Annotation of imach/src/imach.c, revision 1.207
1.207 ! brouard 1: /* $Id: imach.c,v 1.206 2015/10/24 07:14:11 brouard Exp $
1.126 brouard 2: $State: Exp $
1.163 brouard 3: $Log: imach.c,v $
1.207 ! brouard 4: Revision 1.206 2015/10/24 07:14:11 brouard
! 5: *** empty log message ***
! 6:
1.206 brouard 7: Revision 1.205 2015/10/23 15:50:53 brouard
8: Summary: 0.98r3 some clarification for graphs on likelihood contributions
9:
1.205 brouard 10: Revision 1.204 2015/10/01 16:20:26 brouard
11: Summary: Some new graphs of contribution to likelihood
12:
1.204 brouard 13: Revision 1.203 2015/09/30 17:45:14 brouard
14: Summary: looking at better estimation of the hessian
15:
16: Also a better criteria for convergence to the period prevalence And
17: therefore adding the number of years needed to converge. (The
18: prevalence in any alive state shold sum to one
19:
1.203 brouard 20: Revision 1.202 2015/09/22 19:45:16 brouard
21: Summary: Adding some overall graph on contribution to likelihood. Might change
22:
1.202 brouard 23: Revision 1.201 2015/09/15 17:34:58 brouard
24: Summary: 0.98r0
25:
26: - Some new graphs like suvival functions
27: - Some bugs fixed like model=1+age+V2.
28:
1.201 brouard 29: Revision 1.200 2015/09/09 16:53:55 brouard
30: Summary: Big bug thanks to Flavia
31:
32: Even model=1+age+V2. did not work anymore
33:
1.200 brouard 34: Revision 1.199 2015/09/07 14:09:23 brouard
35: Summary: 0.98q6 changing default small png format for graph to vectorized svg.
36:
1.199 brouard 37: Revision 1.198 2015/09/03 07:14:39 brouard
38: Summary: 0.98q5 Flavia
39:
1.198 brouard 40: Revision 1.197 2015/09/01 18:24:39 brouard
41: *** empty log message ***
42:
1.197 brouard 43: Revision 1.196 2015/08/18 23:17:52 brouard
44: Summary: 0.98q5
45:
1.196 brouard 46: Revision 1.195 2015/08/18 16:28:39 brouard
47: Summary: Adding a hack for testing purpose
48:
49: After reading the title, ftol and model lines, if the comment line has
50: a q, starting with #q, the answer at the end of the run is quit. It
51: permits to run test files in batch with ctest. The former workaround was
52: $ echo q | imach foo.imach
53:
1.195 brouard 54: Revision 1.194 2015/08/18 13:32:00 brouard
55: Summary: Adding error when the covariance matrix doesn't contain the exact number of lines required by the model line.
56:
1.194 brouard 57: Revision 1.193 2015/08/04 07:17:42 brouard
58: Summary: 0.98q4
59:
1.193 brouard 60: Revision 1.192 2015/07/16 16:49:02 brouard
61: Summary: Fixing some outputs
62:
1.192 brouard 63: Revision 1.191 2015/07/14 10:00:33 brouard
64: Summary: Some fixes
65:
1.191 brouard 66: Revision 1.190 2015/05/05 08:51:13 brouard
67: Summary: Adding digits in output parameters (7 digits instead of 6)
68:
69: Fix 1+age+.
70:
1.190 brouard 71: Revision 1.189 2015/04/30 14:45:16 brouard
72: Summary: 0.98q2
73:
1.189 brouard 74: Revision 1.188 2015/04/30 08:27:53 brouard
75: *** empty log message ***
76:
1.188 brouard 77: Revision 1.187 2015/04/29 09:11:15 brouard
78: *** empty log message ***
79:
1.187 brouard 80: Revision 1.186 2015/04/23 12:01:52 brouard
81: Summary: V1*age is working now, version 0.98q1
82:
83: Some codes had been disabled in order to simplify and Vn*age was
84: working in the optimization phase, ie, giving correct MLE parameters,
85: but, as usual, outputs were not correct and program core dumped.
86:
1.186 brouard 87: Revision 1.185 2015/03/11 13:26:42 brouard
88: Summary: Inclusion of compile and links command line for Intel Compiler
89:
1.185 brouard 90: Revision 1.184 2015/03/11 11:52:39 brouard
91: Summary: Back from Windows 8. Intel Compiler
92:
1.184 brouard 93: Revision 1.183 2015/03/10 20:34:32 brouard
94: Summary: 0.98q0, trying with directest, mnbrak fixed
95:
96: We use directest instead of original Powell test; probably no
97: incidence on the results, but better justifications;
98: We fixed Numerical Recipes mnbrak routine which was wrong and gave
99: wrong results.
100:
1.183 brouard 101: Revision 1.182 2015/02/12 08:19:57 brouard
102: Summary: Trying to keep directest which seems simpler and more general
103: Author: Nicolas Brouard
104:
1.182 brouard 105: Revision 1.181 2015/02/11 23:22:24 brouard
106: Summary: Comments on Powell added
107:
108: Author:
109:
1.181 brouard 110: Revision 1.180 2015/02/11 17:33:45 brouard
111: Summary: Finishing move from main to function (hpijx and prevalence_limit)
112:
1.180 brouard 113: Revision 1.179 2015/01/04 09:57:06 brouard
114: Summary: back to OS/X
115:
1.179 brouard 116: Revision 1.178 2015/01/04 09:35:48 brouard
117: *** empty log message ***
118:
1.178 brouard 119: Revision 1.177 2015/01/03 18:40:56 brouard
120: Summary: Still testing ilc32 on OSX
121:
1.177 brouard 122: Revision 1.176 2015/01/03 16:45:04 brouard
123: *** empty log message ***
124:
1.176 brouard 125: Revision 1.175 2015/01/03 16:33:42 brouard
126: *** empty log message ***
127:
1.175 brouard 128: Revision 1.174 2015/01/03 16:15:49 brouard
129: Summary: Still in cross-compilation
130:
1.174 brouard 131: Revision 1.173 2015/01/03 12:06:26 brouard
132: Summary: trying to detect cross-compilation
133:
1.173 brouard 134: Revision 1.172 2014/12/27 12:07:47 brouard
135: Summary: Back from Visual Studio and Intel, options for compiling for Windows XP
136:
1.172 brouard 137: Revision 1.171 2014/12/23 13:26:59 brouard
138: Summary: Back from Visual C
139:
140: Still problem with utsname.h on Windows
141:
1.171 brouard 142: Revision 1.170 2014/12/23 11:17:12 brouard
143: Summary: Cleaning some \%% back to %%
144:
145: The escape was mandatory for a specific compiler (which one?), but too many warnings.
146:
1.170 brouard 147: Revision 1.169 2014/12/22 23:08:31 brouard
148: Summary: 0.98p
149:
150: Outputs some informations on compiler used, OS etc. Testing on different platforms.
151:
1.169 brouard 152: Revision 1.168 2014/12/22 15:17:42 brouard
1.170 brouard 153: Summary: update
1.169 brouard 154:
1.168 brouard 155: Revision 1.167 2014/12/22 13:50:56 brouard
156: Summary: Testing uname and compiler version and if compiled 32 or 64
157:
158: Testing on Linux 64
159:
1.167 brouard 160: Revision 1.166 2014/12/22 11:40:47 brouard
161: *** empty log message ***
162:
1.166 brouard 163: Revision 1.165 2014/12/16 11:20:36 brouard
164: Summary: After compiling on Visual C
165:
166: * imach.c (Module): Merging 1.61 to 1.162
167:
1.165 brouard 168: Revision 1.164 2014/12/16 10:52:11 brouard
169: Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
170:
171: * imach.c (Module): Merging 1.61 to 1.162
172:
1.164 brouard 173: Revision 1.163 2014/12/16 10:30:11 brouard
174: * imach.c (Module): Merging 1.61 to 1.162
175:
1.163 brouard 176: Revision 1.162 2014/09/25 11:43:39 brouard
177: Summary: temporary backup 0.99!
178:
1.162 brouard 179: Revision 1.1 2014/09/16 11:06:58 brouard
180: Summary: With some code (wrong) for nlopt
181:
182: Author:
183:
184: Revision 1.161 2014/09/15 20:41:41 brouard
185: Summary: Problem with macro SQR on Intel compiler
186:
1.161 brouard 187: Revision 1.160 2014/09/02 09:24:05 brouard
188: *** empty log message ***
189:
1.160 brouard 190: Revision 1.159 2014/09/01 10:34:10 brouard
191: Summary: WIN32
192: Author: Brouard
193:
1.159 brouard 194: Revision 1.158 2014/08/27 17:11:51 brouard
195: *** empty log message ***
196:
1.158 brouard 197: Revision 1.157 2014/08/27 16:26:55 brouard
198: Summary: Preparing windows Visual studio version
199: Author: Brouard
200:
201: In order to compile on Visual studio, time.h is now correct and time_t
202: and tm struct should be used. difftime should be used but sometimes I
203: just make the differences in raw time format (time(&now).
204: Trying to suppress #ifdef LINUX
205: Add xdg-open for __linux in order to open default browser.
206:
1.157 brouard 207: Revision 1.156 2014/08/25 20:10:10 brouard
208: *** empty log message ***
209:
1.156 brouard 210: Revision 1.155 2014/08/25 18:32:34 brouard
211: Summary: New compile, minor changes
212: Author: Brouard
213:
1.155 brouard 214: Revision 1.154 2014/06/20 17:32:08 brouard
215: Summary: Outputs now all graphs of convergence to period prevalence
216:
1.154 brouard 217: Revision 1.153 2014/06/20 16:45:46 brouard
218: Summary: If 3 live state, convergence to period prevalence on same graph
219: Author: Brouard
220:
1.153 brouard 221: Revision 1.152 2014/06/18 17:54:09 brouard
222: Summary: open browser, use gnuplot on same dir than imach if not found in the path
223:
1.152 brouard 224: Revision 1.151 2014/06/18 16:43:30 brouard
225: *** empty log message ***
226:
1.151 brouard 227: Revision 1.150 2014/06/18 16:42:35 brouard
228: Summary: If gnuplot is not in the path try on same directory than imach binary (OSX)
229: Author: brouard
230:
1.150 brouard 231: Revision 1.149 2014/06/18 15:51:14 brouard
232: Summary: Some fixes in parameter files errors
233: Author: Nicolas Brouard
234:
1.149 brouard 235: Revision 1.148 2014/06/17 17:38:48 brouard
236: Summary: Nothing new
237: Author: Brouard
238:
239: Just a new packaging for OS/X version 0.98nS
240:
1.148 brouard 241: Revision 1.147 2014/06/16 10:33:11 brouard
242: *** empty log message ***
243:
1.147 brouard 244: Revision 1.146 2014/06/16 10:20:28 brouard
245: Summary: Merge
246: Author: Brouard
247:
248: Merge, before building revised version.
249:
1.146 brouard 250: Revision 1.145 2014/06/10 21:23:15 brouard
251: Summary: Debugging with valgrind
252: Author: Nicolas Brouard
253:
254: Lot of changes in order to output the results with some covariates
255: After the Edimburgh REVES conference 2014, it seems mandatory to
256: improve the code.
257: No more memory valgrind error but a lot has to be done in order to
258: continue the work of splitting the code into subroutines.
259: Also, decodemodel has been improved. Tricode is still not
260: optimal. nbcode should be improved. Documentation has been added in
261: the source code.
262:
1.144 brouard 263: Revision 1.143 2014/01/26 09:45:38 brouard
264: Summary: Version 0.98nR (to be improved, but gives same optimization results as 0.98k. Nice, promising
265:
266: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
267: (Module): Version 0.98nR Running ok, but output format still only works for three covariates.
268:
1.143 brouard 269: Revision 1.142 2014/01/26 03:57:36 brouard
270: Summary: gnuplot changed plot w l 1 has to be changed to plot w l lt 2
271:
272: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
273:
1.142 brouard 274: Revision 1.141 2014/01/26 02:42:01 brouard
275: * imach.c (Module): Trying to merge old staffs together while being at Tokyo. Not tested...
276:
1.141 brouard 277: Revision 1.140 2011/09/02 10:37:54 brouard
278: Summary: times.h is ok with mingw32 now.
279:
1.140 brouard 280: Revision 1.139 2010/06/14 07:50:17 brouard
281: After the theft of my laptop, I probably lost some lines of codes which were not uploaded to the CVS tree.
282: I remember having already fixed agemin agemax which are pointers now but not cvs saved.
283:
1.139 brouard 284: Revision 1.138 2010/04/30 18:19:40 brouard
285: *** empty log message ***
286:
1.138 brouard 287: Revision 1.137 2010/04/29 18:11:38 brouard
288: (Module): Checking covariates for more complex models
289: than V1+V2. A lot of change to be done. Unstable.
290:
1.137 brouard 291: Revision 1.136 2010/04/26 20:30:53 brouard
292: (Module): merging some libgsl code. Fixing computation
293: of likelione (using inter/intrapolation if mle = 0) in order to
294: get same likelihood as if mle=1.
295: Some cleaning of code and comments added.
296:
1.136 brouard 297: Revision 1.135 2009/10/29 15:33:14 brouard
298: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
299:
1.135 brouard 300: Revision 1.134 2009/10/29 13:18:53 brouard
301: (Module): Now imach stops if date of birth, at least year of birth, is not given. Some cleaning of the code.
302:
1.134 brouard 303: Revision 1.133 2009/07/06 10:21:25 brouard
304: just nforces
305:
1.133 brouard 306: Revision 1.132 2009/07/06 08:22:05 brouard
307: Many tings
308:
1.132 brouard 309: Revision 1.131 2009/06/20 16:22:47 brouard
310: Some dimensions resccaled
311:
1.131 brouard 312: Revision 1.130 2009/05/26 06:44:34 brouard
313: (Module): Max Covariate is now set to 20 instead of 8. A
314: lot of cleaning with variables initialized to 0. Trying to make
315: V2+V3*age+V1+V4 strb=V3*age+V1+V4 working better.
316:
1.130 brouard 317: Revision 1.129 2007/08/31 13:49:27 lievre
318: Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting
319:
1.129 lievre 320: Revision 1.128 2006/06/30 13:02:05 brouard
321: (Module): Clarifications on computing e.j
322:
1.128 brouard 323: Revision 1.127 2006/04/28 18:11:50 brouard
324: (Module): Yes the sum of survivors was wrong since
325: imach-114 because nhstepm was no more computed in the age
326: loop. Now we define nhstepma in the age loop.
327: (Module): In order to speed up (in case of numerous covariates) we
328: compute health expectancies (without variances) in a first step
329: and then all the health expectancies with variances or standard
330: deviation (needs data from the Hessian matrices) which slows the
331: computation.
332: In the future we should be able to stop the program is only health
333: expectancies and graph are needed without standard deviations.
334:
1.127 brouard 335: Revision 1.126 2006/04/28 17:23:28 brouard
336: (Module): Yes the sum of survivors was wrong since
337: imach-114 because nhstepm was no more computed in the age
338: loop. Now we define nhstepma in the age loop.
339: Version 0.98h
340:
1.126 brouard 341: Revision 1.125 2006/04/04 15:20:31 lievre
342: Errors in calculation of health expectancies. Age was not initialized.
343: Forecasting file added.
344:
345: Revision 1.124 2006/03/22 17:13:53 lievre
346: Parameters are printed with %lf instead of %f (more numbers after the comma).
347: The log-likelihood is printed in the log file
348:
349: Revision 1.123 2006/03/20 10:52:43 brouard
350: * imach.c (Module): <title> changed, corresponds to .htm file
351: name. <head> headers where missing.
352:
353: * imach.c (Module): Weights can have a decimal point as for
354: English (a comma might work with a correct LC_NUMERIC environment,
355: otherwise the weight is truncated).
356: Modification of warning when the covariates values are not 0 or
357: 1.
358: Version 0.98g
359:
360: Revision 1.122 2006/03/20 09:45:41 brouard
361: (Module): Weights can have a decimal point as for
362: English (a comma might work with a correct LC_NUMERIC environment,
363: otherwise the weight is truncated).
364: Modification of warning when the covariates values are not 0 or
365: 1.
366: Version 0.98g
367:
368: Revision 1.121 2006/03/16 17:45:01 lievre
369: * imach.c (Module): Comments concerning covariates added
370:
371: * imach.c (Module): refinements in the computation of lli if
372: status=-2 in order to have more reliable computation if stepm is
373: not 1 month. Version 0.98f
374:
375: Revision 1.120 2006/03/16 15:10:38 lievre
376: (Module): refinements in the computation of lli if
377: status=-2 in order to have more reliable computation if stepm is
378: not 1 month. Version 0.98f
379:
380: Revision 1.119 2006/03/15 17:42:26 brouard
381: (Module): Bug if status = -2, the loglikelihood was
382: computed as likelihood omitting the logarithm. Version O.98e
383:
384: Revision 1.118 2006/03/14 18:20:07 brouard
385: (Module): varevsij Comments added explaining the second
386: table of variances if popbased=1 .
387: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
388: (Module): Function pstamp added
389: (Module): Version 0.98d
390:
391: Revision 1.117 2006/03/14 17:16:22 brouard
392: (Module): varevsij Comments added explaining the second
393: table of variances if popbased=1 .
394: (Module): Covariances of eij, ekl added, graphs fixed, new html link.
395: (Module): Function pstamp added
396: (Module): Version 0.98d
397:
398: Revision 1.116 2006/03/06 10:29:27 brouard
399: (Module): Variance-covariance wrong links and
400: varian-covariance of ej. is needed (Saito).
401:
402: Revision 1.115 2006/02/27 12:17:45 brouard
403: (Module): One freematrix added in mlikeli! 0.98c
404:
405: Revision 1.114 2006/02/26 12:57:58 brouard
406: (Module): Some improvements in processing parameter
407: filename with strsep.
408:
409: Revision 1.113 2006/02/24 14:20:24 brouard
410: (Module): Memory leaks checks with valgrind and:
411: datafile was not closed, some imatrix were not freed and on matrix
412: allocation too.
413:
414: Revision 1.112 2006/01/30 09:55:26 brouard
415: (Module): Back to gnuplot.exe instead of wgnuplot.exe
416:
417: Revision 1.111 2006/01/25 20:38:18 brouard
418: (Module): Lots of cleaning and bugs added (Gompertz)
419: (Module): Comments can be added in data file. Missing date values
420: can be a simple dot '.'.
421:
422: Revision 1.110 2006/01/25 00:51:50 brouard
423: (Module): Lots of cleaning and bugs added (Gompertz)
424:
425: Revision 1.109 2006/01/24 19:37:15 brouard
426: (Module): Comments (lines starting with a #) are allowed in data.
427:
428: Revision 1.108 2006/01/19 18:05:42 lievre
429: Gnuplot problem appeared...
430: To be fixed
431:
432: Revision 1.107 2006/01/19 16:20:37 brouard
433: Test existence of gnuplot in imach path
434:
435: Revision 1.106 2006/01/19 13:24:36 brouard
436: Some cleaning and links added in html output
437:
438: Revision 1.105 2006/01/05 20:23:19 lievre
439: *** empty log message ***
440:
441: Revision 1.104 2005/09/30 16:11:43 lievre
442: (Module): sump fixed, loop imx fixed, and simplifications.
443: (Module): If the status is missing at the last wave but we know
444: that the person is alive, then we can code his/her status as -2
445: (instead of missing=-1 in earlier versions) and his/her
446: contributions to the likelihood is 1 - Prob of dying from last
447: health status (= 1-p13= p11+p12 in the easiest case of somebody in
448: the healthy state at last known wave). Version is 0.98
449:
450: Revision 1.103 2005/09/30 15:54:49 lievre
451: (Module): sump fixed, loop imx fixed, and simplifications.
452:
453: Revision 1.102 2004/09/15 17:31:30 brouard
454: Add the possibility to read data file including tab characters.
455:
456: Revision 1.101 2004/09/15 10:38:38 brouard
457: Fix on curr_time
458:
459: Revision 1.100 2004/07/12 18:29:06 brouard
460: Add version for Mac OS X. Just define UNIX in Makefile
461:
462: Revision 1.99 2004/06/05 08:57:40 brouard
463: *** empty log message ***
464:
465: Revision 1.98 2004/05/16 15:05:56 brouard
466: New version 0.97 . First attempt to estimate force of mortality
467: directly from the data i.e. without the need of knowing the health
468: state at each age, but using a Gompertz model: log u =a + b*age .
469: This is the basic analysis of mortality and should be done before any
470: other analysis, in order to test if the mortality estimated from the
471: cross-longitudinal survey is different from the mortality estimated
472: from other sources like vital statistic data.
473:
474: The same imach parameter file can be used but the option for mle should be -3.
475:
1.133 brouard 476: Agnès, who wrote this part of the code, tried to keep most of the
1.126 brouard 477: former routines in order to include the new code within the former code.
478:
479: The output is very simple: only an estimate of the intercept and of
480: the slope with 95% confident intervals.
481:
482: Current limitations:
483: A) Even if you enter covariates, i.e. with the
484: model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
485: B) There is no computation of Life Expectancy nor Life Table.
486:
487: Revision 1.97 2004/02/20 13:25:42 lievre
488: Version 0.96d. Population forecasting command line is (temporarily)
489: suppressed.
490:
491: Revision 1.96 2003/07/15 15:38:55 brouard
492: * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
493: rewritten within the same printf. Workaround: many printfs.
494:
495: Revision 1.95 2003/07/08 07:54:34 brouard
496: * imach.c (Repository):
497: (Repository): Using imachwizard code to output a more meaningful covariance
498: matrix (cov(a12,c31) instead of numbers.
499:
500: Revision 1.94 2003/06/27 13:00:02 brouard
501: Just cleaning
502:
503: Revision 1.93 2003/06/25 16:33:55 brouard
504: (Module): On windows (cygwin) function asctime_r doesn't
505: exist so I changed back to asctime which exists.
506: (Module): Version 0.96b
507:
508: Revision 1.92 2003/06/25 16:30:45 brouard
509: (Module): On windows (cygwin) function asctime_r doesn't
510: exist so I changed back to asctime which exists.
511:
512: Revision 1.91 2003/06/25 15:30:29 brouard
513: * imach.c (Repository): Duplicated warning errors corrected.
514: (Repository): Elapsed time after each iteration is now output. It
515: helps to forecast when convergence will be reached. Elapsed time
516: is stamped in powell. We created a new html file for the graphs
517: concerning matrix of covariance. It has extension -cov.htm.
518:
519: Revision 1.90 2003/06/24 12:34:15 brouard
520: (Module): Some bugs corrected for windows. Also, when
521: mle=-1 a template is output in file "or"mypar.txt with the design
522: of the covariance matrix to be input.
523:
524: Revision 1.89 2003/06/24 12:30:52 brouard
525: (Module): Some bugs corrected for windows. Also, when
526: mle=-1 a template is output in file "or"mypar.txt with the design
527: of the covariance matrix to be input.
528:
529: Revision 1.88 2003/06/23 17:54:56 brouard
530: * 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.
531:
532: Revision 1.87 2003/06/18 12:26:01 brouard
533: Version 0.96
534:
535: Revision 1.86 2003/06/17 20:04:08 brouard
536: (Module): Change position of html and gnuplot routines and added
537: routine fileappend.
