/
1183: int *ivector(long nl,long nh)
1184: {
1185: int *v;
1186: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1187: if (!v) nrerror("allocation failure in ivector");
1188: return v-nl+NR_END;
1189: }
1190:
1191: /******************free ivector **************************/
1192: void free_ivector(int *v, long nl, long nh)
1193: {
1194: free((FREE_ARG)(v+nl-NR_END));
1195: }
1196:
1197: /************************lvector *******************************/
1198: long *lvector(long nl,long nh)
1199: {
1200: long *v;
1201: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1202: if (!v) nrerror("allocation failure in ivector");
1203: return v-nl+NR_END;
1204: }
1205:
1206: /******************free lvector **************************/
1207: void free_lvector(long *v, long nl, long nh)
1208: {
1209: free((FREE_ARG)(v+nl-NR_END));
1210: }
1211:
1212: /******************* imatrix *******************************/
1213: int **imatrix(long nrl, long nrh, long ncl, long nch)
1214: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1215: {
1216: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1217: int **m;
1218:
1219: /* allocate pointers to rows */
1220: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1221: if (!m) nrerror("allocation failure 1 in matrix()");
1222: m += NR_END;
1223: m -= nrl;
1224:
1225:
1226: /* allocate rows and set pointers to them */
1227: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1228: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1229: m[nrl] += NR_END;
1230: m[nrl] -= ncl;
1231:
1232: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1233:
1234: /* return pointer to array of pointers to rows */
1235: return m;
1236: }
1237:
1238: /****************** free_imatrix *************************/
1239: void free_imatrix(m,nrl,nrh,ncl,nch)
1240: int **m;
1241: long nch,ncl,nrh,nrl;
1242: /* free an int matrix allocated by imatrix() */
1243: {
1244: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1245: free((FREE_ARG) (m+nrl-NR_END));
1246: }
1247:
1248: /******************* matrix *******************************/
1249: double **matrix(long nrl, long nrh, long ncl, long nch)
1250: {
1251: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1252: double **m;
1253:
1254: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1255: if (!m) nrerror("allocation failure 1 in matrix()");
1256: m += NR_END;
1257: m -= nrl;
1258:
1259: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1260: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1261: m[nrl] += NR_END;
1262: m[nrl] -= ncl;
1263:
1264: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1265: return m;
1.145 brouard 1266: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1267: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1268: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1269: */
1270: }
1271:
1272: /*************************free matrix ************************/
1273: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1274: {
1275: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1276: free((FREE_ARG)(m+nrl-NR_END));
1277: }
1278:
1279: /******************* ma3x *******************************/
1280: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1281: {
1282: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1283: double ***m;
1284:
1285: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1286: if (!m) nrerror("allocation failure 1 in matrix()");
1287: m += NR_END;
1288: m -= nrl;
1289:
1290: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1291: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1292: m[nrl] += NR_END;
1293: m[nrl] -= ncl;
1294:
1295: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1296:
1297: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1298: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1299: m[nrl][ncl] += NR_END;
1300: m[nrl][ncl] -= nll;
1301: for (j=ncl+1; j<=nch; j++)
1302: m[nrl][j]=m[nrl][j-1]+nlay;
1303:
1304: for (i=nrl+1; i<=nrh; i++) {
1305: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1306: for (j=ncl+1; j<=nch; j++)
1307: m[i][j]=m[i][j-1]+nlay;
1308: }
1309: return m;
1310: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1311: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1312: */
1313: }
1314:
1315: /*************************free ma3x ************************/
1316: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1317: {
1318: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1319: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1320: free((FREE_ARG)(m+nrl-NR_END));
1321: }
1322:
1323: /*************** function subdirf ***********/
1324: char *subdirf(char fileres[])
1325: {
1326: /* Caution optionfilefiname is hidden */
1327: strcpy(tmpout,optionfilefiname);
1328: strcat(tmpout,"/"); /* Add to the right */
1329: strcat(tmpout,fileres);
1330: return tmpout;
1331: }
1332:
1333: /*************** function subdirf2 ***********/
1334: char *subdirf2(char fileres[], char *preop)
1335: {
1336:
1337: /* Caution optionfilefiname is hidden */
1338: strcpy(tmpout,optionfilefiname);
1339: strcat(tmpout,"/");
1340: strcat(tmpout,preop);
1341: strcat(tmpout,fileres);
1342: return tmpout;
1343: }
1344:
1345: /*************** function subdirf3 ***********/
1346: char *subdirf3(char fileres[], char *preop, char *preop2)
1347: {
1348:
1349: /* Caution optionfilefiname is hidden */
1350: strcpy(tmpout,optionfilefiname);
1351: strcat(tmpout,"/");
1352: strcat(tmpout,preop);
1353: strcat(tmpout,preop2);
1354: strcat(tmpout,fileres);
1355: return tmpout;
1356: }
1357:
1.162 brouard 1358: char *asc_diff_time(long time_sec, char ascdiff[])
1359: {
1360: long sec_left, days, hours, minutes;
1361: days = (time_sec) / (60*60*24);
1362: sec_left = (time_sec) % (60*60*24);
1363: hours = (sec_left) / (60*60) ;
1364: sec_left = (sec_left) %(60*60);
1365: minutes = (sec_left) /60;
1366: sec_left = (sec_left) % (60);
1367: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1368: return ascdiff;
1369: }
1370:
1.126 brouard 1371: /***************** f1dim *************************/
1372: extern int ncom;
1373: extern double *pcom,*xicom;
1374: extern double (*nrfunc)(double []);
1375:
1376: double f1dim(double x)
1377: {
1378: int j;
1379: double f;
1380: double *xt;
1381:
1382: xt=vector(1,ncom);
1383: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1384: f=(*nrfunc)(xt);
1385: free_vector(xt,1,ncom);
1386: return f;
1387: }
1388:
1389: /*****************brent *************************/
1390: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1391: {
1392: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1393: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1394: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1395: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1396: * returned function value.
1397: */
1.126 brouard 1398: int iter;
1399: double a,b,d,etemp;
1.159 brouard 1400: double fu=0,fv,fw,fx;
1.164 brouard 1401: double ftemp=0.;
1.126 brouard 1402: double p,q,r,tol1,tol2,u,v,w,x,xm;
1403: double e=0.0;
1404:
1405: a=(ax < cx ? ax : cx);
1406: b=(ax > cx ? ax : cx);
1407: x=w=v=bx;
1408: fw=fv=fx=(*f)(x);
1409: for (iter=1;iter<=ITMAX;iter++) {
1410: xm=0.5*(a+b);
1411: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1412: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1413: printf(".");fflush(stdout);
1414: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1415: #ifdef DEBUGBRENT
1.126 brouard 1416: 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);
1417: 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);
1418: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1419: #endif
1420: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1421: *xmin=x;
1422: return fx;
1423: }
1424: ftemp=fu;
1425: if (fabs(e) > tol1) {
1426: r=(x-w)*(fx-fv);
1427: q=(x-v)*(fx-fw);
1428: p=(x-v)*q-(x-w)*r;
1429: q=2.0*(q-r);
1430: if (q > 0.0) p = -p;
1431: q=fabs(q);
1432: etemp=e;
1433: e=d;
1434: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1435: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1436: else {
1437: d=p/q;
1438: u=x+d;
1439: if (u-a < tol2 || b-u < tol2)
1440: d=SIGN(tol1,xm-x);
1441: }
1442: } else {
1443: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1444: }
1445: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1446: fu=(*f)(u);
1447: if (fu <= fx) {
1448: if (u >= x) a=x; else b=x;
1449: SHFT(v,w,x,u)
1.183 brouard 1450: SHFT(fv,fw,fx,fu)
1451: } else {
1452: if (u < x) a=u; else b=u;
1453: if (fu <= fw || w == x) {
1454: v=w;
1455: w=u;
1456: fv=fw;
1457: fw=fu;
1458: } else if (fu <= fv || v == x || v == w) {
1459: v=u;
1460: fv=fu;
1461: }
1462: }
1.126 brouard 1463: }
1464: nrerror("Too many iterations in brent");
1465: *xmin=x;
1466: return fx;
1467: }
1468:
1469: /****************** mnbrak ***********************/
1470:
1471: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1472: double (*func)(double))
1.183 brouard 1473: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1474: the downhill direction (defined by the function as evaluated at the initial points) and returns
1475: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1476: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1477: */
1.126 brouard 1478: double ulim,u,r,q, dum;
1479: double fu;
1.187 brouard 1480:
1481: double scale=10.;
1482: int iterscale=0;
1483:
1484: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1485: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1486:
1487:
1488: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1489: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1490: /* *bx = *ax - (*ax - *bx)/scale; */
1491: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1492: /* } */
1493:
1.126 brouard 1494: if (*fb > *fa) {
1495: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1496: SHFT(dum,*fb,*fa,dum)
1497: }
1.126 brouard 1498: *cx=(*bx)+GOLD*(*bx-*ax);
1499: *fc=(*func)(*cx);
1.183 brouard 1500: #ifdef DEBUG
1501: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1502: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1503: #endif
1504: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1505: r=(*bx-*ax)*(*fb-*fc);
1506: q=(*bx-*cx)*(*fb-*fa);
1507: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1508: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1509: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1510: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1511: fu=(*func)(u);
1.163 brouard 1512: #ifdef DEBUG
1513: /* f(x)=A(x-u)**2+f(u) */
1514: double A, fparabu;
1515: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1516: fparabu= *fa - A*(*ax-u)*(*ax-u);
1517: 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);
1518: 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 1519: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1520: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1521: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1522: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1523: #endif
1.184 brouard 1524: #ifdef MNBRAKORIGINAL
1.183 brouard 1525: #else
1.191 brouard 1526: /* if (fu > *fc) { */
1527: /* #ifdef DEBUG */
1528: /* printf("mnbrak4 fu > fc \n"); */
1529: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1530: /* #endif */
1531: /* /\* 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 *\\/ *\/ */
1532: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1533: /* dum=u; /\* Shifting c and u *\/ */
1534: /* u = *cx; */
1535: /* *cx = dum; */
1536: /* dum = fu; */
1537: /* fu = *fc; */
1538: /* *fc =dum; */
1539: /* } else { /\* end *\/ */
1540: /* #ifdef DEBUG */
1541: /* printf("mnbrak3 fu < fc \n"); */
1542: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1543: /* #endif */
1544: /* dum=u; /\* Shifting c and u *\/ */
1545: /* u = *cx; */
1546: /* *cx = dum; */
1547: /* dum = fu; */
1548: /* fu = *fc; */
1549: /* *fc =dum; */
1550: /* } */
1.183 brouard 1551: #ifdef DEBUG
1.191 brouard 1552: printf("mnbrak34 fu < or >= fc \n");
1553: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1554: #endif
1.191 brouard 1555: dum=u; /* Shifting c and u */
1556: u = *cx;
1557: *cx = dum;
1558: dum = fu;
1559: fu = *fc;
1560: *fc =dum;
1.183 brouard 1561: #endif
1.162 brouard 1562: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1563: #ifdef DEBUG
1564: printf("mnbrak2 u after c but before ulim\n");
1565: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1566: #endif
1.126 brouard 1567: fu=(*func)(u);
1568: if (fu < *fc) {
1.183 brouard 1569: #ifdef DEBUG
1570: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1571: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1572: #endif
1.126 brouard 1573: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1574: SHFT(*fb,*fc,fu,(*func)(u))
1575: }
1.162 brouard 1576: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1577: #ifdef DEBUG
1578: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1579: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1580: #endif
1.126 brouard 1581: u=ulim;
1582: fu=(*func)(u);
1.183 brouard 1583: } else { /* u could be left to b (if r > q parabola has a maximum) */
1584: #ifdef DEBUG
1585: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1586: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1587: #endif
1.126 brouard 1588: u=(*cx)+GOLD*(*cx-*bx);
1589: fu=(*func)(u);
1.183 brouard 1590: } /* end tests */
1.126 brouard 1591: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1592: SHFT(*fa,*fb,*fc,fu)
1593: #ifdef DEBUG
1594: 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);
1595: 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);
1596: #endif
1597: } /* 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 1598: }
1599:
1600: /*************** linmin ************************/
1.162 brouard 1601: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1602: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1603: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1604: the value of func at the returned location p . This is actually all accomplished by calling the
1605: routines mnbrak and brent .*/
1.126 brouard 1606: int ncom;
1607: double *pcom,*xicom;
1608: double (*nrfunc)(double []);
1609:
1610: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1611: {
1612: double brent(double ax, double bx, double cx,
1613: double (*f)(double), double tol, double *xmin);
1614: double f1dim(double x);
1615: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1616: double *fc, double (*func)(double));
1617: int j;
1618: double xx,xmin,bx,ax;
1619: double fx,fb,fa;
1.187 brouard 1620:
1.203 brouard 1621: #ifdef LINMINORIGINAL
1622: #else
1623: double scale=10., axs, xxs; /* Scale added for infinity */
1624: #endif
1625:
1.126 brouard 1626: ncom=n;
1627: pcom=vector(1,n);
1628: xicom=vector(1,n);
1629: nrfunc=func;
1630: for (j=1;j<=n;j++) {
1631: pcom[j]=p[j];
1.202 brouard 1632: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1633: }
1.187 brouard 1634:
1.203 brouard 1635: #ifdef LINMINORIGINAL
1636: xx=1.;
1637: #else
1638: axs=0.0;
1639: xxs=1.;
1640: do{
1641: xx= xxs;
1642: #endif
1.187 brouard 1643: ax=0.;
1644: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1645: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1646: /* 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)) */
1647: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1648: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1649: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1650: /* 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 1651: #ifdef LINMINORIGINAL
1652: #else
1653: if (fx != fx){
1654: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1655: printf("|");
1656: fprintf(ficlog,"|");
1657: #ifdef DEBUGLINMIN
1658: 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);
1659: #endif
1660: }
1661: }while(fx != fx);
1662: #endif
1663:
1.191 brouard 1664: #ifdef DEBUGLINMIN
1665: 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 1666: 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 1667: #endif
1.187 brouard 1668: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1669: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1670: /* fmin = f(p[j] + xmin * xi[j]) */
1671: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1672: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1673: #ifdef DEBUG
1674: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1675: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1676: #endif
1.191 brouard 1677: #ifdef DEBUGLINMIN
1678: printf("linmin end ");
1.202 brouard 1679: fprintf(ficlog,"linmin end ");
1.191 brouard 1680: #endif
1.126 brouard 1681: for (j=1;j<=n;j++) {
1.203 brouard 1682: #ifdef LINMINORIGINAL
1683: xi[j] *= xmin;
1684: #else
1685: #ifdef DEBUGLINMIN
1686: if(xxs <1.0)
1687: printf(" before xi[%d]=%12.8f", j,xi[j]);
1688: #endif
1689: 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) */
1690: #ifdef DEBUGLINMIN
1691: if(xxs <1.0)
1692: 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 );
1693: #endif
1694: #endif
1.187 brouard 1695: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1696: }
1.191 brouard 1697: #ifdef DEBUGLINMIN
1.203 brouard 1698: printf("\n");
1.191 brouard 1699: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1700: 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 1701: for (j=1;j<=n;j++) {
1.202 brouard 1702: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1703: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1704: if(j % ncovmodel == 0){
1.191 brouard 1705: printf("\n");
1.202 brouard 1706: fprintf(ficlog,"\n");
1707: }
1.191 brouard 1708: }
1.203 brouard 1709: #else
1.191 brouard 1710: #endif
1.126 brouard 1711: free_vector(xicom,1,n);
1712: free_vector(pcom,1,n);
1713: }
1714:
1715:
1716: /*************** powell ************************/
1.162 brouard 1717: /*
1718: Minimization of a function func of n variables. Input consists of an initial starting point
1719: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1720: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1721: such that failure to decrease by more than this amount on one iteration signals doneness. On
1722: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1723: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1724: */
1.126 brouard 1725: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1726: double (*func)(double []))
1727: {
1728: void linmin(double p[], double xi[], int n, double *fret,
1729: double (*func)(double []));
1730: int i,ibig,j;
1731: double del,t,*pt,*ptt,*xit;
1.181 brouard 1732: double directest;
1.126 brouard 1733: double fp,fptt;
1734: double *xits;
1735: int niterf, itmp;
1736:
1737: pt=vector(1,n);
1738: ptt=vector(1,n);
1739: xit=vector(1,n);
1740: xits=vector(1,n);
1741: *fret=(*func)(p);
1742: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1743: rcurr_time = time(NULL);
1.126 brouard 1744: for (*iter=1;;++(*iter)) {
1.187 brouard 1745: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1746: ibig=0;
1747: del=0.0;
1.157 brouard 1748: rlast_time=rcurr_time;
1749: /* (void) gettimeofday(&curr_time,&tzp); */
1750: rcurr_time = time(NULL);
1751: curr_time = *localtime(&rcurr_time);
1752: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1753: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1754: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1755: for (i=1;i<=n;i++) {
1.126 brouard 1756: printf(" %d %.12f",i, p[i]);
1757: fprintf(ficlog," %d %.12lf",i, p[i]);
1758: fprintf(ficrespow," %.12lf", p[i]);
1759: }
1760: printf("\n");
1761: fprintf(ficlog,"\n");
1762: fprintf(ficrespow,"\n");fflush(ficrespow);
1763: if(*iter <=3){
1.157 brouard 1764: tml = *localtime(&rcurr_time);
1765: strcpy(strcurr,asctime(&tml));
1766: rforecast_time=rcurr_time;
1.126 brouard 1767: itmp = strlen(strcurr);
1768: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1769: strcurr[itmp-1]='\0';
1.162 brouard 1770: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1771: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1772: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1773: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1774: forecast_time = *localtime(&rforecast_time);
1775: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1776: itmp = strlen(strfor);
1777: if(strfor[itmp-1]=='\n')
1778: strfor[itmp-1]='\0';
1.157 brouard 1779: 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);
1780: 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 1781: }
1782: }
1.187 brouard 1783: for (i=1;i<=n;i++) { /* For each direction i */
1784: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1785: fptt=(*fret);
1786: #ifdef DEBUG
1.203 brouard 1787: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1788: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1789: #endif
1.203 brouard 1790: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1791: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1792: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1793: /* Outputs are fret(new point p) p is updated and xit rescaled */
1794: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1795: /* because that direction will be replaced unless the gain del is small */
1796: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1797: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1798: /* with the new direction. */
1.126 brouard 1799: del=fabs(fptt-(*fret));
1800: ibig=i;
1801: }
1802: #ifdef DEBUG
1803: printf("%d %.12e",i,(*fret));
1804: fprintf(ficlog,"%d %.12e",i,(*fret));
1805: for (j=1;j<=n;j++) {
1806: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1807: printf(" x(%d)=%.12e",j,xit[j]);
1808: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1809: }
1810: for(j=1;j<=n;j++) {
1.162 brouard 1811: printf(" p(%d)=%.12e",j,p[j]);
1812: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1813: }
1814: printf("\n");
1815: fprintf(ficlog,"\n");
1816: #endif
1.187 brouard 1817: } /* end loop on each direction i */
1818: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1819: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1820: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1821: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1822: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1823: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1824: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1825: /* decreased of more than 3.84 */
1826: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1827: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1828: /* By adding 10 parameters more the gain should be 18.31 */
1829:
1830: /* Starting the program with initial values given by a former maximization will simply change */
1831: /* the scales of the directions and the directions, because the are reset to canonical directions */
1832: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1833: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1834: #ifdef DEBUG
1835: int k[2],l;
1836: k[0]=1;
1837: k[1]=-1;
1838: printf("Max: %.12e",(*func)(p));
1839: fprintf(ficlog,"Max: %.12e",(*func)(p));
1840: for (j=1;j<=n;j++) {
1841: printf(" %.12e",p[j]);
1842: fprintf(ficlog," %.12e",p[j]);
1843: }
1844: printf("\n");
1845: fprintf(ficlog,"\n");
1846: for(l=0;l<=1;l++) {
1847: for (j=1;j<=n;j++) {
1848: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1849: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1850: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1851: }
1852: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1853: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1854: }
1855: #endif
1856:
1857:
1858: free_vector(xit,1,n);
1859: free_vector(xits,1,n);
1860: free_vector(ptt,1,n);
1861: free_vector(pt,1,n);
1862: return;
1.192 brouard 1863: } /* enough precision */
1.126 brouard 1864: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1865: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1866: ptt[j]=2.0*p[j]-pt[j];
1867: xit[j]=p[j]-pt[j];
1868: pt[j]=p[j];
1869: }
1.181 brouard 1870: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1871: #ifdef POWELLF1F3
1872: #else
1.161 brouard 1873: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1874: #endif
1.162 brouard 1875: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1876: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1877: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1878: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1879: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1880: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1881: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1882: #ifdef NRCORIGINAL
1883: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1884: #else
1885: 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 1886: t= t- del*SQR(fp-fptt);
1.183 brouard 1887: #endif
1.202 brouard 1888: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1889: #ifdef DEBUG
1.181 brouard 1890: 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);
1891: 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 1892: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1893: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1894: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1895: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1896: 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);
1897: 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);
1898: #endif
1.183 brouard 1899: #ifdef POWELLORIGINAL
1900: if (t < 0.0) { /* Then we use it for new direction */
1901: #else
1.182 brouard 1902: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1903: 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 1904: 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 1905: 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 1906: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1907: }
1.181 brouard 1908: if (directest < 0.0) { /* Then we use it for new direction */
1909: #endif
1.191 brouard 1910: #ifdef DEBUGLINMIN
1911: printf("Before linmin in direction P%d-P0\n",n);
1912: for (j=1;j<=n;j++) {
1.202 brouard 1913: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1914: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1915: if(j % ncovmodel == 0){
1.191 brouard 1916: printf("\n");
1.202 brouard 1917: fprintf(ficlog,"\n");
1918: }
1.191 brouard 1919: }
1920: #endif
1.187 brouard 1921: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1922: #ifdef DEBUGLINMIN
1923: for (j=1;j<=n;j++) {
1924: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1925: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1926: if(j % ncovmodel == 0){
1.191 brouard 1927: printf("\n");
1.202 brouard 1928: fprintf(ficlog,"\n");
1929: }
1.191 brouard 1930: }
1931: #endif
1.126 brouard 1932: for (j=1;j<=n;j++) {
1.181 brouard 1933: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1934: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1935: }
1.181 brouard 1936: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1937: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1938:
1.126 brouard 1939: #ifdef DEBUG
1.164 brouard 1940: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1941: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1942: for(j=1;j<=n;j++){
1943: printf(" %.12e",xit[j]);
1944: fprintf(ficlog," %.12e",xit[j]);
1945: }
1946: printf("\n");
1947: fprintf(ficlog,"\n");
1948: #endif
1.192 brouard 1949: } /* end of t or directest negative */
1950: #ifdef POWELLF1F3
1951: #else
1.162 brouard 1952: } /* end if (fptt < fp) */
1.192 brouard 1953: #endif
1954: } /* loop iteration */
1.126 brouard 1955: }
1956:
1957: /**** Prevalence limit (stable or period prevalence) ****************/
1958:
1.203 brouard 1959: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1960: {
1961: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1962: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 ! brouard 1963: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
! 1964: /* Wx is row vector: population in state 1, population in state 2, population dead */
! 1965: /* or prevalence in state 1, prevalence in state 2, 0 */
! 1966: /* newm is the matrix after multiplications, its rows are identical at a factor */
! 1967: /* Initial matrix pimij */
! 1968: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
! 1969: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
! 1970: /* 0, 0 , 1} */
! 1971: /*
! 1972: * and after some iteration: */
! 1973: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
! 1974: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
! 1975: /* 0, 0 , 1} */
! 1976: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
! 1977: /* {0.51571254859325999, 0.4842874514067399, */
! 1978: /* 0.51326036147820708, 0.48673963852179264} */
! 1979: /* If we start from prlim again, prlim tends to a constant matrix */
! 1980:
1.126 brouard 1981: int i, ii,j,k;
1982: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1983: /* double **matprod2(); */ /* test */
1.131 brouard 1984: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1985: double **newm;
1.202 brouard 1986: double agefin, delaymax=100 ; /* Max number of years to converge */
1.203 brouard 1987: int ncvloop=0;
1.169 brouard 1988:
1.126 brouard 1989: for (ii=1;ii<=nlstate+ndeath;ii++)
1990: for (j=1;j<=nlstate+ndeath;j++){
1991: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1992: }
1.169 brouard 1993:
1994: cov[1]=1.;
1995:
1996: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 1997: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 1998: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 1999: ncvloop++;
1.126 brouard 2000: newm=savm;
2001: /* Covariates have to be included here again */
1.138 brouard 2002: cov[2]=agefin;
1.187 brouard 2003: if(nagesqr==1)
2004: cov[3]= agefin*agefin;;
1.138 brouard 2005: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2006: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2007: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2008: /* 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 2009: }
1.186 brouard 2010: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2011: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2012: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2013: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2014: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2015: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2016:
2017: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2018: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2019: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2020: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2021: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2022: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2023:
1.126 brouard 2024: savm=oldm;
2025: oldm=newm;
2026: maxmax=0.;
2027: for(j=1;j<=nlstate;j++){
2028: min=1.;
2029: max=0.;
2030: for(i=1; i<=nlstate; i++) {
2031: sumnew=0;
2032: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2033: prlim[i][j]= newm[i][j]/(1-sumnew);
2034: max=FMAX(max,prlim[i][j]);
2035: min=FMIN(min,prlim[i][j]);
1.206 ! brouard 2036: printf(" age= %d prevalim i=%d, j=%d, prmlim[%d][%d]=%f, agefin=%d max=%f min=%f\n", (int)age, i, j, i, j, prlim[i][j],(int)agefin, max, min);
1.126 brouard 2037: }
1.203 brouard 2038: maxmin=(max-min)/(max+min)*2;
1.126 brouard 2039: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 2040: } /* j loop */
1.203 brouard 2041: *ncvyear= (int)age- (int)agefin;
1.206 ! brouard 2042: printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear);
1.126 brouard 2043: if(maxmax < ftolpl){
1.203 brouard 2044: /* printf("maxmax=%lf maxmin=%lf ncvloop=%ld, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear); */
1.126 brouard 2045: return prlim;
2046: }
1.169 brouard 2047: } /* age loop */
1.203 brouard 2048: printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
2049: Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
2050: /* 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); */
1.169 brouard 2051: return prlim; /* should not reach here */
1.126 brouard 2052: }
2053:
2054: /*************** transition probabilities ***************/
2055:
2056: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2057: {
1.138 brouard 2058: /* According to parameters values stored in x and the covariate's values stored in cov,
2059: computes the probability to be observed in state j being in state i by appying the
2060: model to the ncovmodel covariates (including constant and age).