538:
539: Revision 1.85 2003/06/17 13:12:43 brouard
540: * imach.c (Repository): Check when date of death was earlier that
541: current date of interview. It may happen when the death was just
542: prior to the death. In this case, dh was negative and likelihood
543: was wrong (infinity). We still send an "Error" but patch by
544: assuming that the date of death was just one stepm after the
545: interview.
546: (Repository): Because some people have very long ID (first column)
547: we changed int to long in num[] and we added a new lvector for
548: memory allocation. But we also truncated to 8 characters (left
549: truncation)
550: (Repository): No more line truncation errors.
551:
552: Revision 1.84 2003/06/13 21:44:43 brouard
553: * imach.c (Repository): Replace "freqsummary" at a correct
554: place. It differs from routine "prevalence" which may be called
555: many times. Probs is memory consuming and must be used with
556: parcimony.
557: Version 0.95a3 (should output exactly the same maximization than 0.8a2)
558:
559: Revision 1.83 2003/06/10 13:39:11 lievre
560: *** empty log message ***
561:
562: Revision 1.82 2003/06/05 15:57:20 brouard
563: Add log in imach.c and fullversion number is now printed.
564:
565: */
566: /*
567: Interpolated Markov Chain
568:
569: Short summary of the programme:
570:
571: This program computes Healthy Life Expectancies from
572: cross-longitudinal data. Cross-longitudinal data consist in: -1- a
573: first survey ("cross") where individuals from different ages are
574: interviewed on their health status or degree of disability (in the
575: case of a health survey which is our main interest) -2- at least a
576: second wave of interviews ("longitudinal") which measure each change
577: (if any) in individual health status. Health expectancies are
578: computed from the time spent in each health state according to a
579: model. More health states you consider, more time is necessary to reach the
580: Maximum Likelihood of the parameters involved in the model. The
581: simplest model is the multinomial logistic model where pij is the
582: probability to be observed in state j at the second wave
583: conditional to be observed in state i at the first wave. Therefore
584: the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
585: 'age' is age and 'sex' is a covariate. If you want to have a more
586: complex model than "constant and age", you should modify the program
587: where the markup *Covariates have to be included here again* invites
588: you to do it. More covariates you add, slower the
589: convergence.
590:
591: The advantage of this computer programme, compared to a simple
592: multinomial logistic model, is clear when the delay between waves is not
593: identical for each individual. Also, if a individual missed an
594: intermediate interview, the information is lost, but taken into
595: account using an interpolation or extrapolation.
596:
597: hPijx is the probability to be observed in state i at age x+h
598: conditional to the observed state i at age x. The delay 'h' can be
599: split into an exact number (nh*stepm) of unobserved intermediate
600: states. This elementary transition (by month, quarter,
601: semester or year) is modelled as a multinomial logistic. The hPx
602: matrix is simply the matrix product of nh*stepm elementary matrices
603: and the contribution of each individual to the likelihood is simply
604: hPijx.
605:
606: Also this programme outputs the covariance matrix of the parameters but also
607: of the life expectancies. It also computes the period (stable) prevalence.
608:
1.133 brouard 609: Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
610: Institut national d'études démographiques, Paris.
1.126 brouard 611: This software have been partly granted by Euro-REVES, a concerted action
612: from the European Union.
613: It is copyrighted identically to a GNU software product, ie programme and
614: software can be distributed freely for non commercial use. Latest version
615: can be accessed at http://euroreves.ined.fr/imach .
616:
617: Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
618: or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
619:
620: **********************************************************************/
621: /*
622: main
623: read parameterfile
624: read datafile
625: concatwav
626: freqsummary
627: if (mle >= 1)
628: mlikeli
629: print results files
630: if mle==1
631: computes hessian
632: read end of parameter file: agemin, agemax, bage, fage, estepm
633: begin-prev-date,...
634: open gnuplot file
635: open html file
1.145 brouard 636: period (stable) prevalence | pl_nom 1-1 2-2 etc by covariate
637: for age prevalim() | #****** V1=0 V2=1 V3=1 V4=0 ******
638: | 65 1 0 2 1 3 1 4 0 0.96326 0.03674
639: freexexit2 possible for memory heap.
640:
641: h Pij x | pij_nom ficrestpij
642: # Cov Agex agex+h hpijx with i,j= 1-1 1-2 1-3 2-1 2-2 2-3
643: 1 85 85 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000
644: 1 85 86 0.68299 0.22291 0.09410 0.71093 0.00000 0.28907
645:
646: 1 65 99 0.00364 0.00322 0.99314 0.00350 0.00310 0.99340
647: 1 65 100 0.00214 0.00204 0.99581 0.00206 0.00196 0.99597
648: variance of p one-step probabilities varprob | prob_nom ficresprob #One-step probabilities and stand. devi in ()
649: Standard deviation of one-step probabilities | probcor_nom ficresprobcor #One-step probabilities and correlation matrix
650: Matrix of variance covariance of one-step probabilities | probcov_nom ficresprobcov #One-step probabilities and covariance matrix
651:
1.126 brouard 652: forecasting if prevfcast==1 prevforecast call prevalence()
653: health expectancies
654: Variance-covariance of DFLE
655: prevalence()
656: movingaverage()
657: varevsij()
658: if popbased==1 varevsij(,popbased)
659: total life expectancies
660: Variance of period (stable) prevalence
661: end
662: */
663:
1.187 brouard 664: /* #define DEBUG */
665: /* #define DEBUGBRENT */
1.203 brouard 666: /* #define DEBUGLINMIN */
667: /* #define DEBUGHESS */
668: #define DEBUGHESSIJ
669: /* #define LINMINORIGINAL /\* Don't use loop on scale in linmin (accepting nan)*\/ */
1.165 brouard 670: #define POWELL /* Instead of NLOPT */
1.192 brouard 671: #define POWELLF1F3 /* Skip test */
1.186 brouard 672: /* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test *\/ */
673: /* #define MNBRAKORIGINAL /\* Don't use mnbrak fix *\/ */
1.126 brouard 674:
675: #include <math.h>
676: #include <stdio.h>
677: #include <stdlib.h>
678: #include <string.h>
1.159 brouard 679:
680: #ifdef _WIN32
681: #include <io.h>
1.172 brouard 682: #include <windows.h>
683: #include <tchar.h>
1.159 brouard 684: #else
1.126 brouard 685: #include <unistd.h>
1.159 brouard 686: #endif
1.126 brouard 687:
688: #include <limits.h>
689: #include <sys/types.h>
1.171 brouard 690:
691: #if defined(__GNUC__)
692: #include <sys/utsname.h> /* Doesn't work on Windows */
693: #endif
694:
1.126 brouard 695: #include <sys/stat.h>
696: #include <errno.h>
1.159 brouard 697: /* extern int errno; */
1.126 brouard 698:
1.157 brouard 699: /* #ifdef LINUX */
700: /* #include <time.h> */
701: /* #include "timeval.h" */
702: /* #else */
703: /* #include <sys/time.h> */
704: /* #endif */
705:
1.126 brouard 706: #include <time.h>
707:
1.136 brouard 708: #ifdef GSL
709: #include <gsl/gsl_errno.h>
710: #include <gsl/gsl_multimin.h>
711: #endif
712:
1.167 brouard 713:
1.162 brouard 714: #ifdef NLOPT
715: #include <nlopt.h>
716: typedef struct {
717: double (* function)(double [] );
718: } myfunc_data ;
719: #endif
720:
1.126 brouard 721: /* #include <libintl.h> */
722: /* #define _(String) gettext (String) */
723:
1.141 brouard 724: #define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */
1.126 brouard 725:
726: #define GNUPLOTPROGRAM "gnuplot"
727: /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
728: #define FILENAMELENGTH 132
729:
730: #define GLOCK_ERROR_NOPATH -1 /* empty path */
731: #define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
732:
1.144 brouard 733: #define MAXPARM 128 /**< Maximum number of parameters for the optimization */
734: #define NPARMAX 64 /**< (nlstate+ndeath-1)*nlstate*ncovmodel */
1.126 brouard 735:
736: #define NINTERVMAX 8
1.144 brouard 737: #define NLSTATEMAX 8 /**< Maximum number of live states (for func) */
738: #define NDEATHMAX 8 /**< Maximum number of dead states (for func) */
739: #define NCOVMAX 20 /**< Maximum number of covariates, including generated covariates V1*V2 */
1.197 brouard 740: #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
1.126 brouard 741: #define MAXN 20000
1.144 brouard 742: #define YEARM 12. /**< Number of months per year */
1.126 brouard 743: #define AGESUP 130
744: #define AGEBASE 40
1.194 brouard 745: #define AGEOVERFLOW 1.e20
1.164 brouard 746: #define AGEGOMP 10 /**< Minimal age for Gompertz adjustment */
1.157 brouard 747: #ifdef _WIN32
748: #define DIRSEPARATOR '\\'
749: #define CHARSEPARATOR "\\"
750: #define ODIRSEPARATOR '/'
751: #else
1.126 brouard 752: #define DIRSEPARATOR '/'
753: #define CHARSEPARATOR "/"
754: #define ODIRSEPARATOR '\\'
755: #endif
756:
1.207 ! brouard 757: /* $Id: imach.c,v 1.206 2015/10/24 07:14:11 brouard Exp $ */
1.126 brouard 758: /* $State: Exp $ */
1.196 brouard 759: #include "version.h"
760: char version[]=__IMACH_VERSION__;
1.204 brouard 761: 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";
1.207 ! brouard 762: char fullversion[]="$Revision: 1.206 $ $Date: 2015/10/24 07:14:11 $";
1.126 brouard 763: char strstart[80];
764: char optionfilext[10], optionfilefiname[FILENAMELENGTH];
1.130 brouard 765: int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
1.187 brouard 766: int nagesqr=0, nforce=0; /* nagesqr=1 if model is including age*age, number of forces */
1.145 brouard 767: /* Number of covariates model=V2+V1+ V3*age+V2*V4 */
768: int cptcovn=0; /**< cptcovn number of covariates added in the model (excepting constant and age and age*product) */
769: int cptcovt=0; /**< cptcovt number of covariates added in the model (excepting constant and age) */
770: int cptcovs=0; /**< cptcovs number of simple covariates V2+V1 =2 */
771: int cptcovage=0; /**< Number of covariates with age: V3*age only =1 */
772: int cptcovprodnoage=0; /**< Number of covariate products without age */
773: int cptcoveff=0; /* Total number of covariates to vary for printing results */
774: int cptcov=0; /* Working variable */
1.126 brouard 775: int npar=NPARMAX;
776: int nlstate=2; /* Number of live states */
777: int ndeath=1; /* Number of dead states */
1.130 brouard 778: int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
1.126 brouard 779: int popbased=0;
780:
781: int *wav; /* Number of waves for this individuual 0 is possible */
1.130 brouard 782: int maxwav=0; /* Maxim number of waves */
783: int jmin=0, jmax=0; /* min, max spacing between 2 waves */
784: int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
785: int gipmx=0, gsw=0; /* Global variables on the number of contributions
1.126 brouard 786: to the likelihood and the sum of weights (done by funcone)*/
1.130 brouard 787: int mle=1, weightopt=0;
1.126 brouard 788: int **mw; /* mw[mi][i] is number of the mi wave for this individual */
789: int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
790: int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
791: * wave mi and wave mi+1 is not an exact multiple of stepm. */
1.162 brouard 792: int countcallfunc=0; /* Count the number of calls to func */
1.130 brouard 793: double jmean=1; /* Mean space between 2 waves */
1.145 brouard 794: double **matprod2(); /* test */
1.126 brouard 795: double **oldm, **newm, **savm; /* Working pointers to matrices */
796: double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
1.136 brouard 797: /*FILE *fic ; */ /* Used in readdata only */
798: FILE *ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
1.126 brouard 799: FILE *ficlog, *ficrespow;
1.130 brouard 800: int globpr=0; /* Global variable for printing or not */
1.126 brouard 801: double fretone; /* Only one call to likelihood */
1.130 brouard 802: long ipmx=0; /* Number of contributions */
1.126 brouard 803: double sw; /* Sum of weights */
804: char filerespow[FILENAMELENGTH];
805: char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
806: FILE *ficresilk;
807: FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
808: FILE *ficresprobmorprev;
809: FILE *fichtm, *fichtmcov; /* Html File */
810: FILE *ficreseij;
811: char filerese[FILENAMELENGTH];
812: FILE *ficresstdeij;
813: char fileresstde[FILENAMELENGTH];
814: FILE *ficrescveij;
815: char filerescve[FILENAMELENGTH];
816: FILE *ficresvij;
817: char fileresv[FILENAMELENGTH];
818: FILE *ficresvpl;
819: char fileresvpl[FILENAMELENGTH];
820: char title[MAXLINE];
821: char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
822: char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
823: char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
824: char command[FILENAMELENGTH];
825: int outcmd=0;
826:
827: char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
1.202 brouard 828: char fileresu[FILENAMELENGTH]; /* fileres without r in front */
1.126 brouard 829: char filelog[FILENAMELENGTH]; /* Log file */
830: char filerest[FILENAMELENGTH];
831: char fileregp[FILENAMELENGTH];
832: char popfile[FILENAMELENGTH];
833:
834: char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
835:
1.157 brouard 836: /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
837: /* struct timezone tzp; */
838: /* extern int gettimeofday(); */
839: struct tm tml, *gmtime(), *localtime();
840:
841: extern time_t time();
842:
843: struct tm start_time, end_time, curr_time, last_time, forecast_time;
844: time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
845: struct tm tm;
846:
1.126 brouard 847: char strcurr[80], strfor[80];
848:
849: char *endptr;
850: long lval;
851: double dval;
852:
853: #define NR_END 1
854: #define FREE_ARG char*
855: #define FTOL 1.0e-10
856:
857: #define NRANSI
858: #define ITMAX 200
859:
860: #define TOL 2.0e-4
861:
862: #define CGOLD 0.3819660
863: #define ZEPS 1.0e-10
864: #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
865:
866: #define GOLD 1.618034
867: #define GLIMIT 100.0
868: #define TINY 1.0e-20
869:
870: static double maxarg1,maxarg2;
871: #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
872: #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
873:
874: #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
875: #define rint(a) floor(a+0.5)
1.166 brouard 876: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/myutils_8h-source.html */
1.183 brouard 877: #define mytinydouble 1.0e-16
1.166 brouard 878: /* #define DEQUAL(a,b) (fabs((a)-(b))<mytinydouble) */
879: /* http://www.thphys.uni-heidelberg.de/~robbers/cmbeasy/doc/html/mynrutils_8h-source.html */
880: /* static double dsqrarg; */
881: /* #define DSQR(a) (DEQUAL((dsqrarg=(a)),0.0) ? 0.0 : dsqrarg*dsqrarg) */
1.126 brouard 882: static double sqrarg;
883: #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
884: #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
885: int agegomp= AGEGOMP;
886:
887: int imx;
888: int stepm=1;
889: /* Stepm, step in month: minimum step interpolation*/
890:
891: int estepm;
892: /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
893:
894: int m,nb;
895: long *num;
1.197 brouard 896: int firstpass=0, lastpass=4,*cod, *cens;
1.192 brouard 897: int *ncodemax; /* ncodemax[j]= Number of modalities of the j th
898: covariate for which somebody answered excluding
899: undefined. Usually 2: 0 and 1. */
900: int *ncodemaxwundef; /* ncodemax[j]= Number of modalities of the j th
901: covariate for which somebody answered including
902: undefined. Usually 3: -1, 0 and 1. */
1.126 brouard 903: double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
904: double **pmmij, ***probs;
905: double *ageexmed,*agecens;
906: double dateintmean=0;
907:
908: double *weight;
909: int **s; /* Status */
1.141 brouard 910: double *agedc;
1.145 brouard 911: double **covar; /**< covar[j,i], value of jth covariate for individual i,
1.141 brouard 912: * covar=matrix(0,NCOVMAX,1,n);
1.187 brouard 913: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*age; */
1.141 brouard 914: double idx;
915: int **nbcode, *Tvar; /**< model=V2 => Tvar[1]= 2 */
1.197 brouard 916: int *Tage;
1.145 brouard 917: int *Ndum; /** Freq of modality (tricode */
1.200 brouard 918: /* int **codtab;*/ /**< codtab=imatrix(1,100,1,10); */
1.141 brouard 919: int **Tvard, *Tprod, cptcovprod, *Tvaraff;
1.126 brouard 920: double *lsurv, *lpop, *tpop;
921:
1.143 brouard 922: double ftol=FTOL; /**< Tolerance for computing Max Likelihood */
923: double ftolhess; /**< Tolerance for computing hessian */
1.126 brouard 924:
925: /**************** split *************************/
926: static int split( char *path, char *dirc, char *name, char *ext, char *finame )
927: {
928: /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
929: the name of the file (name), its extension only (ext) and its first part of the name (finame)
930: */
931: char *ss; /* pointer */
1.186 brouard 932: int l1=0, l2=0; /* length counters */
1.126 brouard 933:
934: l1 = strlen(path ); /* length of path */
935: if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
936: ss= strrchr( path, DIRSEPARATOR ); /* find last / */
937: if ( ss == NULL ) { /* no directory, so determine current directory */
938: strcpy( name, path ); /* we got the fullname name because no directory */
939: /*if(strrchr(path, ODIRSEPARATOR )==NULL)
940: printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
941: /* get current working directory */
942: /* extern char* getcwd ( char *buf , int len);*/
1.184 brouard 943: #ifdef WIN32
944: if (_getcwd( dirc, FILENAME_MAX ) == NULL ) {
945: #else
946: if (getcwd(dirc, FILENAME_MAX) == NULL) {
947: #endif
1.126 brouard 948: return( GLOCK_ERROR_GETCWD );
949: }
950: /* got dirc from getcwd*/
951: printf(" DIRC = %s \n",dirc);
1.205 brouard 952: } else { /* strip directory from path */
1.126 brouard 953: ss++; /* after this, the filename */
954: l2 = strlen( ss ); /* length of filename */
955: if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
956: strcpy( name, ss ); /* save file name */
957: strncpy( dirc, path, l1 - l2 ); /* now the directory */
1.186 brouard 958: dirc[l1-l2] = '\0'; /* add zero */
1.126 brouard 959: printf(" DIRC2 = %s \n",dirc);
960: }
961: /* We add a separator at the end of dirc if not exists */
962: l1 = strlen( dirc ); /* length of directory */
963: if( dirc[l1-1] != DIRSEPARATOR ){
964: dirc[l1] = DIRSEPARATOR;
965: dirc[l1+1] = 0;
966: printf(" DIRC3 = %s \n",dirc);
967: }
968: ss = strrchr( name, '.' ); /* find last / */
969: if (ss >0){
970: ss++;
971: strcpy(ext,ss); /* save extension */
972: l1= strlen( name);
973: l2= strlen(ss)+1;
974: strncpy( finame, name, l1-l2);
975: finame[l1-l2]= 0;
976: }
977:
978: return( 0 ); /* we're done */
979: }
980:
981:
982: /******************************************/
983:
984: void replace_back_to_slash(char *s, char*t)
985: {
986: int i;
987: int lg=0;
988: i=0;
989: lg=strlen(t);
990: for(i=0; i<= lg; i++) {
991: (s[i] = t[i]);
992: if (t[i]== '\\') s[i]='/';
993: }
994: }
995:
1.132 brouard 996: char *trimbb(char *out, char *in)
1.137 brouard 997: { /* Trim multiple blanks in line but keeps first blanks if line starts with blanks */
1.132 brouard 998: char *s;
999: s=out;
1000: while (*in != '\0'){
1.137 brouard 1001: while( *in == ' ' && *(in+1) == ' '){ /* && *(in+1) != '\0'){*/
1.132 brouard 1002: in++;
1003: }
1004: *out++ = *in++;
1005: }
1006: *out='\0';
1007: return s;
1008: }
1009:
1.187 brouard 1010: /* char *substrchaine(char *out, char *in, char *chain) */
1011: /* { */
1012: /* /\* Substract chain 'chain' from 'in', return and output 'out' *\/ */
1013: /* char *s, *t; */
1014: /* t=in;s=out; */
1015: /* while ((*in != *chain) && (*in != '\0')){ */
1016: /* *out++ = *in++; */
1017: /* } */
1018:
1019: /* /\* *in matches *chain *\/ */
1020: /* while ((*in++ == *chain++) && (*in != '\0')){ */
1021: /* printf("*in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1022: /* } */
1023: /* in--; chain--; */
1024: /* while ( (*in != '\0')){ */
1025: /* printf("Bef *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1026: /* *out++ = *in++; */
1027: /* printf("Aft *in = %c, *out= %c *chain= %c \n", *in, *out, *chain); */
1028: /* } */
1029: /* *out='\0'; */
1030: /* out=s; */
1031: /* return out; */
1032: /* } */
1033: char *substrchaine(char *out, char *in, char *chain)
1034: {
1035: /* Substract chain 'chain' from 'in', return and output 'out' */
1036: /* in="V1+V1*age+age*age+V2", chain="age*age" */
1037:
1038: char *strloc;
1039:
1040: strcpy (out, in);
1041: strloc = strstr(out, chain); /* strloc points to out at age*age+V2 */
1042: printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);
1043: if(strloc != NULL){
1044: /* will affect out */ /* strloc+strlenc(chain)=+V2 */ /* Will also work in Unicode */
1045: memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);
1046: /* strcpy (strloc, strloc +strlen(chain));*/
1047: }
1048: printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);
1049: return out;
1050: }
1051:
1052:
1.145 brouard 1053: char *cutl(char *blocc, char *alocc, char *in, char occ)
1054: {
1.187 brouard 1055: /* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
1.145 brouard 1056: and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1.187 brouard 1057: gives blocc="abcdef" and alocc="ghi2j".
1.145 brouard 1058: If occ is not found blocc is null and alocc is equal to in. Returns blocc
1059: */
1.160 brouard 1060: char *s, *t;
1.145 brouard 1061: t=in;s=in;
1062: while ((*in != occ) && (*in != '\0')){
1063: *alocc++ = *in++;
1064: }
1065: if( *in == occ){
1066: *(alocc)='\0';
1067: s=++in;
1068: }
1069:
1070: if (s == t) {/* occ not found */
1071: *(alocc-(in-s))='\0';
1072: in=s;
1073: }
1074: while ( *in != '\0'){
1075: *blocc++ = *in++;
1076: }
1077:
1078: *blocc='\0';
1079: return t;
1080: }
1.137 brouard 1081: char *cutv(char *blocc, char *alocc, char *in, char occ)
1082: {
1.187 brouard 1083: /* cuts string in into blocc and alocc where blocc ends before LAST occurence of char 'occ'
1.137 brouard 1084: and alocc starts after last occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')
1085: gives blocc="abcdef2ghi" and alocc="j".