2061: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2062: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2063: ncth covariate in the global vector x is given by the formula:
2064: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2065: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2066: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2067: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2068: Outputs ps[i][j] the probability to be observed in j being in j according to
2069: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2070: */
2071: double s1, lnpijopii;
1.126 brouard 2072: /*double t34;*/
1.164 brouard 2073: int i,j, nc, ii, jj;
1.126 brouard 2074:
2075: for(i=1; i<= nlstate; i++){
2076: for(j=1; j<i;j++){
1.138 brouard 2077: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2078: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2079: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2080: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2081: }
1.138 brouard 2082: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2083: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2084: }
2085: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2086: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2087: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2088: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2089: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2090: }
1.138 brouard 2091: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2092: }
2093: }
2094:
2095: for(i=1; i<= nlstate; i++){
2096: s1=0;
1.131 brouard 2097: for(j=1; j<i; j++){
1.138 brouard 2098: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2099: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2100: }
2101: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2102: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2103: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2104: }
1.138 brouard 2105: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2106: ps[i][i]=1./(s1+1.);
1.138 brouard 2107: /* Computing other pijs */
1.126 brouard 2108: for(j=1; j<i; j++)
2109: ps[i][j]= exp(ps[i][j])*ps[i][i];
2110: for(j=i+1; j<=nlstate+ndeath; j++)
2111: ps[i][j]= exp(ps[i][j])*ps[i][i];
2112: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2113: } /* end i */
2114:
2115: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2116: for(jj=1; jj<= nlstate+ndeath; jj++){
2117: ps[ii][jj]=0;
2118: ps[ii][ii]=1;
2119: }
2120: }
2121:
1.145 brouard 2122:
2123: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2124: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2125: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2126: /* } */
2127: /* printf("\n "); */
2128: /* } */
2129: /* printf("\n ");printf("%lf ",cov[2]);*/
2130: /*
1.126 brouard 2131: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2132: goto end;*/
2133: return ps;
2134: }
2135:
2136: /**************** Product of 2 matrices ******************/
2137:
1.145 brouard 2138: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2139: {
2140: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2141: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2142: /* in, b, out are matrice of pointers which should have been initialized
2143: before: only the contents of out is modified. The function returns
2144: a pointer to pointers identical to out */
1.145 brouard 2145: int i, j, k;
1.126 brouard 2146: for(i=nrl; i<= nrh; i++)
1.145 brouard 2147: for(k=ncolol; k<=ncoloh; k++){
2148: out[i][k]=0.;
2149: for(j=ncl; j<=nch; j++)
2150: out[i][k] +=in[i][j]*b[j][k];
2151: }
1.126 brouard 2152: return out;
2153: }
2154:
2155:
2156: /************* Higher Matrix Product ***************/
2157:
2158: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2159: {
2160: /* Computes the transition matrix starting at age 'age' over
2161: 'nhstepm*hstepm*stepm' months (i.e. until
2162: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2163: nhstepm*hstepm matrices.
2164: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2165: (typically every 2 years instead of every month which is too big
2166: for the memory).
2167: Model is determined by parameters x and covariates have to be
2168: included manually here.
2169:
2170: */
2171:
2172: int i, j, d, h, k;
1.131 brouard 2173: double **out, cov[NCOVMAX+1];
1.126 brouard 2174: double **newm;
1.187 brouard 2175: double agexact;
1.126 brouard 2176:
2177: /* Hstepm could be zero and should return the unit matrix */
2178: for (i=1;i<=nlstate+ndeath;i++)
2179: for (j=1;j<=nlstate+ndeath;j++){
2180: oldm[i][j]=(i==j ? 1.0 : 0.0);
2181: po[i][j][0]=(i==j ? 1.0 : 0.0);
2182: }
2183: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2184: for(h=1; h <=nhstepm; h++){
2185: for(d=1; d <=hstepm; d++){
2186: newm=savm;
2187: /* Covariates have to be included here again */
2188: cov[1]=1.;
1.187 brouard 2189: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2190: cov[2]=agexact;
2191: if(nagesqr==1)
2192: cov[3]= agexact*agexact;
1.131 brouard 2193: for (k=1; k<=cptcovn;k++)
1.200 brouard 2194: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2195: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2196: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2197: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2198: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2199: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2200: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2201: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2202: /* 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 2203:
2204:
2205: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2206: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2207: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2208: pmij(pmmij,cov,ncovmodel,x,nlstate));
2209: savm=oldm;
2210: oldm=newm;
2211: }
2212: for(i=1; i<=nlstate+ndeath; i++)
2213: for(j=1;j<=nlstate+ndeath;j++) {
2214: po[i][j][h]=newm[i][j];
1.128 brouard 2215: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2216: }
1.128 brouard 2217: /*printf("h=%d ",h);*/
1.126 brouard 2218: } /* end h */
1.128 brouard 2219: /* printf("\n H=%d \n",h); */
1.126 brouard 2220: return po;
2221: }
2222:
1.162 brouard 2223: #ifdef NLOPT
2224: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2225: double fret;
2226: double *xt;
2227: int j;
2228: myfunc_data *d2 = (myfunc_data *) pd;
2229: /* xt = (p1-1); */
2230: xt=vector(1,n);
2231: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2232:
2233: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2234: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2235: printf("Function = %.12lf ",fret);
2236: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2237: printf("\n");
2238: free_vector(xt,1,n);
2239: return fret;
2240: }
2241: #endif
1.126 brouard 2242:
2243: /*************** log-likelihood *************/
2244: double func( double *x)
2245: {
2246: int i, ii, j, k, mi, d, kk;
1.131 brouard 2247: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2248: double **out;
2249: double sw; /* Sum of weights */
2250: double lli; /* Individual log likelihood */
2251: int s1, s2;
2252: double bbh, survp;
2253: long ipmx;
1.187 brouard 2254: double agexact;
1.126 brouard 2255: /*extern weight */
2256: /* We are differentiating ll according to initial status */
2257: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2258: /*for(i=1;i<imx;i++)
2259: printf(" %d\n",s[4][i]);
2260: */
1.162 brouard 2261:
2262: ++countcallfunc;
2263:
1.126 brouard 2264: cov[1]=1.;
2265:
2266: for(k=1; k<=nlstate; k++) ll[k]=0.;
2267:
2268: if(mle==1){
2269: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2270: /* Computes the values of the ncovmodel covariates of the model
2271: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2272: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2273: to be observed in j being in i according to the model.
2274: */
1.145 brouard 2275: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2276: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2277: }
1.137 brouard 2278: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2279: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2280: has been calculated etc */
1.126 brouard 2281: for(mi=1; mi<= wav[i]-1; mi++){
2282: for (ii=1;ii<=nlstate+ndeath;ii++)
2283: for (j=1;j<=nlstate+ndeath;j++){
2284: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2285: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2286: }
2287: for(d=0; d<dh[mi][i]; d++){
2288: newm=savm;
1.187 brouard 2289: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2290: cov[2]=agexact;
2291: if(nagesqr==1)
2292: cov[3]= agexact*agexact;
1.126 brouard 2293: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2294: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2295: }
2296: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2297: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2298: savm=oldm;
2299: oldm=newm;
2300: } /* end mult */
2301:
2302: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2303: /* But now since version 0.9 we anticipate for bias at large stepm.
2304: * If stepm is larger than one month (smallest stepm) and if the exact delay
2305: * (in months) between two waves is not a multiple of stepm, we rounded to
2306: * the nearest (and in case of equal distance, to the lowest) interval but now
2307: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2308: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2309: * probability in order to take into account the bias as a fraction of the way
2310: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2311: * -stepm/2 to stepm/2 .
2312: * For stepm=1 the results are the same as for previous versions of Imach.
2313: * For stepm > 1 the results are less biased than in previous versions.
2314: */
2315: s1=s[mw[mi][i]][i];
2316: s2=s[mw[mi+1][i]][i];
2317: bbh=(double)bh[mi][i]/(double)stepm;
2318: /* bias bh is positive if real duration
2319: * is higher than the multiple of stepm and negative otherwise.
2320: */
2321: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2322: if( s2 > nlstate){
2323: /* i.e. if s2 is a death state and if the date of death is known
2324: then the contribution to the likelihood is the probability to
2325: die between last step unit time and current step unit time,
2326: which is also equal to probability to die before dh
2327: minus probability to die before dh-stepm .
2328: In version up to 0.92 likelihood was computed
2329: as if date of death was unknown. Death was treated as any other
2330: health state: the date of the interview describes the actual state
2331: and not the date of a change in health state. The former idea was
2332: to consider that at each interview the state was recorded
2333: (healthy, disable or death) and IMaCh was corrected; but when we
2334: introduced the exact date of death then we should have modified
2335: the contribution of an exact death to the likelihood. This new
2336: contribution is smaller and very dependent of the step unit
2337: stepm. It is no more the probability to die between last interview
2338: and month of death but the probability to survive from last
2339: interview up to one month before death multiplied by the
2340: probability to die within a month. Thanks to Chris
2341: Jackson for correcting this bug. Former versions increased
2342: mortality artificially. The bad side is that we add another loop
2343: which slows down the processing. The difference can be up to 10%
2344: lower mortality.
2345: */
1.183 brouard 2346: /* If, at the beginning of the maximization mostly, the
2347: cumulative probability or probability to be dead is
2348: constant (ie = 1) over time d, the difference is equal to
2349: 0. out[s1][3] = savm[s1][3]: probability, being at state
2350: s1 at precedent wave, to be dead a month before current
2351: wave is equal to probability, being at state s1 at
2352: precedent wave, to be dead at mont of the current
2353: wave. Then the observed probability (that this person died)
2354: is null according to current estimated parameter. In fact,
2355: it should be very low but not zero otherwise the log go to
2356: infinity.
2357: */
2358: /* #ifdef INFINITYORIGINAL */
2359: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2360: /* #else */
2361: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2362: /* lli=log(mytinydouble); */
2363: /* else */
2364: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2365: /* #endif */
2366: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2367:
2368: } else if (s2==-2) {
2369: for (j=1,survp=0. ; j<=nlstate; j++)
2370: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2371: /*survp += out[s1][j]; */
2372: lli= log(survp);
2373: }
2374:
2375: else if (s2==-4) {
2376: for (j=3,survp=0. ; j<=nlstate; j++)
2377: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2378: lli= log(survp);
2379: }
2380:
2381: else if (s2==-5) {
2382: for (j=1,survp=0. ; j<=2; j++)
2383: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2384: lli= log(survp);
2385: }
2386:
2387: else{
2388: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2389: /* 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 */
2390: }
2391: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2392: /*if(lli ==000.0)*/
2393: /*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); */
2394: ipmx +=1;
2395: sw += weight[i];
2396: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2397: /* if (lli < log(mytinydouble)){ */
2398: /* 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); */
2399: /* 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]); */
2400: /* } */
1.126 brouard 2401: } /* end of wave */
2402: } /* end of individual */
2403: } else if(mle==2){
2404: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2405: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2406: for(mi=1; mi<= wav[i]-1; mi++){
2407: for (ii=1;ii<=nlstate+ndeath;ii++)
2408: for (j=1;j<=nlstate+ndeath;j++){
2409: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2410: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2411: }
2412: for(d=0; d<=dh[mi][i]; d++){
2413: newm=savm;
1.187 brouard 2414: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2415: cov[2]=agexact;
2416: if(nagesqr==1)
2417: cov[3]= agexact*agexact;
1.126 brouard 2418: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2419: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2420: }
2421: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2422: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2423: savm=oldm;
2424: oldm=newm;
2425: } /* end mult */
2426:
2427: s1=s[mw[mi][i]][i];
2428: s2=s[mw[mi+1][i]][i];
2429: bbh=(double)bh[mi][i]/(double)stepm;
2430: 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 */
2431: ipmx +=1;
2432: sw += weight[i];
2433: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2434: } /* end of wave */
2435: } /* end of individual */
2436: } else if(mle==3){ /* exponential inter-extrapolation */
2437: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2438: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2439: for(mi=1; mi<= wav[i]-1; mi++){
2440: for (ii=1;ii<=nlstate+ndeath;ii++)
2441: for (j=1;j<=nlstate+ndeath;j++){
2442: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2443: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2444: }
2445: for(d=0; d<dh[mi][i]; d++){
2446: newm=savm;
1.187 brouard 2447: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2448: cov[2]=agexact;
2449: if(nagesqr==1)
2450: cov[3]= agexact*agexact;
1.126 brouard 2451: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2452: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2453: }
2454: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2455: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2456: savm=oldm;
2457: oldm=newm;
2458: } /* end mult */
2459:
2460: s1=s[mw[mi][i]][i];
2461: s2=s[mw[mi+1][i]][i];
2462: bbh=(double)bh[mi][i]/(double)stepm;
2463: 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 */
2464: ipmx +=1;
2465: sw += weight[i];
2466: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2467: } /* end of wave */
2468: } /* end of individual */
2469: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2470: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2471: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2472: for(mi=1; mi<= wav[i]-1; mi++){
2473: for (ii=1;ii<=nlstate+ndeath;ii++)
2474: for (j=1;j<=nlstate+ndeath;j++){
2475: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2476: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2477: }
2478: for(d=0; d<dh[mi][i]; d++){
2479: newm=savm;
1.187 brouard 2480: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2481: cov[2]=agexact;
2482: if(nagesqr==1)
2483: cov[3]= agexact*agexact;
1.126 brouard 2484: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2485: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2486: }
2487:
2488: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2489: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2490: savm=oldm;
2491: oldm=newm;
2492: } /* end mult */
2493:
2494: s1=s[mw[mi][i]][i];
2495: s2=s[mw[mi+1][i]][i];
2496: if( s2 > nlstate){
2497: lli=log(out[s1][s2] - savm[s1][s2]);
2498: }else{
2499: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2500: }
2501: ipmx +=1;
2502: sw += weight[i];
2503: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2504: /* 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]); */
2505: } /* end of wave */
2506: } /* end of individual */
2507: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2508: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2509: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2510: for(mi=1; mi<= wav[i]-1; mi++){
2511: for (ii=1;ii<=nlstate+ndeath;ii++)
2512: for (j=1;j<=nlstate+ndeath;j++){
2513: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2514: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2515: }
2516: for(d=0; d<dh[mi][i]; d++){
2517: newm=savm;
1.187 brouard 2518: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2519: cov[2]=agexact;
2520: if(nagesqr==1)
2521: cov[3]= agexact*agexact;
1.126 brouard 2522: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2523: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2524: }
2525:
2526: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2527: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2528: savm=oldm;
2529: oldm=newm;
2530: } /* end mult */
2531:
2532: s1=s[mw[mi][i]][i];
2533: s2=s[mw[mi+1][i]][i];
2534: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2535: ipmx +=1;
2536: sw += weight[i];
2537: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2538: /*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]);*/
2539: } /* end of wave */
2540: } /* end of individual */
2541: } /* End of if */
2542: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2543: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2544: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2545: return -l;
2546: }
2547:
2548: /*************** log-likelihood *************/
2549: double funcone( double *x)
2550: {
2551: /* Same as likeli but slower because of a lot of printf and if */
2552: int i, ii, j, k, mi, d, kk;
1.131 brouard 2553: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2554: double **out;
2555: double lli; /* Individual log likelihood */
2556: double llt;
2557: int s1, s2;
2558: double bbh, survp;
1.187 brouard 2559: double agexact;
1.126 brouard 2560: /*extern weight */
2561: /* We are differentiating ll according to initial status */
2562: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2563: /*for(i=1;i<imx;i++)
2564: printf(" %d\n",s[4][i]);
2565: */
2566: cov[1]=1.;
2567:
2568: for(k=1; k<=nlstate; k++) ll[k]=0.;
2569:
2570: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2571: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2572: for(mi=1; mi<= wav[i]-1; mi++){
2573: for (ii=1;ii<=nlstate+ndeath;ii++)
2574: for (j=1;j<=nlstate+ndeath;j++){
2575: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2576: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2577: }
2578: for(d=0; d<dh[mi][i]; d++){
2579: newm=savm;
1.187 brouard 2580: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2581: cov[2]=agexact;
2582: if(nagesqr==1)
2583: cov[3]= agexact*agexact;
1.126 brouard 2584: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2585: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2586: }
1.187 brouard 2587:
1.145 brouard 2588: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2589: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2590: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2591: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2592: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2593: savm=oldm;
2594: oldm=newm;
2595: } /* end mult */
2596:
2597: s1=s[mw[mi][i]][i];
2598: s2=s[mw[mi+1][i]][i];
2599: bbh=(double)bh[mi][i]/(double)stepm;
2600: /* bias is positive if real duration
2601: * is higher than the multiple of stepm and negative otherwise.
2602: */
2603: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2604: lli=log(out[s1][s2] - savm[s1][s2]);
2605: } else if (s2==-2) {
2606: for (j=1,survp=0. ; j<=nlstate; j++)
2607: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2608: lli= log(survp);
2609: }else if (mle==1){
2610: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2611: } else if(mle==2){
2612: 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 */
2613: } else if(mle==3){ /* exponential inter-extrapolation */
2614: 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 */
2615: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2616: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2617: } else{ /* mle=0 back to 1 */
2618: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2619: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2620: } /* End of if */
2621: ipmx +=1;
2622: sw += weight[i];
2623: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2624: /*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 2625: if(globpr){
1.205 brouard 2626: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2627: %11.6f %11.6f %11.6f ", \
1.205 brouard 2628: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2629: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2630: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2631: llt +=ll[k]*gipmx/gsw;
2632: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2633: }
2634: fprintf(ficresilk," %10.6f\n", -llt);
2635: }
2636: } /* end of wave */
2637: } /* end of individual */
2638: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2639: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2640: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2641: if(globpr==0){ /* First time we count the contributions and weights */
2642: gipmx=ipmx;
2643: gsw=sw;
2644: }
2645: return -l;
2646: }
2647:
2648:
2649: /*************** function likelione ***********/
2650: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2651: {
2652: /* This routine should help understanding what is done with
2653: the selection of individuals/waves and
2654: to check the exact contribution to the likelihood.
2655: Plotting could be done.