1086: If occ is not found blocc is null and alocc is equal to in. Returns alocc
1087: */
1088: char *s, *t;
1089: t=in;s=in;
1090: while (*in != '\0'){
1091: while( *in == occ){
1092: *blocc++ = *in++;
1093: s=in;
1094: }
1095: *blocc++ = *in++;
1096: }
1097: if (s == t) /* occ not found */
1098: *(blocc-(in-s))='\0';
1099: else
1100: *(blocc-(in-s)-1)='\0';
1101: in=s;
1102: while ( *in != '\0'){
1103: *alocc++ = *in++;
1104: }
1105:
1106: *alocc='\0';
1107: return s;
1108: }
1109:
1.126 brouard 1110: int nbocc(char *s, char occ)
1111: {
1112: int i,j=0;
1113: int lg=20;
1114: i=0;
1115: lg=strlen(s);
1116: for(i=0; i<= lg; i++) {
1117: if (s[i] == occ ) j++;
1118: }
1119: return j;
1120: }
1121:
1.137 brouard 1122: /* void cutv(char *u,char *v, char*t, char occ) */
1123: /* { */
1124: /* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
1125: /* and v starts after last occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') */
1126: /* gives u="abcdef2ghi" and v="j" *\/ */
1127: /* int i,lg,j,p=0; */
1128: /* i=0; */
1129: /* lg=strlen(t); */
1130: /* for(j=0; j<=lg-1; j++) { */
1131: /* if((t[j]!= occ) && (t[j+1]== occ)) p=j+1; */
1132: /* } */
1.126 brouard 1133:
1.137 brouard 1134: /* for(j=0; j<p; j++) { */
1135: /* (u[j] = t[j]); */
1136: /* } */
1137: /* u[p]='\0'; */
1.126 brouard 1138:
1.137 brouard 1139: /* for(j=0; j<= lg; j++) { */
1140: /* if (j>=(p+1))(v[j-p-1] = t[j]); */
1141: /* } */
1142: /* } */
1.126 brouard 1143:
1.160 brouard 1144: #ifdef _WIN32
1145: char * strsep(char **pp, const char *delim)
1146: {
1147: char *p, *q;
1148:
1149: if ((p = *pp) == NULL)
1150: return 0;
1151: if ((q = strpbrk (p, delim)) != NULL)
1152: {
1153: *pp = q + 1;
1154: *q = '\0';
1155: }
1156: else
1157: *pp = 0;
1158: return p;
1159: }
1160: #endif
1161:
1.126 brouard 1162: /********************** nrerror ********************/
1163:
1164: void nrerror(char error_text[])
1165: {
1166: fprintf(stderr,"ERREUR ...\n");
1167: fprintf(stderr,"%s\n",error_text);
1168: exit(EXIT_FAILURE);
1169: }
1170: /*********************** vector *******************/
1171: double *vector(int nl, int nh)
1172: {
1173: double *v;
1174: v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
1175: if (!v) nrerror("allocation failure in vector");
1176: return v-nl+NR_END;
1177: }
1178:
1179: /************************ free vector ******************/
1180: void free_vector(double*v, int nl, int nh)
1181: {
1182: free((FREE_ARG)(v+nl-NR_END));
1183: }
1184:
1185: /************************ivector *******************************/
1186: int *ivector(long nl,long nh)
1187: {
1188: int *v;
1189: v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
1190: if (!v) nrerror("allocation failure in ivector");
1191: return v-nl+NR_END;
1192: }
1193:
1194: /******************free ivector **************************/
1195: void free_ivector(int *v, long nl, long nh)
1196: {
1197: free((FREE_ARG)(v+nl-NR_END));
1198: }
1199:
1200: /************************lvector *******************************/
1201: long *lvector(long nl,long nh)
1202: {
1203: long *v;
1204: v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
1205: if (!v) nrerror("allocation failure in ivector");
1206: return v-nl+NR_END;
1207: }
1208:
1209: /******************free lvector **************************/
1210: void free_lvector(long *v, long nl, long nh)
1211: {
1212: free((FREE_ARG)(v+nl-NR_END));
1213: }
1214:
1215: /******************* imatrix *******************************/
1216: int **imatrix(long nrl, long nrh, long ncl, long nch)
1217: /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
1218: {
1219: long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
1220: int **m;
1221:
1222: /* allocate pointers to rows */
1223: m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
1224: if (!m) nrerror("allocation failure 1 in matrix()");
1225: m += NR_END;
1226: m -= nrl;
1227:
1228:
1229: /* allocate rows and set pointers to them */
1230: m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
1231: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1232: m[nrl] += NR_END;
1233: m[nrl] -= ncl;
1234:
1235: for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
1236:
1237: /* return pointer to array of pointers to rows */
1238: return m;
1239: }
1240:
1241: /****************** free_imatrix *************************/
1242: void free_imatrix(m,nrl,nrh,ncl,nch)
1243: int **m;
1244: long nch,ncl,nrh,nrl;
1245: /* free an int matrix allocated by imatrix() */
1246: {
1247: free((FREE_ARG) (m[nrl]+ncl-NR_END));
1248: free((FREE_ARG) (m+nrl-NR_END));
1249: }
1250:
1251: /******************* matrix *******************************/
1252: double **matrix(long nrl, long nrh, long ncl, long nch)
1253: {
1254: long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
1255: double **m;
1256:
1257: m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1258: if (!m) nrerror("allocation failure 1 in matrix()");
1259: m += NR_END;
1260: m -= nrl;
1261:
1262: m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1263: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1264: m[nrl] += NR_END;
1265: m[nrl] -= ncl;
1266:
1267: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1268: return m;
1.145 brouard 1269: /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) or &(m[1][0])
1270: m[i] = address of ith row of the table. &(m[i]) is its value which is another adress
1271: that of m[i][0]. In order to get the value p m[i][0] but it is unitialized.
1.126 brouard 1272: */
1273: }
1274:
1275: /*************************free matrix ************************/
1276: void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
1277: {
1278: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1279: free((FREE_ARG)(m+nrl-NR_END));
1280: }
1281:
1282: /******************* ma3x *******************************/
1283: double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
1284: {
1285: long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
1286: double ***m;
1287:
1288: m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
1289: if (!m) nrerror("allocation failure 1 in matrix()");
1290: m += NR_END;
1291: m -= nrl;
1292:
1293: m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
1294: if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
1295: m[nrl] += NR_END;
1296: m[nrl] -= ncl;
1297:
1298: for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
1299:
1300: m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
1301: if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
1302: m[nrl][ncl] += NR_END;
1303: m[nrl][ncl] -= nll;
1304: for (j=ncl+1; j<=nch; j++)
1305: m[nrl][j]=m[nrl][j-1]+nlay;
1306:
1307: for (i=nrl+1; i<=nrh; i++) {
1308: m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
1309: for (j=ncl+1; j<=nch; j++)
1310: m[i][j]=m[i][j-1]+nlay;
1311: }
1312: return m;
1313: /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
1314: &(m[i][j][k]) <=> *((*(m+i) + j)+k)
1315: */
1316: }
1317:
1318: /*************************free ma3x ************************/
1319: void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
1320: {
1321: free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
1322: free((FREE_ARG)(m[nrl]+ncl-NR_END));
1323: free((FREE_ARG)(m+nrl-NR_END));
1324: }
1325:
1326: /*************** function subdirf ***********/
1327: char *subdirf(char fileres[])
1328: {
1329: /* Caution optionfilefiname is hidden */
1330: strcpy(tmpout,optionfilefiname);
1331: strcat(tmpout,"/"); /* Add to the right */
1332: strcat(tmpout,fileres);
1333: return tmpout;
1334: }
1335:
1336: /*************** function subdirf2 ***********/
1337: char *subdirf2(char fileres[], char *preop)
1338: {
1339:
1340: /* Caution optionfilefiname is hidden */
1341: strcpy(tmpout,optionfilefiname);
1342: strcat(tmpout,"/");
1343: strcat(tmpout,preop);
1344: strcat(tmpout,fileres);
1345: return tmpout;
1346: }
1347:
1348: /*************** function subdirf3 ***********/
1349: char *subdirf3(char fileres[], char *preop, char *preop2)
1350: {
1351:
1352: /* Caution optionfilefiname is hidden */
1353: strcpy(tmpout,optionfilefiname);
1354: strcat(tmpout,"/");
1355: strcat(tmpout,preop);
1356: strcat(tmpout,preop2);
1357: strcat(tmpout,fileres);
1358: return tmpout;
1359: }
1360:
1.162 brouard 1361: char *asc_diff_time(long time_sec, char ascdiff[])
1362: {
1363: long sec_left, days, hours, minutes;
1364: days = (time_sec) / (60*60*24);
1365: sec_left = (time_sec) % (60*60*24);
1366: hours = (sec_left) / (60*60) ;
1367: sec_left = (sec_left) %(60*60);
1368: minutes = (sec_left) /60;
1369: sec_left = (sec_left) % (60);
1370: sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);
1371: return ascdiff;
1372: }
1373:
1.126 brouard 1374: /***************** f1dim *************************/
1375: extern int ncom;
1376: extern double *pcom,*xicom;
1377: extern double (*nrfunc)(double []);
1378:
1379: double f1dim(double x)
1380: {
1381: int j;
1382: double f;
1383: double *xt;
1384:
1385: xt=vector(1,ncom);
1386: for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
1387: f=(*nrfunc)(xt);
1388: free_vector(xt,1,ncom);
1389: return f;
1390: }
1391:
1392: /*****************brent *************************/
1393: double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
1.187 brouard 1394: {
1395: /* Given a function f, and given a bracketing triplet of abscissas ax, bx, cx (such that bx is
1396: * between ax and cx, and f(bx) is less than both f(ax) and f(cx) ), this routine isolates
1397: * the minimum to a fractional precision of about tol using Brent’s method. The abscissa of
1398: * the minimum is returned as xmin, and the minimum function value is returned as brent , the
1399: * returned function value.
1400: */
1.126 brouard 1401: int iter;
1402: double a,b,d,etemp;
1.159 brouard 1403: double fu=0,fv,fw,fx;
1.164 brouard 1404: double ftemp=0.;
1.126 brouard 1405: double p,q,r,tol1,tol2,u,v,w,x,xm;
1406: double e=0.0;
1407:
1408: a=(ax < cx ? ax : cx);
1409: b=(ax > cx ? ax : cx);
1410: x=w=v=bx;
1411: fw=fv=fx=(*f)(x);
1412: for (iter=1;iter<=ITMAX;iter++) {
1413: xm=0.5*(a+b);
1414: tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
1415: /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
1416: printf(".");fflush(stdout);
1417: fprintf(ficlog,".");fflush(ficlog);
1.162 brouard 1418: #ifdef DEBUGBRENT
1.126 brouard 1419: 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);
1420: 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);
1421: /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
1422: #endif
1423: if (fabs(x-xm) <= (tol2-0.5*(b-a))){
1424: *xmin=x;
1425: return fx;
1426: }
1427: ftemp=fu;
1428: if (fabs(e) > tol1) {
1429: r=(x-w)*(fx-fv);
1430: q=(x-v)*(fx-fw);
1431: p=(x-v)*q-(x-w)*r;
1432: q=2.0*(q-r);
1433: if (q > 0.0) p = -p;
1434: q=fabs(q);
1435: etemp=e;
1436: e=d;
1437: if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
1438: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1439: else {
1440: d=p/q;
1441: u=x+d;
1442: if (u-a < tol2 || b-u < tol2)
1443: d=SIGN(tol1,xm-x);
1444: }
1445: } else {
1446: d=CGOLD*(e=(x >= xm ? a-x : b-x));
1447: }
1448: u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
1449: fu=(*f)(u);
1450: if (fu <= fx) {
1451: if (u >= x) a=x; else b=x;
1452: SHFT(v,w,x,u)
1.183 brouard 1453: SHFT(fv,fw,fx,fu)
1454: } else {
1455: if (u < x) a=u; else b=u;
1456: if (fu <= fw || w == x) {
1457: v=w;
1458: w=u;
1459: fv=fw;
1460: fw=fu;
1461: } else if (fu <= fv || v == x || v == w) {
1462: v=u;
1463: fv=fu;
1464: }
1465: }
1.126 brouard 1466: }
1467: nrerror("Too many iterations in brent");
1468: *xmin=x;
1469: return fx;
1470: }
1471:
1472: /****************** mnbrak ***********************/
1473:
1474: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
1475: double (*func)(double))
1.183 brouard 1476: { /* Given a function func , and given distinct initial points ax and bx , this routine searches in
1477: the downhill direction (defined by the function as evaluated at the initial points) and returns
1478: new points ax , bx , cx that bracket a minimum of the function. Also returned are the function
1479: values at the three points, fa, fb , and fc such that fa > fb and fb < fc.
1480: */
1.126 brouard 1481: double ulim,u,r,q, dum;
1482: double fu;
1.187 brouard 1483:
1484: double scale=10.;
1485: int iterscale=0;
1486:
1487: *fa=(*func)(*ax); /* xta[j]=pcom[j]+(*ax)*xicom[j]; fa=f(xta[j])*/
1488: *fb=(*func)(*bx); /* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) */
1489:
1490:
1491: /* while(*fb != *fb){ /\* *ax should be ok, reducing distance to *ax *\/ */
1492: /* printf("Warning mnbrak *fb = %lf, *bx=%lf *ax=%lf *fa==%lf iter=%d\n",*fb, *bx, *ax, *fa, iterscale++); */
1493: /* *bx = *ax - (*ax - *bx)/scale; */
1494: /* *fb=(*func)(*bx); /\* xtb[j]=pcom[j]+(*bx)*xicom[j]; fb=f(xtb[j]) *\/ */
1495: /* } */
1496:
1.126 brouard 1497: if (*fb > *fa) {
1498: SHFT(dum,*ax,*bx,dum)
1.183 brouard 1499: SHFT(dum,*fb,*fa,dum)
1500: }
1.126 brouard 1501: *cx=(*bx)+GOLD*(*bx-*ax);
1502: *fc=(*func)(*cx);
1.183 brouard 1503: #ifdef DEBUG
1504: printf("mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1505: fprintf(ficlog,"mnbrak0 *fb=%.12e *fc=%.12e\n",*fb,*fc);
1506: #endif
1507: while (*fb > *fc) { /* Declining a,b,c with fa> fb > fc */
1.126 brouard 1508: r=(*bx-*ax)*(*fb-*fc);
1509: q=(*bx-*cx)*(*fb-*fa);
1510: u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
1.183 brouard 1511: (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscissa of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
1512: ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscissa where function should be evaluated */
1513: if ((*bx-u)*(u-*cx) > 0.0) { /* if u_p is between b and c */
1.126 brouard 1514: fu=(*func)(u);
1.163 brouard 1515: #ifdef DEBUG
1516: /* f(x)=A(x-u)**2+f(u) */
1517: double A, fparabu;
1518: A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
1519: fparabu= *fa - A*(*ax-u)*(*ax-u);
1520: 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);
1521: 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 1522: /* And thus,it can be that fu > *fc even if fparabu < *fc */
1523: /* mnbrak (*ax=7.666299858533, *fa=299039.693133272231), (*bx=8.595447774979, *fb=298976.598289369489),
1524: (*cx=10.098840694817, *fc=298946.631474258087), (*u=9.852501168332, fu=298948.773013752128, fparabu=298945.434711494134) */
1525: /* In that case, there is no bracket in the output! Routine is wrong with many consequences.*/
1.163 brouard 1526: #endif
1.184 brouard 1527: #ifdef MNBRAKORIGINAL
1.183 brouard 1528: #else
1.191 brouard 1529: /* if (fu > *fc) { */
1530: /* #ifdef DEBUG */
1531: /* printf("mnbrak4 fu > fc \n"); */
1532: /* fprintf(ficlog, "mnbrak4 fu > fc\n"); */
1533: /* #endif */
1534: /* /\* 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 *\\/ *\/ */
1535: /* /\* SHFT(*fa,*fc,fu,*fc) /\\* (b, u, c) is a bracket while test fb > fc will be fu > fc will exit *\\/ *\/ */
1536: /* dum=u; /\* Shifting c and u *\/ */
1537: /* u = *cx; */
1538: /* *cx = dum; */
1539: /* dum = fu; */
1540: /* fu = *fc; */
1541: /* *fc =dum; */
1542: /* } else { /\* end *\/ */
1543: /* #ifdef DEBUG */
1544: /* printf("mnbrak3 fu < fc \n"); */
1545: /* fprintf(ficlog, "mnbrak3 fu < fc\n"); */
1546: /* #endif */
1547: /* dum=u; /\* Shifting c and u *\/ */
1548: /* u = *cx; */
1549: /* *cx = dum; */
1550: /* dum = fu; */
1551: /* fu = *fc; */
1552: /* *fc =dum; */
1553: /* } */
1.183 brouard 1554: #ifdef DEBUG
1.191 brouard 1555: printf("mnbrak34 fu < or >= fc \n");
1556: fprintf(ficlog, "mnbrak34 fu < fc\n");
1.183 brouard 1557: #endif
1.191 brouard 1558: dum=u; /* Shifting c and u */
1559: u = *cx;
1560: *cx = dum;
1561: dum = fu;
1562: fu = *fc;
1563: *fc =dum;
1.183 brouard 1564: #endif
1.162 brouard 1565: } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
1.183 brouard 1566: #ifdef DEBUG
1567: printf("mnbrak2 u after c but before ulim\n");
1568: fprintf(ficlog, "mnbrak2 u after c but before ulim\n");
1569: #endif
1.126 brouard 1570: fu=(*func)(u);
1571: if (fu < *fc) {
1.183 brouard 1572: #ifdef DEBUG
1573: printf("mnbrak2 u after c but before ulim AND fu < fc\n");
1574: fprintf(ficlog, "mnbrak2 u after c but before ulim AND fu <fc \n");
1575: #endif
1.126 brouard 1576: SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
1.183 brouard 1577: SHFT(*fb,*fc,fu,(*func)(u))
1578: }
1.162 brouard 1579: } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
1.183 brouard 1580: #ifdef DEBUG
1581: printf("mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1582: fprintf(ficlog, "mnbrak2 u outside ulim (verifying that ulim is beyond c)\n");
1583: #endif
1.126 brouard 1584: u=ulim;
1585: fu=(*func)(u);
1.183 brouard 1586: } else { /* u could be left to b (if r > q parabola has a maximum) */
1587: #ifdef DEBUG
1588: printf("mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1589: fprintf(ficlog, "mnbrak2 u could be left to b (if r > q parabola has a maximum)\n");
1590: #endif
1.126 brouard 1591: u=(*cx)+GOLD*(*cx-*bx);
1592: fu=(*func)(u);
1.183 brouard 1593: } /* end tests */
1.126 brouard 1594: SHFT(*ax,*bx,*cx,u)
1.183 brouard 1595: SHFT(*fa,*fb,*fc,fu)
1596: #ifdef DEBUG
1597: 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);
1598: 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);
1599: #endif
1600: } /* 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 1601: }
1602:
1603: /*************** linmin ************************/
1.162 brouard 1604: /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
1605: resets p to where the function func(p) takes on a minimum along the direction xi from p ,
1606: and replaces xi by the actual vector displacement that p was moved. Also returns as fret
1607: the value of func at the returned location p . This is actually all accomplished by calling the
1608: routines mnbrak and brent .*/
1.126 brouard 1609: int ncom;
1610: double *pcom,*xicom;
1611: double (*nrfunc)(double []);
1612:
1613: void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
1614: {
1615: double brent(double ax, double bx, double cx,
1616: double (*f)(double), double tol, double *xmin);
1617: double f1dim(double x);
1618: void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
1619: double *fc, double (*func)(double));
1620: int j;
1621: double xx,xmin,bx,ax;
1622: double fx,fb,fa;
1.187 brouard 1623:
1.203 brouard 1624: #ifdef LINMINORIGINAL
1625: #else
1626: double scale=10., axs, xxs; /* Scale added for infinity */
1627: #endif
1628:
1.126 brouard 1629: ncom=n;
1630: pcom=vector(1,n);
1631: xicom=vector(1,n);
1632: nrfunc=func;
1633: for (j=1;j<=n;j++) {
1634: pcom[j]=p[j];
1.202 brouard 1635: xicom[j]=xi[j]; /* Former scale xi[j] of currrent direction i */
1.126 brouard 1636: }
1.187 brouard 1637:
1.203 brouard 1638: #ifdef LINMINORIGINAL
1639: xx=1.;
1640: #else
1641: axs=0.0;
1642: xxs=1.;
1643: do{
1644: xx= xxs;
1645: #endif
1.187 brouard 1646: ax=0.;
1647: mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Outputs: xtx[j]=pcom[j]+(*xx)*xicom[j]; fx=f(xtx[j]) */
1648: /* brackets with inputs ax=0 and xx=1, but points, pcom=p, and directions values, xicom=xi, are sent via f1dim(x) */
1649: /* 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)) */
1650: /* Outputs: fa=f(p(j)) and fx=f(p(j) + xxs * xi(j) ) and f(bx)= f(p(j)+ bx* xi(j)) */
1651: /* Given input ax=axs and xx=xxs, xx might be too far from ax to get a finite f(xx) */
1652: /* Searches on line, outputs (ax, xx, bx) such that fx < min(fa and fb) */
1653: /* 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 1654: #ifdef LINMINORIGINAL
1655: #else
1656: if (fx != fx){
1657: xxs=xxs/scale; /* Trying a smaller xx, closer to initial ax=0 */
1658: printf("|");
1659: fprintf(ficlog,"|");
1660: #ifdef DEBUGLINMIN
1661: 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);
1662: #endif
1663: }
1664: }while(fx != fx);
1665: #endif
1666:
1.191 brouard 1667: #ifdef DEBUGLINMIN
1668: 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 1669: 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 1670: #endif
1.187 brouard 1671: *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Giving a bracketting triplet (ax, xx, bx), find a minimum, xmin, according to f1dim, *fret(xmin),*/
1672: /* fa = f(p[j] + ax * xi[j]), fx = f(p[j] + xx * xi[j]), fb = f(p[j] + bx * xi[j]) */
1673: /* fmin = f(p[j] + xmin * xi[j]) */
1674: /* P+lambda n in that direction (lambdamin), with TOL between abscisses */
1675: /* f1dim(xmin): for (j=1;j<=ncom;j++) xt[j]=pcom[j]+xmin*xicom[j]; */
1.126 brouard 1676: #ifdef DEBUG
1677: printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1678: fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
1679: #endif
1.191 brouard 1680: #ifdef DEBUGLINMIN
1681: printf("linmin end ");
1.202 brouard 1682: fprintf(ficlog,"linmin end ");
1.191 brouard 1683: #endif
1.126 brouard 1684: for (j=1;j<=n;j++) {
1.203 brouard 1685: #ifdef LINMINORIGINAL
1686: xi[j] *= xmin;
1687: #else
1688: #ifdef DEBUGLINMIN
1689: if(xxs <1.0)
1690: printf(" before xi[%d]=%12.8f", j,xi[j]);
1691: #endif
1692: 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) */
1693: #ifdef DEBUGLINMIN
1694: if(xxs <1.0)
1695: 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 );
1696: #endif
1697: #endif
1.187 brouard 1698: p[j] += xi[j]; /* Parameters values are updated accordingly */
1.126 brouard 1699: }
1.191 brouard 1700: #ifdef DEBUGLINMIN
1.203 brouard 1701: printf("\n");
1.191 brouard 1702: printf("Comparing last *frec(xmin=%12.8f)=%12.8f from Brent and frec(0.)=%12.8f \n", xmin, *fret, (*func)(p));
1.202 brouard 1703: 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 1704: for (j=1;j<=n;j++) {
1.202 brouard 1705: printf(" xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1706: fprintf(ficlog," xi[%d]= %14.10f p[%d]= %12.7f",j,xi[j],j,p[j]);
1707: if(j % ncovmodel == 0){
1.191 brouard 1708: printf("\n");
1.202 brouard 1709: fprintf(ficlog,"\n");
1710: }
1.191 brouard 1711: }
1.203 brouard 1712: #else
1.191 brouard 1713: #endif
1.126 brouard 1714: free_vector(xicom,1,n);
1715: free_vector(pcom,1,n);
1716: }
1717:
1718:
1719: /*************** powell ************************/
1.162 brouard 1720: /*
1721: Minimization of a function func of n variables. Input consists of an initial starting point
1722: p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
1723: rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
1724: such that failure to decrease by more than this amount on one iteration signals doneness. On
1725: output, p is set to the best point found, xi is the then-current direction set, fret is the returned
1726: function value at p , and iter is the number of iterations taken. The routine linmin is used.