2656: */
2657: int k;
2658:
2659: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2660: strcpy(fileresilk,"ILK_");
1.202 brouard 2661: strcat(fileresilk,fileresu);
1.126 brouard 2662: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2663: printf("Problem with resultfile: %s\n", fileresilk);
2664: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2665: }
1.205 brouard 2666: fprintf(ficresilk, "#individual(line's_record) count age 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");
2667: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %weight 2wlli out sav ");
1.126 brouard 2668: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2669: for(k=1; k<=nlstate; k++)
2670: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2671: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2672: }
2673:
2674: *fretone=(*funcone)(p);
2675: if(*globpri !=0){
2676: fclose(ficresilk);
1.205 brouard 2677: if (mle ==0)
2678: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2679: else if(mle >=1)
2680: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2681: 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));
2682:
2683: 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 2684: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 2685: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2686: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 2687: fflush(fichtm);
2688:
2689: for (k=1; k<= nlstate ; k++) {
2690: fprintf(fichtm,"<br>- Probability p%dj by origin %d and destination j <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
1.204 brouard 2691: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
1.205 brouard 2692: }
2693: }
1.126 brouard 2694: return;
2695: }
2696:
2697:
2698: /*********** Maximum Likelihood Estimation ***************/
2699:
2700: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2701: {
1.165 brouard 2702: int i,j, iter=0;
1.126 brouard 2703: double **xi;
2704: double fret;
2705: double fretone; /* Only one call to likelihood */
2706: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2707:
2708: #ifdef NLOPT
2709: int creturn;
2710: nlopt_opt opt;
2711: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2712: double *lb;
2713: double minf; /* the minimum objective value, upon return */
2714: double * p1; /* Shifted parameters from 0 instead of 1 */
2715: myfunc_data dinst, *d = &dinst;
2716: #endif
2717:
2718:
1.126 brouard 2719: xi=matrix(1,npar,1,npar);
2720: for (i=1;i<=npar;i++)
2721: for (j=1;j<=npar;j++)
2722: xi[i][j]=(i==j ? 1.0 : 0.0);
2723: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2724: strcpy(filerespow,"POW_");
1.126 brouard 2725: strcat(filerespow,fileres);
2726: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2727: printf("Problem with resultfile: %s\n", filerespow);
2728: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2729: }
2730: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2731: for (i=1;i<=nlstate;i++)
2732: for(j=1;j<=nlstate+ndeath;j++)
2733: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2734: fprintf(ficrespow,"\n");
1.162 brouard 2735: #ifdef POWELL
1.126 brouard 2736: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2737: #endif
1.126 brouard 2738:
1.162 brouard 2739: #ifdef NLOPT
2740: #ifdef NEWUOA
2741: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2742: #else
2743: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2744: #endif
2745: lb=vector(0,npar-1);
2746: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2747: nlopt_set_lower_bounds(opt, lb);
2748: nlopt_set_initial_step1(opt, 0.1);
2749:
2750: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2751: d->function = func;
2752: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2753: nlopt_set_min_objective(opt, myfunc, d);
2754: nlopt_set_xtol_rel(opt, ftol);
2755: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2756: printf("nlopt failed! %d\n",creturn);
2757: }
2758: else {
2759: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2760: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2761: iter=1; /* not equal */
2762: }
2763: nlopt_destroy(opt);
2764: #endif
1.126 brouard 2765: free_matrix(xi,1,npar,1,npar);
2766: fclose(ficrespow);
1.203 brouard 2767: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2768: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2769: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2770:
2771: }
2772:
2773: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2774: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2775: {
2776: double **a,**y,*x,pd;
1.203 brouard 2777: /* double **hess; */
1.164 brouard 2778: int i, j;
1.126 brouard 2779: int *indx;
2780:
2781: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2782: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2783: void lubksb(double **a, int npar, int *indx, double b[]) ;
2784: void ludcmp(double **a, int npar, int *indx, double *d) ;
2785: double gompertz(double p[]);
1.203 brouard 2786: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2787:
2788: printf("\nCalculation of the hessian matrix. Wait...\n");
2789: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2790: for (i=1;i<=npar;i++){
1.203 brouard 2791: printf("%d-",i);fflush(stdout);
2792: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2793:
2794: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2795:
2796: /* printf(" %f ",p[i]);
2797: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2798: }
2799:
2800: for (i=1;i<=npar;i++) {
2801: for (j=1;j<=npar;j++) {
2802: if (j>i) {
1.203 brouard 2803: printf(".%d-%d",i,j);fflush(stdout);
2804: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2805: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2806:
2807: hess[j][i]=hess[i][j];
2808: /*printf(" %lf ",hess[i][j]);*/
2809: }
2810: }
2811: }
2812: printf("\n");
2813: fprintf(ficlog,"\n");
2814:
2815: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2816: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2817:
2818: a=matrix(1,npar,1,npar);
2819: y=matrix(1,npar,1,npar);
2820: x=vector(1,npar);
2821: indx=ivector(1,npar);
2822: for (i=1;i<=npar;i++)
2823: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2824: ludcmp(a,npar,indx,&pd);
2825:
2826: for (j=1;j<=npar;j++) {
2827: for (i=1;i<=npar;i++) x[i]=0;
2828: x[j]=1;
2829: lubksb(a,npar,indx,x);
2830: for (i=1;i<=npar;i++){
2831: matcov[i][j]=x[i];
2832: }
2833: }
2834:
2835: printf("\n#Hessian matrix#\n");
2836: fprintf(ficlog,"\n#Hessian matrix#\n");
2837: for (i=1;i<=npar;i++) {
2838: for (j=1;j<=npar;j++) {
1.203 brouard 2839: printf("%.6e ",hess[i][j]);
2840: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2841: }
2842: printf("\n");
2843: fprintf(ficlog,"\n");
2844: }
2845:
1.203 brouard 2846: /* printf("\n#Covariance matrix#\n"); */
2847: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2848: /* for (i=1;i<=npar;i++) { */
2849: /* for (j=1;j<=npar;j++) { */
2850: /* printf("%.6e ",matcov[i][j]); */
2851: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2852: /* } */
2853: /* printf("\n"); */
2854: /* fprintf(ficlog,"\n"); */
2855: /* } */
2856:
1.126 brouard 2857: /* Recompute Inverse */
1.203 brouard 2858: /* for (i=1;i<=npar;i++) */
2859: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2860: /* ludcmp(a,npar,indx,&pd); */
2861:
2862: /* printf("\n#Hessian matrix recomputed#\n"); */
2863:
2864: /* for (j=1;j<=npar;j++) { */
2865: /* for (i=1;i<=npar;i++) x[i]=0; */
2866: /* x[j]=1; */
2867: /* lubksb(a,npar,indx,x); */
2868: /* for (i=1;i<=npar;i++){ */
2869: /* y[i][j]=x[i]; */
2870: /* printf("%.3e ",y[i][j]); */
2871: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2872: /* } */
2873: /* printf("\n"); */
2874: /* fprintf(ficlog,"\n"); */
2875: /* } */
2876:
2877: /* Verifying the inverse matrix */
2878: #ifdef DEBUGHESS
2879: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2880:
1.203 brouard 2881: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2882: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2883:
2884: for (j=1;j<=npar;j++) {
2885: for (i=1;i<=npar;i++){
1.203 brouard 2886: printf("%.2f ",y[i][j]);
2887: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2888: }
2889: printf("\n");
2890: fprintf(ficlog,"\n");
2891: }
1.203 brouard 2892: #endif
1.126 brouard 2893:
2894: free_matrix(a,1,npar,1,npar);
2895: free_matrix(y,1,npar,1,npar);
2896: free_vector(x,1,npar);
2897: free_ivector(indx,1,npar);
1.203 brouard 2898: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2899:
2900:
2901: }
2902:
2903: /*************** hessian matrix ****************/
2904: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2905: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2906: int i;
2907: int l=1, lmax=20;
1.203 brouard 2908: double k1,k2, res, fx;
1.132 brouard 2909: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2910: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2911: int k=0,kmax=10;
2912: double l1;
2913:
2914: fx=func(x);
2915: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2916: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2917: l1=pow(10,l);
2918: delts=delt;
2919: for(k=1 ; k <kmax; k=k+1){
2920: delt = delta*(l1*k);
2921: p2[theta]=x[theta] +delt;
1.145 brouard 2922: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2923: p2[theta]=x[theta]-delt;
2924: k2=func(p2)-fx;
2925: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2926: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2927:
1.203 brouard 2928: #ifdef DEBUGHESSII
1.126 brouard 2929: 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);
2930: 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);
2931: #endif
2932: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2933: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2934: k=kmax;
2935: }
2936: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2937: k=kmax; l=lmax*10;
1.126 brouard 2938: }
2939: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2940: delts=delt;
2941: }
1.203 brouard 2942: } /* End loop k */
1.126 brouard 2943: }
2944: delti[theta]=delts;
2945: return res;
2946:
2947: }
2948:
1.203 brouard 2949: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2950: {
2951: int i;
1.164 brouard 2952: int l=1, lmax=20;
1.126 brouard 2953: double k1,k2,k3,k4,res,fx;
1.132 brouard 2954: double p2[MAXPARM+1];
1.203 brouard 2955: int k, kmax=1;
2956: double v1, v2, cv12, lc1, lc2;
2957:
1.126 brouard 2958: fx=func(x);
1.203 brouard 2959: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2960: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 2961: p2[thetai]=x[thetai]+delti[thetai]*k;
2962: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2963: k1=func(p2)-fx;
2964:
1.203 brouard 2965: p2[thetai]=x[thetai]+delti[thetai]*k;
2966: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2967: k2=func(p2)-fx;
2968:
1.203 brouard 2969: p2[thetai]=x[thetai]-delti[thetai]*k;
2970: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2971: k3=func(p2)-fx;
2972:
1.203 brouard 2973: p2[thetai]=x[thetai]-delti[thetai]*k;
2974: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2975: k4=func(p2)-fx;
1.203 brouard 2976: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
2977: if(k1*k2*k3*k4 <0.){
2978: kmax=kmax+10;
2979: if(kmax >=10){
2980: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2981: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2982: 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);
2983: 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);
2984: }
2985: }
2986: #ifdef DEBUGHESSIJ
2987: v1=hess[thetai][thetai];
2988: v2=hess[thetaj][thetaj];
2989: cv12=res;
2990: /* Computing eigen value of Hessian matrix */
2991: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2992: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2993: if ((lc2 <0) || (lc1 <0) ){
2994: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2995: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2996: 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);
2997: 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);
2998: }
1.126 brouard 2999: #endif
3000: }
3001: return res;
3002: }
3003:
1.203 brouard 3004: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3005: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3006: /* { */
3007: /* int i; */
3008: /* int l=1, lmax=20; */
3009: /* double k1,k2,k3,k4,res,fx; */
3010: /* double p2[MAXPARM+1]; */
3011: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3012: /* int k=0,kmax=10; */
3013: /* double l1; */
3014:
3015: /* fx=func(x); */
3016: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3017: /* l1=pow(10,l); */
3018: /* delts=delt; */
3019: /* for(k=1 ; k <kmax; k=k+1){ */
3020: /* delt = delti*(l1*k); */
3021: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3022: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3023: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3024: /* k1=func(p2)-fx; */
3025:
3026: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3027: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3028: /* k2=func(p2)-fx; */
3029:
3030: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3031: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3032: /* k3=func(p2)-fx; */
3033:
3034: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3035: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3036: /* k4=func(p2)-fx; */
3037: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3038: /* #ifdef DEBUGHESSIJ */
3039: /* 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); */
3040: /* 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); */
3041: /* #endif */
3042: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3043: /* k=kmax; */
3044: /* } */
3045: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3046: /* k=kmax; l=lmax*10; */
3047: /* } */
3048: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3049: /* delts=delt; */
3050: /* } */
3051: /* } /\* End loop k *\/ */
3052: /* } */
3053: /* delti[theta]=delts; */
3054: /* return res; */
3055: /* } */
3056:
3057:
1.126 brouard 3058: /************** Inverse of matrix **************/
3059: void ludcmp(double **a, int n, int *indx, double *d)
3060: {
3061: int i,imax,j,k;
3062: double big,dum,sum,temp;
3063: double *vv;
3064:
3065: vv=vector(1,n);
3066: *d=1.0;
3067: for (i=1;i<=n;i++) {
3068: big=0.0;
3069: for (j=1;j<=n;j++)
3070: if ((temp=fabs(a[i][j])) > big) big=temp;
3071: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3072: vv[i]=1.0/big;
3073: }
3074: for (j=1;j<=n;j++) {
3075: for (i=1;i<j;i++) {
3076: sum=a[i][j];
3077: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3078: a[i][j]=sum;
3079: }
3080: big=0.0;
3081: for (i=j;i<=n;i++) {
3082: sum=a[i][j];
3083: for (k=1;k<j;k++)
3084: sum -= a[i][k]*a[k][j];
3085: a[i][j]=sum;
3086: if ( (dum=vv[i]*fabs(sum)) >= big) {
3087: big=dum;
3088: imax=i;
3089: }
3090: }
3091: if (j != imax) {
3092: for (k=1;k<=n;k++) {
3093: dum=a[imax][k];
3094: a[imax][k]=a[j][k];
3095: a[j][k]=dum;
3096: }
3097: *d = -(*d);
3098: vv[imax]=vv[j];
3099: }
3100: indx[j]=imax;
3101: if (a[j][j] == 0.0) a[j][j]=TINY;
3102: if (j != n) {
3103: dum=1.0/(a[j][j]);
3104: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3105: }
3106: }
3107: free_vector(vv,1,n); /* Doesn't work */
3108: ;
3109: }
3110:
3111: void lubksb(double **a, int n, int *indx, double b[])
3112: {
3113: int i,ii=0,ip,j;
3114: double sum;
3115:
3116: for (i=1;i<=n;i++) {
3117: ip=indx[i];
3118: sum=b[ip];
3119: b[ip]=b[i];
3120: if (ii)
3121: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3122: else if (sum) ii=i;
3123: b[i]=sum;
3124: }
3125: for (i=n;i>=1;i--) {
3126: sum=b[i];
3127: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3128: b[i]=sum/a[i][i];
3129: }
3130: }
3131:
3132: void pstamp(FILE *fichier)
3133: {
1.196 brouard 3134: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3135: }
3136:
3137: /************ Frequencies ********************/
3138: void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
3139: { /* Some frequencies */
3140:
1.164 brouard 3141: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3142: int first;
3143: double ***freq; /* Frequencies */
3144: double *pp, **prop;
3145: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3146: char fileresp[FILENAMELENGTH];
3147:
3148: pp=vector(1,nlstate);
3149: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3150: strcpy(fileresp,"P_");
3151: strcat(fileresp,fileresu);
1.126 brouard 3152: if((ficresp=fopen(fileresp,"w"))==NULL) {
3153: printf("Problem with prevalence resultfile: %s\n", fileresp);
3154: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3155: exit(0);
3156: }
3157: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3158: j1=0;
3159:
3160: j=cptcoveff;
3161: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3162:
3163: first=1;
3164:
1.169 brouard 3165: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3166: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3167: /* j1++; */
1.145 brouard 3168: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3169: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3170: scanf("%d", i);*/
3171: for (i=-5; i<=nlstate+ndeath; i++)
3172: for (jk=-5; jk<=nlstate+ndeath; jk++)
3173: for(m=iagemin; m <= iagemax+3; m++)
3174: freq[i][jk][m]=0;
1.143 brouard 3175:
3176: for (i=1; i<=nlstate; i++)
3177: for(m=iagemin; m <= iagemax+3; m++)
3178: prop[i][m]=0;
1.126 brouard 3179:
3180: dateintsum=0;
3181: k2cpt=0;
3182: for (i=1; i<=imx; i++) {
3183: bool=1;
1.144 brouard 3184: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3185: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3186: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3187: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3188: bool=0;
1.198 brouard 3189: /* 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",
3190: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3191: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3192: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3193: }
1.126 brouard 3194: }
1.144 brouard 3195:
1.126 brouard 3196: if (bool==1){
3197: for(m=firstpass; m<=lastpass; m++){
3198: k2=anint[m][i]+(mint[m][i]/12.);
3199: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3200: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3201: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3202: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3203: if (m<lastpass) {
3204: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3205: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3206: }
3207:
3208: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3209: dateintsum=dateintsum+k2;
3210: k2cpt++;
3211: }
3212: /*}*/
3213: }
3214: }
1.145 brouard 3215: } /* end i */
1.126 brouard 3216:
3217: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3218: pstamp(ficresp);
3219: if (cptcovn>0) {
3220: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3221: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3222: fprintf(ficresp, "**********\n#");
1.143 brouard 3223: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3224: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3225: fprintf(ficlog, "**********\n#");
1.126 brouard 3226: }
3227: for(i=1; i<=nlstate;i++)
3228: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3229: fprintf(ficresp, "\n");
3230:
3231: for(i=iagemin; i <= iagemax+3; i++){
3232: if(i==iagemax+3){
3233: fprintf(ficlog,"Total");
3234: }else{
3235: if(first==1){
3236: first=0;
3237: printf("See log file for details...\n");
3238: }
3239: fprintf(ficlog,"Age %d", i);
3240: }
3241: for(jk=1; jk <=nlstate ; jk++){
3242: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3243: pp[jk] += freq[jk][m][i];
3244: }
3245: for(jk=1; jk <=nlstate ; jk++){
3246: for(m=-1, pos=0; m <=0 ; m++)
3247: pos += freq[jk][m][i];
3248: if(pp[jk]>=1.e-10){
3249: if(first==1){
1.132 brouard 3250: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3251: }
3252: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3253: }else{
3254: if(first==1)
3255: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3256: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3257: }
3258: }
3259:
3260: for(jk=1; jk <=nlstate ; jk++){
3261: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3262: pp[jk] += freq[jk][m][i];
3263: }
3264: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3265: pos += pp[jk];
3266: posprop += prop[jk][i];
3267: }
3268: for(jk=1; jk <=nlstate ; jk++){
3269: if(pos>=1.e-5){
3270: if(first==1)
3271: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3272: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3273: }else{
3274: if(first==1)
3275: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3276: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3277: }
3278: if( i <= iagemax){
3279: if(pos>=1.e-5){
3280: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3281: /*probs[i][jk][j1]= pp[jk]/pos;*/
3282: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3283: }
3284: else
3285: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3286: }
3287: }
3288:
3289: for(jk=-1; jk <=nlstate+ndeath; jk++)
3290: for(m=-1; m <=nlstate+ndeath; m++)
3291: if(freq[jk][m][i] !=0 ) {
3292: if(first==1)
3293: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3294: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3295: }
3296: if(i <= iagemax)
3297: fprintf(ficresp,"\n");
3298: if(first==1)
3299: printf("Others in log...\n");
3300: fprintf(ficlog,"\n");
3301: }
1.145 brouard 3302: /*}*/
1.126 brouard 3303: }
3304: dateintmean=dateintsum/k2cpt;
3305:
3306: fclose(ficresp);
3307: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3308: free_vector(pp,1,nlstate);
3309: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3310: /* End of Freq */
3311: }
3312:
3313: /************ Prevalence ********************/
3314: 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)
3315: {
3316: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3317: in each health status at the date of interview (if between dateprev1 and dateprev2).
3318: We still use firstpass and lastpass as another selection.
3319: */
3320:
1.164 brouard 3321: int i, m, jk, j1, bool, z1,j;
3322:
3323: double **prop;
3324: double posprop;
1.126 brouard 3325: double y2; /* in fractional years */
3326: int iagemin, iagemax;
1.145 brouard 3327: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3328:
3329: iagemin= (int) agemin;
3330: iagemax= (int) agemax;
3331: /*pp=vector(1,nlstate);*/
3332: prop=matrix(1,nlstate,iagemin,iagemax+3);
3333: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3334: j1=0;
3335:
1.145 brouard 3336: /*j=cptcoveff;*/
1.126 brouard 3337: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3338:
1.145 brouard 3339: first=1;
3340: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3341: /*for(i1=1; i1<=ncodemax[k1];i1++){
3342: j1++;*/
1.126 brouard 3343:
3344: for (i=1; i<=nlstate; i++)
3345: for(m=iagemin; m <= iagemax+3; m++)
3346: prop[i][m]=0.0;
3347:
3348: for (i=1; i<=imx; i++) { /* Each individual */
3349: bool=1;
3350: if (cptcovn>0) {
3351: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3352: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3353: bool=0;
3354: }
3355: if (bool==1) {
3356: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3357: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3358: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3359: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3360: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3361: 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);
3362: if (s[m][i]>0 && s[m][i]<=nlstate) {
3363: /*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]]);*/
3364: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3365: prop[s[m][i]][iagemax+3] += weight[i];
3366: }
3367: }
3368: } /* end selection of waves */
3369: }
3370: }
3371: for(i=iagemin; i <= iagemax+3; i++){
3372: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3373: posprop += prop[jk][i];
3374: }
1.145 brouard 3375:
1.126 brouard 3376: for(jk=1; jk <=nlstate ; jk++){
3377: if( i <= iagemax){
3378: if(posprop>=1.e-5){
3379: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3380: } else{
3381: if(first==1){
3382: first=0;
3383: 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]);
3384: }
3385: }
1.126 brouard 3386: }
3387: }/* end jk */
3388: }/* end i */
1.145 brouard 3389: /*} *//* end i1 */
3390: } /* end j1 */
1.126 brouard 3391:
3392: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3393: /*free_vector(pp,1,nlstate);*/
3394: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3395: } /* End of prevalence */
3396:
3397: /************* Waves Concatenation ***************/
3398:
3399: 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)
3400: {
3401: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3402: Death is a valid wave (if date is known).
3403: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3404: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3405: and mw[mi+1][i]. dh depends on stepm.
3406: */
3407:
3408: int i, mi, m;
3409: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3410: double sum=0., jmean=0.;*/
3411: int first;
3412: int j, k=0,jk, ju, jl;
3413: double sum=0.;
3414: first=0;
1.164 brouard 3415: jmin=100000;
1.126 brouard 3416: jmax=-1;
3417: jmean=0.;
3418: for(i=1; i<=imx; i++){
3419: mi=0;
3420: m=firstpass;
3421: while(s[m][i] <= nlstate){
3422: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3423: mw[++mi][i]=m;
3424: if(m >=lastpass)
3425: break;
3426: else
3427: m++;
3428: }/* end while */
3429: if (s[m][i] > nlstate){
3430: mi++; /* Death is another wave */
3431: /* if(mi==0) never been interviewed correctly before death */
3432: /* Only death is a correct wave */
3433: mw[mi][i]=m;
3434: }
3435:
3436: wav[i]=mi;
3437: if(mi==0){
3438: nbwarn++;
3439: if(first==0){
3440: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3441: first=1;
3442: }
3443: if(first==1){
3444: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3445: }
3446: } /* end mi==0 */
3447: } /* End individuals */
3448:
3449: for(i=1; i<=imx; i++){
3450: for(mi=1; mi<wav[i];mi++){
3451: if (stepm <=0)
3452: dh[mi][i]=1;
3453: else{
3454: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3455: if (agedc[i] < 2*AGESUP) {
3456: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3457: if(j==0) j=1; /* Survives at least one month after exam */
3458: else if(j<0){
3459: nberr++;
3460: 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]);
3461: j=1; /* Temporary Dangerous patch */
3462: 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);
3463: 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]);
3464: 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);
3465: }
3466: k=k+1;
3467: if (j >= jmax){
3468: jmax=j;
3469: ijmax=i;
3470: }
3471: if (j <= jmin){
3472: jmin=j;
3473: ijmin=i;
3474: }
3475: sum=sum+j;
3476: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3477: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3478: }
3479: }
3480: else{
3481: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3482: /* 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]); */
3483:
3484: k=k+1;
3485: if (j >= jmax) {
3486: jmax=j;
3487: ijmax=i;
3488: }
3489: else if (j <= jmin){
3490: jmin=j;
3491: ijmin=i;
3492: }
3493: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3494: /*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]);*/
3495: if(j<0){
3496: nberr++;
3497: 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]);
3498: 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]);
3499: }
3500: sum=sum+j;
3501: }
3502: jk= j/stepm;
3503: jl= j -jk*stepm;
3504: ju= j -(jk+1)*stepm;
3505: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3506: if(jl==0){
3507: dh[mi][i]=jk;
3508: bh[mi][i]=0;
3509: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3510: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3511: dh[mi][i]=jk+1;
3512: bh[mi][i]=ju;
3513: }
3514: }else{
3515: if(jl <= -ju){
3516: dh[mi][i]=jk;
3517: bh[mi][i]=jl; /* bias is positive if real duration
3518: * is higher than the multiple of stepm and negative otherwise.
3519: */
3520: }
3521: else{
3522: dh[mi][i]=jk+1;
3523: bh[mi][i]=ju;
3524: }
3525: if(dh[mi][i]==0){
3526: dh[mi][i]=1; /* At least one step */
3527: bh[mi][i]=ju; /* At least one step */
3528: /* 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);*/
3529: }
3530: } /* end if mle */
3531: }
3532: } /* end wave */
3533: }
3534: jmean=sum/k;
3535: 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 3536: 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 3537: }
3538:
3539: /*********** Tricode ****************************/
1.145 brouard 3540: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3541: {
1.144 brouard 3542: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3543: /* 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 3544: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3545: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3546: * nbcode[Tvar[j]][1]=
1.144 brouard 3547: */
1.130 brouard 3548:
1.145 brouard 3549: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3550: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3551: int cptcode=0; /* Modality max of covariates j */
3552: int modmincovj=0; /* Modality min of covariates j */
3553:
3554:
1.126 brouard 3555: cptcoveff=0;
3556:
1.144 brouard 3557: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3558:
1.145 brouard 3559: /* Loop on covariates without age and products */
1.186 brouard 3560: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3561: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3562: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3563: modality of this covariate Vj*/
1.145 brouard 3564: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3565: * If product of Vn*Vm, still boolean *:
3566: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3567: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3568: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3569: modality of the nth covariate of individual i. */
1.145 brouard 3570: if (ij > modmaxcovj)
3571: modmaxcovj=ij;
3572: else if (ij < modmincovj)
3573: modmincovj=ij;
3574: if ((ij < -1) && (ij > NCOVMAX)){
3575: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3576: exit(1);
3577: }else
1.136 brouard 3578: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3579: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3580: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3581: /* getting the maximum value of the modality of the covariate
3582: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3583: female is 1, then modmaxcovj=1.*/
1.192 brouard 3584: } /* end for loop on individuals i */
1.145 brouard 3585: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3586: 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 3587: cptcode=modmaxcovj;
1.137 brouard 3588: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3589: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3590: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3591: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3592: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3593: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3594: if( k != -1){
3595: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3596: covariate for which somebody answered excluding
3597: undefined. Usually 2: 0 and 1. */
3598: }
3599: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3600: covariate for which somebody answered including
3601: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3602: }
3603: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3604: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3605: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3606:
1.136 brouard 3607: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3608: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3609: 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 3610: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3611: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3612: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3613: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3614: nbcode[Tvar[j]][ij]=k;
3615: nbcode[Tvar[j]][1]=0;
3616: nbcode[Tvar[j]][2]=1;
3617: nbcode[Tvar[j]][3]=2;
1.197 brouard 3618: To be continued (not working yet).
1.145 brouard 3619: */
1.197 brouard 3620: ij=0; /* ij is similar to i but can jump over null modalities */
3621: 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*/
3622: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3623: break;
3624: }
3625: ij++;
1.197 brouard 3626: 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 3627: cptcode = ij; /* New max modality for covar j */
3628: } /* end of loop on modality i=-1 to 1 or more */
3629:
3630: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3631: /* /\*recode from 0 *\/ */
3632: /* k is a modality. If we have model=V1+V1*sex */
3633: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3634: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3635: /* } */
3636: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3637: /* if (ij > ncodemax[j]) { */
3638: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3639: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3640: /* break; */
3641: /* } */
3642: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3643: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3644:
1.145 brouard 3645: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3646:
1.187 brouard 3647: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3648: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3649: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3650: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3651: }
1.126 brouard 3652:
1.192 brouard 3653: ij=0;
1.145 brouard 3654: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3655: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3656: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3657: ij++;
1.145 brouard 3658: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3659: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3660: }else{
3661: /* Tvaraff[ij]=0; */
3662: }
1.126 brouard 3663: }
1.192 brouard 3664: /* ij--; */
1.144 brouard 3665: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3666:
1.126 brouard 3667: }
3668:
1.145 brouard 3669:
1.126 brouard 3670: /*********** Health Expectancies ****************/
3671:
1.127 brouard 3672: 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 3673:
3674: {
3675: /* Health expectancies, no variances */
1.164 brouard 3676: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3677: int nhstepma, nstepma; /* Decreasing with age */
3678: double age, agelim, hf;
3679: double ***p3mat;
3680: double eip;
3681:
3682: pstamp(ficreseij);
3683: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3684: fprintf(ficreseij,"# Age");
3685: for(i=1; i<=nlstate;i++){
3686: for(j=1; j<=nlstate;j++){
3687: fprintf(ficreseij," e%1d%1d ",i,j);
3688: }
3689: fprintf(ficreseij," e%1d. ",i);
3690: }
3691: fprintf(ficreseij,"\n");
3692:
3693:
3694: if(estepm < stepm){
3695: printf ("Problem %d lower than %d\n",estepm, stepm);
3696: }
3697: else hstepm=estepm;
3698: /* We compute the life expectancy from trapezoids spaced every estepm months
3699: * This is mainly to measure the difference between two models: for example
3700: * if stepm=24 months pijx are given only every 2 years and by summing them
3701: * we are calculating an estimate of the Life Expectancy assuming a linear
3702: * progression in between and thus overestimating or underestimating according
3703: * to the curvature of the survival function. If, for the same date, we
3704: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3705: * to compare the new estimate of Life expectancy with the same linear
3706: * hypothesis. A more precise result, taking into account a more precise
3707: * curvature will be obtained if estepm is as small as stepm. */
3708:
3709: /* For example we decided to compute the life expectancy with the smallest unit */
3710: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3711: nhstepm is the number of hstepm from age to agelim
3712: nstepm is the number of stepm from age to agelin.
3713: Look at hpijx to understand the reason of that which relies in memory size
3714: and note for a fixed period like estepm months */
3715: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3716: survival function given by stepm (the optimization length). Unfortunately it
3717: means that if the survival funtion is printed only each two years of age and if
3718: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3719: results. So we changed our mind and took the option of the best precision.
3720: */
3721: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3722:
3723: agelim=AGESUP;
3724: /* If stepm=6 months */
3725: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3726: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3727:
3728: /* nhstepm age range expressed in number of stepm */
3729: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3730: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3731: /* if (stepm >= YEARM) hstepm=1;*/
3732: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3733: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3734:
3735: for (age=bage; age<=fage; age ++){
3736: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3737: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3738: /* if (stepm >= YEARM) hstepm=1;*/
3739: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3740:
3741: /* If stepm=6 months */
3742: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3743: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3744:
3745: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3746:
3747: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3748:
3749: printf("%d|",(int)age);fflush(stdout);
3750: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3751:
3752: /* Computing expectancies */
3753: for(i=1; i<=nlstate;i++)
3754: for(j=1; j<=nlstate;j++)
3755: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3756: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3757:
3758: /* 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]);*/
3759:
3760: }
3761:
3762: fprintf(ficreseij,"%3.0f",age );
3763: for(i=1; i<=nlstate;i++){
3764: eip=0;
3765: for(j=1; j<=nlstate;j++){
3766: eip +=eij[i][j][(int)age];
3767: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3768: }
3769: fprintf(ficreseij,"%9.4f", eip );
3770: }
3771: fprintf(ficreseij,"\n");
3772:
3773: }
3774: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3775: printf("\n");
3776: fprintf(ficlog,"\n");
3777:
3778: }
3779:
1.127 brouard 3780: 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 3781:
3782: {
3783: /* Covariances of health expectancies eij and of total life expectancies according
3784: to initial status i, ei. .
3785: */
3786: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3787: int nhstepma, nstepma; /* Decreasing with age */
3788: double age, agelim, hf;
3789: double ***p3matp, ***p3matm, ***varhe;
3790: double **dnewm,**doldm;
3791: double *xp, *xm;
3792: double **gp, **gm;
3793: double ***gradg, ***trgradg;
3794: int theta;
3795:
3796: double eip, vip;
3797:
3798: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3799: xp=vector(1,npar);
3800: xm=vector(1,npar);
3801: dnewm=matrix(1,nlstate*nlstate,1,npar);
3802: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3803:
3804: pstamp(ficresstdeij);
3805: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3806: fprintf(ficresstdeij,"# Age");
3807: for(i=1; i<=nlstate;i++){
3808: for(j=1; j<=nlstate;j++)
3809: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3810: fprintf(ficresstdeij," e%1d. ",i);
3811: }
3812: fprintf(ficresstdeij,"\n");
3813:
3814: pstamp(ficrescveij);
3815: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3816: fprintf(ficrescveij,"# Age");
3817: for(i=1; i<=nlstate;i++)
3818: for(j=1; j<=nlstate;j++){
3819: cptj= (j-1)*nlstate+i;
3820: for(i2=1; i2<=nlstate;i2++)
3821: for(j2=1; j2<=nlstate;j2++){
3822: cptj2= (j2-1)*nlstate+i2;
3823: if(cptj2 <= cptj)
3824: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3825: }
3826: }
3827: fprintf(ficrescveij,"\n");
3828:
3829: if(estepm < stepm){
3830: printf ("Problem %d lower than %d\n",estepm, stepm);
3831: }
3832: else hstepm=estepm;
3833: /* We compute the life expectancy from trapezoids spaced every estepm months
3834: * This is mainly to measure the difference between two models: for example
3835: * if stepm=24 months pijx are given only every 2 years and by summing them
3836: * we are calculating an estimate of the Life Expectancy assuming a linear
3837: * progression in between and thus overestimating or underestimating according
3838: * to the curvature of the survival function. If, for the same date, we
3839: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3840: * to compare the new estimate of Life expectancy with the same linear
3841: * hypothesis. A more precise result, taking into account a more precise
3842: * curvature will be obtained if estepm is as small as stepm. */
3843:
3844: /* For example we decided to compute the life expectancy with the smallest unit */
3845: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3846: nhstepm is the number of hstepm from age to agelim
3847: nstepm is the number of stepm from age to agelin.