1727: */
1.126 brouard 1728: void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
1729: double (*func)(double []))
1730: {
1731: void linmin(double p[], double xi[], int n, double *fret,
1732: double (*func)(double []));
1733: int i,ibig,j;
1734: double del,t,*pt,*ptt,*xit;
1.181 brouard 1735: double directest;
1.126 brouard 1736: double fp,fptt;
1737: double *xits;
1738: int niterf, itmp;
1739:
1740: pt=vector(1,n);
1741: ptt=vector(1,n);
1742: xit=vector(1,n);
1743: xits=vector(1,n);
1744: *fret=(*func)(p);
1745: for (j=1;j<=n;j++) pt[j]=p[j];
1.202 brouard 1746: rcurr_time = time(NULL);
1.126 brouard 1747: for (*iter=1;;++(*iter)) {
1.187 brouard 1748: fp=(*fret); /* From former iteration or initial value */
1.126 brouard 1749: ibig=0;
1750: del=0.0;
1.157 brouard 1751: rlast_time=rcurr_time;
1752: /* (void) gettimeofday(&curr_time,&tzp); */
1753: rcurr_time = time(NULL);
1754: curr_time = *localtime(&rcurr_time);
1755: printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
1756: fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
1757: /* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
1.192 brouard 1758: for (i=1;i<=n;i++) {
1.126 brouard 1759: printf(" %d %.12f",i, p[i]);
1760: fprintf(ficlog," %d %.12lf",i, p[i]);
1761: fprintf(ficrespow," %.12lf", p[i]);
1762: }
1763: printf("\n");
1764: fprintf(ficlog,"\n");
1765: fprintf(ficrespow,"\n");fflush(ficrespow);
1766: if(*iter <=3){
1.157 brouard 1767: tml = *localtime(&rcurr_time);
1768: strcpy(strcurr,asctime(&tml));
1769: rforecast_time=rcurr_time;
1.126 brouard 1770: itmp = strlen(strcurr);
1771: if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
1772: strcurr[itmp-1]='\0';
1.162 brouard 1773: printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.157 brouard 1774: fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
1.126 brouard 1775: for(niterf=10;niterf<=30;niterf+=10){
1.157 brouard 1776: rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
1777: forecast_time = *localtime(&rforecast_time);
1778: strcpy(strfor,asctime(&forecast_time));
1.126 brouard 1779: itmp = strlen(strfor);
1780: if(strfor[itmp-1]=='\n')
1781: strfor[itmp-1]='\0';
1.157 brouard 1782: 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);
1783: 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 1784: }
1785: }
1.187 brouard 1786: for (i=1;i<=n;i++) { /* For each direction i */
1787: for (j=1;j<=n;j++) xit[j]=xi[j][i]; /* Directions stored from previous iteration with previous scales */
1.126 brouard 1788: fptt=(*fret);
1789: #ifdef DEBUG
1.203 brouard 1790: printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1791: fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
1.126 brouard 1792: #endif
1.203 brouard 1793: printf("%d",i);fflush(stdout); /* print direction (parameter) i */
1.126 brouard 1794: fprintf(ficlog,"%d",i);fflush(ficlog);
1.188 brouard 1795: linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
1796: /* Outputs are fret(new point p) p is updated and xit rescaled */
1797: if (fabs(fptt-(*fret)) > del) { /* We are keeping the max gain on each of the n directions */
1798: /* because that direction will be replaced unless the gain del is small */
1799: /* in comparison with the 'probable' gain, mu^2, with the last average direction. */
1800: /* Unless the n directions are conjugate some gain in the determinant may be obtained */
1801: /* with the new direction. */
1.126 brouard 1802: del=fabs(fptt-(*fret));
1803: ibig=i;
1804: }
1805: #ifdef DEBUG
1806: printf("%d %.12e",i,(*fret));
1807: fprintf(ficlog,"%d %.12e",i,(*fret));
1808: for (j=1;j<=n;j++) {
1809: xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
1810: printf(" x(%d)=%.12e",j,xit[j]);
1811: fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
1812: }
1813: for(j=1;j<=n;j++) {
1.162 brouard 1814: printf(" p(%d)=%.12e",j,p[j]);
1815: fprintf(ficlog," p(%d)=%.12e",j,p[j]);
1.126 brouard 1816: }
1817: printf("\n");
1818: fprintf(ficlog,"\n");
1819: #endif
1.187 brouard 1820: } /* end loop on each direction i */
1821: /* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
1.188 brouard 1822: /* But p and xit have been updated at the end of linmin, *fret corresponds to new p, xit */
1.187 brouard 1823: /* New value of last point Pn is not computed, P(n-1) */
1.182 brouard 1824: if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) { /* Did we reach enough precision? */
1.188 brouard 1825: /* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
1826: /* By adding age*age in a model, the new -2LL should be lower and the difference follows a */
1827: /* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
1828: /* decreased of more than 3.84 */
1829: /* By adding age*age and V1*age the gain (-2LL) should be more than 5.99 (ddl=2) */
1830: /* By using V1+V2+V3, the gain should be 7.82, compared with basic 1+age. */
1831: /* By adding 10 parameters more the gain should be 18.31 */
1832:
1833: /* Starting the program with initial values given by a former maximization will simply change */
1834: /* the scales of the directions and the directions, because the are reset to canonical directions */
1835: /* Thus the first calls to linmin will give new points and better maximizations until fp-(*fret) is */
1836: /* under the tolerance value. If the tolerance is very small 1.e-9, it could last long. */
1.126 brouard 1837: #ifdef DEBUG
1838: int k[2],l;
1839: k[0]=1;
1840: k[1]=-1;
1841: printf("Max: %.12e",(*func)(p));
1842: fprintf(ficlog,"Max: %.12e",(*func)(p));
1843: for (j=1;j<=n;j++) {
1844: printf(" %.12e",p[j]);
1845: fprintf(ficlog," %.12e",p[j]);
1846: }
1847: printf("\n");
1848: fprintf(ficlog,"\n");
1849: for(l=0;l<=1;l++) {
1850: for (j=1;j<=n;j++) {
1851: ptt[j]=p[j]+(p[j]-pt[j])*k[l];
1852: printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1853: fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
1854: }
1855: printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1856: fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
1857: }
1858: #endif
1859:
1860:
1861: free_vector(xit,1,n);
1862: free_vector(xits,1,n);
1863: free_vector(ptt,1,n);
1864: free_vector(pt,1,n);
1865: return;
1.192 brouard 1866: } /* enough precision */
1.126 brouard 1867: if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
1.181 brouard 1868: for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
1.126 brouard 1869: ptt[j]=2.0*p[j]-pt[j];
1870: xit[j]=p[j]-pt[j];
1871: pt[j]=p[j];
1872: }
1.181 brouard 1873: fptt=(*func)(ptt); /* f_3 */
1.192 brouard 1874: #ifdef POWELLF1F3
1875: #else
1.161 brouard 1876: if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
1.192 brouard 1877: #endif
1.162 brouard 1878: /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
1.161 brouard 1879: /* From x1 (P0) distance of x2 is at h and x3 is 2h */
1.162 brouard 1880: /* Let f"(x2) be the 2nd derivative equal everywhere. */
1881: /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
1882: /* will reach at f3 = fm + h^2/2 f"m ; f" = (f1 -2f2 +f3 ) / h**2 */
1.181 brouard 1883: /* Conditional for using this new direction is that mu^2 = (f1-2f2+f3)^2 /2 < del */
1.161 brouard 1884: /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
1.183 brouard 1885: #ifdef NRCORIGINAL
1886: t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)- del*SQR(fp-fptt); /* Original Numerical Recipes in C*/
1887: #else
1888: 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 1889: t= t- del*SQR(fp-fptt);
1.183 brouard 1890: #endif
1.202 brouard 1891: directest = fp-2.0*(*fret)+fptt - 2.0 * del; /* If delta was big enough we change it for a new direction */
1.161 brouard 1892: #ifdef DEBUG
1.181 brouard 1893: 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);
1894: 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 1895: printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1896: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1897: fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
1898: (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
1899: 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);
1900: 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);
1901: #endif
1.183 brouard 1902: #ifdef POWELLORIGINAL
1903: if (t < 0.0) { /* Then we use it for new direction */
1904: #else
1.182 brouard 1905: if (directest*t < 0.0) { /* Contradiction between both tests */
1.202 brouard 1906: 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 1907: 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 1908: 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 1909: fprintf(ficlog,"f1-2f2+f3= %.12lf, f1-f2-del= %.12lf, f1-f3= %.12lf\n",fp-2.0*(*fret)+fptt, fp -(*fret) -del, fp-fptt);
1910: }
1.181 brouard 1911: if (directest < 0.0) { /* Then we use it for new direction */
1912: #endif
1.191 brouard 1913: #ifdef DEBUGLINMIN
1914: printf("Before linmin in direction P%d-P0\n",n);
1915: for (j=1;j<=n;j++) {
1.202 brouard 1916: printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1917: fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1918: if(j % ncovmodel == 0){
1.191 brouard 1919: printf("\n");
1.202 brouard 1920: fprintf(ficlog,"\n");
1921: }
1.191 brouard 1922: }
1923: #endif
1.187 brouard 1924: linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
1.191 brouard 1925: #ifdef DEBUGLINMIN
1926: for (j=1;j<=n;j++) {
1927: printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1.202 brouard 1928: fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
1929: if(j % ncovmodel == 0){
1.191 brouard 1930: printf("\n");
1.202 brouard 1931: fprintf(ficlog,"\n");
1932: }
1.191 brouard 1933: }
1934: #endif
1.126 brouard 1935: for (j=1;j<=n;j++) {
1.181 brouard 1936: xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
1937: xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
1.126 brouard 1938: }
1.181 brouard 1939: printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1940: fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
1.161 brouard 1941:
1.126 brouard 1942: #ifdef DEBUG
1.164 brouard 1943: printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1944: fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
1.126 brouard 1945: for(j=1;j<=n;j++){
1946: printf(" %.12e",xit[j]);
1947: fprintf(ficlog," %.12e",xit[j]);
1948: }
1949: printf("\n");
1950: fprintf(ficlog,"\n");
1951: #endif
1.192 brouard 1952: } /* end of t or directest negative */
1953: #ifdef POWELLF1F3
1954: #else
1.162 brouard 1955: } /* end if (fptt < fp) */
1.192 brouard 1956: #endif
1957: } /* loop iteration */
1.126 brouard 1958: }
1959:
1960: /**** Prevalence limit (stable or period prevalence) ****************/
1961:
1.203 brouard 1962: double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int *ncvyear, int ij)
1.126 brouard 1963: {
1964: /* Computes the prevalence limit in each live state at age x by left multiplying the unit
1.203 brouard 1965: matrix by transitions matrix until convergence is reached with precision ftolpl */
1.206 brouard 1966: /* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
1967: /* Wx is row vector: population in state 1, population in state 2, population dead */
1968: /* or prevalence in state 1, prevalence in state 2, 0 */
1969: /* newm is the matrix after multiplications, its rows are identical at a factor */
1970: /* Initial matrix pimij */
1971: /* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
1972: /* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
1973: /* 0, 0 , 1} */
1974: /*
1975: * and after some iteration: */
1976: /* {0.45504275246439968, 0.42731458730878791, 0.11764266022681241, */
1977: /* 0.45201005341706885, 0.42865420071559901, 0.11933574586733192, */
1978: /* 0, 0 , 1} */
1979: /* And prevalence by suppressing the deaths are close to identical rows in prlim: */
1980: /* {0.51571254859325999, 0.4842874514067399, */
1981: /* 0.51326036147820708, 0.48673963852179264} */
1982: /* If we start from prlim again, prlim tends to a constant matrix */
1983:
1.126 brouard 1984: int i, ii,j,k;
1985: double min, max, maxmin, maxmax,sumnew=0.;
1.145 brouard 1986: /* double **matprod2(); */ /* test */
1.131 brouard 1987: double **out, cov[NCOVMAX+1], **pmij();
1.126 brouard 1988: double **newm;
1.202 brouard 1989: double agefin, delaymax=100 ; /* Max number of years to converge */
1.203 brouard 1990: int ncvloop=0;
1.169 brouard 1991:
1.126 brouard 1992: for (ii=1;ii<=nlstate+ndeath;ii++)
1993: for (j=1;j<=nlstate+ndeath;j++){
1994: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
1995: }
1.169 brouard 1996:
1997: cov[1]=1.;
1998:
1999: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
1.202 brouard 2000: /* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
1.126 brouard 2001: for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
1.202 brouard 2002: ncvloop++;
1.126 brouard 2003: newm=savm;
2004: /* Covariates have to be included here again */
1.138 brouard 2005: cov[2]=agefin;
1.187 brouard 2006: if(nagesqr==1)
2007: cov[3]= agefin*agefin;;
1.138 brouard 2008: for (k=1; k<=cptcovn;k++) {
1.200 brouard 2009: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
2010: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
1.198 brouard 2011: /* 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 2012: }
1.186 brouard 2013: /*wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2014: /* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]*cov[2]; */
2015: for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
1.186 brouard 2016: for (k=1; k<=cptcovprod;k++) /* Useless */
1.200 brouard 2017: /* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
2018: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
1.138 brouard 2019:
2020: /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
2021: /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
2022: /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
1.145 brouard 2023: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
2024: /* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind *\/ */
1.142 brouard 2025: out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */
1.138 brouard 2026:
1.126 brouard 2027: savm=oldm;
2028: oldm=newm;
2029: maxmax=0.;
2030: for(j=1;j<=nlstate;j++){
2031: min=1.;
2032: max=0.;
2033: for(i=1; i<=nlstate; i++) {
2034: sumnew=0;
2035: for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
2036: prlim[i][j]= newm[i][j]/(1-sumnew);
2037: max=FMAX(max,prlim[i][j]);
2038: min=FMIN(min,prlim[i][j]);
1.206 brouard 2039: 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 2040: }
1.203 brouard 2041: maxmin=(max-min)/(max+min)*2;
1.126 brouard 2042: maxmax=FMAX(maxmax,maxmin);
1.169 brouard 2043: } /* j loop */
1.203 brouard 2044: *ncvyear= (int)age- (int)agefin;
1.207 ! brouard 2045: printf("maxmax=%lf maxmin=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, maxmin, ncvloop, (int)age, (int)agefin, *ncvyear);
1.126 brouard 2046: if(maxmax < ftolpl){
1.203 brouard 2047: /* 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 2048: return prlim;
2049: }
1.169 brouard 2050: } /* age loop */
1.203 brouard 2051: printf("Warning: the stable prevalence at age %d did not converge with the required precision %g > ftolpl=%g. \n\
2052: 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);
2053: /* 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 2054: return prlim; /* should not reach here */
1.126 brouard 2055: }
2056:
2057: /*************** transition probabilities ***************/
2058:
2059: double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
2060: {
1.138 brouard 2061: /* According to parameters values stored in x and the covariate's values stored in cov,
2062: computes the probability to be observed in state j being in state i by appying the
2063: model to the ncovmodel covariates (including constant and age).
2064: lnpijopii=ln(pij/pii)= aij+bij*age+cij*v1+dij*v2+... = sum_nc=1^ncovmodel xij(nc)*cov[nc]
2065: and, according on how parameters are entered, the position of the coefficient xij(nc) of the
2066: ncth covariate in the global vector x is given by the formula:
2067: j<i nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel
2068: j>=i nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel
2069: Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
2070: sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
2071: Outputs ps[i][j] the probability to be observed in j being in j according to
2072: the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
2073: */
2074: double s1, lnpijopii;
1.126 brouard 2075: /*double t34;*/
1.164 brouard 2076: int i,j, nc, ii, jj;
1.126 brouard 2077:
2078: for(i=1; i<= nlstate; i++){
2079: for(j=1; j<i;j++){
1.138 brouard 2080: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2081: /*lnpijopii += param[i][j][nc]*cov[nc];*/
2082: lnpijopii += x[nc+((i-1)*(nlstate+ndeath-1)+j-1)*ncovmodel]*cov[nc];
2083: /* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2084: }
1.138 brouard 2085: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
2086: /* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
1.126 brouard 2087: }
2088: for(j=i+1; j<=nlstate+ndeath;j++){
1.138 brouard 2089: for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
2090: /*lnpijopii += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];*/
2091: lnpijopii += x[nc + ((i-1)*(nlstate+ndeath-1)+(j-2))*ncovmodel]*cov[nc];
2092: /* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
1.126 brouard 2093: }
1.138 brouard 2094: ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
1.126 brouard 2095: }
2096: }
2097:
2098: for(i=1; i<= nlstate; i++){
2099: s1=0;
1.131 brouard 2100: for(j=1; j<i; j++){
1.138 brouard 2101: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2102: /*printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2103: }
2104: for(j=i+1; j<=nlstate+ndeath; j++){
1.138 brouard 2105: s1+=exp(ps[i][j]); /* In fact sums pij/pii */
1.131 brouard 2106: /*printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
2107: }
1.138 brouard 2108: /* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
1.126 brouard 2109: ps[i][i]=1./(s1+1.);
1.138 brouard 2110: /* Computing other pijs */
1.126 brouard 2111: for(j=1; j<i; j++)
2112: ps[i][j]= exp(ps[i][j])*ps[i][i];
2113: for(j=i+1; j<=nlstate+ndeath; j++)
2114: ps[i][j]= exp(ps[i][j])*ps[i][i];
2115: /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
2116: } /* end i */
2117:
2118: for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
2119: for(jj=1; jj<= nlstate+ndeath; jj++){
2120: ps[ii][jj]=0;
2121: ps[ii][ii]=1;
2122: }
2123: }
2124:
1.145 brouard 2125:
2126: /* for(ii=1; ii<= nlstate+ndeath; ii++){ */
2127: /* for(jj=1; jj<= nlstate+ndeath; jj++){ */
2128: /* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
2129: /* } */
2130: /* printf("\n "); */
2131: /* } */
2132: /* printf("\n ");printf("%lf ",cov[2]);*/
2133: /*
1.126 brouard 2134: for(i=1; i<= npar; i++) printf("%f ",x[i]);
2135: goto end;*/
2136: return ps;
2137: }
2138:
2139: /**************** Product of 2 matrices ******************/
2140:
1.145 brouard 2141: double **matprod2(double **out, double **in,int nrl, int nrh, int ncl, int nch, int ncolol, int ncoloh, double **b)
1.126 brouard 2142: {
2143: /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
2144: b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
2145: /* in, b, out are matrice of pointers which should have been initialized
2146: before: only the contents of out is modified. The function returns
2147: a pointer to pointers identical to out */
1.145 brouard 2148: int i, j, k;
1.126 brouard 2149: for(i=nrl; i<= nrh; i++)
1.145 brouard 2150: for(k=ncolol; k<=ncoloh; k++){
2151: out[i][k]=0.;
2152: for(j=ncl; j<=nch; j++)
2153: out[i][k] +=in[i][j]*b[j][k];
2154: }
1.126 brouard 2155: return out;
2156: }
2157:
2158:
2159: /************* Higher Matrix Product ***************/
2160:
2161: double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
2162: {
2163: /* Computes the transition matrix starting at age 'age' over
2164: 'nhstepm*hstepm*stepm' months (i.e. until
2165: age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
2166: nhstepm*hstepm matrices.
2167: Output is stored in matrix po[i][j][h] for h every 'hstepm' step
2168: (typically every 2 years instead of every month which is too big
2169: for the memory).
2170: Model is determined by parameters x and covariates have to be
2171: included manually here.
2172:
2173: */
2174:
2175: int i, j, d, h, k;
1.131 brouard 2176: double **out, cov[NCOVMAX+1];
1.126 brouard 2177: double **newm;
1.187 brouard 2178: double agexact;
1.126 brouard 2179:
2180: /* Hstepm could be zero and should return the unit matrix */
2181: for (i=1;i<=nlstate+ndeath;i++)
2182: for (j=1;j<=nlstate+ndeath;j++){
2183: oldm[i][j]=(i==j ? 1.0 : 0.0);
2184: po[i][j][0]=(i==j ? 1.0 : 0.0);
2185: }
2186: /* Even if hstepm = 1, at least one multiplication by the unit matrix */
2187: for(h=1; h <=nhstepm; h++){
2188: for(d=1; d <=hstepm; d++){
2189: newm=savm;
2190: /* Covariates have to be included here again */
2191: cov[1]=1.;
1.187 brouard 2192: agexact=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
2193: cov[2]=agexact;
2194: if(nagesqr==1)
2195: cov[3]= agexact*agexact;
1.131 brouard 2196: for (k=1; k<=cptcovn;k++)
1.200 brouard 2197: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
2198: /* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.186 brouard 2199: for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
2200: /* cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 2201: cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
2202: /* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]*cov[2]; */
1.145 brouard 2203: for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */
1.200 brouard 2204: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
2205: /* 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 2206:
2207:
2208: /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
2209: /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
2210: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
2211: pmij(pmmij,cov,ncovmodel,x,nlstate));
2212: savm=oldm;
2213: oldm=newm;
2214: }
2215: for(i=1; i<=nlstate+ndeath; i++)
2216: for(j=1;j<=nlstate+ndeath;j++) {
2217: po[i][j][h]=newm[i][j];
1.128 brouard 2218: /*if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);*/
1.126 brouard 2219: }
1.128 brouard 2220: /*printf("h=%d ",h);*/
1.126 brouard 2221: } /* end h */
1.128 brouard 2222: /* printf("\n H=%d \n",h); */
1.126 brouard 2223: return po;
2224: }
2225:
1.162 brouard 2226: #ifdef NLOPT
2227: double myfunc(unsigned n, const double *p1, double *grad, void *pd){
2228: double fret;
2229: double *xt;
2230: int j;
2231: myfunc_data *d2 = (myfunc_data *) pd;
2232: /* xt = (p1-1); */
2233: xt=vector(1,n);
2234: for (j=1;j<=n;j++) xt[j]=p1[j-1]; /* xt[1]=p1[0] */
2235:
2236: fret=(d2->function)(xt); /* p xt[1]@8 is fine */
2237: /* fret=(*func)(xt); /\* p xt[1]@8 is fine *\/ */
2238: printf("Function = %.12lf ",fret);
2239: for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]);
2240: printf("\n");
2241: free_vector(xt,1,n);
2242: return fret;
2243: }
2244: #endif
1.126 brouard 2245:
2246: /*************** log-likelihood *************/
2247: double func( double *x)
2248: {
2249: int i, ii, j, k, mi, d, kk;
1.131 brouard 2250: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2251: double **out;
2252: double sw; /* Sum of weights */
2253: double lli; /* Individual log likelihood */
2254: int s1, s2;
2255: double bbh, survp;
2256: long ipmx;
1.187 brouard 2257: double agexact;
1.126 brouard 2258: /*extern weight */
2259: /* We are differentiating ll according to initial status */
2260: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2261: /*for(i=1;i<imx;i++)
2262: printf(" %d\n",s[4][i]);
2263: */
1.162 brouard 2264:
2265: ++countcallfunc;
2266:
1.126 brouard 2267: cov[1]=1.;
2268:
2269: for(k=1; k<=nlstate; k++) ll[k]=0.;
2270:
2271: if(mle==1){
2272: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.138 brouard 2273: /* Computes the values of the ncovmodel covariates of the model
2274: depending if the covariates are fixed or variying (age dependent) and stores them in cov[]
2275: Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
2276: to be observed in j being in i according to the model.
2277: */
1.145 brouard 2278: for (k=1; k<=cptcovn;k++){ /* Simple and product covariates without age* products */
1.187 brouard 2279: cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.145 brouard 2280: }
1.137 brouard 2281: /* In model V2+V1*V4+age*V3+V3*V2 Tvar[1] is V2, Tvar[2=V1*V4]
1.138 brouard 2282: is 6, Tvar[3=age*V3] should not be computed because of age Tvar[4=V3*V2]
1.137 brouard 2283: has been calculated etc */
1.126 brouard 2284: for(mi=1; mi<= wav[i]-1; mi++){
2285: for (ii=1;ii<=nlstate+ndeath;ii++)
2286: for (j=1;j<=nlstate+ndeath;j++){
2287: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2288: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2289: }
2290: for(d=0; d<dh[mi][i]; d++){
2291: newm=savm;
1.187 brouard 2292: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2293: cov[2]=agexact;
2294: if(nagesqr==1)
2295: cov[3]= agexact*agexact;
1.126 brouard 2296: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2297: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact; /* Tage[kk] gives the data-covariate associated with age */
1.126 brouard 2298: }
2299: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2300: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2301: savm=oldm;
2302: oldm=newm;
2303: } /* end mult */
2304:
2305: /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
2306: /* But now since version 0.9 we anticipate for bias at large stepm.
2307: * If stepm is larger than one month (smallest stepm) and if the exact delay
2308: * (in months) between two waves is not a multiple of stepm, we rounded to
2309: * the nearest (and in case of equal distance, to the lowest) interval but now
2310: * we keep into memory the bias bh[mi][i] and also the previous matrix product
2311: * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
2312: * probability in order to take into account the bias as a fraction of the way
2313: * from savm to out if bh is negative or even beyond if bh is positive. bh varies
2314: * -stepm/2 to stepm/2 .
2315: * For stepm=1 the results are the same as for previous versions of Imach.
2316: * For stepm > 1 the results are less biased than in previous versions.
2317: */
2318: s1=s[mw[mi][i]][i];
2319: s2=s[mw[mi+1][i]][i];
2320: bbh=(double)bh[mi][i]/(double)stepm;
2321: /* bias bh is positive if real duration
2322: * is higher than the multiple of stepm and negative otherwise.
2323: */
2324: /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
2325: if( s2 > nlstate){
2326: /* i.e. if s2 is a death state and if the date of death is known
2327: then the contribution to the likelihood is the probability to
2328: die between last step unit time and current step unit time,
2329: which is also equal to probability to die before dh
2330: minus probability to die before dh-stepm .
2331: In version up to 0.92 likelihood was computed
2332: as if date of death was unknown. Death was treated as any other
2333: health state: the date of the interview describes the actual state
2334: and not the date of a change in health state. The former idea was
2335: to consider that at each interview the state was recorded
2336: (healthy, disable or death) and IMaCh was corrected; but when we
2337: introduced the exact date of death then we should have modified
2338: the contribution of an exact death to the likelihood. This new
2339: contribution is smaller and very dependent of the step unit
2340: stepm. It is no more the probability to die between last interview
2341: and month of death but the probability to survive from last
2342: interview up to one month before death multiplied by the
2343: probability to die within a month. Thanks to Chris
2344: Jackson for correcting this bug. Former versions increased
2345: mortality artificially. The bad side is that we add another loop
2346: which slows down the processing. The difference can be up to 10%
2347: lower mortality.
2348: */
1.183 brouard 2349: /* If, at the beginning of the maximization mostly, the
2350: cumulative probability or probability to be dead is
2351: constant (ie = 1) over time d, the difference is equal to
2352: 0. out[s1][3] = savm[s1][3]: probability, being at state
2353: s1 at precedent wave, to be dead a month before current
2354: wave is equal to probability, being at state s1 at
2355: precedent wave, to be dead at mont of the current
2356: wave. Then the observed probability (that this person died)
2357: is null according to current estimated parameter. In fact,
2358: it should be very low but not zero otherwise the log go to
2359: infinity.
2360: */
2361: /* #ifdef INFINITYORIGINAL */
2362: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2363: /* #else */
2364: /* if ((out[s1][s2] - savm[s1][s2]) < mytinydouble) */
2365: /* lli=log(mytinydouble); */
2366: /* else */
2367: /* lli=log(out[s1][s2] - savm[s1][s2]); */
2368: /* #endif */
2369: lli=log(out[s1][s2] - savm[s1][s2]);
1.126 brouard 2370:
2371: } else if (s2==-2) {
2372: for (j=1,survp=0. ; j<=nlstate; j++)
2373: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2374: /*survp += out[s1][j]; */
2375: lli= log(survp);
2376: }
2377:
2378: else if (s2==-4) {
2379: for (j=3,survp=0. ; j<=nlstate; j++)
2380: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2381: lli= log(survp);
2382: }
2383:
2384: else if (s2==-5) {
2385: for (j=1,survp=0. ; j<=2; j++)
2386: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2387: lli= log(survp);
2388: }
2389:
2390: else{
2391: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2392: /* 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 */
2393: }
2394: /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
2395: /*if(lli ==000.0)*/
2396: /*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); */
2397: ipmx +=1;
2398: sw += weight[i];
2399: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.183 brouard 2400: /* if (lli < log(mytinydouble)){ */
2401: /* 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); */
2402: /* 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]); */
2403: /* } */
1.126 brouard 2404: } /* end of wave */
2405: } /* end of individual */
2406: } else if(mle==2){
2407: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2408: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2409: for(mi=1; mi<= wav[i]-1; mi++){
2410: for (ii=1;ii<=nlstate+ndeath;ii++)
2411: for (j=1;j<=nlstate+ndeath;j++){
2412: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2413: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2414: }
2415: for(d=0; d<=dh[mi][i]; d++){
2416: newm=savm;
1.187 brouard 2417: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2418: cov[2]=agexact;
2419: if(nagesqr==1)
2420: cov[3]= agexact*agexact;
1.126 brouard 2421: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2422: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2423: }
2424: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2425: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2426: savm=oldm;
2427: oldm=newm;
2428: } /* end mult */
2429:
2430: s1=s[mw[mi][i]][i];
2431: s2=s[mw[mi+1][i]][i];
2432: bbh=(double)bh[mi][i]/(double)stepm;
2433: 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 */
2434: ipmx +=1;
2435: sw += weight[i];
2436: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2437: } /* end of wave */
2438: } /* end of individual */
2439: } else if(mle==3){ /* exponential inter-extrapolation */
2440: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2441: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2442: for(mi=1; mi<= wav[i]-1; mi++){
2443: for (ii=1;ii<=nlstate+ndeath;ii++)
2444: for (j=1;j<=nlstate+ndeath;j++){
2445: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2446: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2447: }
2448: for(d=0; d<dh[mi][i]; d++){
2449: newm=savm;
1.187 brouard 2450: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2451: cov[2]=agexact;
2452: if(nagesqr==1)
2453: cov[3]= agexact*agexact;
1.126 brouard 2454: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2455: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2456: }
2457: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2458: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2459: savm=oldm;
2460: oldm=newm;
2461: } /* end mult */
2462:
2463: s1=s[mw[mi][i]][i];
2464: s2=s[mw[mi+1][i]][i];
2465: bbh=(double)bh[mi][i]/(double)stepm;
2466: 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 */
2467: ipmx +=1;
2468: sw += weight[i];
2469: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2470: } /* end of wave */
2471: } /* end of individual */
2472: }else if (mle==4){ /* ml=4 no inter-extrapolation */
2473: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2474: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2475: for(mi=1; mi<= wav[i]-1; mi++){
2476: for (ii=1;ii<=nlstate+ndeath;ii++)
2477: for (j=1;j<=nlstate+ndeath;j++){
2478: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2479: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2480: }
2481: for(d=0; d<dh[mi][i]; d++){
2482: newm=savm;
1.187 brouard 2483: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2484: cov[2]=agexact;
2485: if(nagesqr==1)
2486: cov[3]= agexact*agexact;
1.126 brouard 2487: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2488: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2489: }
2490:
2491: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2492: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2493: savm=oldm;
2494: oldm=newm;
2495: } /* end mult */
2496:
2497: s1=s[mw[mi][i]][i];
2498: s2=s[mw[mi+1][i]][i];
2499: if( s2 > nlstate){
2500: lli=log(out[s1][s2] - savm[s1][s2]);
2501: }else{
2502: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2503: }
2504: ipmx +=1;
2505: sw += weight[i];
2506: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2507: /* 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]); */
2508: } /* end of wave */
2509: } /* end of individual */
2510: }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
2511: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2512: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2513: for(mi=1; mi<= wav[i]-1; mi++){
2514: for (ii=1;ii<=nlstate+ndeath;ii++)
2515: for (j=1;j<=nlstate+ndeath;j++){
2516: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2517: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2518: }
2519: for(d=0; d<dh[mi][i]; d++){
2520: newm=savm;
1.187 brouard 2521: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2522: cov[2]=agexact;
2523: if(nagesqr==1)
2524: cov[3]= agexact*agexact;
1.126 brouard 2525: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2526: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2527: }
2528:
2529: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2530: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
2531: savm=oldm;
2532: oldm=newm;
2533: } /* end mult */
2534:
2535: s1=s[mw[mi][i]][i];
2536: s2=s[mw[mi+1][i]][i];
2537: lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
2538: ipmx +=1;
2539: sw += weight[i];
2540: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
2541: /*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]);*/
2542: } /* end of wave */
2543: } /* end of individual */
2544: } /* End of if */
2545: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2546: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2547: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2548: return -l;
2549: }
2550:
2551: /*************** log-likelihood *************/
2552: double funcone( double *x)
2553: {
2554: /* Same as likeli but slower because of a lot of printf and if */
2555: int i, ii, j, k, mi, d, kk;
1.131 brouard 2556: double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
1.126 brouard 2557: double **out;
2558: double lli; /* Individual log likelihood */
2559: double llt;
2560: int s1, s2;
2561: double bbh, survp;
1.187 brouard 2562: double agexact;
1.126 brouard 2563: /*extern weight */
2564: /* We are differentiating ll according to initial status */
2565: /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
2566: /*for(i=1;i<imx;i++)
2567: printf(" %d\n",s[4][i]);
2568: */
2569: cov[1]=1.;
2570:
2571: for(k=1; k<=nlstate; k++) ll[k]=0.;
2572:
2573: for (i=1,ipmx=0, sw=0.; i<=imx; i++){
1.187 brouard 2574: for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];
1.126 brouard 2575: for(mi=1; mi<= wav[i]-1; mi++){
2576: for (ii=1;ii<=nlstate+ndeath;ii++)
2577: for (j=1;j<=nlstate+ndeath;j++){
2578: oldm[ii][j]=(ii==j ? 1.0 : 0.0);
2579: savm[ii][j]=(ii==j ? 1.0 : 0.0);
2580: }
2581: for(d=0; d<dh[mi][i]; d++){
2582: newm=savm;
1.187 brouard 2583: agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
2584: cov[2]=agexact;
2585: if(nagesqr==1)
2586: cov[3]= agexact*agexact;
1.126 brouard 2587: for (kk=1; kk<=cptcovage;kk++) {
1.187 brouard 2588: cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
1.126 brouard 2589: }
1.187 brouard 2590:
1.145 brouard 2591: /* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
1.126 brouard 2592: out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
2593: 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
1.145 brouard 2594: /* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
2595: /* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
1.126 brouard 2596: savm=oldm;
2597: oldm=newm;
2598: } /* end mult */
2599:
2600: s1=s[mw[mi][i]][i];
2601: s2=s[mw[mi+1][i]][i];
2602: bbh=(double)bh[mi][i]/(double)stepm;
2603: /* bias is positive if real duration
2604: * is higher than the multiple of stepm and negative otherwise.
2605: */
2606: if( s2 > nlstate && (mle <5) ){ /* Jackson */
2607: lli=log(out[s1][s2] - savm[s1][s2]);
2608: } else if (s2==-2) {
2609: for (j=1,survp=0. ; j<=nlstate; j++)
2610: survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
2611: lli= log(survp);
2612: }else if (mle==1){
2613: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2614: } else if(mle==2){
2615: 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 */
2616: } else if(mle==3){ /* exponential inter-extrapolation */
2617: 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 */
2618: } else if (mle==4){ /* mle=4 no inter-extrapolation */
2619: lli=log(out[s1][s2]); /* Original formula */
1.136 brouard 2620: } else{ /* mle=0 back to 1 */
2621: lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
2622: /*lli=log(out[s1][s2]); */ /* Original formula */
1.126 brouard 2623: } /* End of if */
2624: ipmx +=1;
2625: sw += weight[i];
2626: ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
1.132 brouard 2627: /*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 2628: if(globpr){
1.205 brouard 2629: fprintf(ficresilk,"%9ld %6.1f %6d %2d %2d %2d %2d %3d %11.6f %8.4f %8.3f\
1.126 brouard 2630: %11.6f %11.6f %11.6f ", \
1.205 brouard 2631: num[i], agexact, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
1.126 brouard 2632: 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
2633: for(k=1,llt=0.,l=0.; k<=nlstate; k++){
2634: llt +=ll[k]*gipmx/gsw;
2635: fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
2636: }
2637: fprintf(ficresilk," %10.6f\n", -llt);
2638: }
2639: } /* end of wave */
2640: } /* end of individual */
2641: for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
2642: /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
2643: l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
2644: if(globpr==0){ /* First time we count the contributions and weights */
2645: gipmx=ipmx;
2646: gsw=sw;
2647: }
2648: return -l;
2649: }
2650:
2651:
2652: /*************** function likelione ***********/
2653: void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
2654: {
2655: /* This routine should help understanding what is done with
2656: the selection of individuals/waves and
2657: to check the exact contribution to the likelihood.
2658: Plotting could be done.
2659: */
2660: int k;
2661:
2662: if(*globpri !=0){ /* Just counts and sums, no printings */
1.201 brouard 2663: strcpy(fileresilk,"ILK_");
1.202 brouard 2664: strcat(fileresilk,fileresu);
1.126 brouard 2665: if((ficresilk=fopen(fileresilk,"w"))==NULL) {
2666: printf("Problem with resultfile: %s\n", fileresilk);
2667: fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
2668: }
1.205 brouard 2669: 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");
1.207 ! brouard 2670: fprintf(ficresilk, "#num_i age i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
1.126 brouard 2671: /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
2672: for(k=1; k<=nlstate; k++)
2673: fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
2674: fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
2675: }
2676:
2677: *fretone=(*funcone)(p);
2678: if(*globpri !=0){
2679: fclose(ficresilk);
1.205 brouard 2680: if (mle ==0)
2681: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with initial parameters and mle = %d.",mle);
2682: else if(mle >=1)
2683: fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
2684: fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
1.207 ! brouard 2685:
! 2686: 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 2687: <img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 ! brouard 2688: fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
1.204 brouard 2689: <img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
1.207 ! brouard 2690: fflush(fichtm);
1.205 brouard 2691:
1.207 ! brouard 2692: for (k=1; k<= nlstate ; k++) {
! 2693: 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 2694: <img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
1.207 ! brouard 2695: }
1.205 brouard 2696: }
1.126 brouard 2697: return;
2698: }
2699:
2700:
2701: /*********** Maximum Likelihood Estimation ***************/
2702:
2703: void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
2704: {
1.165 brouard 2705: int i,j, iter=0;
1.126 brouard 2706: double **xi;
2707: double fret;
2708: double fretone; /* Only one call to likelihood */
2709: /* char filerespow[FILENAMELENGTH];*/
1.162 brouard 2710:
2711: #ifdef NLOPT
2712: int creturn;
2713: nlopt_opt opt;
2714: /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
2715: double *lb;
2716: double minf; /* the minimum objective value, upon return */
2717: double * p1; /* Shifted parameters from 0 instead of 1 */
2718: myfunc_data dinst, *d = &dinst;
2719: #endif
2720:
2721:
1.126 brouard 2722: xi=matrix(1,npar,1,npar);
2723: for (i=1;i<=npar;i++)
2724: for (j=1;j<=npar;j++)
2725: xi[i][j]=(i==j ? 1.0 : 0.0);
2726: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.201 brouard 2727: strcpy(filerespow,"POW_");
1.126 brouard 2728: strcat(filerespow,fileres);
2729: if((ficrespow=fopen(filerespow,"w"))==NULL) {
2730: printf("Problem with resultfile: %s\n", filerespow);
2731: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
2732: }
2733: fprintf(ficrespow,"# Powell\n# iter -2*LL");
2734: for (i=1;i<=nlstate;i++)
2735: for(j=1;j<=nlstate+ndeath;j++)
2736: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
2737: fprintf(ficrespow,"\n");
1.162 brouard 2738: #ifdef POWELL
1.126 brouard 2739: powell(p,xi,npar,ftol,&iter,&fret,func);
1.162 brouard 2740: #endif
1.126 brouard 2741:
1.162 brouard 2742: #ifdef NLOPT
2743: #ifdef NEWUOA
2744: opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
2745: #else
2746: opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
2747: #endif
2748: lb=vector(0,npar-1);
2749: for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
2750: nlopt_set_lower_bounds(opt, lb);
2751: nlopt_set_initial_step1(opt, 0.1);
2752:
2753: p1= (p+1); /* p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
2754: d->function = func;
2755: printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
2756: nlopt_set_min_objective(opt, myfunc, d);
2757: nlopt_set_xtol_rel(opt, ftol);
2758: if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
2759: printf("nlopt failed! %d\n",creturn);
2760: }
2761: else {
2762: printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
2763: printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
2764: iter=1; /* not equal */
2765: }
2766: nlopt_destroy(opt);
2767: #endif
1.126 brouard 2768: free_matrix(xi,1,npar,1,npar);
2769: fclose(ficrespow);
1.203 brouard 2770: printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
2771: fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.180 brouard 2772: fprintf(ficres,"#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
1.126 brouard 2773:
2774: }
2775:
2776: /**** Computes Hessian and covariance matrix ***/
1.203 brouard 2777: void hesscov(double **matcov, double **hess, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
1.126 brouard 2778: {
2779: double **a,**y,*x,pd;
1.203 brouard 2780: /* double **hess; */
1.164 brouard 2781: int i, j;
1.126 brouard 2782: int *indx;
2783:
2784: double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
1.203 brouard 2785: double hessij(double p[], double **hess, double delti[], int i, int j,double (*func)(double []),int npar);
1.126 brouard 2786: void lubksb(double **a, int npar, int *indx, double b[]) ;
2787: void ludcmp(double **a, int npar, int *indx, double *d) ;
2788: double gompertz(double p[]);
1.203 brouard 2789: /* hess=matrix(1,npar,1,npar); */
1.126 brouard 2790:
2791: printf("\nCalculation of the hessian matrix. Wait...\n");
2792: fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
2793: for (i=1;i<=npar;i++){
1.203 brouard 2794: printf("%d-",i);fflush(stdout);
2795: fprintf(ficlog,"%d-",i);fflush(ficlog);
1.126 brouard 2796:
2797: hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
2798:
2799: /* printf(" %f ",p[i]);
2800: printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
2801: }
2802:
2803: for (i=1;i<=npar;i++) {
2804: for (j=1;j<=npar;j++) {
2805: if (j>i) {
1.203 brouard 2806: printf(".%d-%d",i,j);fflush(stdout);
2807: fprintf(ficlog,".%d-%d",i,j);fflush(ficlog);
2808: hess[i][j]=hessij(p,hess, delti,i,j,func,npar);
1.126 brouard 2809:
2810: hess[j][i]=hess[i][j];
2811: /*printf(" %lf ",hess[i][j]);*/
2812: }
2813: }
2814: }
2815: printf("\n");
2816: fprintf(ficlog,"\n");
2817:
2818: printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
2819: fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
2820:
2821: a=matrix(1,npar,1,npar);
2822: y=matrix(1,npar,1,npar);
2823: x=vector(1,npar);
2824: indx=ivector(1,npar);
2825: for (i=1;i<=npar;i++)
2826: for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
2827: ludcmp(a,npar,indx,&pd);
2828:
2829: for (j=1;j<=npar;j++) {
2830: for (i=1;i<=npar;i++) x[i]=0;
2831: x[j]=1;
2832: lubksb(a,npar,indx,x);
2833: for (i=1;i<=npar;i++){
2834: matcov[i][j]=x[i];
2835: }
2836: }
2837:
2838: printf("\n#Hessian matrix#\n");
2839: fprintf(ficlog,"\n#Hessian matrix#\n");
2840: for (i=1;i<=npar;i++) {
2841: for (j=1;j<=npar;j++) {