3848: Look at hpijx to understand the reason of that which relies in memory size
3849: and note for a fixed period like estepm months */
3850: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3851: survival function given by stepm (the optimization length). Unfortunately it
3852: means that if the survival funtion is printed only each two years of age and if
3853: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3854: results. So we changed our mind and took the option of the best precision.
3855: */
3856: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3857:
3858: /* If stepm=6 months */
3859: /* nhstepm age range expressed in number of stepm */
3860: agelim=AGESUP;
3861: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3862: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3863: /* if (stepm >= YEARM) hstepm=1;*/
3864: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3865:
3866: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3867: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3868: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3869: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3870: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3871: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3872:
3873: for (age=bage; age<=fage; age ++){
3874: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3875: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3876: /* if (stepm >= YEARM) hstepm=1;*/
3877: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3878:
3879: /* If stepm=6 months */
3880: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3881: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3882:
3883: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3884:
3885: /* Computing Variances of health expectancies */
3886: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3887: decrease memory allocation */
3888: for(theta=1; theta <=npar; theta++){
3889: for(i=1; i<=npar; i++){
3890: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3891: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3892: }
3893: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3894: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3895:
3896: for(j=1; j<= nlstate; j++){
3897: for(i=1; i<=nlstate; i++){
3898: for(h=0; h<=nhstepm-1; h++){
3899: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3900: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3901: }
3902: }
3903: }
3904:
3905: for(ij=1; ij<= nlstate*nlstate; ij++)
3906: for(h=0; h<=nhstepm-1; h++){
3907: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3908: }
3909: }/* End theta */
3910:
3911:
3912: for(h=0; h<=nhstepm-1; h++)
3913: for(j=1; j<=nlstate*nlstate;j++)
3914: for(theta=1; theta <=npar; theta++)
3915: trgradg[h][j][theta]=gradg[h][theta][j];
3916:
3917:
3918: for(ij=1;ij<=nlstate*nlstate;ij++)
3919: for(ji=1;ji<=nlstate*nlstate;ji++)
3920: varhe[ij][ji][(int)age] =0.;
3921:
3922: printf("%d|",(int)age);fflush(stdout);
3923: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3924: for(h=0;h<=nhstepm-1;h++){
3925: for(k=0;k<=nhstepm-1;k++){
3926: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3927: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3928: for(ij=1;ij<=nlstate*nlstate;ij++)
3929: for(ji=1;ji<=nlstate*nlstate;ji++)
3930: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3931: }
3932: }
3933:
3934: /* Computing expectancies */
3935: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3936: for(i=1; i<=nlstate;i++)
3937: for(j=1; j<=nlstate;j++)
3938: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3939: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3940:
3941: /* 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]);*/
3942:
3943: }
3944:
3945: fprintf(ficresstdeij,"%3.0f",age );
3946: for(i=1; i<=nlstate;i++){
3947: eip=0.;
3948: vip=0.;
3949: for(j=1; j<=nlstate;j++){
3950: eip += eij[i][j][(int)age];
3951: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3952: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3953: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3954: }
3955: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3956: }
3957: fprintf(ficresstdeij,"\n");
3958:
3959: fprintf(ficrescveij,"%3.0f",age );
3960: for(i=1; i<=nlstate;i++)
3961: for(j=1; j<=nlstate;j++){
3962: cptj= (j-1)*nlstate+i;
3963: for(i2=1; i2<=nlstate;i2++)
3964: for(j2=1; j2<=nlstate;j2++){
3965: cptj2= (j2-1)*nlstate+i2;
3966: if(cptj2 <= cptj)
3967: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3968: }
3969: }
3970: fprintf(ficrescveij,"\n");
3971:
3972: }
3973: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3974: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3975: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3976: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3977: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3978: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3979: printf("\n");
3980: fprintf(ficlog,"\n");
3981:
3982: free_vector(xm,1,npar);
3983: free_vector(xp,1,npar);
3984: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3985: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3986: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3987: }
3988:
3989: /************ Variance ******************/
1.203 brouard 3990: 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 *ncvyear, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
1.126 brouard 3991: {
3992: /* Variance of health expectancies */
3993: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3994: /* double **newm;*/
1.169 brouard 3995: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3996:
3997: int movingaverage();
1.126 brouard 3998: double **dnewm,**doldm;
3999: double **dnewmp,**doldmp;
4000: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4001: int k;
1.126 brouard 4002: double *xp;
4003: double **gp, **gm; /* for var eij */
4004: double ***gradg, ***trgradg; /*for var eij */
4005: double **gradgp, **trgradgp; /* for var p point j */
4006: double *gpp, *gmp; /* for var p point j */
4007: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4008: double ***p3mat;
4009: double age,agelim, hf;
4010: double ***mobaverage;
4011: int theta;
4012: char digit[4];
4013: char digitp[25];
4014:
4015: char fileresprobmorprev[FILENAMELENGTH];
4016:
4017: if(popbased==1){
4018: if(mobilav!=0)
1.201 brouard 4019: strcpy(digitp,"-POPULBASED-MOBILAV_");
4020: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4021: }
4022: else
1.201 brouard 4023: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4024:
4025: if (mobilav!=0) {
4026: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4027: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4028: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4029: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4030: }
4031: }
4032:
1.201 brouard 4033: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4034: sprintf(digit,"%-d",ij);
4035: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4036: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4037: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4038: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4039: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4040: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4041: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4042: }
4043: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4044:
4045: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4046: pstamp(ficresprobmorprev);
4047: 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);
4048: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4049: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4050: fprintf(ficresprobmorprev," p.%-d SE",j);
4051: for(i=1; i<=nlstate;i++)
4052: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4053: }
4054: fprintf(ficresprobmorprev,"\n");
4055: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4056: fprintf(ficgp,"\nunset title \n");
4057: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4058: 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");
4059: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4060: /* } */
4061: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4062: pstamp(ficresvij);
4063: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4064: if(popbased==1)
1.128 brouard 4065: 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 4066: else
4067: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4068: fprintf(ficresvij,"# Age");
4069: for(i=1; i<=nlstate;i++)
4070: for(j=1; j<=nlstate;j++)
4071: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4072: fprintf(ficresvij,"\n");
4073:
4074: xp=vector(1,npar);
4075: dnewm=matrix(1,nlstate,1,npar);
4076: doldm=matrix(1,nlstate,1,nlstate);
4077: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4078: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4079:
4080: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4081: gpp=vector(nlstate+1,nlstate+ndeath);
4082: gmp=vector(nlstate+1,nlstate+ndeath);
4083: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4084:
4085: if(estepm < stepm){
4086: printf ("Problem %d lower than %d\n",estepm, stepm);
4087: }
4088: else hstepm=estepm;
4089: /* For example we decided to compute the life expectancy with the smallest unit */
4090: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4091: nhstepm is the number of hstepm from age to agelim
4092: nstepm is the number of stepm from age to agelin.
1.128 brouard 4093: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 4094: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4095: survival function given by stepm (the optimization length). Unfortunately it
4096: means that if the survival funtion is printed every two years of age and if
4097: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4098: results. So we changed our mind and took the option of the best precision.
4099: */
4100: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4101: agelim = AGESUP;
4102: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4103: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4104: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4105: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4106: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4107: gp=matrix(0,nhstepm,1,nlstate);
4108: gm=matrix(0,nhstepm,1,nlstate);
4109:
4110:
4111: for(theta=1; theta <=npar; theta++){
4112: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4113: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4114: }
4115: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4116: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4117:
4118: if (popbased==1) {
4119: if(mobilav ==0){
4120: for(i=1; i<=nlstate;i++)
4121: prlim[i][i]=probs[(int)age][i][ij];
4122: }else{ /* mobilav */
4123: for(i=1; i<=nlstate;i++)
4124: prlim[i][i]=mobaverage[(int)age][i][ij];
4125: }
4126: }
4127:
4128: for(j=1; j<= nlstate; j++){
4129: for(h=0; h<=nhstepm; h++){
4130: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4131: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4132: }
4133: }
4134: /* This for computing probability of death (h=1 means
4135: computed over hstepm matrices product = hstepm*stepm months)
4136: as a weighted average of prlim.
4137: */
4138: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4139: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4140: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4141: }
4142: /* end probability of death */
4143:
4144: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4145: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4146: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4147: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
1.126 brouard 4148:
4149: if (popbased==1) {
4150: if(mobilav ==0){
4151: for(i=1; i<=nlstate;i++)
4152: prlim[i][i]=probs[(int)age][i][ij];
4153: }else{ /* mobilav */
4154: for(i=1; i<=nlstate;i++)
4155: prlim[i][i]=mobaverage[(int)age][i][ij];
4156: }
4157: }
4158:
1.128 brouard 4159: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4160: for(h=0; h<=nhstepm; h++){
4161: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4162: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4163: }
4164: }
4165: /* This for computing probability of death (h=1 means
4166: computed over hstepm matrices product = hstepm*stepm months)
4167: as a weighted average of prlim.
4168: */
4169: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4170: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4171: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4172: }
4173: /* end probability of death */
4174:
4175: for(j=1; j<= nlstate; j++) /* vareij */
4176: for(h=0; h<=nhstepm; h++){
4177: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4178: }
4179:
4180: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4181: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4182: }
4183:
4184: } /* End theta */
4185:
4186: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4187:
4188: for(h=0; h<=nhstepm; h++) /* veij */
4189: for(j=1; j<=nlstate;j++)
4190: for(theta=1; theta <=npar; theta++)
4191: trgradg[h][j][theta]=gradg[h][theta][j];
4192:
4193: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4194: for(theta=1; theta <=npar; theta++)
4195: trgradgp[j][theta]=gradgp[theta][j];
4196:
4197:
4198: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4199: for(i=1;i<=nlstate;i++)
4200: for(j=1;j<=nlstate;j++)
4201: vareij[i][j][(int)age] =0.;
4202:
4203: for(h=0;h<=nhstepm;h++){
4204: for(k=0;k<=nhstepm;k++){
4205: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4206: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4207: for(i=1;i<=nlstate;i++)
4208: for(j=1;j<=nlstate;j++)
4209: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4210: }
4211: }
4212:
4213: /* pptj */
4214: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4215: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4216: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4217: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4218: varppt[j][i]=doldmp[j][i];
4219: /* end ppptj */
4220: /* x centered again */
4221: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4222: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4223:
4224: if (popbased==1) {
4225: if(mobilav ==0){
4226: for(i=1; i<=nlstate;i++)
4227: prlim[i][i]=probs[(int)age][i][ij];
4228: }else{ /* mobilav */
4229: for(i=1; i<=nlstate;i++)
4230: prlim[i][i]=mobaverage[(int)age][i][ij];
4231: }
4232: }
4233:
4234: /* This for computing probability of death (h=1 means
4235: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4236: as a weighted average of prlim.
4237: */
4238: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4239: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4240: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4241: }
4242: /* end probability of death */
4243:
4244: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4245: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4246: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4247: for(i=1; i<=nlstate;i++){
4248: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4249: }
4250: }
4251: fprintf(ficresprobmorprev,"\n");
4252:
4253: fprintf(ficresvij,"%.0f ",age );
4254: for(i=1; i<=nlstate;i++)
4255: for(j=1; j<=nlstate;j++){
4256: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4257: }
4258: fprintf(ficresvij,"\n");
4259: free_matrix(gp,0,nhstepm,1,nlstate);
4260: free_matrix(gm,0,nhstepm,1,nlstate);
4261: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4262: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4263: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4264: } /* End age */
4265: free_vector(gpp,nlstate+1,nlstate+ndeath);
4266: free_vector(gmp,nlstate+1,nlstate+ndeath);
4267: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4268: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4269: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4270: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4271: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4272: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4273: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4274: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4275: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4276: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4277: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4278: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4279: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4280: 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 4281: 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 4282: /* 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 4283: */
1.199 brouard 4284: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4285: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4286:
4287: free_vector(xp,1,npar);
4288: free_matrix(doldm,1,nlstate,1,nlstate);
4289: free_matrix(dnewm,1,nlstate,1,npar);
4290: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4291: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4292: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4293: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4294: fclose(ficresprobmorprev);
4295: fflush(ficgp);
4296: fflush(fichtm);
4297: } /* end varevsij */
4298:
4299: /************ Variance of prevlim ******************/
1.203 brouard 4300: 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 *ncvyear, int ij, char strstart[])
1.126 brouard 4301: {
1.205 brouard 4302: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4303: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4304:
1.126 brouard 4305: double **dnewm,**doldm;
4306: int i, j, nhstepm, hstepm;
4307: double *xp;
4308: double *gp, *gm;
4309: double **gradg, **trgradg;
4310: double age,agelim;
4311: int theta;
4312:
4313: pstamp(ficresvpl);
4314: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4315: fprintf(ficresvpl,"# Age");
4316: for(i=1; i<=nlstate;i++)
4317: fprintf(ficresvpl," %1d-%1d",i,i);
4318: fprintf(ficresvpl,"\n");
4319:
4320: xp=vector(1,npar);
4321: dnewm=matrix(1,nlstate,1,npar);
4322: doldm=matrix(1,nlstate,1,nlstate);
4323:
4324: hstepm=1*YEARM; /* Every year of age */
4325: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4326: agelim = AGESUP;
4327: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4328: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4329: if (stepm >= YEARM) hstepm=1;
4330: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4331: gradg=matrix(1,npar,1,nlstate);
4332: gp=vector(1,nlstate);
4333: gm=vector(1,nlstate);
4334:
4335: for(theta=1; theta <=npar; theta++){
4336: for(i=1; i<=npar; i++){ /* Computes gradient */
4337: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4338: }
1.203 brouard 4339: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4340: for(i=1;i<=nlstate;i++)
4341: gp[i] = prlim[i][i];
4342:
4343: for(i=1; i<=npar; i++) /* Computes gradient */
4344: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.203 brouard 4345: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4346: for(i=1;i<=nlstate;i++)
4347: gm[i] = prlim[i][i];
4348:
4349: for(i=1;i<=nlstate;i++)
4350: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4351: } /* End theta */
4352:
4353: trgradg =matrix(1,nlstate,1,npar);
4354:
4355: for(j=1; j<=nlstate;j++)
4356: for(theta=1; theta <=npar; theta++)
4357: trgradg[j][theta]=gradg[theta][j];
4358:
4359: for(i=1;i<=nlstate;i++)
4360: varpl[i][(int)age] =0.;
1.205 brouard 4361: if((int)age==67 ||(int)age== 66 ){
4362: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4363: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4364: }else{
1.126 brouard 4365: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4366: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4367: }
1.126 brouard 4368: for(i=1;i<=nlstate;i++)
4369: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4370:
4371: fprintf(ficresvpl,"%.0f ",age );
4372: for(i=1; i<=nlstate;i++)
4373: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4374: fprintf(ficresvpl,"\n");
4375: free_vector(gp,1,nlstate);
4376: free_vector(gm,1,nlstate);
4377: free_matrix(gradg,1,npar,1,nlstate);
4378: free_matrix(trgradg,1,nlstate,1,npar);
4379: } /* End age */
4380:
4381: free_vector(xp,1,npar);
4382: free_matrix(doldm,1,nlstate,1,npar);
4383: free_matrix(dnewm,1,nlstate,1,nlstate);
4384:
4385: }
4386:
4387: /************ Variance of one-step probabilities ******************/
4388: 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[])
4389: {
1.164 brouard 4390: int i, j=0, k1, l1, tj;
1.126 brouard 4391: int k2, l2, j1, z1;
1.164 brouard 4392: int k=0, l;
1.145 brouard 4393: int first=1, first1, first2;
1.126 brouard 4394: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4395: double **dnewm,**doldm;
4396: double *xp;
4397: double *gp, *gm;
4398: double **gradg, **trgradg;
4399: double **mu;
1.164 brouard 4400: double age, cov[NCOVMAX+1];
1.126 brouard 4401: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4402: int theta;
4403: char fileresprob[FILENAMELENGTH];
4404: char fileresprobcov[FILENAMELENGTH];
4405: char fileresprobcor[FILENAMELENGTH];
4406: double ***varpij;
4407:
1.201 brouard 4408: strcpy(fileresprob,"PROB_");
1.126 brouard 4409: strcat(fileresprob,fileres);
4410: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4411: printf("Problem with resultfile: %s\n", fileresprob);
4412: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4413: }
1.201 brouard 4414: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4415: strcat(fileresprobcov,fileresu);
1.126 brouard 4416: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4417: printf("Problem with resultfile: %s\n", fileresprobcov);
4418: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4419: }
1.201 brouard 4420: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4421: strcat(fileresprobcor,fileresu);
1.126 brouard 4422: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4423: printf("Problem with resultfile: %s\n", fileresprobcor);
4424: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4425: }
4426: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4427: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4428: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4429: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4430: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4431: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4432: pstamp(ficresprob);
4433: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4434: fprintf(ficresprob,"# Age");
4435: pstamp(ficresprobcov);
4436: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4437: fprintf(ficresprobcov,"# Age");
4438: pstamp(ficresprobcor);
4439: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4440: fprintf(ficresprobcor,"# Age");
4441:
4442:
4443: for(i=1; i<=nlstate;i++)
4444: for(j=1; j<=(nlstate+ndeath);j++){
4445: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4446: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4447: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4448: }
4449: /* fprintf(ficresprob,"\n");
4450: fprintf(ficresprobcov,"\n");
4451: fprintf(ficresprobcor,"\n");
4452: */
1.131 brouard 4453: xp=vector(1,npar);
1.126 brouard 4454: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4455: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4456: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4457: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4458: first=1;
4459: fprintf(ficgp,"\n# Routine varprob");
4460: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4461: fprintf(fichtm,"\n");
4462:
1.200 brouard 4463: 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 4464: 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);
4465: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4466: and drawn. It helps understanding how is the covariance between two incidences.\
4467: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4468: 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. \
4469: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4470: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4471: standard deviations wide on each axis. <br>\
4472: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4473: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4474: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4475:
4476: cov[1]=1;
1.145 brouard 4477: /* tj=cptcoveff; */
4478: tj = (int) pow(2,cptcoveff);
1.126 brouard 4479: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4480: j1=0;
1.145 brouard 4481: for(j1=1; j1<=tj;j1++){
4482: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4483: /*j1++;*/
1.126 brouard 4484: if (cptcovn>0) {
4485: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4486: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4487: fprintf(ficresprob, "**********\n#\n");
4488: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4489: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4490: fprintf(ficresprobcov, "**********\n#\n");
4491:
4492: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4493: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4494: fprintf(ficgp, "**********\n#\n");
4495:
4496:
4497: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4498: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4499: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4500:
4501: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4502: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4503: fprintf(ficresprobcor, "**********\n#");
4504: }
4505:
1.145 brouard 4506: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4507: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4508: gp=vector(1,(nlstate)*(nlstate+ndeath));
4509: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4510: for (age=bage; age<=fage; age ++){
4511: cov[2]=age;
1.187 brouard 4512: if(nagesqr==1)
4513: cov[3]= age*age;
1.126 brouard 4514: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4515: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4516: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4517: * 1 1 1 1 1
4518: * 2 2 1 1 1
4519: * 3 1 2 1 1
4520: */
4521: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4522: }
1.186 brouard 4523: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4524: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4525: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4526: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4527:
4528:
4529: for(theta=1; theta <=npar; theta++){
4530: for(i=1; i<=npar; i++)
4531: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4532:
4533: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4534:
4535: k=0;
4536: for(i=1; i<= (nlstate); i++){
4537: for(j=1; j<=(nlstate+ndeath);j++){
4538: k=k+1;
4539: gp[k]=pmmij[i][j];
4540: }
4541: }
4542:
4543: for(i=1; i<=npar; i++)
4544: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4545:
4546: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4547: k=0;
4548: for(i=1; i<=(nlstate); i++){
4549: for(j=1; j<=(nlstate+ndeath);j++){
4550: k=k+1;
4551: gm[k]=pmmij[i][j];
4552: }
4553: }
4554:
4555: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4556: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4557: }
4558:
4559: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4560: for(theta=1; theta <=npar; theta++)
4561: trgradg[j][theta]=gradg[theta][j];
4562:
4563: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4564: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4565:
4566: pmij(pmmij,cov,ncovmodel,x,nlstate);
4567:
4568: k=0;
4569: for(i=1; i<=(nlstate); i++){
4570: for(j=1; j<=(nlstate+ndeath);j++){
4571: k=k+1;
4572: mu[k][(int) age]=pmmij[i][j];
4573: }
4574: }
4575: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4576: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4577: varpij[i][j][(int)age] = doldm[i][j];
4578:
4579: /*printf("\n%d ",(int)age);
4580: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4581: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4582: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4583: }*/
4584:
4585: fprintf(ficresprob,"\n%d ",(int)age);
4586: fprintf(ficresprobcov,"\n%d ",(int)age);
4587: fprintf(ficresprobcor,"\n%d ",(int)age);
4588:
4589: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4590: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4591: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4592: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4593: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4594: }
4595: i=0;
4596: for (k=1; k<=(nlstate);k++){
4597: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4598: i++;
1.126 brouard 4599: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4600: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4601: for (j=1; j<=i;j++){
1.145 brouard 4602: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4603: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4604: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4605: }
4606: }
4607: }/* end of loop for state */
4608: } /* end of loop for age */
1.145 brouard 4609: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4610: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4611: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4612: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4613:
1.126 brouard 4614: /* Confidence intervalle of pij */
4615: /*
1.131 brouard 4616: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4617: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4618: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4619: 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);
4620: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4621: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4622: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4623: */
4624:
4625: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4626: first1=1;first2=2;
1.126 brouard 4627: for (k2=1; k2<=(nlstate);k2++){
4628: for (l2=1; l2<=(nlstate+ndeath);l2++){
4629: if(l2==k2) continue;
4630: j=(k2-1)*(nlstate+ndeath)+l2;
4631: for (k1=1; k1<=(nlstate);k1++){
4632: for (l1=1; l1<=(nlstate+ndeath);l1++){
4633: if(l1==k1) continue;
4634: i=(k1-1)*(nlstate+ndeath)+l1;
4635: if(i<=j) continue;
4636: for (age=bage; age<=fage; age ++){
4637: if ((int)age %5==0){
4638: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4639: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4640: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4641: mu1=mu[i][(int) age]/stepm*YEARM ;
4642: mu2=mu[j][(int) age]/stepm*YEARM;
4643: c12=cv12/sqrt(v1*v2);
4644: /* Computing eigen value of matrix of covariance */
4645: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4646: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4647: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4648: if(first2==1){
4649: first1=0;
4650: 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);
4651: }
4652: 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);
4653: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4654: /* lc2=fabs(lc2); */
1.135 brouard 4655: }
4656:
1.126 brouard 4657: /* Eigen vectors */
4658: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4659: /*v21=sqrt(1.-v11*v11); *//* error */
4660: v21=(lc1-v1)/cv12*v11;
4661: v12=-v21;
4662: v22=v11;
4663: tnalp=v21/v11;
4664: if(first1==1){
4665: first1=0;
4666: 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);
4667: }
4668: 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);
4669: /*printf(fignu*/
4670: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4671: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4672: if(first==1){
4673: first=0;
1.200 brouard 4674: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4675: fprintf(ficgp,"\nset parametric;unset label");
4676: 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 4677: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4678: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4679: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4680: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4681: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4682: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4683: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4684: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4685: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4686: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4687: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4688: 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",\
4689: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4690: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4691: }else{
4692: first=0;
4693: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4694: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4695: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4696: 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",\
4697: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4698: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4699: }/* if first */
4700: } /* age mod 5 */
4701: } /* end loop age */
1.201 brouard 4702: 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 4703: first=1;
4704: } /*l12 */
4705: } /* k12 */
4706: } /*l1 */
4707: }/* k1 */
1.169 brouard 4708: /* } */ /* loop covariates */
1.126 brouard 4709: }
4710: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4711: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4712: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4713: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4714: free_vector(xp,1,npar);
4715: fclose(ficresprob);
4716: fclose(ficresprobcov);
4717: fclose(ficresprobcor);
4718: fflush(ficgp);