1.203 brouard 2842: printf("%.6e ",hess[i][j]);
2843: fprintf(ficlog,"%.6e ",hess[i][j]);
1.126 brouard 2844: }
2845: printf("\n");
2846: fprintf(ficlog,"\n");
2847: }
2848:
1.203 brouard 2849: /* printf("\n#Covariance matrix#\n"); */
2850: /* fprintf(ficlog,"\n#Covariance matrix#\n"); */
2851: /* for (i=1;i<=npar;i++) { */
2852: /* for (j=1;j<=npar;j++) { */
2853: /* printf("%.6e ",matcov[i][j]); */
2854: /* fprintf(ficlog,"%.6e ",matcov[i][j]); */
2855: /* } */
2856: /* printf("\n"); */
2857: /* fprintf(ficlog,"\n"); */
2858: /* } */
2859:
1.126 brouard 2860: /* Recompute Inverse */
1.203 brouard 2861: /* for (i=1;i<=npar;i++) */
2862: /* for (j=1;j<=npar;j++) a[i][j]=matcov[i][j]; */
2863: /* ludcmp(a,npar,indx,&pd); */
2864:
2865: /* printf("\n#Hessian matrix recomputed#\n"); */
2866:
2867: /* for (j=1;j<=npar;j++) { */
2868: /* for (i=1;i<=npar;i++) x[i]=0; */
2869: /* x[j]=1; */
2870: /* lubksb(a,npar,indx,x); */
2871: /* for (i=1;i<=npar;i++){ */
2872: /* y[i][j]=x[i]; */
2873: /* printf("%.3e ",y[i][j]); */
2874: /* fprintf(ficlog,"%.3e ",y[i][j]); */
2875: /* } */
2876: /* printf("\n"); */
2877: /* fprintf(ficlog,"\n"); */
2878: /* } */
2879:
2880: /* Verifying the inverse matrix */
2881: #ifdef DEBUGHESS
2882: y=matprod2(y,hess,1,npar,1,npar,1,npar,matcov);
1.126 brouard 2883:
1.203 brouard 2884: printf("\n#Verification: multiplying the matrix of covariance by the Hessian matrix, should be unity:#\n");
2885: fprintf(ficlog,"\n#Verification: multiplying the matrix of covariance by the Hessian matrix. Should be unity:#\n");
1.126 brouard 2886:
2887: for (j=1;j<=npar;j++) {
2888: for (i=1;i<=npar;i++){
1.203 brouard 2889: printf("%.2f ",y[i][j]);
2890: fprintf(ficlog,"%.2f ",y[i][j]);
1.126 brouard 2891: }
2892: printf("\n");
2893: fprintf(ficlog,"\n");
2894: }
1.203 brouard 2895: #endif
1.126 brouard 2896:
2897: free_matrix(a,1,npar,1,npar);
2898: free_matrix(y,1,npar,1,npar);
2899: free_vector(x,1,npar);
2900: free_ivector(indx,1,npar);
1.203 brouard 2901: /* free_matrix(hess,1,npar,1,npar); */
1.126 brouard 2902:
2903:
2904: }
2905:
2906: /*************** hessian matrix ****************/
2907: double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
1.203 brouard 2908: { /* Around values of x, computes the function func and returns the scales delti and hessian */
1.126 brouard 2909: int i;
2910: int l=1, lmax=20;
1.203 brouard 2911: double k1,k2, res, fx;
1.132 brouard 2912: double p2[MAXPARM+1]; /* identical to x */
1.126 brouard 2913: double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
2914: int k=0,kmax=10;
2915: double l1;
2916:
2917: fx=func(x);
2918: for (i=1;i<=npar;i++) p2[i]=x[i];
1.145 brouard 2919: for(l=0 ; l <=lmax; l++){ /* Enlarging the zone around the Maximum */
1.126 brouard 2920: l1=pow(10,l);
2921: delts=delt;
2922: for(k=1 ; k <kmax; k=k+1){
2923: delt = delta*(l1*k);
2924: p2[theta]=x[theta] +delt;
1.145 brouard 2925: k1=func(p2)-fx; /* Might be negative if too close to the theoretical maximum */
1.126 brouard 2926: p2[theta]=x[theta]-delt;
2927: k2=func(p2)-fx;
2928: /*res= (k1-2.0*fx+k2)/delt/delt; */
1.203 brouard 2929: res= (k1+k2)/delt/delt/2.; /* Divided by 2 because L and not 2*L */
1.126 brouard 2930:
1.203 brouard 2931: #ifdef DEBUGHESSII
1.126 brouard 2932: 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);
2933: 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);
2934: #endif
2935: /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
2936: if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
2937: k=kmax;
2938: }
2939: else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
1.164 brouard 2940: k=kmax; l=lmax*10;
1.126 brouard 2941: }
2942: else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
2943: delts=delt;
2944: }
1.203 brouard 2945: } /* End loop k */
1.126 brouard 2946: }
2947: delti[theta]=delts;
2948: return res;
2949:
2950: }
2951:
1.203 brouard 2952: double hessij( double x[], double **hess, double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
1.126 brouard 2953: {
2954: int i;
1.164 brouard 2955: int l=1, lmax=20;
1.126 brouard 2956: double k1,k2,k3,k4,res,fx;
1.132 brouard 2957: double p2[MAXPARM+1];
1.203 brouard 2958: int k, kmax=1;
2959: double v1, v2, cv12, lc1, lc2;
2960:
1.126 brouard 2961: fx=func(x);
1.203 brouard 2962: for (k=1; k<=kmax; k=k+10) {
1.126 brouard 2963: for (i=1;i<=npar;i++) p2[i]=x[i];
1.203 brouard 2964: p2[thetai]=x[thetai]+delti[thetai]*k;
2965: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2966: k1=func(p2)-fx;
2967:
1.203 brouard 2968: p2[thetai]=x[thetai]+delti[thetai]*k;
2969: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2970: k2=func(p2)-fx;
2971:
1.203 brouard 2972: p2[thetai]=x[thetai]-delti[thetai]*k;
2973: p2[thetaj]=x[thetaj]+delti[thetaj]*k;
1.126 brouard 2974: k3=func(p2)-fx;
2975:
1.203 brouard 2976: p2[thetai]=x[thetai]-delti[thetai]*k;
2977: p2[thetaj]=x[thetaj]-delti[thetaj]*k;
1.126 brouard 2978: k4=func(p2)-fx;
1.203 brouard 2979: res=(k1-k2-k3+k4)/4.0/delti[thetai]/k/delti[thetaj]/k/2.; /* Because of L not 2*L */
2980: if(k1*k2*k3*k4 <0.){
2981: kmax=kmax+10;
2982: if(kmax >=10){
2983: printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2984: fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; increase ftol=%.2e\n",thetai,thetaj, ftol);
2985: 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);
2986: 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);
2987: }
2988: }
2989: #ifdef DEBUGHESSIJ
2990: v1=hess[thetai][thetai];
2991: v2=hess[thetaj][thetaj];
2992: cv12=res;
2993: /* Computing eigen value of Hessian matrix */
2994: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2995: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
2996: if ((lc2 <0) || (lc1 <0) ){
2997: printf("Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2998: fprintf(ficlog, "Warning: sub Hessian matrix '%d%d' does not have positive eigen values \n",thetai,thetaj);
2999: 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);
3000: 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);
3001: }
1.126 brouard 3002: #endif
3003: }
3004: return res;
3005: }
3006:
1.203 brouard 3007: /* Not done yet: Was supposed to fix if not exactly at the maximum */
3008: /* double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar) */
3009: /* { */
3010: /* int i; */
3011: /* int l=1, lmax=20; */
3012: /* double k1,k2,k3,k4,res,fx; */
3013: /* double p2[MAXPARM+1]; */
3014: /* double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4; */
3015: /* int k=0,kmax=10; */
3016: /* double l1; */
3017:
3018: /* fx=func(x); */
3019: /* for(l=0 ; l <=lmax; l++){ /\* Enlarging the zone around the Maximum *\/ */
3020: /* l1=pow(10,l); */
3021: /* delts=delt; */
3022: /* for(k=1 ; k <kmax; k=k+1){ */
3023: /* delt = delti*(l1*k); */
3024: /* for (i=1;i<=npar;i++) p2[i]=x[i]; */
3025: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3026: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3027: /* k1=func(p2)-fx; */
3028:
3029: /* p2[thetai]=x[thetai]+delti[thetai]/k; */
3030: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3031: /* k2=func(p2)-fx; */
3032:
3033: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3034: /* p2[thetaj]=x[thetaj]+delti[thetaj]/k; */
3035: /* k3=func(p2)-fx; */
3036:
3037: /* p2[thetai]=x[thetai]-delti[thetai]/k; */
3038: /* p2[thetaj]=x[thetaj]-delti[thetaj]/k; */
3039: /* k4=func(p2)-fx; */
3040: /* res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /\* Because of L not 2*L *\/ */
3041: /* #ifdef DEBUGHESSIJ */
3042: /* 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); */
3043: /* 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); */
3044: /* #endif */
3045: /* if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)|| (k4 <khi/nkhi/2.)){ */
3046: /* k=kmax; */
3047: /* } */
3048: /* else if((k1 >khi/nkhif) || (k2 >khi/nkhif) || (k4 >khi/nkhif) || (k4 >khi/nkhif)){ /\* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. *\/ */
3049: /* k=kmax; l=lmax*10; */
3050: /* } */
3051: /* else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ */
3052: /* delts=delt; */
3053: /* } */
3054: /* } /\* End loop k *\/ */
3055: /* } */
3056: /* delti[theta]=delts; */
3057: /* return res; */
3058: /* } */
3059:
3060:
1.126 brouard 3061: /************** Inverse of matrix **************/
3062: void ludcmp(double **a, int n, int *indx, double *d)
3063: {
3064: int i,imax,j,k;
3065: double big,dum,sum,temp;
3066: double *vv;
3067:
3068: vv=vector(1,n);
3069: *d=1.0;
3070: for (i=1;i<=n;i++) {
3071: big=0.0;
3072: for (j=1;j<=n;j++)
3073: if ((temp=fabs(a[i][j])) > big) big=temp;
3074: if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
3075: vv[i]=1.0/big;
3076: }
3077: for (j=1;j<=n;j++) {
3078: for (i=1;i<j;i++) {
3079: sum=a[i][j];
3080: for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
3081: a[i][j]=sum;
3082: }
3083: big=0.0;
3084: for (i=j;i<=n;i++) {
3085: sum=a[i][j];
3086: for (k=1;k<j;k++)
3087: sum -= a[i][k]*a[k][j];
3088: a[i][j]=sum;
3089: if ( (dum=vv[i]*fabs(sum)) >= big) {
3090: big=dum;
3091: imax=i;
3092: }
3093: }
3094: if (j != imax) {
3095: for (k=1;k<=n;k++) {
3096: dum=a[imax][k];
3097: a[imax][k]=a[j][k];
3098: a[j][k]=dum;
3099: }
3100: *d = -(*d);
3101: vv[imax]=vv[j];
3102: }
3103: indx[j]=imax;
3104: if (a[j][j] == 0.0) a[j][j]=TINY;
3105: if (j != n) {
3106: dum=1.0/(a[j][j]);
3107: for (i=j+1;i<=n;i++) a[i][j] *= dum;
3108: }
3109: }
3110: free_vector(vv,1,n); /* Doesn't work */
3111: ;
3112: }
3113:
3114: void lubksb(double **a, int n, int *indx, double b[])
3115: {
3116: int i,ii=0,ip,j;
3117: double sum;
3118:
3119: for (i=1;i<=n;i++) {
3120: ip=indx[i];
3121: sum=b[ip];
3122: b[ip]=b[i];
3123: if (ii)
3124: for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
3125: else if (sum) ii=i;
3126: b[i]=sum;
3127: }
3128: for (i=n;i>=1;i--) {
3129: sum=b[i];
3130: for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
3131: b[i]=sum/a[i][i];
3132: }
3133: }
3134:
3135: void pstamp(FILE *fichier)
3136: {
1.196 brouard 3137: fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
1.126 brouard 3138: }
3139:
3140: /************ Frequencies ********************/
3141: 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[])
3142: { /* Some frequencies */
3143:
1.164 brouard 3144: int i, m, jk, j1, bool, z1,j;
1.126 brouard 3145: int first;
3146: double ***freq; /* Frequencies */
3147: double *pp, **prop;
3148: double pos,posprop, k2, dateintsum=0,k2cpt=0;
3149: char fileresp[FILENAMELENGTH];
3150:
3151: pp=vector(1,nlstate);
3152: prop=matrix(1,nlstate,iagemin,iagemax+3);
1.201 brouard 3153: strcpy(fileresp,"P_");
3154: strcat(fileresp,fileresu);
1.126 brouard 3155: if((ficresp=fopen(fileresp,"w"))==NULL) {
3156: printf("Problem with prevalence resultfile: %s\n", fileresp);
3157: fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
3158: exit(0);
3159: }
3160: freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
3161: j1=0;
3162:
3163: j=cptcoveff;
3164: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3165:
3166: first=1;
3167:
1.169 brouard 3168: /* for(k1=1; k1<=j ; k1++){ */ /* Loop on covariates */
3169: /* for(i1=1; i1<=ncodemax[k1];i1++){ */ /* Now it is 2 */
3170: /* j1++; */
1.145 brouard 3171: for (j1 = 1; j1 <= (int) pow(2,cptcoveff); j1++){
1.126 brouard 3172: /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
3173: scanf("%d", i);*/
3174: for (i=-5; i<=nlstate+ndeath; i++)
3175: for (jk=-5; jk<=nlstate+ndeath; jk++)
3176: for(m=iagemin; m <= iagemax+3; m++)
3177: freq[i][jk][m]=0;
1.143 brouard 3178:
3179: for (i=1; i<=nlstate; i++)
3180: for(m=iagemin; m <= iagemax+3; m++)
3181: prop[i][m]=0;
1.126 brouard 3182:
3183: dateintsum=0;
3184: k2cpt=0;
3185: for (i=1; i<=imx; i++) {
3186: bool=1;
1.144 brouard 3187: if (cptcovn>0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
3188: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3189: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
1.145 brouard 3190: /* Tests if the value of each of the covariates of i is equal to filter j1 */
1.144 brouard 3191: bool=0;
1.198 brouard 3192: /* 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",
3193: bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
3194: j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
3195: /* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
1.144 brouard 3196: }
1.126 brouard 3197: }
1.144 brouard 3198:
1.126 brouard 3199: if (bool==1){
3200: for(m=firstpass; m<=lastpass; m++){
3201: k2=anint[m][i]+(mint[m][i]/12.);
3202: /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
3203: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3204: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3205: if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
3206: if (m<lastpass) {
3207: freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
3208: freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
3209: }
3210:
3211: if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
3212: dateintsum=dateintsum+k2;
3213: k2cpt++;
3214: }
3215: /*}*/
3216: }
3217: }
1.145 brouard 3218: } /* end i */
1.126 brouard 3219:
3220: /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
3221: pstamp(ficresp);
3222: if (cptcovn>0) {
3223: fprintf(ficresp, "\n#********** Variable ");
1.198 brouard 3224: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 3225: fprintf(ficresp, "**********\n#");
1.143 brouard 3226: fprintf(ficlog, "\n#********** Variable ");
1.198 brouard 3227: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.143 brouard 3228: fprintf(ficlog, "**********\n#");
1.126 brouard 3229: }
3230: for(i=1; i<=nlstate;i++)
3231: fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
3232: fprintf(ficresp, "\n");
3233:
3234: for(i=iagemin; i <= iagemax+3; i++){
3235: if(i==iagemax+3){
3236: fprintf(ficlog,"Total");
3237: }else{
3238: if(first==1){
3239: first=0;
3240: printf("See log file for details...\n");
3241: }
3242: fprintf(ficlog,"Age %d", i);
3243: }
3244: for(jk=1; jk <=nlstate ; jk++){
3245: for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
3246: pp[jk] += freq[jk][m][i];
3247: }
3248: for(jk=1; jk <=nlstate ; jk++){
3249: for(m=-1, pos=0; m <=0 ; m++)
3250: pos += freq[jk][m][i];
3251: if(pp[jk]>=1.e-10){
3252: if(first==1){
1.132 brouard 3253: printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
1.126 brouard 3254: }
3255: fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
3256: }else{
3257: if(first==1)
3258: printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3259: fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
3260: }
3261: }
3262:
3263: for(jk=1; jk <=nlstate ; jk++){
3264: for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
3265: pp[jk] += freq[jk][m][i];
3266: }
3267: for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
3268: pos += pp[jk];
3269: posprop += prop[jk][i];
3270: }
3271: for(jk=1; jk <=nlstate ; jk++){
3272: if(pos>=1.e-5){
3273: if(first==1)
3274: printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3275: fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
3276: }else{
3277: if(first==1)
3278: printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3279: fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
3280: }
3281: if( i <= iagemax){
3282: if(pos>=1.e-5){
3283: fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
3284: /*probs[i][jk][j1]= pp[jk]/pos;*/
3285: /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
3286: }
3287: else
3288: fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
3289: }
3290: }
3291:
3292: for(jk=-1; jk <=nlstate+ndeath; jk++)
3293: for(m=-1; m <=nlstate+ndeath; m++)
3294: if(freq[jk][m][i] !=0 ) {
3295: if(first==1)
3296: printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
3297: fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
3298: }
3299: if(i <= iagemax)
3300: fprintf(ficresp,"\n");
3301: if(first==1)
3302: printf("Others in log...\n");
3303: fprintf(ficlog,"\n");
3304: }
1.145 brouard 3305: /*}*/
1.126 brouard 3306: }
3307: dateintmean=dateintsum/k2cpt;
3308:
3309: fclose(ficresp);
3310: free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
3311: free_vector(pp,1,nlstate);
3312: free_matrix(prop,1,nlstate,iagemin, iagemax+3);
3313: /* End of Freq */
3314: }
3315:
3316: /************ Prevalence ********************/
3317: 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)
3318: {
3319: /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
3320: in each health status at the date of interview (if between dateprev1 and dateprev2).
3321: We still use firstpass and lastpass as another selection.
3322: */
3323:
1.164 brouard 3324: int i, m, jk, j1, bool, z1,j;
3325:
3326: double **prop;
3327: double posprop;
1.126 brouard 3328: double y2; /* in fractional years */
3329: int iagemin, iagemax;
1.145 brouard 3330: int first; /** to stop verbosity which is redirected to log file */
1.126 brouard 3331:
3332: iagemin= (int) agemin;
3333: iagemax= (int) agemax;
3334: /*pp=vector(1,nlstate);*/
3335: prop=matrix(1,nlstate,iagemin,iagemax+3);
3336: /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
3337: j1=0;
3338:
1.145 brouard 3339: /*j=cptcoveff;*/
1.126 brouard 3340: if (cptcovn<1) {j=1;ncodemax[1]=1;}
3341:
1.145 brouard 3342: first=1;
3343: for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){
3344: /*for(i1=1; i1<=ncodemax[k1];i1++){
3345: j1++;*/
1.126 brouard 3346:
3347: for (i=1; i<=nlstate; i++)
3348: for(m=iagemin; m <= iagemax+3; m++)
3349: prop[i][m]=0.0;
3350:
3351: for (i=1; i<=imx; i++) { /* Each individual */
3352: bool=1;
3353: if (cptcovn>0) {
3354: for (z1=1; z1<=cptcoveff; z1++)
1.198 brouard 3355: if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)])
1.126 brouard 3356: bool=0;
3357: }
3358: if (bool==1) {
3359: for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
3360: y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
3361: if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
3362: if(agev[m][i]==0) agev[m][i]=iagemax+1;
3363: if(agev[m][i]==1) agev[m][i]=iagemax+2;
3364: 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);
3365: if (s[m][i]>0 && s[m][i]<=nlstate) {
3366: /*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]]);*/
3367: prop[s[m][i]][(int)agev[m][i]] += weight[i];
3368: prop[s[m][i]][iagemax+3] += weight[i];
3369: }
3370: }
3371: } /* end selection of waves */
3372: }
3373: }
3374: for(i=iagemin; i <= iagemax+3; i++){
3375: for(jk=1,posprop=0; jk <=nlstate ; jk++) {
3376: posprop += prop[jk][i];
3377: }
1.145 brouard 3378:
1.126 brouard 3379: for(jk=1; jk <=nlstate ; jk++){
3380: if( i <= iagemax){
3381: if(posprop>=1.e-5){
3382: probs[i][jk][j1]= prop[jk][i]/posprop;
1.145 brouard 3383: } else{
3384: if(first==1){
3385: first=0;
3386: 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]);
3387: }
3388: }
1.126 brouard 3389: }
3390: }/* end jk */
3391: }/* end i */
1.145 brouard 3392: /*} *//* end i1 */
3393: } /* end j1 */
1.126 brouard 3394:
3395: /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
3396: /*free_vector(pp,1,nlstate);*/
3397: free_matrix(prop,1,nlstate, iagemin,iagemax+3);
3398: } /* End of prevalence */
3399:
3400: /************* Waves Concatenation ***************/
3401:
3402: 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)
3403: {
3404: /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
3405: Death is a valid wave (if date is known).
3406: mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
3407: dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
3408: and mw[mi+1][i]. dh depends on stepm.
3409: */
3410:
3411: int i, mi, m;
3412: /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
3413: double sum=0., jmean=0.;*/
3414: int first;
3415: int j, k=0,jk, ju, jl;
3416: double sum=0.;
3417: first=0;
1.164 brouard 3418: jmin=100000;
1.126 brouard 3419: jmax=-1;
3420: jmean=0.;
3421: for(i=1; i<=imx; i++){
3422: mi=0;
3423: m=firstpass;
3424: while(s[m][i] <= nlstate){
3425: if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
3426: mw[++mi][i]=m;
3427: if(m >=lastpass)
3428: break;
3429: else
3430: m++;
3431: }/* end while */
3432: if (s[m][i] > nlstate){
3433: mi++; /* Death is another wave */
3434: /* if(mi==0) never been interviewed correctly before death */
3435: /* Only death is a correct wave */
3436: mw[mi][i]=m;
3437: }
3438:
3439: wav[i]=mi;
3440: if(mi==0){
3441: nbwarn++;
3442: if(first==0){
3443: printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
3444: first=1;
3445: }
3446: if(first==1){
3447: fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
3448: }
3449: } /* end mi==0 */
3450: } /* End individuals */
3451:
3452: for(i=1; i<=imx; i++){
3453: for(mi=1; mi<wav[i];mi++){
3454: if (stepm <=0)
3455: dh[mi][i]=1;
3456: else{
3457: if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
3458: if (agedc[i] < 2*AGESUP) {
3459: j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
3460: if(j==0) j=1; /* Survives at least one month after exam */
3461: else if(j<0){
3462: nberr++;
3463: 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]);
3464: j=1; /* Temporary Dangerous patch */
3465: 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);
3466: 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]);
3467: 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);
3468: }
3469: k=k+1;
3470: if (j >= jmax){
3471: jmax=j;
3472: ijmax=i;
3473: }
3474: if (j <= jmin){
3475: jmin=j;
3476: ijmin=i;
3477: }
3478: sum=sum+j;
3479: /*if (j<0) printf("j=%d num=%d \n",j,i);*/
3480: /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
3481: }
3482: }
3483: else{
3484: j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
3485: /* 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]); */
3486:
3487: k=k+1;
3488: if (j >= jmax) {
3489: jmax=j;
3490: ijmax=i;
3491: }
3492: else if (j <= jmin){
3493: jmin=j;
3494: ijmin=i;
3495: }
3496: /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
3497: /*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]);*/
3498: if(j<0){
3499: nberr++;
3500: 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]);
3501: 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]);
3502: }
3503: sum=sum+j;
3504: }
3505: jk= j/stepm;
3506: jl= j -jk*stepm;
3507: ju= j -(jk+1)*stepm;
3508: if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
3509: if(jl==0){
3510: dh[mi][i]=jk;
3511: bh[mi][i]=0;
3512: }else{ /* We want a negative bias in order to only have interpolation ie
1.136 brouard 3513: * to avoid the price of an extra matrix product in likelihood */
1.126 brouard 3514: dh[mi][i]=jk+1;
3515: bh[mi][i]=ju;
3516: }
3517: }else{
3518: if(jl <= -ju){
3519: dh[mi][i]=jk;
3520: bh[mi][i]=jl; /* bias is positive if real duration
3521: * is higher than the multiple of stepm and negative otherwise.