4719: fflush(fichtmcov);
4720: }
4721:
4722:
4723: /******************* Printing html file ***********/
1.201 brouard 4724: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4725: int lastpass, int stepm, int weightopt, char model[],\
4726: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4727: int popforecast, int estepm ,\
4728: double jprev1, double mprev1,double anprev1, \
4729: double jprev2, double mprev2,double anprev2){
4730: int jj1, k1, i1, cpt;
4731:
4732: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4733: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4734: </ul>");
4735: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4736: - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
1.201 brouard 4737: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4738: fprintf(fichtm,"\
4739: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4740: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4741: fprintf(fichtm,"\
4742: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4743: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4744: fprintf(fichtm,"\
1.128 brouard 4745: - (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
1.126 brouard 4746: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4747: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4748: fprintf(fichtm,"\
4749: - Population projections by age and states: \
1.201 brouard 4750: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4751:
4752: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4753:
1.145 brouard 4754: m=pow(2,cptcoveff);
1.126 brouard 4755: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4756:
4757: jj1=0;
4758: for(k1=1; k1<=m;k1++){
1.192 brouard 4759: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4760: jj1++;
4761: if (cptcovn > 0) {
4762: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4763: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4764: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4765: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4766: }
1.126 brouard 4767: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4768: }
1.201 brouard 4769: /* aij, bij */
4770: fprintf(fichtm,"<br>- Logit model, 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> \
4771: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4772: /* Pij */
1.202 brouard 4773: fprintf(fichtm,"<br>\n- Pij 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 4774: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4775: /* Quasi-incidences */
1.201 brouard 4776: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4777: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4778: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4779: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4780: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4781: /* Survival functions (period) in state j */
4782: for(cpt=1; cpt<=nlstate;cpt++){
4783: 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> \
4784: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4785: }
4786: /* State specific survival functions (period) */
4787: for(cpt=1; cpt<=nlstate;cpt++){
4788: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
4789: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4790: <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);
4791: }
4792: /* Period (stable) prevalence in each health state */
4793: for(cpt=1; cpt<=nlstate;cpt++){
4794: 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> \
4795: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4796: }
1.126 brouard 4797: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4798: 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 4799: <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 4800: }
1.192 brouard 4801: /* } /\* end i1 *\/ */
1.126 brouard 4802: }/* End k1 */
4803: fprintf(fichtm,"</ul>");
4804:
4805: fprintf(fichtm,"\
4806: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4807: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4808: - 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 4809: But because parameters are usually highly correlated (a higher incidence of disability \
4810: and a higher incidence of recovery can give very close observed transition) it might \
4811: be very useful to look not only at linear confidence intervals estimated from the \
4812: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4813: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4814: covariance matrix of the one-step probabilities. \
4815: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4816:
1.193 brouard 4817: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4818: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4819: fprintf(fichtm,"\
4820: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4821: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4822:
4823: fprintf(fichtm,"\
4824: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4825: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4826: fprintf(fichtm,"\
4827: - 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): \
4828: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4829: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4830: fprintf(fichtm,"\
4831: - (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): \
4832: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4833: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4834: fprintf(fichtm,"\
1.128 brouard 4835: - 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 4836: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4837: fprintf(fichtm,"\
1.128 brouard 4838: - 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 4839: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4840: fprintf(fichtm,"\
4841: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4842: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4843:
4844: /* if(popforecast==1) fprintf(fichtm,"\n */
4845: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4846: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4847: /* <br>",fileres,fileres,fileres,fileres); */
4848: /* else */
4849: /* 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); */
4850: fflush(fichtm);
4851: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4852:
1.145 brouard 4853: m=pow(2,cptcoveff);
1.126 brouard 4854: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4855:
4856: jj1=0;
4857: for(k1=1; k1<=m;k1++){
1.192 brouard 4858: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4859: jj1++;
4860: if (cptcovn > 0) {
4861: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4862: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4863: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4864: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4865: }
4866: for(cpt=1; cpt<=nlstate;cpt++) {
4867: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4868: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4869: <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 4870: }
4871: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4872: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4873: true period expectancies (those weighted with period prevalences are also\
4874: drawn in addition to the population based expectancies computed using\
1.205 brouard 4875: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4876: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4877: /* } /\* end i1 *\/ */
1.126 brouard 4878: }/* End k1 */
4879: fprintf(fichtm,"</ul>");
4880: fflush(fichtm);
4881: }
4882:
4883: /******************* Gnuplot file **************/
1.201 brouard 4884: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4885:
4886: char dirfileres[132],optfileres[132];
1.164 brouard 4887: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4888: int ng=0;
1.201 brouard 4889: int vpopbased;
1.126 brouard 4890: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4891: /* printf("Problem with file %s",optionfilegnuplot); */
4892: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4893: /* } */
4894:
4895: /*#ifdef windows */
4896: fprintf(ficgp,"cd \"%s\" \n",pathc);
4897: /*#endif */
4898: m=pow(2,cptcoveff);
4899:
1.202 brouard 4900: /* Contribution to likelihood */
4901: /* Plot the probability implied in the likelihood */
4902: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4903: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4904: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4905: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4906: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4907: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4908: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4909: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 4910: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4911: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):5 t \"All sample, transitions colored by destination\" with dots lc variable; set out;\n",subdirf(fileresilk));
1.204 brouard 4912: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4913: fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$12):4 t \"All sample, transitions colored by origin\" with dots lc variable; set out;\n\n",subdirf(fileresilk));
1.204 brouard 4914: for (i=1; i<= nlstate ; i ++) {
4915: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 4916: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
4917: fprintf(ficgp," u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable \\\n",i,1,i,1);
1.204 brouard 4918: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 4919: fprintf(ficgp,",\\\n \"\" u 2:($4 == %d && $5==%d ? $9 : 1/0):($11/4.):5 t \"p%d%d\" with points pointtype 7 ps variable lc variable ",i,j,i,j);
1.204 brouard 4920: }
4921: fprintf(ficgp,";\nset out; unset ylabel;\n");
4922: }
4923: /* 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 */
4924: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
4925: /* 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 4926: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4927: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4928:
1.126 brouard 4929: strcpy(dirfileres,optionfilefiname);
4930: strcpy(optfileres,"vpl");
4931: /* 1eme*/
1.201 brouard 4932: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4933: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4934: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4935: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4936: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4937: fprintf(ficgp,"set xlabel \"Age\" \n\
4938: set ylabel \"Probability\" \n\
1.199 brouard 4939: set ter svg size 640, 480\n\
1.201 brouard 4940: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4941:
4942: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4943: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4944: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4945: }
1.201 brouard 4946: 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 4947: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4948: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4949: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4950: }
1.201 brouard 4951: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4952: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4953: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4954: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4955: }
1.201 brouard 4956: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
4957: fprintf(ficgp,"\nset out \n");
4958: } /* k1 */
4959: } /* cpt */
1.126 brouard 4960: /*2 eme*/
1.153 brouard 4961: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4962: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 4963: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
4964: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
4965: if(vpopbased==0)
4966: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
4967: else
4968: fprintf(ficgp,"\nreplot ");
4969: for (i=1; i<= nlstate+1 ; i ++) {
4970: k=2*i;
4971: 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);
4972: for (j=1; j<= nlstate+1 ; j ++) {
4973: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4974: else fprintf(ficgp," %%*lf (%%*lf)");
4975: }
4976: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
4977: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
4978: 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);
4979: for (j=1; j<= nlstate+1 ; j ++) {
4980: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4981: else fprintf(ficgp," %%*lf (%%*lf)");
4982: }
4983: fprintf(ficgp,"\" t\"\" w l lt 0,");
4984: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4985: for (j=1; j<= nlstate+1 ; j ++) {
4986: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4987: else fprintf(ficgp," %%*lf (%%*lf)");
4988: }
4989: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4990: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
4991: } /* state */
4992: } /* vpopbased */
4993: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
4994: } /* k1 */
1.126 brouard 4995: /*3eme*/
4996:
4997: for (k1=1; k1<= m ; k1 ++) {
4998: for (cpt=1; cpt<= nlstate ; cpt ++) {
4999: /* k=2+nlstate*(2*cpt-2); */
5000: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5001: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5002: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5003: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5004: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5005: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5006: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5007: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5008: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5009: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5010:
5011: */
5012: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5013: 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 5014: /* 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);*/
5015:
5016: }
1.201 brouard 5017: 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 5018: }
5019: }
5020:
1.201 brouard 5021: /* Survival functions (period) from state i in state j by initial state i */
5022: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5023: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5024: k=3;
5025: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
5026: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5027: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5028: set ter svg size 640, 480\n\
5029: unset log y\n\
5030: plot [%.f:%.f] ", ageminpar, agemaxpar);
5031: for (i=1; i<= nlstate ; i ++){
5032: if(i==1)
5033: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5034: else
5035: fprintf(ficgp,", '' ");
5036: l=(nlstate+ndeath)*(i-1)+1;
5037: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5038: for (j=2; j<= nlstate+ndeath ; j ++)
5039: fprintf(ficgp,"+$%d",k+l+j-1);
5040: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5041: } /* nlstate */
5042: fprintf(ficgp,"\nset out\n");
5043: } /* end cpt state*/
5044: } /* end covariate */
5045:
5046: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5047: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5048: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5049: k=3;
5050: 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);
5051: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5052: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5053: set ter svg size 640, 480\n\
5054: unset log y\n\
5055: plot [%.f:%.f] ", ageminpar, agemaxpar);
5056: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5057: if(j==1)
5058: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5059: else
5060: fprintf(ficgp,", '' ");
5061: l=(nlstate+ndeath)*(cpt-1) +j;
5062: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5063: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5064: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5065: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5066: } /* nlstate */
5067: fprintf(ficgp,", '' ");
5068: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5069: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5070: l=(nlstate+ndeath)*(cpt-1) +j;
5071: if(j < nlstate)
5072: fprintf(ficgp,"$%d +",k+l);
5073: else
5074: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5075: }
5076: fprintf(ficgp,"\nset out\n");
5077: } /* end cpt state*/
5078: } /* end covariate */
5079:
1.202 brouard 5080: /* CV preval stable (period) for each covariate */
5081: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5082: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5083: k=3;
1.153 brouard 5084: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5085: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5086: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5087: set ter svg size 640, 480\n\
1.126 brouard 5088: unset log y\n\
1.153 brouard 5089: plot [%.f:%.f] ", ageminpar, agemaxpar);
5090: for (i=1; i<= nlstate ; i ++){
5091: if(i==1)
1.201 brouard 5092: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5093: else
5094: fprintf(ficgp,", '' ");
1.154 brouard 5095: l=(nlstate+ndeath)*(i-1)+1;
5096: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5097: for (j=2; j<= nlstate ; j ++)
5098: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5099: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5100: } /* nlstate */
1.201 brouard 5101: fprintf(ficgp,"\nset out\n");
1.153 brouard 5102: } /* end cpt state*/
5103: } /* end covariate */
1.201 brouard 5104:
1.126 brouard 5105: /* proba elementaires */
1.187 brouard 5106: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5107: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5108: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5109: for(k=1; k <=(nlstate+ndeath); k++){
5110: if (k != i) {
1.187 brouard 5111: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5112: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5113: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5114: jk++;
5115: }
1.187 brouard 5116: fprintf(ficgp,"\n");
1.126 brouard 5117: }
5118: }
5119: }
1.187 brouard 5120: fprintf(ficgp,"##############\n#\n");
5121:
1.145 brouard 5122: /*goto avoid;*/
1.200 brouard 5123: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5124: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5125: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5126: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5127: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5128: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5129: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5130: fprintf(ficgp,"# p11=1/(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5131: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5132: fprintf(ficgp,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5133: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5134: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5135: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5136: fprintf(ficgp,"#\n");
1.201 brouard 5137: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5138: fprintf(ficgp,"# ng=%d\n",ng);
5139: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5140: for(jk=1; jk <=m; jk++) {
1.187 brouard 5141: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5142: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5143: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5144: if (ng==1){
5145: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5146: fprintf(ficgp,"\nunset log y");
5147: }else if (ng==2){
5148: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5149: fprintf(ficgp,"\nset log y");
5150: }else if (ng==3){
1.126 brouard 5151: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5152: fprintf(ficgp,"\nset log y");
5153: }else
5154: fprintf(ficgp,"\nunset title ");
5155: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5156: i=1;
5157: for(k2=1; k2<=nlstate; k2++) {
5158: k3=i;
5159: for(k=1; k<=(nlstate+ndeath); k++) {
5160: if (k != k2){
1.201 brouard 5161: switch( ng) {
5162: case 1:
1.187 brouard 5163: if(nagesqr==0)
1.201 brouard 5164: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5165: else /* nagesqr =1 */
1.201 brouard 5166: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5167: break;
5168: case 2: /* ng=2 */
1.187 brouard 5169: if(nagesqr==0)
5170: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5171: else /* nagesqr =1 */
1.201 brouard 5172: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5173: break;
5174: case 3:
5175: if(nagesqr==0)
5176: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5177: else /* nagesqr =1 */
5178: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5179: break;
5180: }
1.141 brouard 5181: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5182: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5183: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5184: if(ij <=cptcovage) { /* Bug valgrind */
5185: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5186: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5187: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5188: ij++;
5189: }
1.186 brouard 5190: }
5191: else
1.198 brouard 5192: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5193: }
1.201 brouard 5194: if(ng != 1){
5195: fprintf(ficgp,")/(1");
1.126 brouard 5196:
1.201 brouard 5197: for(k1=1; k1 <=nlstate; k1++){
5198: if(nagesqr==0)
5199: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5200: else /* nagesqr =1 */
5201: 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);
5202:
5203: ij=1;
5204: for(j=3; j <=ncovmodel-nagesqr; j++){
5205: if(ij <=cptcovage) { /* Bug valgrind */
5206: if((j-2)==Tage[ij]) { /* Bug valgrind */
5207: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5208: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5209: ij++;
5210: }
1.197 brouard 5211: }
1.201 brouard 5212: else
5213: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5214: }
1.201 brouard 5215: fprintf(ficgp,")");
1.126 brouard 5216: }
5217: fprintf(ficgp,")");
1.201 brouard 5218: if(ng ==2)
5219: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5220: else /* ng= 3 */
5221: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5222: }else{ /* end ng <> 1 */
5223: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5224: }
5225: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5226: i=i+ncovmodel;
5227: }
5228: } /* end k */
5229: } /* end k2 */
1.201 brouard 5230: fprintf(ficgp,"\n set out\n");
1.126 brouard 5231: } /* end jk */
5232: } /* end ng */
1.164 brouard 5233: /* avoid: */
1.126 brouard 5234: fflush(ficgp);
5235: } /* end gnuplot */
5236:
5237:
5238: /*************** Moving average **************/
5239: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5240:
5241: int i, cpt, cptcod;
5242: int modcovmax =1;
5243: int mobilavrange, mob;
5244: double age;
5245:
5246: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5247: a covariate has 2 modalities */
5248: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5249:
5250: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5251: if(mobilav==1) mobilavrange=5; /* default */
5252: else mobilavrange=mobilav;
5253: for (age=bage; age<=fage; age++)
5254: for (i=1; i<=nlstate;i++)
5255: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5256: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5257: /* We keep the original values on the extreme ages bage, fage and for
5258: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5259: we use a 5 terms etc. until the borders are no more concerned.
5260: */
5261: for (mob=3;mob <=mobilavrange;mob=mob+2){
5262: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5263: for (i=1; i<=nlstate;i++){
5264: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5265: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5266: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5267: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5268: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5269: }
5270: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5271: }
5272: }
5273: }/* end age */
5274: }/* end mob */
5275: }else return -1;
5276: return 0;
5277: }/* End movingaverage */
5278:
5279:
5280: /************** Forecasting ******************/
1.169 brouard 5281: 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 5282: /* proj1, year, month, day of starting projection
5283: agemin, agemax range of age
5284: dateprev1 dateprev2 range of dates during which prevalence is computed
5285: anproj2 year of en of projection (same day and month as proj1).
5286: */
1.164 brouard 5287: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5288: double agec; /* generic age */
5289: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5290: double *popeffectif,*popcount;
5291: double ***p3mat;
5292: double ***mobaverage;
5293: char fileresf[FILENAMELENGTH];
5294:
5295: agelim=AGESUP;
5296: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5297:
1.201 brouard 5298: strcpy(fileresf,"F_");
5299: strcat(fileresf,fileresu);
1.126 brouard 5300: if((ficresf=fopen(fileresf,"w"))==NULL) {
5301: printf("Problem with forecast resultfile: %s\n", fileresf);
5302: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5303: }
5304: printf("Computing forecasting: result on file '%s' \n", fileresf);
5305: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5306:
5307: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5308:
5309: if (mobilav!=0) {
5310: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5311: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5312: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5313: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5314: }
5315: }
5316:
5317: stepsize=(int) (stepm+YEARM-1)/YEARM;
5318: if (stepm<=12) stepsize=1;
5319: if(estepm < stepm){
5320: printf ("Problem %d lower than %d\n",estepm, stepm);
5321: }
5322: else hstepm=estepm;
5323:
5324: hstepm=hstepm/stepm;
5325: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5326: fractional in yp1 */
5327: anprojmean=yp;
5328: yp2=modf((yp1*12),&yp);
5329: mprojmean=yp;
5330: yp1=modf((yp2*30.5),&yp);
5331: jprojmean=yp;
5332: if(jprojmean==0) jprojmean=1;
5333: if(mprojmean==0) jprojmean=1;
5334:
5335: i1=cptcoveff;
5336: if (cptcovn < 1){i1=1;}
5337:
5338: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5339:
5340: fprintf(ficresf,"#****** Routine prevforecast **\n");
5341:
5342: /* if (h==(int)(YEARM*yearp)){ */
5343: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5344: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5345: k=k+1;
5346: fprintf(ficresf,"\n#******");
5347: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5348: fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5349: }
5350: fprintf(ficresf,"******\n");
5351: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5352: for(j=1; j<=nlstate+ndeath;j++){
5353: for(i=1; i<=nlstate;i++)
5354: fprintf(ficresf," p%d%d",i,j);
5355: fprintf(ficresf," p.%d",j);
5356: }
5357: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5358: fprintf(ficresf,"\n");
5359: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5360:
5361: for (agec=fage; agec>=(ageminpar-1); agec--){
5362: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5363: nhstepm = nhstepm/hstepm;
5364: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5365: oldm=oldms;savm=savms;
5366: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5367:
5368: for (h=0; h<=nhstepm; h++){
5369: if (h*hstepm/YEARM*stepm ==yearp) {
5370: fprintf(ficresf,"\n");
5371: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5372: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5373: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5374: }
5375: for(j=1; j<=nlstate+ndeath;j++) {
5376: ppij=0.;
5377: for(i=1; i<=nlstate;i++) {
5378: if (mobilav==1)
5379: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5380: else {
5381: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5382: }
5383: if (h*hstepm/YEARM*stepm== yearp) {
5384: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5385: }
5386: } /* end i */
5387: if (h*hstepm/YEARM*stepm==yearp) {
5388: fprintf(ficresf," %.3f", ppij);
5389: }
5390: }/* end j */
5391: } /* end h */
5392: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5393: } /* end agec */
5394: } /* end yearp */
5395: } /* end cptcod */
5396: } /* end cptcov */
5397:
5398: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5399:
5400: fclose(ficresf);
5401: }
5402:
5403: /************** Forecasting *****not tested NB*************/
1.169 brouard 5404: 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 5405:
5406: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5407: int *popage;
5408: double calagedatem, agelim, kk1, kk2;
5409: double *popeffectif,*popcount;
5410: double ***p3mat,***tabpop,***tabpopprev;
5411: double ***mobaverage;
5412: char filerespop[FILENAMELENGTH];
5413:
5414: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5415: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5416: agelim=AGESUP;
5417: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5418:
5419: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5420:
5421:
1.201 brouard 5422: strcpy(filerespop,"POP_");
5423: strcat(filerespop,fileresu);
1.126 brouard 5424: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5425: printf("Problem with forecast resultfile: %s\n", filerespop);
5426: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5427: }
5428: printf("Computing forecasting: result on file '%s' \n", filerespop);
5429: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5430:
5431: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5432:
5433: if (mobilav!=0) {
5434: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5435: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5436: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5437: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5438: }
5439: }
5440:
5441: stepsize=(int) (stepm+YEARM-1)/YEARM;
5442: if (stepm<=12) stepsize=1;
5443:
5444: agelim=AGESUP;
5445:
5446: hstepm=1;
5447: hstepm=hstepm/stepm;
5448:
5449: if (popforecast==1) {
5450: if((ficpop=fopen(popfile,"r"))==NULL) {
5451: printf("Problem with population file : %s\n",popfile);exit(0);
5452: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5453: }
5454: popage=ivector(0,AGESUP);
5455: popeffectif=vector(0,AGESUP);
5456: popcount=vector(0,AGESUP);
5457:
5458: i=1;
5459: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5460:
5461: imx=i;
5462: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5463: }
5464:
5465: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5466: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5467: k=k+1;
5468: fprintf(ficrespop,"\n#******");
5469: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5470: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5471: }
5472: fprintf(ficrespop,"******\n");
5473: fprintf(ficrespop,"# Age");
5474: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5475: if (popforecast==1) fprintf(ficrespop," [Population]");
5476:
5477: for (cpt=0; cpt<=0;cpt++) {
5478: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5479:
5480: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5481: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5482: nhstepm = nhstepm/hstepm;
5483:
5484: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5485: oldm=oldms;savm=savms;
5486: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5487:
5488: for (h=0; h<=nhstepm; h++){
5489: if (h==(int) (calagedatem+YEARM*cpt)) {
5490: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5491: }
5492: for(j=1; j<=nlstate+ndeath;j++) {
5493: kk1=0.;kk2=0;
5494: for(i=1; i<=nlstate;i++) {
5495: if (mobilav==1)
5496: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5497: else {
5498: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5499: }
5500: }
5501: if (h==(int)(calagedatem+12*cpt)){
5502: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5503: /*fprintf(ficrespop," %.3f", kk1);
5504: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5505: }
5506: }
5507: for(i=1; i<=nlstate;i++){
5508: kk1=0.;
5509: for(j=1; j<=nlstate;j++){
5510: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5511: }
5512: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5513: }
5514:
5515: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5516: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5517: }
5518: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5519: }
5520: }
5521:
5522: /******/
5523:
5524: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5525: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5526: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5527: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5528: nhstepm = nhstepm/hstepm;
5529:
5530: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5531: oldm=oldms;savm=savms;
5532: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5533: for (h=0; h<=nhstepm; h++){
5534: if (h==(int) (calagedatem+YEARM*cpt)) {
5535: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5536: }
5537: for(j=1; j<=nlstate+ndeath;j++) {
5538: kk1=0.;kk2=0;
5539: for(i=1; i<=nlstate;i++) {
5540: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5541: }
5542: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5543: }
5544: }
5545: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5546: }
5547: }
5548: }
5549: }
5550:
5551: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5552:
5553: if (popforecast==1) {
5554: free_ivector(popage,0,AGESUP);
5555: free_vector(popeffectif,0,AGESUP);
5556: free_vector(popcount,0,AGESUP);
5557: }
5558: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5559: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5560: fclose(ficrespop);
5561: } /* End of popforecast */
5562:
5563: int fileappend(FILE *fichier, char *optionfich)