3522: */
3523: }
3524: else{
3525: dh[mi][i]=jk+1;
3526: bh[mi][i]=ju;
3527: }
3528: if(dh[mi][i]==0){
3529: dh[mi][i]=1; /* At least one step */
3530: bh[mi][i]=ju; /* At least one step */
3531: /* 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);*/
3532: }
3533: } /* end if mle */
3534: }
3535: } /* end wave */
3536: }
3537: jmean=sum/k;
3538: 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 3539: 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 3540: }
3541:
3542: /*********** Tricode ****************************/
1.145 brouard 3543: void tricode(int *Tvar, int **nbcode, int imx, int *Ndum)
1.126 brouard 3544: {
1.144 brouard 3545: /**< Uses cptcovn+2*cptcovprod as the number of covariates */
3546: /* 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 3547: * Boring subroutine which should only output nbcode[Tvar[j]][k]
1.145 brouard 3548: * Tvar[5] in V2+V1+V3*age+V2*V4 is 2 (V2)
1.169 brouard 3549: * nbcode[Tvar[j]][1]=
1.144 brouard 3550: */
1.130 brouard 3551:
1.145 brouard 3552: int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
1.136 brouard 3553: int modmaxcovj=0; /* Modality max of covariates j */
1.145 brouard 3554: int cptcode=0; /* Modality max of covariates j */
3555: int modmincovj=0; /* Modality min of covariates j */
3556:
3557:
1.126 brouard 3558: cptcoveff=0;
3559:
1.144 brouard 3560: for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
1.126 brouard 3561:
1.145 brouard 3562: /* Loop on covariates without age and products */
1.186 brouard 3563: for (j=1; j<=(cptcovs); j++) { /* From model V1 + V2*age+ V3 + V3*V4 keeps V1 + V3 = 2 only */
1.192 brouard 3564: for (k=-1; k < maxncov; k++) Ndum[k]=0;
1.186 brouard 3565: for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the
1.136 brouard 3566: modality of this covariate Vj*/
1.145 brouard 3567: ij=(int)(covar[Tvar[j]][i]); /* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
3568: * If product of Vn*Vm, still boolean *:
3569: * If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
3570: * 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
3571: /* Finds for covariate j, n=Tvar[j] of Vn . ij is the
1.136 brouard 3572: modality of the nth covariate of individual i. */
1.145 brouard 3573: if (ij > modmaxcovj)
3574: modmaxcovj=ij;
3575: else if (ij < modmincovj)
3576: modmincovj=ij;
3577: if ((ij < -1) && (ij > NCOVMAX)){
3578: printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
3579: exit(1);
3580: }else
1.136 brouard 3581: Ndum[ij]++; /*counts and stores the occurence of this modality 0, 1, -1*/
1.145 brouard 3582: /* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
1.126 brouard 3583: /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
1.136 brouard 3584: /* getting the maximum value of the modality of the covariate
3585: (should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
3586: female is 1, then modmaxcovj=1.*/
1.192 brouard 3587: } /* end for loop on individuals i */
1.145 brouard 3588: printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", j, Tvar[j], modmincovj, modmaxcovj);
1.192 brouard 3589: 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 3590: cptcode=modmaxcovj;
1.137 brouard 3591: /* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
1.145 brouard 3592: /*for (i=0; i<=cptcode; i++) {*/
1.192 brouard 3593: for (k=modmincovj; k<=modmaxcovj; k++) { /* k=-1 ? 0 and 1*//* For each value k of the modality of model-cov j */
3594: printf("Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3595: fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", j, Tvar[j], k, Ndum[k]);
3596: if( Ndum[k] != 0 ){ /* Counts if nobody answered modality k ie empty modality, we skip it and reorder */
3597: if( k != -1){
3598: ncodemax[j]++; /* ncodemax[j]= Number of modalities of the j th
3599: covariate for which somebody answered excluding
3600: undefined. Usually 2: 0 and 1. */
3601: }
3602: ncodemaxwundef[j]++; /* ncodemax[j]= Number of modalities of the j th
3603: covariate for which somebody answered including
3604: undefined. Usually 3: -1, 0 and 1. */
1.145 brouard 3605: }
3606: /* In fact ncodemax[j]=2 (dichotom. variables only) but it could be more for
3607: historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
1.131 brouard 3608: } /* Ndum[-1] number of undefined modalities */
1.126 brouard 3609:
1.136 brouard 3610: /* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
1.186 brouard 3611: /* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7.
3612: 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 3613: modmincovj=3; modmaxcovj = 7;
1.186 brouard 3614: There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3;
3615: which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10;
3616: defining two dummy variables: variables V1_1 and V1_2.
1.145 brouard 3617: nbcode[Tvar[j]][ij]=k;
3618: nbcode[Tvar[j]][1]=0;
3619: nbcode[Tvar[j]][2]=1;
3620: nbcode[Tvar[j]][3]=2;
1.197 brouard 3621: To be continued (not working yet).
1.145 brouard 3622: */
1.197 brouard 3623: ij=0; /* ij is similar to i but can jump over null modalities */
3624: 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*/
3625: if (Ndum[i] == 0) { /* If nobody responded to this modality k */
1.192 brouard 3626: break;
3627: }
3628: ij++;
1.197 brouard 3629: 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 3630: cptcode = ij; /* New max modality for covar j */
3631: } /* end of loop on modality i=-1 to 1 or more */
3632:
3633: /* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 *\//\* Could be 1 to 4 *\//\* cptcode=modmaxcovj *\/ */
3634: /* /\*recode from 0 *\/ */
3635: /* k is a modality. If we have model=V1+V1*sex */
3636: /* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
3637: /* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode *\/ */
3638: /* } */
3639: /* /\* cptcode = ij; *\/ /\* New max modality for covar j *\/ */
3640: /* if (ij > ncodemax[j]) { */
3641: /* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3642: /* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
3643: /* break; */
3644: /* } */
3645: /* } /\* end of loop on modality k *\/ */
1.137 brouard 3646: } /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/
3647:
1.145 brouard 3648: for (k=-1; k< maxncov; k++) Ndum[k]=0;
1.137 brouard 3649:
1.187 brouard 3650: for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually age*age */
1.145 brouard 3651: /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
3652: ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
1.187 brouard 3653: Ndum[ij]++; /* Might be supersed V1 + V1*age */
1.145 brouard 3654: }
1.126 brouard 3655:
1.192 brouard 3656: ij=0;
1.145 brouard 3657: for (i=0; i<= maxncov-1; i++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(age*V3), 5(V3*V2) 6(V1*V4) */
3658: /*printf("Ndum[%d]=%d\n",i, Ndum[i]);*/
1.126 brouard 3659: if((Ndum[i]!=0) && (i<=ncovcol)){
1.192 brouard 3660: ij++;
1.145 brouard 3661: /*printf("diff Ndum[%d]=%d\n",i, Ndum[i]);*/
3662: Tvaraff[ij]=i; /*For printing (unclear) */
1.192 brouard 3663: }else{
3664: /* Tvaraff[ij]=0; */
3665: }
1.126 brouard 3666: }
1.192 brouard 3667: /* ij--; */
1.144 brouard 3668: cptcoveff=ij; /*Number of total covariates*/
1.145 brouard 3669:
1.126 brouard 3670: }
3671:
1.145 brouard 3672:
1.126 brouard 3673: /*********** Health Expectancies ****************/
3674:
1.127 brouard 3675: 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 3676:
3677: {
3678: /* Health expectancies, no variances */
1.164 brouard 3679: int i, j, nhstepm, hstepm, h, nstepm;
1.126 brouard 3680: int nhstepma, nstepma; /* Decreasing with age */
3681: double age, agelim, hf;
3682: double ***p3mat;
3683: double eip;
3684:
3685: pstamp(ficreseij);
3686: fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
3687: fprintf(ficreseij,"# Age");
3688: for(i=1; i<=nlstate;i++){
3689: for(j=1; j<=nlstate;j++){
3690: fprintf(ficreseij," e%1d%1d ",i,j);
3691: }
3692: fprintf(ficreseij," e%1d. ",i);
3693: }
3694: fprintf(ficreseij,"\n");
3695:
3696:
3697: if(estepm < stepm){
3698: printf ("Problem %d lower than %d\n",estepm, stepm);
3699: }
3700: else hstepm=estepm;
3701: /* We compute the life expectancy from trapezoids spaced every estepm months
3702: * This is mainly to measure the difference between two models: for example
3703: * if stepm=24 months pijx are given only every 2 years and by summing them
3704: * we are calculating an estimate of the Life Expectancy assuming a linear
3705: * progression in between and thus overestimating or underestimating according
3706: * to the curvature of the survival function. If, for the same date, we
3707: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3708: * to compare the new estimate of Life expectancy with the same linear
3709: * hypothesis. A more precise result, taking into account a more precise
3710: * curvature will be obtained if estepm is as small as stepm. */
3711:
3712: /* For example we decided to compute the life expectancy with the smallest unit */
3713: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3714: nhstepm is the number of hstepm from age to agelim
3715: nstepm is the number of stepm from age to agelin.
3716: Look at hpijx to understand the reason of that which relies in memory size
3717: and note for a fixed period like estepm months */
3718: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3719: survival function given by stepm (the optimization length). Unfortunately it
3720: means that if the survival funtion is printed only each two years of age and if
3721: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3722: results. So we changed our mind and took the option of the best precision.
3723: */
3724: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3725:
3726: agelim=AGESUP;
3727: /* If stepm=6 months */
3728: /* Computed by stepm unit matrices, product of hstepm matrices, stored
3729: in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
3730:
3731: /* nhstepm age range expressed in number of stepm */
3732: nstepm=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3733: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3734: /* if (stepm >= YEARM) hstepm=1;*/
3735: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3736: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3737:
3738: for (age=bage; age<=fage; age ++){
3739: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3740: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3741: /* if (stepm >= YEARM) hstepm=1;*/
3742: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3743:
3744: /* If stepm=6 months */
3745: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3746: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3747:
3748: hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3749:
3750: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3751:
3752: printf("%d|",(int)age);fflush(stdout);
3753: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3754:
3755: /* Computing expectancies */
3756: for(i=1; i<=nlstate;i++)
3757: for(j=1; j<=nlstate;j++)
3758: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3759: eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
3760:
3761: /* 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]);*/
3762:
3763: }
3764:
3765: fprintf(ficreseij,"%3.0f",age );
3766: for(i=1; i<=nlstate;i++){
3767: eip=0;
3768: for(j=1; j<=nlstate;j++){
3769: eip +=eij[i][j][(int)age];
3770: fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
3771: }
3772: fprintf(ficreseij,"%9.4f", eip );
3773: }
3774: fprintf(ficreseij,"\n");
3775:
3776: }
3777: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3778: printf("\n");
3779: fprintf(ficlog,"\n");
3780:
3781: }
3782:
1.127 brouard 3783: 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 3784:
3785: {
3786: /* Covariances of health expectancies eij and of total life expectancies according
3787: to initial status i, ei. .
3788: */
3789: int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
3790: int nhstepma, nstepma; /* Decreasing with age */
3791: double age, agelim, hf;
3792: double ***p3matp, ***p3matm, ***varhe;
3793: double **dnewm,**doldm;
3794: double *xp, *xm;
3795: double **gp, **gm;
3796: double ***gradg, ***trgradg;
3797: int theta;
3798:
3799: double eip, vip;
3800:
3801: varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
3802: xp=vector(1,npar);
3803: xm=vector(1,npar);
3804: dnewm=matrix(1,nlstate*nlstate,1,npar);
3805: doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
3806:
3807: pstamp(ficresstdeij);
3808: fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
3809: fprintf(ficresstdeij,"# Age");
3810: for(i=1; i<=nlstate;i++){
3811: for(j=1; j<=nlstate;j++)
3812: fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
3813: fprintf(ficresstdeij," e%1d. ",i);
3814: }
3815: fprintf(ficresstdeij,"\n");
3816:
3817: pstamp(ficrescveij);
3818: fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
3819: fprintf(ficrescveij,"# Age");
3820: for(i=1; i<=nlstate;i++)
3821: for(j=1; j<=nlstate;j++){
3822: cptj= (j-1)*nlstate+i;
3823: for(i2=1; i2<=nlstate;i2++)
3824: for(j2=1; j2<=nlstate;j2++){
3825: cptj2= (j2-1)*nlstate+i2;
3826: if(cptj2 <= cptj)
3827: fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
3828: }
3829: }
3830: fprintf(ficrescveij,"\n");
3831:
3832: if(estepm < stepm){
3833: printf ("Problem %d lower than %d\n",estepm, stepm);
3834: }
3835: else hstepm=estepm;
3836: /* We compute the life expectancy from trapezoids spaced every estepm months
3837: * This is mainly to measure the difference between two models: for example
3838: * if stepm=24 months pijx are given only every 2 years and by summing them
3839: * we are calculating an estimate of the Life Expectancy assuming a linear
3840: * progression in between and thus overestimating or underestimating according
3841: * to the curvature of the survival function. If, for the same date, we
3842: * estimate the model with stepm=1 month, we can keep estepm to 24 months
3843: * to compare the new estimate of Life expectancy with the same linear
3844: * hypothesis. A more precise result, taking into account a more precise
3845: * curvature will be obtained if estepm is as small as stepm. */
3846:
3847: /* For example we decided to compute the life expectancy with the smallest unit */
3848: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
3849: nhstepm is the number of hstepm from age to agelim
3850: nstepm is the number of stepm from age to agelin.
3851: Look at hpijx to understand the reason of that which relies in memory size
3852: and note for a fixed period like estepm months */
3853: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
3854: survival function given by stepm (the optimization length). Unfortunately it
3855: means that if the survival funtion is printed only each two years of age and if
3856: you sum them up and add 1 year (area under the trapezoids) you won't get the same
3857: results. So we changed our mind and took the option of the best precision.
3858: */
3859: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
3860:
3861: /* If stepm=6 months */
3862: /* nhstepm age range expressed in number of stepm */
3863: agelim=AGESUP;
3864: nstepm=(int) rint((agelim-bage)*YEARM/stepm);
3865: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3866: /* if (stepm >= YEARM) hstepm=1;*/
3867: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
3868:
3869: p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3870: p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3871: gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
3872: trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
3873: gp=matrix(0,nhstepm,1,nlstate*nlstate);
3874: gm=matrix(0,nhstepm,1,nlstate*nlstate);
3875:
3876: for (age=bage; age<=fage; age ++){
3877: nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
3878: /* Typically if 20 years nstepm = 20*12/6=40 stepm */
3879: /* if (stepm >= YEARM) hstepm=1;*/
3880: nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
3881:
3882: /* If stepm=6 months */
3883: /* Computed by stepm unit matrices, product of hstepma matrices, stored
3884: in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
3885:
3886: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
3887:
3888: /* Computing Variances of health expectancies */
3889: /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
3890: decrease memory allocation */
3891: for(theta=1; theta <=npar; theta++){
3892: for(i=1; i<=npar; i++){
3893: xp[i] = x[i] + (i==theta ?delti[theta]:0);
3894: xm[i] = x[i] - (i==theta ?delti[theta]:0);
3895: }
3896: hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
3897: hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
3898:
3899: for(j=1; j<= nlstate; j++){
3900: for(i=1; i<=nlstate; i++){
3901: for(h=0; h<=nhstepm-1; h++){
3902: gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
3903: gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
3904: }
3905: }
3906: }
3907:
3908: for(ij=1; ij<= nlstate*nlstate; ij++)
3909: for(h=0; h<=nhstepm-1; h++){
3910: gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
3911: }
3912: }/* End theta */
3913:
3914:
3915: for(h=0; h<=nhstepm-1; h++)
3916: for(j=1; j<=nlstate*nlstate;j++)
3917: for(theta=1; theta <=npar; theta++)
3918: trgradg[h][j][theta]=gradg[h][theta][j];
3919:
3920:
3921: for(ij=1;ij<=nlstate*nlstate;ij++)
3922: for(ji=1;ji<=nlstate*nlstate;ji++)
3923: varhe[ij][ji][(int)age] =0.;
3924:
3925: printf("%d|",(int)age);fflush(stdout);
3926: fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
3927: for(h=0;h<=nhstepm-1;h++){
3928: for(k=0;k<=nhstepm-1;k++){
3929: matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
3930: matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
3931: for(ij=1;ij<=nlstate*nlstate;ij++)
3932: for(ji=1;ji<=nlstate*nlstate;ji++)
3933: varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
3934: }
3935: }
3936:
3937: /* Computing expectancies */
3938: hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
3939: for(i=1; i<=nlstate;i++)
3940: for(j=1; j<=nlstate;j++)
3941: for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
3942: eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
3943:
3944: /* 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]);*/
3945:
3946: }
3947:
3948: fprintf(ficresstdeij,"%3.0f",age );
3949: for(i=1; i<=nlstate;i++){
3950: eip=0.;
3951: vip=0.;
3952: for(j=1; j<=nlstate;j++){
3953: eip += eij[i][j][(int)age];
3954: for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
3955: vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
3956: fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
3957: }
3958: fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
3959: }
3960: fprintf(ficresstdeij,"\n");
3961:
3962: fprintf(ficrescveij,"%3.0f",age );
3963: for(i=1; i<=nlstate;i++)
3964: for(j=1; j<=nlstate;j++){
3965: cptj= (j-1)*nlstate+i;
3966: for(i2=1; i2<=nlstate;i2++)
3967: for(j2=1; j2<=nlstate;j2++){
3968: cptj2= (j2-1)*nlstate+i2;
3969: if(cptj2 <= cptj)
3970: fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
3971: }
3972: }
3973: fprintf(ficrescveij,"\n");
3974:
3975: }
3976: free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
3977: free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
3978: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
3979: free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
3980: free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3981: free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
3982: printf("\n");
3983: fprintf(ficlog,"\n");
3984:
3985: free_vector(xm,1,npar);
3986: free_vector(xp,1,npar);
3987: free_matrix(dnewm,1,nlstate*nlstate,1,npar);
3988: free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
3989: free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
3990: }
3991:
3992: /************ Variance ******************/
1.203 brouard 3993: 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 3994: {
3995: /* Variance of health expectancies */
3996: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
3997: /* double **newm;*/
1.169 brouard 3998: /* int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav)*/
3999:
4000: int movingaverage();
1.126 brouard 4001: double **dnewm,**doldm;
4002: double **dnewmp,**doldmp;
4003: int i, j, nhstepm, hstepm, h, nstepm ;
1.164 brouard 4004: int k;
1.126 brouard 4005: double *xp;
4006: double **gp, **gm; /* for var eij */
4007: double ***gradg, ***trgradg; /*for var eij */
4008: double **gradgp, **trgradgp; /* for var p point j */
4009: double *gpp, *gmp; /* for var p point j */
4010: double **varppt; /* for var p point j nlstate to nlstate+ndeath */
4011: double ***p3mat;
4012: double age,agelim, hf;
4013: double ***mobaverage;
4014: int theta;
4015: char digit[4];
4016: char digitp[25];
4017:
4018: char fileresprobmorprev[FILENAMELENGTH];
4019:
4020: if(popbased==1){
4021: if(mobilav!=0)
1.201 brouard 4022: strcpy(digitp,"-POPULBASED-MOBILAV_");
4023: else strcpy(digitp,"-POPULBASED-NOMOBIL_");
1.126 brouard 4024: }
4025: else
1.201 brouard 4026: strcpy(digitp,"-STABLBASED_");
1.126 brouard 4027:
4028: if (mobilav!=0) {
4029: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4030: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
4031: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
4032: printf(" Error in movingaverage mobilav=%d\n",mobilav);
4033: }
4034: }
4035:
1.201 brouard 4036: strcpy(fileresprobmorprev,"PRMORPREV-");
1.126 brouard 4037: sprintf(digit,"%-d",ij);
4038: /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
4039: strcat(fileresprobmorprev,digit); /* Tvar to be done */
4040: strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
1.202 brouard 4041: strcat(fileresprobmorprev,fileresu);
1.126 brouard 4042: if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
4043: printf("Problem with resultfile: %s\n", fileresprobmorprev);
4044: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
4045: }
4046: printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4047:
4048: fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
4049: pstamp(ficresprobmorprev);
4050: 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);
4051: fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
4052: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4053: fprintf(ficresprobmorprev," p.%-d SE",j);
4054: for(i=1; i<=nlstate;i++)
4055: fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
4056: }
4057: fprintf(ficresprobmorprev,"\n");
4058: fprintf(ficgp,"\n# Routine varevsij");
1.200 brouard 4059: fprintf(ficgp,"\nunset title \n");
4060: /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
1.126 brouard 4061: 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");
4062: fprintf(fichtm,"\n<br>%s <br>\n",digitp);
4063: /* } */
4064: varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4065: pstamp(ficresvij);
4066: fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
4067: if(popbased==1)
1.128 brouard 4068: 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 4069: else
4070: fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
4071: fprintf(ficresvij,"# Age");
4072: for(i=1; i<=nlstate;i++)
4073: for(j=1; j<=nlstate;j++)
4074: fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
4075: fprintf(ficresvij,"\n");
4076:
4077: xp=vector(1,npar);
4078: dnewm=matrix(1,nlstate,1,npar);
4079: doldm=matrix(1,nlstate,1,nlstate);
4080: dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
4081: doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4082:
4083: gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
4084: gpp=vector(nlstate+1,nlstate+ndeath);
4085: gmp=vector(nlstate+1,nlstate+ndeath);
4086: trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
4087:
4088: if(estepm < stepm){
4089: printf ("Problem %d lower than %d\n",estepm, stepm);
4090: }
4091: else hstepm=estepm;
4092: /* For example we decided to compute the life expectancy with the smallest unit */
4093: /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
4094: nhstepm is the number of hstepm from age to agelim
4095: nstepm is the number of stepm from age to agelin.
1.128 brouard 4096: Look at function hpijx to understand why (it is linked to memory size questions) */
1.126 brouard 4097: /* We decided (b) to get a life expectancy respecting the most precise curvature of the
4098: survival function given by stepm (the optimization length). Unfortunately it
4099: means that if the survival funtion is printed every two years of age and if
4100: you sum them up and add 1 year (area under the trapezoids) you won't get the same
4101: results. So we changed our mind and took the option of the best precision.
4102: */
4103: hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
4104: agelim = AGESUP;
4105: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4106: nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4107: nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
4108: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4109: gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
4110: gp=matrix(0,nhstepm,1,nlstate);
4111: gm=matrix(0,nhstepm,1,nlstate);
4112:
4113:
4114: for(theta=1; theta <=npar; theta++){
4115: for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
4116: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4117: }
4118: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4119: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4120:
4121: if (popbased==1) {
4122: if(mobilav ==0){
4123: for(i=1; i<=nlstate;i++)
4124: prlim[i][i]=probs[(int)age][i][ij];
4125: }else{ /* mobilav */
4126: for(i=1; i<=nlstate;i++)
4127: prlim[i][i]=mobaverage[(int)age][i][ij];
4128: }
4129: }
4130:
4131: for(j=1; j<= nlstate; j++){
4132: for(h=0; h<=nhstepm; h++){
4133: for(i=1, gp[h][j]=0.;i<=nlstate;i++)
4134: gp[h][j] += prlim[i][i]*p3mat[i][j][h];
4135: }
4136: }
4137: /* This for computing probability of death (h=1 means
4138: computed over hstepm matrices product = hstepm*stepm months)
4139: as a weighted average of prlim.