5564: {
5565: if((fichier=fopen(optionfich,"a"))==NULL) {
5566: printf("Problem with file: %s\n", optionfich);
5567: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5568: return (0);
5569: }
5570: fflush(fichier);
5571: return (1);
5572: }
5573:
5574:
5575: /**************** function prwizard **********************/
5576: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5577: {
5578:
5579: /* Wizard to print covariance matrix template */
5580:
1.164 brouard 5581: char ca[32], cb[32];
5582: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5583: int numlinepar;
5584:
5585: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5586: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5587: for(i=1; i <=nlstate; i++){
5588: jj=0;
5589: for(j=1; j <=nlstate+ndeath; j++){
5590: if(j==i) continue;
5591: jj++;
5592: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5593: printf("%1d%1d",i,j);
5594: fprintf(ficparo,"%1d%1d",i,j);
5595: for(k=1; k<=ncovmodel;k++){
5596: /* printf(" %lf",param[i][j][k]); */
5597: /* fprintf(ficparo," %lf",param[i][j][k]); */
5598: printf(" 0.");
5599: fprintf(ficparo," 0.");
5600: }
5601: printf("\n");
5602: fprintf(ficparo,"\n");
5603: }
5604: }
5605: printf("# Scales (for hessian or gradient estimation)\n");
5606: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5607: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5608: for(i=1; i <=nlstate; i++){
5609: jj=0;
5610: for(j=1; j <=nlstate+ndeath; j++){
5611: if(j==i) continue;
5612: jj++;
5613: fprintf(ficparo,"%1d%1d",i,j);
5614: printf("%1d%1d",i,j);
5615: fflush(stdout);
5616: for(k=1; k<=ncovmodel;k++){
5617: /* printf(" %le",delti3[i][j][k]); */
5618: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5619: printf(" 0.");
5620: fprintf(ficparo," 0.");
5621: }
5622: numlinepar++;
5623: printf("\n");
5624: fprintf(ficparo,"\n");
5625: }
5626: }
5627: printf("# Covariance matrix\n");
5628: /* # 121 Var(a12)\n\ */
5629: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5630: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5631: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5632: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5633: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5634: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5635: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5636: fflush(stdout);
5637: fprintf(ficparo,"# Covariance matrix\n");
5638: /* # 121 Var(a12)\n\ */
5639: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5640: /* # ...\n\ */
5641: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5642:
5643: for(itimes=1;itimes<=2;itimes++){
5644: jj=0;
5645: for(i=1; i <=nlstate; i++){
5646: for(j=1; j <=nlstate+ndeath; j++){
5647: if(j==i) continue;
5648: for(k=1; k<=ncovmodel;k++){
5649: jj++;
5650: ca[0]= k+'a'-1;ca[1]='\0';
5651: if(itimes==1){
5652: printf("#%1d%1d%d",i,j,k);
5653: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5654: }else{
5655: printf("%1d%1d%d",i,j,k);
5656: fprintf(ficparo,"%1d%1d%d",i,j,k);
5657: /* printf(" %.5le",matcov[i][j]); */
5658: }
5659: ll=0;
5660: for(li=1;li <=nlstate; li++){
5661: for(lj=1;lj <=nlstate+ndeath; lj++){
5662: if(lj==li) continue;
5663: for(lk=1;lk<=ncovmodel;lk++){
5664: ll++;
5665: if(ll<=jj){
5666: cb[0]= lk +'a'-1;cb[1]='\0';
5667: if(ll<jj){
5668: if(itimes==1){
5669: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5670: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5671: }else{
5672: printf(" 0.");
5673: fprintf(ficparo," 0.");
5674: }
5675: }else{
5676: if(itimes==1){
5677: printf(" Var(%s%1d%1d)",ca,i,j);
5678: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5679: }else{
5680: printf(" 0.");
5681: fprintf(ficparo," 0.");
5682: }
5683: }
5684: }
5685: } /* end lk */
5686: } /* end lj */
5687: } /* end li */
5688: printf("\n");
5689: fprintf(ficparo,"\n");
5690: numlinepar++;
5691: } /* end k*/
5692: } /*end j */
5693: } /* end i */
5694: } /* end itimes */
5695:
5696: } /* end of prwizard */
5697: /******************* Gompertz Likelihood ******************************/
5698: double gompertz(double x[])
5699: {
5700: double A,B,L=0.0,sump=0.,num=0.;
5701: int i,n=0; /* n is the size of the sample */
5702:
5703: for (i=0;i<=imx-1 ; i++) {
5704: sump=sump+weight[i];
5705: /* sump=sump+1;*/
5706: num=num+1;
5707: }
5708:
5709:
5710: /* for (i=0; i<=imx; i++)
5711: 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]);*/
5712:
5713: for (i=1;i<=imx ; i++)
5714: {
5715: if (cens[i] == 1 && wav[i]>1)
5716: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5717:
5718: if (cens[i] == 0 && wav[i]>1)
5719: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5720: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5721:
5722: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5723: if (wav[i] > 1 ) { /* ??? */
5724: L=L+A*weight[i];
5725: /* 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]);*/
5726: }
5727: }
5728:
5729: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5730:
5731: return -2*L*num/sump;
5732: }
5733:
1.136 brouard 5734: #ifdef GSL
5735: /******************* Gompertz_f Likelihood ******************************/
5736: double gompertz_f(const gsl_vector *v, void *params)
5737: {
5738: double A,B,LL=0.0,sump=0.,num=0.;
5739: double *x= (double *) v->data;
5740: int i,n=0; /* n is the size of the sample */
5741:
5742: for (i=0;i<=imx-1 ; i++) {
5743: sump=sump+weight[i];
5744: /* sump=sump+1;*/
5745: num=num+1;
5746: }
5747:
5748:
5749: /* for (i=0; i<=imx; i++)
5750: 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]);*/
5751: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5752: for (i=1;i<=imx ; i++)
5753: {
5754: if (cens[i] == 1 && wav[i]>1)
5755: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5756:
5757: if (cens[i] == 0 && wav[i]>1)
5758: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5759: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5760:
5761: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5762: if (wav[i] > 1 ) { /* ??? */
5763: LL=LL+A*weight[i];
5764: /* 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]);*/
5765: }
5766: }
5767:
5768: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5769: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5770:
5771: return -2*LL*num/sump;
5772: }
5773: #endif
5774:
1.126 brouard 5775: /******************* Printing html file ***********/
1.201 brouard 5776: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5777: int lastpass, int stepm, int weightopt, char model[],\
5778: int imx, double p[],double **matcov,double agemortsup){
5779: int i,k;
5780:
5781: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5782: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5783: for (i=1;i<=2;i++)
5784: 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 5785: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5786: fprintf(fichtm,"</ul>");
5787:
5788: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5789:
5790: 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>");
5791:
5792: for (k=agegomp;k<(agemortsup-2);k++)
5793: 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]);
5794:
5795:
5796: fflush(fichtm);
5797: }
5798:
5799: /******************* Gnuplot file **************/
1.201 brouard 5800: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5801:
5802: char dirfileres[132],optfileres[132];
1.164 brouard 5803:
1.126 brouard 5804: int ng;
5805:
5806:
5807: /*#ifdef windows */
5808: fprintf(ficgp,"cd \"%s\" \n",pathc);
5809: /*#endif */
5810:
5811:
5812: strcpy(dirfileres,optionfilefiname);
5813: strcpy(optfileres,"vpl");
1.199 brouard 5814: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5815: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5816: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5817: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5818: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5819:
5820: }
5821:
1.136 brouard 5822: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5823: {
1.126 brouard 5824:
1.136 brouard 5825: /*-------- data file ----------*/
5826: FILE *fic;
5827: char dummy[]=" ";
1.164 brouard 5828: int i=0, j=0, n=0;
1.136 brouard 5829: int linei, month, year,iout;
5830: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5831: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5832: char *stratrunc;
5833: int lstra;
1.126 brouard 5834:
5835:
1.136 brouard 5836: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5837: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5838: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5839: }
1.126 brouard 5840:
1.136 brouard 5841: i=1;
5842: linei=0;
5843: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5844: linei=linei+1;
5845: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5846: if(line[j] == '\t')
5847: line[j] = ' ';
5848: }
5849: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5850: ;
5851: };
5852: line[j+1]=0; /* Trims blanks at end of line */
5853: if(line[0]=='#'){
5854: fprintf(ficlog,"Comment line\n%s\n",line);
5855: printf("Comment line\n%s\n",line);
5856: continue;
5857: }
5858: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5859: strcpy(line, linetmp);
1.136 brouard 5860:
1.126 brouard 5861:
1.136 brouard 5862: for (j=maxwav;j>=1;j--){
1.137 brouard 5863: cutv(stra, strb, line, ' ');
1.136 brouard 5864: if(strb[0]=='.') { /* Missing status */
5865: lval=-1;
5866: }else{
5867: errno=0;
5868: lval=strtol(strb,&endptr,10);
5869: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5870: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5871: 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);
5872: 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 5873: return 1;
5874: }
5875: }
5876: s[j][i]=lval;
5877:
5878: strcpy(line,stra);
5879: cutv(stra, strb,line,' ');
1.169 brouard 5880: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5881: }
1.169 brouard 5882: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5883: month=99;
5884: year=9999;
5885: }else{
1.141 brouard 5886: 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);
5887: 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 5888: return 1;
5889: }
5890: anint[j][i]= (double) year;
5891: mint[j][i]= (double)month;
5892: strcpy(line,stra);
5893: } /* ENd Waves */
5894:
5895: cutv(stra, strb,line,' ');
1.169 brouard 5896: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5897: }
1.169 brouard 5898: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5899: month=99;
5900: year=9999;
5901: }else{
1.141 brouard 5902: 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);
5903: 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 5904: return 1;
5905: }
5906: andc[i]=(double) year;
5907: moisdc[i]=(double) month;
5908: strcpy(line,stra);
5909:
5910: cutv(stra, strb,line,' ');
1.169 brouard 5911: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5912: }
1.169 brouard 5913: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5914: month=99;
5915: year=9999;
5916: }else{
1.141 brouard 5917: 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);
5918: 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 5919: return 1;
5920: }
5921: if (year==9999) {
1.141 brouard 5922: 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);
5923: 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 5924: return 1;
1.126 brouard 5925:
1.136 brouard 5926: }
5927: annais[i]=(double)(year);
5928: moisnais[i]=(double)(month);
5929: strcpy(line,stra);
5930:
5931: cutv(stra, strb,line,' ');
5932: errno=0;
5933: dval=strtod(strb,&endptr);
5934: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5935: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5936: 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 5937: fflush(ficlog);
5938: return 1;
5939: }
5940: weight[i]=dval;
5941: strcpy(line,stra);
5942:
5943: for (j=ncovcol;j>=1;j--){
5944: cutv(stra, strb,line,' ');
5945: if(strb[0]=='.') { /* Missing status */
5946: lval=-1;
5947: }else{
5948: errno=0;
5949: lval=strtol(strb,&endptr,10);
5950: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5951: 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);
5952: 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 5953: return 1;
5954: }
5955: }
5956: if(lval <-1 || lval >1){
1.141 brouard 5957: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5958: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5959: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5960: For example, for multinomial values like 1, 2 and 3,\n \
5961: build V1=0 V2=0 for the reference value (1),\n \
5962: V1=1 V2=0 for (2) \n \
5963: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5964: output of IMaCh is often meaningless.\n \
5965: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5966: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5967: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5968: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5969: For example, for multinomial values like 1, 2 and 3,\n \
5970: build V1=0 V2=0 for the reference value (1),\n \
5971: V1=1 V2=0 for (2) \n \
5972: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5973: output of IMaCh is often meaningless.\n \
5974: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5975: return 1;
5976: }
5977: covar[j][i]=(double)(lval);
5978: strcpy(line,stra);
5979: }
5980: lstra=strlen(stra);
5981:
5982: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5983: stratrunc = &(stra[lstra-9]);
5984: num[i]=atol(stratrunc);
5985: }
5986: else
5987: num[i]=atol(stra);
5988: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5989: 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;}*/
5990:
5991: i=i+1;
5992: } /* End loop reading data */
1.126 brouard 5993:
1.136 brouard 5994: *imax=i-1; /* Number of individuals */
5995: fclose(fic);
5996:
5997: return (0);
1.164 brouard 5998: /* endread: */
1.136 brouard 5999: printf("Exiting readdata: ");
6000: fclose(fic);
6001: return (1);
1.126 brouard 6002:
6003:
6004:
1.136 brouard 6005: }
1.145 brouard 6006: void removespace(char *str) {
6007: char *p1 = str, *p2 = str;
6008: do
6009: while (*p2 == ' ')
6010: p2++;
1.169 brouard 6011: while (*p1++ == *p2++);
1.145 brouard 6012: }
6013:
6014: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6015: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6016: * - nagesqr = 1 if age*age in the model, otherwise 0.
6017: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6018: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6019: * - cptcovage number of covariates with age*products =2
6020: * - cptcovs number of simple covariates
6021: * - 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
6022: * which is a new column after the 9 (ncovcol) variables.
6023: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6024: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6025: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6026: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6027: */
1.136 brouard 6028: {
1.145 brouard 6029: int i, j, k, ks;
1.164 brouard 6030: int j1, k1, k2;
1.136 brouard 6031: char modelsav[80];
1.145 brouard 6032: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6033: char *strpt;
1.136 brouard 6034:
1.145 brouard 6035: /*removespace(model);*/
1.136 brouard 6036: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6037: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6038: if (strstr(model,"AGE") !=0){
1.192 brouard 6039: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6040: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6041: return 1;
6042: }
1.141 brouard 6043: if (strstr(model,"v") !=0){
6044: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6045: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6046: return 1;
6047: }
1.187 brouard 6048: strcpy(modelsav,model);
6049: if ((strpt=strstr(model,"age*age")) !=0){
6050: printf(" strpt=%s, model=%s\n",strpt, model);
6051: if(strpt != model){
6052: printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6053: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6054: corresponding column of parameters.\n",model);
6055: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6056: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6057: corresponding column of parameters.\n",model); fflush(ficlog);
6058: return 1;
6059: }
6060:
6061: nagesqr=1;
6062: if (strstr(model,"+age*age") !=0)
6063: substrchaine(modelsav, model, "+age*age");
6064: else if (strstr(model,"age*age+") !=0)
6065: substrchaine(modelsav, model, "age*age+");
6066: else
6067: substrchaine(modelsav, model, "age*age");
6068: }else
6069: nagesqr=0;
6070: if (strlen(modelsav) >1){
6071: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6072: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6073: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6074: cptcovt= j+1; /* Number of total covariates in the model, not including
6075: * cst, age and age*age
6076: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6077: /* including age products which are counted in cptcovage.
6078: * but the covariates which are products must be treated
6079: * separately: ncovn=4- 2=2 (V1+V3). */
6080: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6081: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6082:
6083:
6084: /* Design
6085: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6086: * < ncovcol=8 >
6087: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6088: * k= 1 2 3 4 5 6 7 8
6089: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6090: * covar[k,i], value of kth covariate if not including age for individual i:
6091: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6092: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6093: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6094: * Tage[++cptcovage]=k
6095: * if products, new covar are created after ncovcol with k1
6096: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6097: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6098: * 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
6099: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6100: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6101: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6102: * < ncovcol=8 >
6103: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6104: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6105: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6106: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6107: * p Tprod[1]@2={ 6, 5}
6108: *p Tvard[1][1]@4= {7, 8, 5, 6}
6109: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6110: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6111: *How to reorganize?
6112: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6113: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6114: * {2, 1, 4, 8, 5, 6, 3, 7}
6115: * Struct []
6116: */
1.145 brouard 6117:
1.187 brouard 6118: /* This loop fills the array Tvar from the string 'model'.*/
6119: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6120: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6121: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6122: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6123: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6124: /* k=1 Tvar[1]=2 (from V2) */
6125: /* k=5 Tvar[5] */
6126: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6127: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6128: /* } */
1.198 brouard 6129: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6130: /*
6131: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6132: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6133: Tvar[k]=0;
1.187 brouard 6134: cptcovage=0;
6135: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6136: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6137: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6138: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6139: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6140: /*scanf("%d",i);*/
6141: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6142: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6143: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6144: /* covar is not filled and then is empty */
6145: cptcovprod--;
6146: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6147: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6148: cptcovage++; /* Sums the number of covariates which include age as a product */
6149: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6150: /*printf("stre=%s ", stre);*/
6151: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6152: cptcovprod--;
6153: cutl(stre,strb,strc,'V');
6154: Tvar[k]=atoi(stre);
6155: cptcovage++;
6156: Tage[cptcovage]=k;
6157: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6158: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6159: cptcovn++;
6160: cptcovprodnoage++;k1++;
6161: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6162: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6163: because this model-covariate is a construction we invent a new column
6164: ncovcol + k1
6165: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6166: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6167: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6168: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6169: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6170: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6171: k2=k2+2;
6172: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6173: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6174: for (i=1; i<=lastobs;i++){
6175: /* Computes the new covariate which is a product of
6176: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6177: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6178: }
6179: } /* End age is not in the model */
6180: } /* End if model includes a product */
6181: else { /* no more sum */
6182: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6183: /* scanf("%d",i);*/
6184: cutl(strd,strc,strb,'V');
6185: ks++; /**< Number of simple covariates */
1.145 brouard 6186: cptcovn++;
1.187 brouard 6187: Tvar[k]=atoi(strd);
6188: }
6189: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6190: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6191: scanf("%d",i);*/
6192: } /* end of loop + on total covariates */
6193: } /* end if strlen(modelsave == 0) age*age might exist */
6194: } /* end if strlen(model == 0) */
1.136 brouard 6195:
6196: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6197: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6198:
6199: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6200: printf("cptcovprod=%d ", cptcovprod);
6201: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6202:
6203: scanf("%d ",i);*/
6204:
6205:
1.137 brouard 6206: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6207: /*endread:*/
1.136 brouard 6208: printf("Exiting decodemodel: ");
6209: return (1);
6210: }
6211:
1.169 brouard 6212: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6213: {
6214: int i, m;
6215:
6216: for (i=1; i<=imx; i++) {
6217: for(m=2; (m<= maxwav); m++) {
6218: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6219: anint[m][i]=9999;
6220: s[m][i]=-1;
6221: }
6222: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6223: *nberr = *nberr + 1;
6224: 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);
6225: 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 6226: s[m][i]=-1;
6227: }
6228: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6229: (*nberr)++;
1.136 brouard 6230: 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]);
6231: 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]);
6232: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6233: }
6234: }
6235: }
6236:
6237: for (i=1; i<=imx; i++) {
6238: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6239: for(m=firstpass; (m<= lastpass); m++){
6240: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6241: if (s[m][i] >= nlstate+1) {
1.169 brouard 6242: if(agedc[i]>0){
6243: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6244: agev[m][i]=agedc[i];
6245: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6246: }else {
1.136 brouard 6247: if ((int)andc[i]!=9999){
6248: nbwarn++;
6249: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6250: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6251: agev[m][i]=-1;
6252: }
6253: }
1.169 brouard 6254: } /* agedc > 0 */
1.136 brouard 6255: }
6256: else if(s[m][i] !=9){ /* Standard case, age in fractional
6257: years but with the precision of a month */
6258: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6259: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6260: agev[m][i]=1;
6261: else if(agev[m][i] < *agemin){
6262: *agemin=agev[m][i];
6263: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6264: }
6265: else if(agev[m][i] >*agemax){
6266: *agemax=agev[m][i];
1.156 brouard 6267: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6268: }
6269: /*agev[m][i]=anint[m][i]-annais[i];*/
6270: /* agev[m][i] = age[i]+2*m;*/
6271: }
6272: else { /* =9 */
6273: agev[m][i]=1;
6274: s[m][i]=-1;
6275: }
6276: }
6277: else /*= 0 Unknown */
6278: agev[m][i]=1;
6279: }
6280:
6281: }
6282: for (i=1; i<=imx; i++) {
6283: for(m=firstpass; (m<=lastpass); m++){
6284: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6285: (*nberr)++;
1.136 brouard 6286: 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);
6287: 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);
6288: return 1;
6289: }
6290: }
6291: }
6292:
6293: /*for (i=1; i<=imx; i++){
6294: for (m=firstpass; (m<lastpass); m++){
6295: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6296: }
6297:
6298: }*/
6299:
6300:
1.139 brouard 6301: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6302: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6303:
6304: return (0);
1.164 brouard 6305: /* endread:*/
1.136 brouard 6306: printf("Exiting calandcheckages: ");
6307: return (1);
6308: }
6309:
1.172 brouard 6310: #if defined(_MSC_VER)
6311: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6312: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6313: //#include "stdafx.h"
6314: //#include <stdio.h>
6315: //#include <tchar.h>
6316: //#include <windows.h>
6317: //#include <iostream>
6318: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6319:
6320: LPFN_ISWOW64PROCESS fnIsWow64Process;
6321:
6322: BOOL IsWow64()
6323: {
6324: BOOL bIsWow64 = FALSE;
6325:
6326: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6327: // (HANDLE, PBOOL);
6328:
6329: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6330:
6331: HMODULE module = GetModuleHandle(_T("kernel32"));
6332: const char funcName[] = "IsWow64Process";
6333: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6334: GetProcAddress(module, funcName);
6335:
6336: if (NULL != fnIsWow64Process)
6337: {
6338: if (!fnIsWow64Process(GetCurrentProcess(),
6339: &bIsWow64))
6340: //throw std::exception("Unknown error");
6341: printf("Unknown error\n");
6342: }
6343: return bIsWow64 != FALSE;
6344: }
6345: #endif
1.177 brouard 6346:
1.191 brouard 6347: void syscompilerinfo(int logged)
1.167 brouard 6348: {
6349: /* #include "syscompilerinfo.h"*/
1.185 brouard 6350: /* command line Intel compiler 32bit windows, XP compatible:*/
6351: /* /GS /W3 /Gy
6352: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6353: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6354: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6355: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6356: */
6357: /* 64 bits */
1.185 brouard 6358: /*
6359: /GS /W3 /Gy
6360: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6361: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6362: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6363: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6364: /* Optimization are useless and O3 is slower than O2 */
6365: /*
6366: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6367: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6368: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6369: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6370: */
1.186 brouard 6371: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6372: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6373: /PDB:"visual studio
6374: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6375: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6376: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6377: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6378: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6379: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6380: uiAccess='false'"
6381: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6382: /NOLOGO /TLBID:1
6383: */
1.177 brouard 6384: #if defined __INTEL_COMPILER
1.178 brouard 6385: #if defined(__GNUC__)
6386: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6387: #endif
1.177 brouard 6388: #elif defined(__GNUC__)
1.179 brouard 6389: #ifndef __APPLE__
1.174 brouard 6390: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6391: #endif
1.177 brouard 6392: struct utsname sysInfo;
1.178 brouard 6393: int cross = CROSS;
6394: if (cross){
6395: printf("Cross-");
1.191 brouard 6396: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6397: }
1.174 brouard 6398: #endif
6399:
1.171 brouard 6400: #include <stdint.h>
1.178 brouard 6401:
1.191 brouard 6402: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6403: #if defined(__clang__)
1.191 brouard 6404: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6405: #endif
6406: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6407: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6408: #endif
6409: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6410: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6411: #endif
6412: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6413: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6414: #endif
6415: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6416: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6417: #endif
6418: #if defined(_MSC_VER)
1.191 brouard 6419: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6420: #endif
6421: #if defined(__PGI)
1.191 brouard 6422: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6423: #endif
6424: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6425: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6426: #endif
1.191 brouard 6427: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6428:
1.167 brouard 6429: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6430: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6431: // Windows (x64 and x86)
1.191 brouard 6432: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6433: #elif __unix__ // all unices, not all compilers
6434: // Unix
1.191 brouard 6435: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6436: #elif __linux__
6437: // linux
1.191 brouard 6438: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6439: #elif __APPLE__
1.174 brouard 6440: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6441: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6442: #endif
6443:
6444: /* __MINGW32__ */
6445: /* __CYGWIN__ */
6446: /* __MINGW64__ */
6447: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6448: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6449: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6450: /* _WIN64 // Defined for applications for Win64. */
6451: /* _M_X64 // Defined for compilations that target x64 processors. */
6452: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6453:
1.167 brouard 6454: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6455: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6456: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6457: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6458: #else
1.191 brouard 6459: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6460: #endif
6461:
1.169 brouard 6462: #if defined(__GNUC__)
6463: # if defined(__GNUC_PATCHLEVEL__)
6464: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6465: + __GNUC_MINOR__ * 100 \
6466: + __GNUC_PATCHLEVEL__)
6467: # else
6468: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6469: + __GNUC_MINOR__ * 100)
6470: # endif
1.174 brouard 6471: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6472: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6473:
6474: if (uname(&sysInfo) != -1) {
6475: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6476: 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 6477: }
6478: else
6479: perror("uname() error");
1.179 brouard 6480: //#ifndef __INTEL_COMPILER
6481: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6482: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6483: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6484: #endif
1.169 brouard 6485: #endif
1.172 brouard 6486:
6487: // void main()
6488: // {
1.169 brouard 6489: #if defined(_MSC_VER)
1.174 brouard 6490: if (IsWow64()){
1.191 brouard 6491: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6492: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6493: }
6494: else{
1.191 brouard 6495: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6496: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6497: }
1.172 brouard 6498: // printf("\nPress Enter to continue...");
6499: // getchar();
6500: // }
6501:
1.169 brouard 6502: #endif
6503:
1.167 brouard 6504:
6505: }
1.136 brouard 6506:
1.203 brouard 6507: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
1.180 brouard 6508: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6509: int i, j, k, i1 ;
1.202 brouard 6510: /* double ftolpl = 1.e-10; */
1.180 brouard 6511: double age, agebase, agelim;
1.203 brouard 6512: double tot;
1.180 brouard 6513:
1.202 brouard 6514: strcpy(filerespl,"PL_");
6515: strcat(filerespl,fileresu);
6516: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6517: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6518: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6519: }
6520: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6521: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6522: pstamp(ficrespl);
1.203 brouard 6523: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6524: fprintf(ficrespl,"#Age ");
6525: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6526: fprintf(ficrespl,"\n");
1.180 brouard 6527:
6528: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6529:
6530: agebase=ageminpar;
6531: agelim=agemaxpar;
6532:
6533: i1=pow(2,cptcoveff);
6534: if (cptcovn < 1){i1=1;}
6535:
6536: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6537: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6538: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6539: k=k+1;
6540: /* to clean */
1.198 brouard 6541: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6542: fprintf(ficrespl,"#******");
6543: printf("#******");
6544: fprintf(ficlog,"#******");
1.180 brouard 6545: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6546: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6547: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6548: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6549: }
6550: fprintf(ficrespl,"******\n");
6551: printf("******\n");
6552: fprintf(ficlog,"******\n");
6553:
6554: fprintf(ficrespl,"#Age ");
6555: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6556: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6557: }
1.203 brouard 6558: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6559: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6560:
6561: for (age=agebase; age<=agelim; age++){
6562: /* for (age=agebase; age<=agebase; age++){ */
1.203 brouard 6563: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
1.180 brouard 6564: fprintf(ficrespl,"%.0f ",age );
6565: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6566: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6567: tot=0.;
6568: for(i=1; i<=nlstate;i++){
6569: tot += prlim[i][i];
1.180 brouard 6570: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6571: }
6572: fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
1.180 brouard 6573: } /* Age */
6574: /* was end of cptcod */
6575: } /* cptcov */
1.184 brouard 6576: return 0;
1.180 brouard 6577: }
6578:
6579: int hPijx(double *p, int bage, int fage){
6580: /*------------- h Pij x at various ages ------------*/
6581:
6582: int stepsize;
6583: int agelim;
6584: int hstepm;
6585: int nhstepm;
6586: int h, i, i1, j, k;
6587:
6588: double agedeb;
6589: double ***p3mat;
6590:
1.201 brouard 6591: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6592: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6593: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6594: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6595: }
6596: printf("Computing pij: result on file '%s' \n", filerespij);
6597: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6598:
6599: stepsize=(int) (stepm+YEARM-1)/YEARM;
6600: /*if (stepm<=24) stepsize=2;*/
6601:
6602: agelim=AGESUP;
6603: hstepm=stepsize*YEARM; /* Every year of age */
6604: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6605:
6606: /* hstepm=1; aff par mois*/
6607: pstamp(ficrespij);
6608: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6609: i1= pow(2,cptcoveff);
1.183 brouard 6610: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6611: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6612: /* k=k+1; */
6613: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6614: fprintf(ficrespij,"\n#****** ");
6615: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6616: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6617: fprintf(ficrespij,"******\n");
6618:
6619: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6620: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6621: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6622:
6623: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6624:
1.183 brouard 6625: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6626: oldm=oldms;savm=savms;
6627: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6628: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6629: for(i=1; i<=nlstate;i++)
6630: for(j=1; j<=nlstate+ndeath;j++)
6631: fprintf(ficrespij," %1d-%1d",i,j);
6632: fprintf(ficrespij,"\n");
6633: for (h=0; h<=nhstepm; h++){
6634: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6635: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6636: for(i=1; i<=nlstate;i++)
6637: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6638: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6639: fprintf(ficrespij,"\n");
6640: }
1.183 brouard 6641: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6642: fprintf(ficrespij,"\n");
6643: }
1.180 brouard 6644: /*}*/
6645: }
1.184 brouard 6646: return 0;
1.180 brouard 6647: }
6648:
6649:
1.136 brouard 6650: /***********************************************/
6651: /**************** Main Program *****************/
6652: /***********************************************/
6653:
6654: int main(int argc, char *argv[])
6655: {
6656: #ifdef GSL
6657: const gsl_multimin_fminimizer_type *T;
6658: size_t iteri = 0, it;
6659: int rval = GSL_CONTINUE;
6660: int status = GSL_SUCCESS;
6661: double ssval;
6662: #endif
6663: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6664: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.203 brouard 6665: int ncvyearnp=0;
6666: int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6667: int jj, ll, li, lj, lk;
1.136 brouard 6668: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6669: int num_filled;
1.136 brouard 6670: int itimes;
6671: int NDIM=2;
6672: int vpopbased=0;
6673:
1.164 brouard 6674: char ca[32], cb[32];
1.136 brouard 6675: /* FILE *fichtm; *//* Html File */
6676: /* FILE *ficgp;*/ /*Gnuplot File */
6677: struct stat info;
1.191 brouard 6678: double agedeb=0.;
1.194 brouard 6679:
6680: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6681:
1.165 brouard 6682: double fret;
1.191 brouard 6683: double dum=0.; /* Dummy variable */
1.136 brouard 6684: double ***p3mat;
6685: double ***mobaverage;
1.164 brouard 6686:
6687: char line[MAXLINE];
1.197 brouard 6688: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6689:
6690: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6691: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6692: char *tok, *val; /* pathtot */
1.136 brouard 6693: int firstobs=1, lastobs=10;
1.195 brouard 6694: int c, h , cpt, c2;
1.191 brouard 6695: int jl=0;
6696: int i1, j1, jk, stepsize=0;
1.194 brouard 6697: int count=0;
6698:
1.164 brouard 6699: int *tab;
1.136 brouard 6700: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6701: int mobilav=0,popforecast=0;
1.191 brouard 6702: int hstepm=0, nhstepm=0;
1.136 brouard 6703: int agemortsup;
6704: float sumlpop=0.;
6705: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6706: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6707:
1.191 brouard 6708: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6709: double ftolpl=FTOL;
6710: double **prlim;
6711: double ***param; /* Matrix of parameters */
6712: double *p;
6713: double **matcov; /* Matrix of covariance */
1.203 brouard 6714: double **hess; /* Hessian matrix */
1.136 brouard 6715: double ***delti3; /* Scale */
6716: double *delti; /* Scale */
6717: double ***eij, ***vareij;
6718: double **varpl; /* Variances of prevalence limits by age */
6719: double *epj, vepp;
1.164 brouard 6720:
1.136 brouard 6721: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6722: double **ximort;
1.145 brouard 6723: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6724: int *dcwave;
6725:
1.164 brouard 6726: char z[1]="c";
1.136 brouard 6727:
6728: /*char *strt;*/
6729: char strtend[80];
1.126 brouard 6730:
1.164 brouard 6731:
1.126 brouard 6732: /* setlocale (LC_ALL, ""); */
6733: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6734: /* textdomain (PACKAGE); */
6735: /* setlocale (LC_CTYPE, ""); */
6736: /* setlocale (LC_MESSAGES, ""); */
6737:
6738: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6739: rstart_time = time(NULL);
6740: /* (void) gettimeofday(&start_time,&tzp);*/
6741: start_time = *localtime(&rstart_time);
1.126 brouard 6742: curr_time=start_time;
1.157 brouard 6743: /*tml = *localtime(&start_time.tm_sec);*/
6744: /* strcpy(strstart,asctime(&tml)); */
6745: strcpy(strstart,asctime(&start_time));
1.126 brouard 6746:
6747: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6748: /* tp.tm_sec = tp.tm_sec +86400; */
6749: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6750: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6751: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6752: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6753: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6754: /* strt=asctime(&tmg); */
6755: /* printf("Time(after) =%s",strstart); */
6756: /* (void) time (&time_value);
6757: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6758: * tm = *localtime(&time_value);
6759: * strstart=asctime(&tm);
6760: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6761: */
6762:
6763: nberr=0; /* Number of errors and warnings */
6764: nbwarn=0;
1.184 brouard 6765: #ifdef WIN32
6766: _getcwd(pathcd, size);
6767: #else
1.126 brouard 6768: getcwd(pathcd, size);
1.184 brouard 6769: #endif
1.191 brouard 6770: syscompilerinfo(0);
1.196 brouard 6771: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6772: if(argc <=1){
6773: printf("\nEnter the parameter file name: ");
1.205 brouard 6774: if(!fgets(pathr,FILENAMELENGTH,stdin)){
6775: printf("ERROR Empty parameter file name\n");
6776: goto end;
6777: }
1.126 brouard 6778: i=strlen(pathr);
6779: if(pathr[i-1]=='\n')
6780: pathr[i-1]='\0';
1.156 brouard 6781: i=strlen(pathr);
1.205 brouard 6782: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 6783: pathr[i-1]='\0';
1.205 brouard 6784: }
6785: i=strlen(pathr);
6786: if( i==0 ){
6787: printf("ERROR Empty parameter file name\n");
6788: goto end;
6789: }
6790: for (tok = pathr; tok != NULL; ){
1.126 brouard 6791: printf("Pathr |%s|\n",pathr);
6792: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6793: printf("val= |%s| pathr=%s\n",val,pathr);
6794: strcpy (pathtot, val);
6795: if(pathr[0] == '\0') break; /* Dirty */
6796: }
6797: }
6798: else{
6799: strcpy(pathtot,argv[1]);
6800: }
6801: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6802: /*cygwin_split_path(pathtot,path,optionfile);
6803: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6804: /* cutv(path,optionfile,pathtot,'\\');*/
6805:
6806: /* Split argv[0], imach program to get pathimach */
6807: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6808: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6809: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6810: /* strcpy(pathimach,argv[0]); */
6811: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6812: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6813: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6814: #ifdef WIN32
6815: _chdir(path); /* Can be a relative path */
6816: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6817: #else
1.126 brouard 6818: chdir(path); /* Can be a relative path */
1.184 brouard 6819: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6820: #endif
6821: printf("Current directory %s!\n",pathcd);
1.126 brouard 6822: strcpy(command,"mkdir ");
6823: strcat(command,optionfilefiname);
6824: if((outcmd=system(command)) != 0){
1.169 brouard 6825: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6826: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6827: /* fclose(ficlog); */
6828: /* exit(1); */
6829: }
6830: /* if((imk=mkdir(optionfilefiname))<0){ */
6831: /* perror("mkdir"); */
6832: /* } */
6833:
6834: /*-------- arguments in the command line --------*/
6835:
1.186 brouard 6836: /* Main Log file */
1.126 brouard 6837: strcat(filelog, optionfilefiname);
6838: strcat(filelog,".log"); /* */
6839: if((ficlog=fopen(filelog,"w"))==NULL) {
6840: printf("Problem with logfile %s\n",filelog);
6841: goto end;
6842: }
6843: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6844: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6845: fprintf(ficlog,"\nEnter the parameter file name: \n");
6846: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6847: path=%s \n\
6848: optionfile=%s\n\
6849: optionfilext=%s\n\
1.156 brouard 6850: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6851:
1.197 brouard 6852: syscompilerinfo(1);
1.167 brouard 6853:
1.126 brouard 6854: printf("Local time (at start):%s",strstart);
6855: fprintf(ficlog,"Local time (at start): %s",strstart);
6856: fflush(ficlog);
6857: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6858: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6859:
6860: /* */
6861: strcpy(fileres,"r");
6862: strcat(fileres, optionfilefiname);
1.201 brouard 6863: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6864: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6865: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6866:
1.186 brouard 6867: /* Main ---------arguments file --------*/
1.126 brouard 6868:
6869: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6870: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6871: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6872: fflush(ficlog);
1.149 brouard 6873: /* goto end; */
6874: exit(70);
1.126 brouard 6875: }
6876:
6877:
6878:
6879: strcpy(filereso,"o");
1.201 brouard 6880: strcat(filereso,fileresu);
1.126 brouard 6881: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6882: printf("Problem with Output resultfile: %s\n", filereso);
6883: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6884: fflush(ficlog);
6885: goto end;
6886: }
6887:
6888: /* Reads comments: lines beginning with '#' */
6889: numlinepar=0;
1.197 brouard 6890:
6891: /* First parameter line */
6892: while(fgets(line, MAXLINE, ficpar)) {
6893: /* If line starts with a # it is a comment */
6894: if (line[0] == '#') {
6895: numlinepar++;
6896: fputs(line,stdout);
6897: fputs(line,ficparo);
6898: fputs(line,ficlog);
6899: continue;
6900: }else
6901: break;
6902: }
6903: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6904: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6905: if (num_filled != 5) {
6906: printf("Should be 5 parameters\n");
6907: }
1.126 brouard 6908: numlinepar++;
1.197 brouard 6909: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6910: }
6911: /* Second parameter line */
6912: while(fgets(line, MAXLINE, ficpar)) {
6913: /* If line starts with a # it is a comment */
6914: if (line[0] == '#') {
6915: numlinepar++;
6916: fputs(line,stdout);
6917: fputs(line,ficparo);
6918: fputs(line,ficlog);
6919: continue;
6920: }else
6921: break;
6922: }
6923: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6924: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6925: if (num_filled != 8) {
6926: printf("Not 8\n");
6927: }
6928: 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 6929: }
1.203 brouard 6930: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
6931: ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6932: /* Third parameter line */
6933: while(fgets(line, MAXLINE, ficpar)) {
6934: /* If line starts with a # it is a comment */
6935: if (line[0] == '#') {
6936: numlinepar++;
6937: fputs(line,stdout);
6938: fputs(line,ficparo);
6939: fputs(line,ficlog);
6940: continue;
6941: }else
6942: break;
6943: }
1.201 brouard 6944: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
6945: if (num_filled == 0)
6946: model[0]='\0';
6947: else if (num_filled != 1){
1.197 brouard 6948: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6949: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6950: model[0]='\0';
6951: goto end;
6952: }
6953: else{
6954: if (model[0]=='+'){
6955: for(i=1; i<=strlen(model);i++)
6956: modeltemp[i-1]=model[i];
1.201 brouard 6957: strcpy(model,modeltemp);
1.197 brouard 6958: }
6959: }
1.199 brouard 6960: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 6961: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 6962: }
6963: /* 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); */
6964: /* numlinepar=numlinepar+3; /\* In general *\/ */
6965: /* 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 6966: 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);
6967: 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 6968: fflush(ficlog);
1.190 brouard 6969: /* if(model[0]=='#'|| model[0]== '\0'){ */
6970: if(model[0]=='#'){
1.187 brouard 6971: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6972: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6973: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6974: if(mle != -1){
6975: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6976: exit(1);
6977: }
6978: }
1.126 brouard 6979: while((c=getc(ficpar))=='#' && c!= EOF){
6980: ungetc(c,ficpar);
6981: fgets(line, MAXLINE, ficpar);
6982: numlinepar++;
1.195 brouard 6983: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6984: z[0]=line[1];
6985: }
6986: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6987: fputs(line, stdout);
6988: //puts(line);
1.126 brouard 6989: fputs(line,ficparo);
6990: fputs(line,ficlog);
6991: }
6992: ungetc(c,ficpar);
6993:
6994:
1.145 brouard 6995: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6996: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
6997: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
6998: v1+v2*age+v2*v3 makes cptcovn = 3
6999: */
7000: if (strlen(model)>1)
1.187 brouard 7001: 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 7002: else
1.187 brouard 7003: ncovmodel=2; /* Constant and age */
1.133 brouard 7004: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7005: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7006: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7007: 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);
7008: 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);
7009: fflush(stdout);
7010: fclose (ficlog);
7011: goto end;
7012: }
1.126 brouard 7013: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7014: delti=delti3[1][1];
7015: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7016: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7017: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7018: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7019: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7020: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7021: fclose (ficparo);
7022: fclose (ficlog);
7023: goto end;
7024: exit(0);
7025: }
1.186 brouard 7026: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7027: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7028: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7029: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7030: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7031: matcov=matrix(1,npar,1,npar);
1.203 brouard 7032: hess=matrix(1,npar,1,npar);
1.126 brouard 7033: }
7034: else{
1.145 brouard 7035: /* Read guessed parameters */
1.126 brouard 7036: /* Reads comments: lines beginning with '#' */
7037: while((c=getc(ficpar))=='#' && c!= EOF){
7038: ungetc(c,ficpar);
7039: fgets(line, MAXLINE, ficpar);
7040: numlinepar++;
1.141 brouard 7041: fputs(line,stdout);
1.126 brouard 7042: fputs(line,ficparo);
7043: fputs(line,ficlog);
7044: }
7045: ungetc(c,ficpar);
7046:
7047: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7048: for(i=1; i <=nlstate; i++){
7049: j=0;
7050: for(jj=1; jj <=nlstate+ndeath; jj++){
7051: if(jj==i) continue;
7052: j++;
7053: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7054: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7055: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7056: It might be a problem of design; if ncovcol and the model are correct\n \
7057: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7058: exit(1);
7059: }
7060: fprintf(ficparo,"%1d%1d",i1,j1);
7061: if(mle==1)
1.193 brouard 7062: printf("%1d%1d",i,jj);
7063: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7064: for(k=1; k<=ncovmodel;k++){
7065: fscanf(ficpar," %lf",¶m[i][j][k]);
7066: if(mle==1){
7067: printf(" %lf",param[i][j][k]);
7068: fprintf(ficlog," %lf",param[i][j][k]);
7069: }
7070: else
7071: fprintf(ficlog," %lf",param[i][j][k]);
7072: fprintf(ficparo," %lf",param[i][j][k]);
7073: }
7074: fscanf(ficpar,"\n");
7075: numlinepar++;
7076: if(mle==1)
7077: printf("\n");
7078: fprintf(ficlog,"\n");
7079: fprintf(ficparo,"\n");
7080: }
7081: }
7082: fflush(ficlog);
7083:
1.145 brouard 7084: /* Reads scales values */
1.126 brouard 7085: p=param[1][1];
7086:
7087: /* Reads comments: lines beginning with '#' */
7088: while((c=getc(ficpar))=='#' && c!= EOF){
7089: ungetc(c,ficpar);
7090: fgets(line, MAXLINE, ficpar);
7091: numlinepar++;
1.141 brouard 7092: fputs(line,stdout);
1.126 brouard 7093: fputs(line,ficparo);
7094: fputs(line,ficlog);
7095: }
7096: ungetc(c,ficpar);
7097:
7098: for(i=1; i <=nlstate; i++){
7099: for(j=1; j <=nlstate+ndeath-1; j++){
7100: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7101: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7102: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7103: exit(1);
7104: }
7105: printf("%1d%1d",i,j);
7106: fprintf(ficparo,"%1d%1d",i1,j1);
7107: fprintf(ficlog,"%1d%1d",i1,j1);
7108: for(k=1; k<=ncovmodel;k++){
7109: fscanf(ficpar,"%le",&delti3[i][j][k]);
7110: printf(" %le",delti3[i][j][k]);
7111: fprintf(ficparo," %le",delti3[i][j][k]);
7112: fprintf(ficlog," %le",delti3[i][j][k]);
7113: }
7114: fscanf(ficpar,"\n");
7115: numlinepar++;
7116: printf("\n");
7117: fprintf(ficparo,"\n");
7118: fprintf(ficlog,"\n");
7119: }
7120: }
7121: fflush(ficlog);
7122:
1.145 brouard 7123: /* Reads covariance matrix */
1.126 brouard 7124: delti=delti3[1][1];
7125:
7126:
7127: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7128:
7129: /* Reads comments: lines beginning with '#' */
7130: while((c=getc(ficpar))=='#' && c!= EOF){
7131: ungetc(c,ficpar);
7132: fgets(line, MAXLINE, ficpar);
7133: numlinepar++;
1.141 brouard 7134: fputs(line,stdout);
1.126 brouard 7135: fputs(line,ficparo);
7136: fputs(line,ficlog);
7137: }
7138: ungetc(c,ficpar);
7139:
7140: matcov=matrix(1,npar,1,npar);
1.203 brouard 7141: hess=matrix(1,npar,1,npar);
1.131 brouard 7142: for(i=1; i <=npar; i++)
7143: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7144:
1.194 brouard 7145: /* Scans npar lines */
1.126 brouard 7146: for(i=1; i <=npar; i++){
1.194 brouard 7147: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7148: if(count != 3){
7149: printf("Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7150: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7151: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7152: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7153: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7154: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7155: exit(1);
7156: }else
1.126 brouard 7157: if(mle==1)
1.194 brouard 7158: printf("%1d%1d%1d",i1,j1,jk);
7159: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7160: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7161: for(j=1; j <=i; j++){
7162: fscanf(ficpar," %le",&matcov[i][j]);
7163: if(mle==1){
7164: printf(" %.5le",matcov[i][j]);
7165: }
7166: fprintf(ficlog," %.5le",matcov[i][j]);
7167: fprintf(ficparo," %.5le",matcov[i][j]);
7168: }
7169: fscanf(ficpar,"\n");
7170: numlinepar++;
7171: if(mle==1)
7172: printf("\n");
7173: fprintf(ficlog,"\n");
7174: fprintf(ficparo,"\n");
7175: }
1.194 brouard 7176: /* End of read covariance matrix npar lines */
1.126 brouard 7177: for(i=1; i <=npar; i++)
7178: for(j=i+1;j<=npar;j++)
7179: matcov[i][j]=matcov[j][i];
7180:
7181: if(mle==1)
7182: printf("\n");
7183: fprintf(ficlog,"\n");
7184:
7185: fflush(ficlog);
7186:
7187: /*-------- Rewriting parameter file ----------*/
7188: strcpy(rfileres,"r"); /* "Rparameterfile */
7189: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7190: strcat(rfileres,"."); /* */
7191: strcat(rfileres,optionfilext); /* Other files have txt extension */
7192: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7193: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7194: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7195: }
7196: fprintf(ficres,"#%s\n",version);
7197: } /* End of mle != -3 */
7198:
1.186 brouard 7199: /* Main data
7200: */
1.126 brouard 7201: n= lastobs;
7202: num=lvector(1,n);
7203: moisnais=vector(1,n);
7204: annais=vector(1,n);
7205: moisdc=vector(1,n);
7206: andc=vector(1,n);
7207: agedc=vector(1,n);
7208: cod=ivector(1,n);
7209: weight=vector(1,n);
7210: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7211: mint=matrix(1,maxwav,1,n);
7212: anint=matrix(1,maxwav,1,n);
1.131 brouard 7213: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7214: tab=ivector(1,NCOVMAX);
1.144 brouard 7215: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7216: 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 7217:
1.136 brouard 7218: /* Reads data from file datafile */
7219: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7220: goto end;
7221:
7222: /* Calculation of the number of parameters from char model */
1.137 brouard 7223: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7224: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7225: k=3 V4 Tvar[k=3]= 4 (from V4)
7226: k=2 V1 Tvar[k=2]= 1 (from V1)
7227: k=1 Tvar[1]=2 (from V2)
7228: */
7229: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7230: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7231: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7232: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7233: */
7234: /* For model-covariate k tells which data-covariate to use but
7235: because this model-covariate is a construction we invent a new column
7236: ncovcol + k1
7237: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7238: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7239: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7240: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7241: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7242: */
1.145 brouard 7243: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7244: 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 7245: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7246: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7247: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7248: 4 covariates (3 plus signs)
7249: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7250: */
1.136 brouard 7251:
1.186 brouard 7252: /* Main decodemodel */
7253:
1.187 brouard 7254:
1.136 brouard 7255: if(decodemodel(model, lastobs) == 1)
7256: goto end;
7257:
1.137 brouard 7258: if((double)(lastobs-imx)/(double)imx > 1.10){
7259: nbwarn++;
7260: 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);
7261: 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);
7262: }
1.136 brouard 7263: /* if(mle==1){*/
1.137 brouard 7264: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7265: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7266: }
7267:
7268: /*-calculation of age at interview from date of interview and age at death -*/
7269: agev=matrix(1,maxwav,1,imx);
7270:
7271: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7272: goto end;
7273:
1.126 brouard 7274:
1.136 brouard 7275: agegomp=(int)agemin;
7276: free_vector(moisnais,1,n);
7277: free_vector(annais,1,n);
1.126 brouard 7278: /* free_matrix(mint,1,maxwav,1,n);
7279: free_matrix(anint,1,maxwav,1,n);*/
7280: free_vector(moisdc,1,n);
7281: free_vector(andc,1,n);
1.145 brouard 7282: /* */
7283:
1.126 brouard 7284: wav=ivector(1,imx);
7285: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7286: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7287: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7288:
7289: /* Concatenates waves */
7290: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7291: /* */
7292:
1.126 brouard 7293: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7294:
7295: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7296: ncodemax[1]=1;
1.145 brouard 7297: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7298: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7299: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7300: /* Nbcode gives the value of the lth modality of jth covariate, in
7301: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7302: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7303:
1.200 brouard 7304: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7305: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7306: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7307: h=0;
7308:
7309:
7310: /*if (cptcovn > 0) */
1.126 brouard 7311:
1.145 brouard 7312:
1.126 brouard 7313: m=pow(2,cptcoveff);
7314:
1.144 brouard 7315: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7316: * For k=4 covariates, h goes from 1 to 2**k
7317: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7318: * h\k 1 2 3 4
1.143 brouard 7319: *______________________________
7320: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7321: * 2 2 1 1 1
7322: * 3 i=2 1 2 1 1
7323: * 4 2 2 1 1
7324: * 5 i=3 1 i=2 1 2 1
7325: * 6 2 1 2 1
7326: * 7 i=4 1 2 2 1
7327: * 8 2 2 2 1
1.197 brouard 7328: * 9 i=5 1 i=3 1 i=2 1 2
7329: * 10 2 1 1 2
7330: * 11 i=6 1 2 1 2
7331: * 12 2 2 1 2
7332: * 13 i=7 1 i=4 1 2 2
7333: * 14 2 1 2 2
7334: * 15 i=8 1 2 2 2
7335: * 16 2 2 2 2
1.143 brouard 7336: */
1.202 brouard 7337: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7338: /* /\* printf("h=%2d ", h); *\/ */
7339: /* /\* for(k=1; k <=10; k++){ *\/ */
7340: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7341: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7342: /* /\* } *\/ */
7343: /* /\* printf("\n"); *\/ */
7344: /* } */
1.197 brouard 7345: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7346: /* 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 *\/ */
7347: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7348: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7349: /* h++; */
7350: /* if (h>m) */
7351: /* h=1; */
7352: /* codtab[h][k]=j; */
7353: /* /\* codtab[12][3]=1; *\/ */
7354: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7355: /* /\* 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]]); *\/ */
7356: /* } */
7357: /* } */
7358: /* } */
7359: /* } */
1.126 brouard 7360: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7361: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7362: /* for(i=1; i <=m ;i++){ */
7363: /* for(k=1; k <=cptcovn; k++){ */
7364: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7365: /* } */
7366: /* printf("\n"); */
7367: /* } */
7368: /* scanf("%d",i);*/
1.145 brouard 7369:
7370: free_ivector(Ndum,-1,NCOVMAX);
7371:
7372:
1.126 brouard 7373:
1.186 brouard 7374: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7375: strcpy(optionfilegnuplot,optionfilefiname);
7376: if(mle==-3)
1.201 brouard 7377: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7378: strcat(optionfilegnuplot,".gp");
7379:
7380: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7381: printf("Problem with file %s",optionfilegnuplot);
7382: }
7383: else{
1.204 brouard 7384: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7385: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7386: //fprintf(ficgp,"set missing 'NaNq'\n");
7387: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7388: }
7389: /* fclose(ficgp);*/
1.186 brouard 7390:
7391:
7392: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7393:
7394: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7395: if(mle==-3)
1.201 brouard 7396: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7397: strcat(optionfilehtm,".htm");
7398: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7399: printf("Problem with %s \n",optionfilehtm);
7400: exit(0);
1.126 brouard 7401: }
7402:
7403: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7404: strcat(optionfilehtmcov,"-cov.htm");
7405: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7406: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7407: }
7408: else{
7409: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7410: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7411: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7412: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7413: }
7414:
1.204 brouard 7415: 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-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</a></font><br> \
7416: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7417: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7418: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7419: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7420: \n\
7421: <hr size=\"2\" color=\"#EC5E5E\">\
7422: <ul><li><h4>Parameter files</h4>\n\
7423: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7424: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7425: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7426: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7427: - Date and time at start: %s</ul>\n",\
7428: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7429: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7430: fileres,fileres,\
7431: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7432: fflush(fichtm);
7433:
7434: strcpy(pathr,path);
7435: strcat(pathr,optionfilefiname);
1.184 brouard 7436: #ifdef WIN32
7437: _chdir(optionfilefiname); /* Move to directory named optionfile */
7438: #else
1.126 brouard 7439: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7440: #endif
7441:
1.126 brouard 7442:
7443: /* Calculates basic frequencies. Computes observed prevalence at single age
7444: and prints on file fileres'p'. */
7445: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7446:
7447: fprintf(fichtm,"\n");
7448: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7449: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7450: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7451: imx,agemin,agemax,jmin,jmax,jmean);
7452: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7453: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7454: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7455: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7456: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7457:
7458:
7459: /* For Powell, parameters are in a vector p[] starting at p[1]
7460: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7461: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7462:
7463: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7464: /* For mortality only */
1.126 brouard 7465: if (mle==-3){
1.136 brouard 7466: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7467: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7468: cens=ivector(1,n);
7469: ageexmed=vector(1,n);
7470: agecens=vector(1,n);
7471: dcwave=ivector(1,n);
7472:
7473: for (i=1; i<=imx; i++){
7474: dcwave[i]=-1;
7475: for (m=firstpass; m<=lastpass; m++)
7476: if (s[m][i]>nlstate) {
7477: dcwave[i]=m;
7478: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7479: break;
7480: }
7481: }
7482:
7483: for (i=1; i<=imx; i++) {
7484: if (wav[i]>0){
7485: ageexmed[i]=agev[mw[1][i]][i];
7486: j=wav[i];
7487: agecens[i]=1.;
7488:
7489: if (ageexmed[i]> 1 && wav[i] > 0){
7490: agecens[i]=agev[mw[j][i]][i];
7491: cens[i]= 1;
7492: }else if (ageexmed[i]< 1)
7493: cens[i]= -1;
7494: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7495: cens[i]=0 ;
7496: }
7497: else cens[i]=-1;
7498: }
7499:
7500: for (i=1;i<=NDIM;i++) {
7501: for (j=1;j<=NDIM;j++)
7502: ximort[i][j]=(i == j ? 1.0 : 0.0);
7503: }
7504:
1.145 brouard 7505: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7506: /*printf("%lf %lf", p[1], p[2]);*/
7507:
7508:
1.136 brouard 7509: #ifdef GSL
7510: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7511: #else
1.126 brouard 7512: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7513: #endif
1.201 brouard 7514: strcpy(filerespow,"POW-MORT_");
7515: strcat(filerespow,fileresu);
1.126 brouard 7516: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7517: printf("Problem with resultfile: %s\n", filerespow);
7518: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7519: }
1.136 brouard 7520: #ifdef GSL
7521: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7522: #else
1.126 brouard 7523: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7524: #endif
1.126 brouard 7525: /* for (i=1;i<=nlstate;i++)
7526: for(j=1;j<=nlstate+ndeath;j++)
7527: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7528: */
7529: fprintf(ficrespow,"\n");
1.136 brouard 7530: #ifdef GSL
7531: /* gsl starts here */
7532: T = gsl_multimin_fminimizer_nmsimplex;
7533: gsl_multimin_fminimizer *sfm = NULL;
7534: gsl_vector *ss, *x;
7535: gsl_multimin_function minex_func;
7536:
7537: /* Initial vertex size vector */
7538: ss = gsl_vector_alloc (NDIM);
7539:
7540: if (ss == NULL){
7541: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7542: }
7543: /* Set all step sizes to 1 */
7544: gsl_vector_set_all (ss, 0.001);
7545:
7546: /* Starting point */
1.126 brouard 7547:
1.136 brouard 7548: x = gsl_vector_alloc (NDIM);
7549:
7550: if (x == NULL){
7551: gsl_vector_free(ss);
7552: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7553: }
7554:
7555: /* Initialize method and iterate */
7556: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7557: /* gsl_vector_set(x, 0, 0.0268); */
7558: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7559: gsl_vector_set(x, 0, p[1]);
7560: gsl_vector_set(x, 1, p[2]);
7561:
7562: minex_func.f = &gompertz_f;
7563: minex_func.n = NDIM;
7564: minex_func.params = (void *)&p; /* ??? */
7565:
7566: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7567: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7568:
7569: printf("Iterations beginning .....\n\n");
7570: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7571:
7572: iteri=0;
7573: while (rval == GSL_CONTINUE){
7574: iteri++;
7575: status = gsl_multimin_fminimizer_iterate(sfm);
7576:
7577: if (status) printf("error: %s\n", gsl_strerror (status));
7578: fflush(0);
7579:
7580: if (status)
7581: break;
7582:
7583: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7584: ssval = gsl_multimin_fminimizer_size (sfm);
7585:
7586: if (rval == GSL_SUCCESS)
7587: printf ("converged to a local maximum at\n");
7588:
7589: printf("%5d ", iteri);
7590: for (it = 0; it < NDIM; it++){
7591: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7592: }
7593: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7594: }
7595:
7596: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7597:
7598: gsl_vector_free(x); /* initial values */
7599: gsl_vector_free(ss); /* inital step size */
7600: for (it=0; it<NDIM; it++){
7601: p[it+1]=gsl_vector_get(sfm->x,it);
7602: fprintf(ficrespow," %.12lf", p[it]);
7603: }
7604: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7605: #endif
7606: #ifdef POWELL
7607: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7608: #endif
1.126 brouard 7609: fclose(ficrespow);
7610:
1.203 brouard 7611: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7612:
7613: for(i=1; i <=NDIM; i++)
7614: for(j=i+1;j<=NDIM;j++)
7615: matcov[i][j]=matcov[j][i];
7616:
7617: printf("\nCovariance matrix\n ");
1.203 brouard 7618: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7619: for(i=1; i <=NDIM; i++) {
7620: for(j=1;j<=NDIM;j++){
7621: printf("%f ",matcov[i][j]);
1.203 brouard 7622: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7623: }
1.203 brouard 7624: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7625: }
7626:
7627: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7628: for (i=1;i<=NDIM;i++) {
1.126 brouard 7629: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7630: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7631: }
1.126 brouard 7632: lsurv=vector(1,AGESUP);
7633: lpop=vector(1,AGESUP);
7634: tpop=vector(1,AGESUP);
7635: lsurv[agegomp]=100000;
7636:
7637: for (k=agegomp;k<=AGESUP;k++) {
7638: agemortsup=k;
7639: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7640: }
7641:
7642: for (k=agegomp;k<agemortsup;k++)
7643: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7644:
7645: for (k=agegomp;k<agemortsup;k++){
7646: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7647: sumlpop=sumlpop+lpop[k];
7648: }
7649:
7650: tpop[agegomp]=sumlpop;
7651: for (k=agegomp;k<(agemortsup-3);k++){
7652: /* tpop[k+1]=2;*/
7653: tpop[k+1]=tpop[k]-lpop[k];
7654: }
7655:
7656:
7657: printf("\nAge lx qx dx Lx Tx e(x)\n");
7658: for (k=agegomp;k<(agemortsup-2);k++)
7659: 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]);
7660:
7661:
7662: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7663: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7664: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7665: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7666: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7667: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7668: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7669: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7670: }else
1.201 brouard 7671: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7672: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7673: stepm, weightopt,\
7674: model,imx,p,matcov,agemortsup);
7675:
7676: free_vector(lsurv,1,AGESUP);
7677: free_vector(lpop,1,AGESUP);
7678: free_vector(tpop,1,AGESUP);
1.136 brouard 7679: #ifdef GSL
7680: free_ivector(cens,1,n);
7681: free_vector(agecens,1,n);
7682: free_ivector(dcwave,1,n);
7683: free_matrix(ximort,1,NDIM,1,NDIM);
7684: #endif
1.186 brouard 7685: } /* Endof if mle==-3 mortality only */
1.205 brouard 7686: /* Standard */
7687: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7688: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7689: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7690: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7691: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7692: for (k=1; k<=npar;k++)
7693: printf(" %d %8.5f",k,p[k]);
7694: printf("\n");
1.205 brouard 7695: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7696: /* mlikeli uses func not funcone */
7697: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7698: }
7699: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7700: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7701: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7702: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7703: }
7704: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7705: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7706: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7707: for (k=1; k<=npar;k++)
7708: printf(" %d %8.5f",k,p[k]);
7709: printf("\n");
7710:
7711: /*--------- results files --------------*/
1.192 brouard 7712: 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 7713:
7714:
7715: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7716: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7717: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7718: for(i=1,jk=1; i <=nlstate; i++){
7719: for(k=1; k <=(nlstate+ndeath); k++){
7720: if (k != i) {
7721: printf("%d%d ",i,k);
7722: fprintf(ficlog,"%d%d ",i,k);
7723: fprintf(ficres,"%1d%1d ",i,k);
7724: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7725: printf("%12.7f ",p[jk]);
7726: fprintf(ficlog,"%12.7f ",p[jk]);
7727: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7728: jk++;
7729: }
7730: printf("\n");
7731: fprintf(ficlog,"\n");
7732: fprintf(ficres,"\n");
7733: }
7734: }
7735: }
1.203 brouard 7736: if(mle != 0){
7737: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7738: ftolhess=ftol; /* Usually correct */
1.203 brouard 7739: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7740: 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");
7741: 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");
7742: for(i=1,jk=1; i <=nlstate; i++){
7743: for(k=1; k <=(nlstate+ndeath); k++){
7744: if (k != i) {
7745: printf("%d%d ",i,k);
7746: fprintf(ficlog,"%d%d ",i,k);
7747: for(j=1; j <=ncovmodel; j++){
7748: 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]));
7749: 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]));
7750: jk++;
7751: }
7752: printf("\n");
7753: fprintf(ficlog,"\n");
1.193 brouard 7754: }
7755: }
7756: }
1.203 brouard 7757: } /* end of hesscov and Wald tests */
1.193 brouard 7758:
1.203 brouard 7759: /* */
1.126 brouard 7760: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7761: printf("# Scales (for hessian or gradient estimation)\n");
7762: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7763: for(i=1,jk=1; i <=nlstate; i++){
7764: for(j=1; j <=nlstate+ndeath; j++){
7765: if (j!=i) {
7766: fprintf(ficres,"%1d%1d",i,j);
7767: printf("%1d%1d",i,j);
7768: fprintf(ficlog,"%1d%1d",i,j);
7769: for(k=1; k<=ncovmodel;k++){
7770: printf(" %.5e",delti[jk]);
7771: fprintf(ficlog," %.5e",delti[jk]);
7772: fprintf(ficres," %.5e",delti[jk]);
7773: jk++;
7774: }
7775: printf("\n");
7776: fprintf(ficlog,"\n");
7777: fprintf(ficres,"\n");
7778: }
7779: }
7780: }
7781:
7782: 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 7783: if(mle >= 1) /* To big for the screen */
1.126 brouard 7784: 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");
7785: 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");
7786: /* # 121 Var(a12)\n\ */
7787: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7788: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7789: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7790: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7791: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7792: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7793: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7794:
7795:
7796: /* Just to have a covariance matrix which will be more understandable
7797: even is we still don't want to manage dictionary of variables
7798: */
7799: for(itimes=1;itimes<=2;itimes++){
7800: jj=0;
7801: for(i=1; i <=nlstate; i++){
7802: for(j=1; j <=nlstate+ndeath; j++){
7803: if(j==i) continue;
7804: for(k=1; k<=ncovmodel;k++){
7805: jj++;
7806: ca[0]= k+'a'-1;ca[1]='\0';
7807: if(itimes==1){
7808: if(mle>=1)
7809: printf("#%1d%1d%d",i,j,k);
7810: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7811: fprintf(ficres,"#%1d%1d%d",i,j,k);
7812: }else{
7813: if(mle>=1)
7814: printf("%1d%1d%d",i,j,k);
7815: fprintf(ficlog,"%1d%1d%d",i,j,k);
7816: fprintf(ficres,"%1d%1d%d",i,j,k);
7817: }
7818: ll=0;
7819: for(li=1;li <=nlstate; li++){
7820: for(lj=1;lj <=nlstate+ndeath; lj++){
7821: if(lj==li) continue;
7822: for(lk=1;lk<=ncovmodel;lk++){
7823: ll++;
7824: if(ll<=jj){
7825: cb[0]= lk +'a'-1;cb[1]='\0';
7826: if(ll<jj){
7827: if(itimes==1){
7828: if(mle>=1)
7829: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7830: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7831: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7832: }else{
7833: if(mle>=1)
7834: printf(" %.5e",matcov[jj][ll]);
7835: fprintf(ficlog," %.5e",matcov[jj][ll]);
7836: fprintf(ficres," %.5e",matcov[jj][ll]);
7837: }
7838: }else{
7839: if(itimes==1){
7840: if(mle>=1)
7841: printf(" Var(%s%1d%1d)",ca,i,j);
7842: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7843: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7844: }else{
7845: if(mle>=1)
1.203 brouard 7846: printf(" %.7e",matcov[jj][ll]);
7847: fprintf(ficlog," %.7e",matcov[jj][ll]);
7848: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7849: }
7850: }
7851: }
7852: } /* end lk */
7853: } /* end lj */
7854: } /* end li */
7855: if(mle>=1)
7856: printf("\n");
7857: fprintf(ficlog,"\n");
7858: fprintf(ficres,"\n");
7859: numlinepar++;
7860: } /* end k*/
7861: } /*end j */
7862: } /* end i */
7863: } /* end itimes */
7864:
7865: fflush(ficlog);
7866: fflush(ficres);
7867:
7868: while((c=getc(ficpar))=='#' && c!= EOF){
7869: ungetc(c,ficpar);
7870: fgets(line, MAXLINE, ficpar);
1.141 brouard 7871: fputs(line,stdout);
1.126 brouard 7872: fputs(line,ficparo);
7873: }
7874: ungetc(c,ficpar);
7875:
7876: estepm=0;
7877: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7878: if (estepm==0 || estepm < stepm) estepm=stepm;
7879: if (fage <= 2) {
7880: bage = ageminpar;
7881: fage = agemaxpar;
7882: }
7883:
7884: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7885: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7886: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7887:
7888: /* Other stuffs, more or less useful */
1.126 brouard 7889: while((c=getc(ficpar))=='#' && c!= EOF){
7890: ungetc(c,ficpar);
7891: fgets(line, MAXLINE, ficpar);
1.141 brouard 7892: fputs(line,stdout);
1.126 brouard 7893: fputs(line,ficparo);
7894: }
7895: ungetc(c,ficpar);
7896:
7897: 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);
7898: 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);
7899: 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);
7900: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7901: 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);
7902:
7903: while((c=getc(ficpar))=='#' && c!= EOF){
7904: ungetc(c,ficpar);
7905: fgets(line, MAXLINE, ficpar);
1.141 brouard 7906: fputs(line,stdout);
1.126 brouard 7907: fputs(line,ficparo);
7908: }
7909: ungetc(c,ficpar);
7910:
7911:
7912: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7913: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7914:
7915: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7916: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7917: fprintf(ficparo,"pop_based=%d\n",popbased);
7918: fprintf(ficres,"pop_based=%d\n",popbased);
7919:
7920: while((c=getc(ficpar))=='#' && c!= EOF){
7921: ungetc(c,ficpar);
7922: fgets(line, MAXLINE, ficpar);
1.141 brouard 7923: fputs(line,stdout);
1.126 brouard 7924: fputs(line,ficparo);
7925: }
7926: ungetc(c,ficpar);
7927:
7928: 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);
7929: 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);
7930: 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);
7931: 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);
7932: 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);
7933: /* day and month of proj2 are not used but only year anproj2.*/
7934:
7935:
7936:
1.145 brouard 7937: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7938: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7939:
7940: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7941: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7942: printf("Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7943: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7944: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7945: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7946: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7947: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7948: }else
1.201 brouard 7949: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7950:
1.201 brouard 7951: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7952: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7953: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7954:
7955: /*------------ free_vector -------------*/
7956: /* chdir(path); */
7957:
7958: free_ivector(wav,1,imx);
7959: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7960: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7961: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7962: free_lvector(num,1,n);
7963: free_vector(agedc,1,n);
7964: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7965: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7966: fclose(ficparo);
7967: fclose(ficres);
7968:
7969:
1.186 brouard 7970: /* Other results (useful)*/
7971:
7972:
1.126 brouard 7973: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7974: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7975: prlim=matrix(1,nlstate,1,nlstate);
1.203 brouard 7976: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);
1.126 brouard 7977: fclose(ficrespl);
7978:
1.145 brouard 7979: #ifdef FREEEXIT2
7980: #include "freeexit2.h"
7981: #endif
7982:
1.126 brouard 7983: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7984: /*#include "hpijx.h"*/
7985: hPijx(p, bage, fage);
1.145 brouard 7986: fclose(ficrespij);
1.126 brouard 7987:
1.145 brouard 7988: /*-------------- Variance of one-step probabilities---*/
7989: k=1;
1.126 brouard 7990: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7991:
7992:
7993: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7994: for(i=1;i<=AGESUP;i++)
7995: for(j=1;j<=NCOVMAX;j++)
7996: for(k=1;k<=NCOVMAX;k++)
7997: probs[i][j][k]=0.;
7998:
7999: /*---------- Forecasting ------------------*/
8000: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8001: if(prevfcast==1){
8002: /* if(stepm ==1){*/
1.201 brouard 8003: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8004: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8005: /* } */
8006: /* else{ */
8007: /* erreur=108; */
8008: /* 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); */
8009: /* 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); */
8010: /* } */
8011: }
1.186 brouard 8012:
8013: /* ------ Other prevalence ratios------------ */
1.126 brouard 8014:
1.127 brouard 8015: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8016:
8017: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8018: /* 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",\
8019: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8020: */
1.126 brouard 8021:
1.127 brouard 8022: if (mobilav!=0) {
8023: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8024: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8025: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8026: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8027: }
1.126 brouard 8028: }
8029:
8030:
1.127 brouard 8031: /*---------- Health expectancies, no variances ------------*/
8032:
1.201 brouard 8033: strcpy(filerese,"E_");
8034: strcat(filerese,fileresu);
1.126 brouard 8035: if((ficreseij=fopen(filerese,"w"))==NULL) {
8036: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8037: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8038: }
8039: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
8040: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 8041: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8042: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8043:
8044: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8045: fprintf(ficreseij,"\n#****** ");
8046: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8047: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8048: }
8049: fprintf(ficreseij,"******\n");
8050:
8051: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8052: oldm=oldms;savm=savms;
8053: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8054:
8055: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8056: /*}*/
1.127 brouard 8057: }
8058: fclose(ficreseij);
8059:
8060:
8061: /*---------- Health expectancies and variances ------------*/
8062:
8063:
1.201 brouard 8064: strcpy(filerest,"T_");
8065: strcat(filerest,fileresu);
1.127 brouard 8066: if((ficrest=fopen(filerest,"w"))==NULL) {
8067: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8068: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8069: }
8070: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8071: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8072:
1.126 brouard 8073:
1.201 brouard 8074: strcpy(fileresstde,"STDE_");
8075: strcat(fileresstde,fileresu);
1.126 brouard 8076: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8077: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8078: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8079: }
8080: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8081: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8082:
1.201 brouard 8083: strcpy(filerescve,"CVE_");
8084: strcat(filerescve,fileresu);
1.126 brouard 8085: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8086: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8087: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8088: }
8089: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8090: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8091:
1.201 brouard 8092: strcpy(fileresv,"V_");
8093: strcat(fileresv,fileresu);
1.126 brouard 8094: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8095: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8096: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8097: }
8098: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8099: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8100:
1.145 brouard 8101: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8102: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8103:
8104: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8105: fprintf(ficrest,"\n#****** ");
1.126 brouard 8106: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8107: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8108: fprintf(ficrest,"******\n");
8109:
8110: fprintf(ficresstdeij,"\n#****** ");
8111: fprintf(ficrescveij,"\n#****** ");
8112: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8113: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8114: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8115: }
8116: fprintf(ficresstdeij,"******\n");
8117: fprintf(ficrescveij,"******\n");
8118:
8119: fprintf(ficresvij,"\n#****** ");
8120: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8121: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8122: fprintf(ficresvij,"******\n");
8123:
8124: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8125: oldm=oldms;savm=savms;
1.127 brouard 8126: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 8127: /*
8128: */
8129: /* goto endfree; */
1.126 brouard 8130:
8131: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8132: pstamp(ficrest);
1.145 brouard 8133:
8134:
1.128 brouard 8135: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 8136: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 8137: cptcod= 0; /* To be deleted */
1.203 brouard 8138: 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 */
1.145 brouard 8139: fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
1.128 brouard 8140: if(vpopbased==1)
8141: 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);
8142: else
8143: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 brouard 8144: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 8145: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8146: fprintf(ficrest,"\n");
1.199 brouard 8147: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 8148: epj=vector(1,nlstate+1);
8149: for(age=bage; age <=fage ;age++){
1.203 brouard 8150: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
1.128 brouard 8151: if (vpopbased==1) {
8152: if(mobilav ==0){
8153: for(i=1; i<=nlstate;i++)
8154: prlim[i][i]=probs[(int)age][i][k];
8155: }else{ /* mobilav */
8156: for(i=1; i<=nlstate;i++)
8157: prlim[i][i]=mobaverage[(int)age][i][k];
8158: }
1.126 brouard 8159: }
8160:
1.201 brouard 8161: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.205 brouard 8162: /* fprintf(ficrest," %4.0f %d %d %d %d",age, vpopbased, mobilav,Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */ /* to be done */
1.199 brouard 8163: /* printf(" age %4.0f ",age); */
1.128 brouard 8164: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8165: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8166: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 8167: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8168: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 8169: }
8170: epj[nlstate+1] +=epj[j];
1.126 brouard 8171: }
1.199 brouard 8172: /* printf(" age %4.0f \n",age); */
1.126 brouard 8173:
1.128 brouard 8174: for(i=1, vepp=0.;i <=nlstate;i++)
8175: for(j=1;j <=nlstate;j++)
8176: vepp += vareij[i][j][(int)age];
8177: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8178: for(j=1;j <=nlstate;j++){
8179: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
8180: }
8181: fprintf(ficrest,"\n");
1.126 brouard 8182: }
8183: }
8184: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8185: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8186: free_vector(epj,1,nlstate+1);
1.145 brouard 8187: /*}*/
1.126 brouard 8188: }
8189: free_vector(weight,1,n);
1.145 brouard 8190: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8191: free_imatrix(s,1,maxwav+1,1,n);
8192: free_matrix(anint,1,maxwav,1,n);
8193: free_matrix(mint,1,maxwav,1,n);
8194: free_ivector(cod,1,n);
8195: free_ivector(tab,1,NCOVMAX);
8196: fclose(ficresstdeij);
8197: fclose(ficrescveij);
8198: fclose(ficresvij);
8199: fclose(ficrest);
8200: fclose(ficpar);
8201:
8202: /*------- Variance of period (stable) prevalence------*/
8203:
1.201 brouard 8204: strcpy(fileresvpl,"VPL_");
8205: strcat(fileresvpl,fileresu);
1.126 brouard 8206: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8207: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8208: exit(0);
8209: }
8210: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
8211:
1.145 brouard 8212: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8213: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8214:
8215: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8216: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8217: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8218: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8219: fprintf(ficresvpl,"******\n");
8220:
8221: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8222: oldm=oldms;savm=savms;
1.203 brouard 8223: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
1.126 brouard 8224: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8225: /*}*/
1.126 brouard 8226: }
8227:
8228: fclose(ficresvpl);
8229:
8230: /*---------- End : free ----------------*/
8231: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8232: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8233: } /* mle==-3 arrives here for freeing */
1.164 brouard 8234: /* endfree:*/
1.141 brouard 8235: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8236: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8237: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8238: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8239: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8240: free_matrix(covar,0,NCOVMAX,1,n);
8241: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8242: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8243: /*free_vector(delti,1,npar);*/
8244: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8245: free_matrix(agev,1,maxwav,1,imx);
8246: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8247:
1.145 brouard 8248: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8249: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8250: free_ivector(Tvar,1,NCOVMAX);
8251: free_ivector(Tprod,1,NCOVMAX);
8252: free_ivector(Tvaraff,1,NCOVMAX);
8253: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8254:
8255: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8256: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8257: fflush(fichtm);
8258: fflush(ficgp);
8259:
8260:
8261: if((nberr >0) || (nbwarn>0)){
8262: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8263: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8264: }else{
8265: printf("End of Imach\n");
8266: fprintf(ficlog,"End of Imach\n");
8267: }
8268: printf("See log file on %s\n",filelog);
8269: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8270: /*(void) gettimeofday(&end_time,&tzp);*/
8271: rend_time = time(NULL);
8272: end_time = *localtime(&rend_time);
8273: /* tml = *localtime(&end_time.tm_sec); */
8274: strcpy(strtend,asctime(&end_time));
1.126 brouard 8275: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8276: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8277: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8278:
1.157 brouard 8279: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8280: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8281: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8282: /* printf("Total time was %d uSec.\n", total_usecs);*/
8283: /* if(fileappend(fichtm,optionfilehtm)){ */
8284: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8285: fclose(fichtm);
8286: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8287: fclose(fichtmcov);
8288: fclose(ficgp);
8289: fclose(ficlog);
8290: /*------ End -----------*/
8291:
8292:
8293: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8294: #ifdef WIN32
8295: if (_chdir(pathcd) != 0)
8296: printf("Can't move to directory %s!\n",path);
8297: if(_getcwd(pathcd,MAXLINE) > 0)
8298: #else
1.126 brouard 8299: if(chdir(pathcd) != 0)
1.184 brouard 8300: printf("Can't move to directory %s!\n", path);
8301: if (getcwd(pathcd, MAXLINE) > 0)
8302: #endif
1.126 brouard 8303: printf("Current directory %s!\n",pathcd);
8304: /*strcat(plotcmd,CHARSEPARATOR);*/
8305: sprintf(plotcmd,"gnuplot");
1.157 brouard 8306: #ifdef _WIN32
1.126 brouard 8307: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8308: #endif
8309: if(!stat(plotcmd,&info)){
1.158 brouard 8310: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8311: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8312: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8313: }else
8314: strcpy(pplotcmd,plotcmd);
1.157 brouard 8315: #ifdef __unix
1.126 brouard 8316: strcpy(plotcmd,GNUPLOTPROGRAM);
8317: if(!stat(plotcmd,&info)){
1.158 brouard 8318: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8319: }else
8320: strcpy(pplotcmd,plotcmd);
8321: #endif
8322: }else
8323: strcpy(pplotcmd,plotcmd);
8324:
8325: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8326: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8327:
8328: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8329: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8330: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8331: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8332: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8333: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8334: }
1.158 brouard 8335: printf(" Successful, please wait...");
1.126 brouard 8336: while (z[0] != 'q') {
8337: /* chdir(path); */
1.154 brouard 8338: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8339: scanf("%s",z);
8340: /* if (z[0] == 'c') system("./imach"); */
8341: if (z[0] == 'e') {
1.158 brouard 8342: #ifdef __APPLE__
1.152 brouard 8343: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8344: #elif __linux
8345: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8346: #else
1.152 brouard 8347: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8348: #endif
8349: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8350: system(pplotcmd);
1.126 brouard 8351: }
8352: else if (z[0] == 'g') system(plotcmd);
8353: else if (z[0] == 'q') exit(0);
8354: }
8355: end:
8356: while (z[0] != 'q') {
1.195 brouard 8357: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8358: scanf("%s",z);
8359: }
8360: }
FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>
![[BACK]](/icons/small/back.gif){kind=icon}
Return to imach.c CVS log ![[TXT]](/icons/small/text.gif){kind=icon}
![[DIR]](/icons/small/dir.gif){kind=icon}
Up to [Local Repository] / imach / src