4140: */
4141: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4142: for(i=1,gpp[j]=0.; i<= nlstate; i++)
4143: gpp[j] += prlim[i][i]*p3mat[i][j][1];
4144: }
4145: /* end probability of death */
4146:
4147: for(i=1; i<=npar; i++) /* Computes gradient x - delta */
4148: xp[i] = x[i] - (i==theta ?delti[theta]:0);
4149: hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4150: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear, ij);
1.126 brouard 4151:
4152: if (popbased==1) {
4153: if(mobilav ==0){
4154: for(i=1; i<=nlstate;i++)
4155: prlim[i][i]=probs[(int)age][i][ij];
4156: }else{ /* mobilav */
4157: for(i=1; i<=nlstate;i++)
4158: prlim[i][i]=mobaverage[(int)age][i][ij];
4159: }
4160: }
4161:
1.128 brouard 4162: for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
1.126 brouard 4163: for(h=0; h<=nhstepm; h++){
4164: for(i=1, gm[h][j]=0.;i<=nlstate;i++)
4165: gm[h][j] += prlim[i][i]*p3mat[i][j][h];
4166: }
4167: }
4168: /* This for computing probability of death (h=1 means
4169: computed over hstepm matrices product = hstepm*stepm months)
4170: as a weighted average of prlim.
4171: */
4172: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4173: for(i=1,gmp[j]=0.; i<= nlstate; i++)
4174: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4175: }
4176: /* end probability of death */
4177:
4178: for(j=1; j<= nlstate; j++) /* vareij */
4179: for(h=0; h<=nhstepm; h++){
4180: gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
4181: }
4182:
4183: for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
4184: gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
4185: }
4186:
4187: } /* End theta */
4188:
4189: trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
4190:
4191: for(h=0; h<=nhstepm; h++) /* veij */
4192: for(j=1; j<=nlstate;j++)
4193: for(theta=1; theta <=npar; theta++)
4194: trgradg[h][j][theta]=gradg[h][theta][j];
4195:
4196: for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
4197: for(theta=1; theta <=npar; theta++)
4198: trgradgp[j][theta]=gradgp[theta][j];
4199:
4200:
4201: hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
4202: for(i=1;i<=nlstate;i++)
4203: for(j=1;j<=nlstate;j++)
4204: vareij[i][j][(int)age] =0.;
4205:
4206: for(h=0;h<=nhstepm;h++){
4207: for(k=0;k<=nhstepm;k++){
4208: matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
4209: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
4210: for(i=1;i<=nlstate;i++)
4211: for(j=1;j<=nlstate;j++)
4212: vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
4213: }
4214: }
4215:
4216: /* pptj */
4217: matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
4218: matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
4219: for(j=nlstate+1;j<=nlstate+ndeath;j++)
4220: for(i=nlstate+1;i<=nlstate+ndeath;i++)
4221: varppt[j][i]=doldmp[j][i];
4222: /* end ppptj */
4223: /* x centered again */
4224: hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
1.203 brouard 4225: prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4226:
4227: if (popbased==1) {
4228: if(mobilav ==0){
4229: for(i=1; i<=nlstate;i++)
4230: prlim[i][i]=probs[(int)age][i][ij];
4231: }else{ /* mobilav */
4232: for(i=1; i<=nlstate;i++)
4233: prlim[i][i]=mobaverage[(int)age][i][ij];
4234: }
4235: }
4236:
4237: /* This for computing probability of death (h=1 means
4238: computed over hstepm (estepm) matrices product = hstepm*stepm months)
4239: as a weighted average of prlim.
4240: */
4241: for(j=nlstate+1;j<=nlstate+ndeath;j++){
4242: for(i=1,gmp[j]=0.;i<= nlstate; i++)
4243: gmp[j] += prlim[i][i]*p3mat[i][j][1];
4244: }
4245: /* end probability of death */
4246:
4247: fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
4248: for(j=nlstate+1; j<=(nlstate+ndeath);j++){
4249: fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
4250: for(i=1; i<=nlstate;i++){
4251: fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
4252: }
4253: }
4254: fprintf(ficresprobmorprev,"\n");
4255:
4256: fprintf(ficresvij,"%.0f ",age );
4257: for(i=1; i<=nlstate;i++)
4258: for(j=1; j<=nlstate;j++){
4259: fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
4260: }
4261: fprintf(ficresvij,"\n");
4262: free_matrix(gp,0,nhstepm,1,nlstate);
4263: free_matrix(gm,0,nhstepm,1,nlstate);
4264: free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
4265: free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
4266: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
4267: } /* End age */
4268: free_vector(gpp,nlstate+1,nlstate+ndeath);
4269: free_vector(gmp,nlstate+1,nlstate+ndeath);
4270: free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
4271: free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
1.199 brouard 4272: /* fprintf(ficgp,"\nunset parametric;unset label; set ter png small size 320, 240"); */
4273: fprintf(ficgp,"\nunset parametric;unset label; set ter svg size 640, 480");
1.126 brouard 4274: /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
1.131 brouard 4275: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
1.201 brouard 4276: fprintf(ficgp,"\nset out \"%s%s.svg\";",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4277: /* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
4278: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
4279: /* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
1.145 brouard 4280: fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l lt 1 ",subdirf(fileresprobmorprev));
1.170 brouard 4281: fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95%% interval\" w l lt 2 ",subdirf(fileresprobmorprev));
1.145 brouard 4282: fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l lt 2 ",subdirf(fileresprobmorprev));
1.126 brouard 4283: 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 4284: 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 4285: /* 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 4286: */
1.199 brouard 4287: /* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.svg\";replot;",digitp,optionfilefiname,digit); */
1.201 brouard 4288: fprintf(ficgp,"\nset out;\nset out \"%s%s.svg\";replot;set out;\n",subdirf3(optionfilefiname,"VARMUPTJGR-",digitp),digit);
1.126 brouard 4289:
4290: free_vector(xp,1,npar);
4291: free_matrix(doldm,1,nlstate,1,nlstate);
4292: free_matrix(dnewm,1,nlstate,1,npar);
4293: free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4294: free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
4295: free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
4296: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
4297: fclose(ficresprobmorprev);
4298: fflush(ficgp);
4299: fflush(fichtm);
4300: } /* end varevsij */
4301:
4302: /************ Variance of prevlim ******************/
1.203 brouard 4303: 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 4304: {
1.205 brouard 4305: /* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
1.126 brouard 4306: /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
1.164 brouard 4307:
1.126 brouard 4308: double **dnewm,**doldm;
4309: int i, j, nhstepm, hstepm;
4310: double *xp;
4311: double *gp, *gm;
4312: double **gradg, **trgradg;
4313: double age,agelim;
4314: int theta;
4315:
4316: pstamp(ficresvpl);
4317: fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
4318: fprintf(ficresvpl,"# Age");
4319: for(i=1; i<=nlstate;i++)
4320: fprintf(ficresvpl," %1d-%1d",i,i);
4321: fprintf(ficresvpl,"\n");
4322:
4323: xp=vector(1,npar);
4324: dnewm=matrix(1,nlstate,1,npar);
4325: doldm=matrix(1,nlstate,1,nlstate);
4326:
4327: hstepm=1*YEARM; /* Every year of age */
4328: hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
4329: agelim = AGESUP;
4330: for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
4331: nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
4332: if (stepm >= YEARM) hstepm=1;
4333: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
4334: gradg=matrix(1,npar,1,nlstate);
4335: gp=vector(1,nlstate);
4336: gm=vector(1,nlstate);
4337:
4338: for(theta=1; theta <=npar; theta++){
4339: for(i=1; i<=npar; i++){ /* Computes gradient */
4340: xp[i] = x[i] + (i==theta ?delti[theta]:0);
4341: }
1.203 brouard 4342: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4343: for(i=1;i<=nlstate;i++)
4344: gp[i] = prlim[i][i];
4345:
4346: for(i=1; i<=npar; i++) /* Computes gradient */
4347: xp[i] = x[i] - (i==theta ?delti[theta]:0);
1.203 brouard 4348: prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyear,ij);
1.126 brouard 4349: for(i=1;i<=nlstate;i++)
4350: gm[i] = prlim[i][i];
4351:
4352: for(i=1;i<=nlstate;i++)
4353: gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
4354: } /* End theta */
4355:
4356: trgradg =matrix(1,nlstate,1,npar);
4357:
4358: for(j=1; j<=nlstate;j++)
4359: for(theta=1; theta <=npar; theta++)
4360: trgradg[j][theta]=gradg[theta][j];
4361:
4362: for(i=1;i<=nlstate;i++)
4363: varpl[i][(int)age] =0.;
1.205 brouard 4364: if((int)age==67 ||(int)age== 66 ){
4365: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4366: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
4367: }else{
1.126 brouard 4368: matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
4369: matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
1.205 brouard 4370: }
1.126 brouard 4371: for(i=1;i<=nlstate;i++)
4372: varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
4373:
4374: fprintf(ficresvpl,"%.0f ",age );
4375: for(i=1; i<=nlstate;i++)
4376: fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
4377: fprintf(ficresvpl,"\n");
4378: free_vector(gp,1,nlstate);
4379: free_vector(gm,1,nlstate);
4380: free_matrix(gradg,1,npar,1,nlstate);
4381: free_matrix(trgradg,1,nlstate,1,npar);
4382: } /* End age */
4383:
4384: free_vector(xp,1,npar);
4385: free_matrix(doldm,1,nlstate,1,npar);
4386: free_matrix(dnewm,1,nlstate,1,nlstate);
4387:
4388: }
4389:
4390: /************ Variance of one-step probabilities ******************/
4391: 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[])
4392: {
1.164 brouard 4393: int i, j=0, k1, l1, tj;
1.126 brouard 4394: int k2, l2, j1, z1;
1.164 brouard 4395: int k=0, l;
1.145 brouard 4396: int first=1, first1, first2;
1.126 brouard 4397: double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
4398: double **dnewm,**doldm;
4399: double *xp;
4400: double *gp, *gm;
4401: double **gradg, **trgradg;
4402: double **mu;
1.164 brouard 4403: double age, cov[NCOVMAX+1];
1.126 brouard 4404: double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
4405: int theta;
4406: char fileresprob[FILENAMELENGTH];
4407: char fileresprobcov[FILENAMELENGTH];
4408: char fileresprobcor[FILENAMELENGTH];
4409: double ***varpij;
4410:
1.201 brouard 4411: strcpy(fileresprob,"PROB_");
1.126 brouard 4412: strcat(fileresprob,fileres);
4413: if((ficresprob=fopen(fileresprob,"w"))==NULL) {
4414: printf("Problem with resultfile: %s\n", fileresprob);
4415: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
4416: }
1.201 brouard 4417: strcpy(fileresprobcov,"PROBCOV_");
1.202 brouard 4418: strcat(fileresprobcov,fileresu);
1.126 brouard 4419: if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
4420: printf("Problem with resultfile: %s\n", fileresprobcov);
4421: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
4422: }
1.201 brouard 4423: strcpy(fileresprobcor,"PROBCOR_");
1.202 brouard 4424: strcat(fileresprobcor,fileresu);
1.126 brouard 4425: if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
4426: printf("Problem with resultfile: %s\n", fileresprobcor);
4427: fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
4428: }
4429: printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4430: fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
4431: printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4432: fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
4433: printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4434: fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
4435: pstamp(ficresprob);
4436: fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
4437: fprintf(ficresprob,"# Age");
4438: pstamp(ficresprobcov);
4439: fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
4440: fprintf(ficresprobcov,"# Age");
4441: pstamp(ficresprobcor);
4442: fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
4443: fprintf(ficresprobcor,"# Age");
4444:
4445:
4446: for(i=1; i<=nlstate;i++)
4447: for(j=1; j<=(nlstate+ndeath);j++){
4448: fprintf(ficresprob," p%1d-%1d (SE)",i,j);
4449: fprintf(ficresprobcov," p%1d-%1d ",i,j);
4450: fprintf(ficresprobcor," p%1d-%1d ",i,j);
4451: }
4452: /* fprintf(ficresprob,"\n");
4453: fprintf(ficresprobcov,"\n");
4454: fprintf(ficresprobcor,"\n");
4455: */
1.131 brouard 4456: xp=vector(1,npar);
1.126 brouard 4457: dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4458: doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4459: mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
4460: varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
4461: first=1;
4462: fprintf(ficgp,"\n# Routine varprob");
4463: fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
4464: fprintf(fichtm,"\n");
4465:
1.200 brouard 4466: 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 4467: 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);
4468: fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
1.126 brouard 4469: and drawn. It helps understanding how is the covariance between two incidences.\
4470: They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
4471: 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. \
4472: It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
4473: would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
4474: standard deviations wide on each axis. <br>\
4475: Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
4476: and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
4477: To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
4478:
4479: cov[1]=1;
1.145 brouard 4480: /* tj=cptcoveff; */
4481: tj = (int) pow(2,cptcoveff);
1.126 brouard 4482: if (cptcovn<1) {tj=1;ncodemax[1]=1;}
4483: j1=0;
1.145 brouard 4484: for(j1=1; j1<=tj;j1++){
4485: /*for(i1=1; i1<=ncodemax[t];i1++){ */
4486: /*j1++;*/
1.126 brouard 4487: if (cptcovn>0) {
4488: fprintf(ficresprob, "\n#********** Variable ");
1.198 brouard 4489: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4490: fprintf(ficresprob, "**********\n#\n");
4491: fprintf(ficresprobcov, "\n#********** Variable ");
1.198 brouard 4492: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4493: fprintf(ficresprobcov, "**********\n#\n");
4494:
4495: fprintf(ficgp, "\n#********** Variable ");
1.198 brouard 4496: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4497: fprintf(ficgp, "**********\n#\n");
4498:
4499:
4500: fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
1.198 brouard 4501: for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4502: fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
4503:
4504: fprintf(ficresprobcor, "\n#********** Variable ");
1.198 brouard 4505: for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
1.126 brouard 4506: fprintf(ficresprobcor, "**********\n#");
4507: }
4508:
1.145 brouard 4509: gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
4510: trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
4511: gp=vector(1,(nlstate)*(nlstate+ndeath));
4512: gm=vector(1,(nlstate)*(nlstate+ndeath));
1.126 brouard 4513: for (age=bage; age<=fage; age ++){
4514: cov[2]=age;
1.187 brouard 4515: if(nagesqr==1)
4516: cov[3]= age*age;
1.126 brouard 4517: for (k=1; k<=cptcovn;k++) {
1.200 brouard 4518: cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];
4519: /*cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];*//* j1 1 2 3 4
1.145 brouard 4520: * 1 1 1 1 1
4521: * 2 2 1 1 1
4522: * 3 1 2 1 1
4523: */
4524: /* nbcode[1][1]=0 nbcode[1][2]=1;*/
1.126 brouard 4525: }
1.186 brouard 4526: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2]; */
1.200 brouard 4527: for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
1.126 brouard 4528: for (k=1; k<=cptcovprod;k++)
1.200 brouard 4529: cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
1.126 brouard 4530:
4531:
4532: for(theta=1; theta <=npar; theta++){
4533: for(i=1; i<=npar; i++)
4534: xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
4535:
4536: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4537:
4538: k=0;
4539: for(i=1; i<= (nlstate); i++){
4540: for(j=1; j<=(nlstate+ndeath);j++){
4541: k=k+1;
4542: gp[k]=pmmij[i][j];
4543: }
4544: }
4545:
4546: for(i=1; i<=npar; i++)
4547: xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
4548:
4549: pmij(pmmij,cov,ncovmodel,xp,nlstate);
4550: k=0;
4551: for(i=1; i<=(nlstate); i++){
4552: for(j=1; j<=(nlstate+ndeath);j++){
4553: k=k+1;
4554: gm[k]=pmmij[i][j];
4555: }
4556: }
4557:
4558: for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
4559: gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
4560: }
4561:
4562: for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
4563: for(theta=1; theta <=npar; theta++)
4564: trgradg[j][theta]=gradg[theta][j];
4565:
4566: matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
4567: matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
4568:
4569: pmij(pmmij,cov,ncovmodel,x,nlstate);
4570:
4571: k=0;
4572: for(i=1; i<=(nlstate); i++){
4573: for(j=1; j<=(nlstate+ndeath);j++){
4574: k=k+1;
4575: mu[k][(int) age]=pmmij[i][j];
4576: }
4577: }
4578: for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
4579: for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
4580: varpij[i][j][(int)age] = doldm[i][j];
4581:
4582: /*printf("\n%d ",(int)age);
4583: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4584: printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4585: fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
4586: }*/
4587:
4588: fprintf(ficresprob,"\n%d ",(int)age);
4589: fprintf(ficresprobcov,"\n%d ",(int)age);
4590: fprintf(ficresprobcor,"\n%d ",(int)age);
4591:
4592: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
4593: fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
4594: for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
4595: fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
4596: fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
4597: }
4598: i=0;
4599: for (k=1; k<=(nlstate);k++){
4600: for (l=1; l<=(nlstate+ndeath);l++){
1.145 brouard 4601: i++;
1.126 brouard 4602: fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
4603: fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
4604: for (j=1; j<=i;j++){
1.145 brouard 4605: /* printf(" k=%d l=%d i=%d j=%d\n",k,l,i,j);fflush(stdout); */
1.126 brouard 4606: fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
4607: fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
4608: }
4609: }
4610: }/* end of loop for state */
4611: } /* end of loop for age */
1.145 brouard 4612: free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
4613: free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
4614: free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4615: free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
4616:
1.126 brouard 4617: /* Confidence intervalle of pij */
4618: /*
1.131 brouard 4619: fprintf(ficgp,"\nunset parametric;unset label");
1.126 brouard 4620: fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
4621: fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
4622: 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);
4623: fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
4624: fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
4625: fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
4626: */
4627:
4628: /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
1.145 brouard 4629: first1=1;first2=2;
1.126 brouard 4630: for (k2=1; k2<=(nlstate);k2++){
4631: for (l2=1; l2<=(nlstate+ndeath);l2++){
4632: if(l2==k2) continue;
4633: j=(k2-1)*(nlstate+ndeath)+l2;
4634: for (k1=1; k1<=(nlstate);k1++){
4635: for (l1=1; l1<=(nlstate+ndeath);l1++){
4636: if(l1==k1) continue;
4637: i=(k1-1)*(nlstate+ndeath)+l1;
4638: if(i<=j) continue;
4639: for (age=bage; age<=fage; age ++){
4640: if ((int)age %5==0){
4641: v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
4642: v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
4643: cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
4644: mu1=mu[i][(int) age]/stepm*YEARM ;
4645: mu2=mu[j][(int) age]/stepm*YEARM;
4646: c12=cv12/sqrt(v1*v2);
4647: /* Computing eigen value of matrix of covariance */
4648: lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
4649: lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
1.135 brouard 4650: if ((lc2 <0) || (lc1 <0) ){
1.145 brouard 4651: if(first2==1){
4652: first1=0;
4653: 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);
4654: }
4655: 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);
4656: /* lc1=fabs(lc1); */ /* If we want to have them positive */
4657: /* lc2=fabs(lc2); */
1.135 brouard 4658: }
4659:
1.126 brouard 4660: /* Eigen vectors */
4661: v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
4662: /*v21=sqrt(1.-v11*v11); *//* error */
4663: v21=(lc1-v1)/cv12*v11;
4664: v12=-v21;
4665: v22=v11;
4666: tnalp=v21/v11;
4667: if(first1==1){
4668: first1=0;
4669: 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);
4670: }
4671: 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);
4672: /*printf(fignu*/
4673: /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
4674: /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
4675: if(first==1){
4676: first=0;
1.200 brouard 4677: fprintf(ficgp,"\n# Ellipsoids of confidence\n#\n");
1.126 brouard 4678: fprintf(ficgp,"\nset parametric;unset label");
4679: 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 4680: fprintf(ficgp,"\nset ter svg size 640, 480");
1.126 brouard 4681: fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
1.201 brouard 4682: :<a href=\"%s_%d%1d%1d-%1d%1d.svg\">\
4683: %s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
4684: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2,\
4685: subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
4686: fprintf(fichtmcov,"\n<br><img src=\"%s_%d%1d%1d-%1d%1d.svg\"> ",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4687: fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
1.201 brouard 4688: fprintf(ficgp,"\nset out \"%s_%d%1d%1d-%1d%1d.svg\"",subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2);
1.126 brouard 4689: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4690: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4691: 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",\
4692: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4693: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4694: }else{
4695: first=0;
4696: fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
4697: fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
4698: fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
4699: 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",\
4700: mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
4701: mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
4702: }/* if first */
4703: } /* age mod 5 */
4704: } /* end loop age */
1.201 brouard 4705: 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 4706: first=1;
4707: } /*l12 */
4708: } /* k12 */
4709: } /*l1 */
4710: }/* k1 */
1.169 brouard 4711: /* } */ /* loop covariates */
1.126 brouard 4712: }
4713: free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
4714: free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
4715: free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
4716: free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
4717: free_vector(xp,1,npar);
4718: fclose(ficresprob);
4719: fclose(ficresprobcov);
4720: fclose(ficresprobcor);
4721: fflush(ficgp);
4722: fflush(fichtmcov);
4723: }
4724:
4725:
4726: /******************* Printing html file ***********/
1.201 brouard 4727: void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 4728: int lastpass, int stepm, int weightopt, char model[],\
4729: int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
4730: int popforecast, int estepm ,\
4731: double jprev1, double mprev1,double anprev1, \
4732: double jprev2, double mprev2,double anprev2){
4733: int jj1, k1, i1, cpt;
4734:
4735: fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
4736: <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
4737: </ul>");
4738: fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
4739: - 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 4740: jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
1.126 brouard 4741: fprintf(fichtm,"\
4742: - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
1.201 brouard 4743: stepm,subdirf2(fileresu,"PIJ_"),subdirf2(fileresu,"PIJ_"));
1.126 brouard 4744: fprintf(fichtm,"\
4745: - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4746: subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
1.126 brouard 4747: fprintf(fichtm,"\
1.128 brouard 4748: - (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 4749: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4750: estepm,subdirf2(fileresu,"E_"),subdirf2(fileresu,"E_"));
1.126 brouard 4751: fprintf(fichtm,"\
4752: - Population projections by age and states: \
1.201 brouard 4753: <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
1.126 brouard 4754:
4755: fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
4756:
1.145 brouard 4757: m=pow(2,cptcoveff);
1.126 brouard 4758: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4759:
4760: jj1=0;
4761: for(k1=1; k1<=m;k1++){
1.192 brouard 4762: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4763: jj1++;
4764: if (cptcovn > 0) {
4765: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
1.192 brouard 4766: for (cpt=1; cpt<=cptcoveff;cpt++){
1.198 brouard 4767: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
4768: printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);
1.192 brouard 4769: }
1.126 brouard 4770: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4771: }
1.201 brouard 4772: /* aij, bij */
4773: 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> \
4774: <img src=\"%s_%d-1.svg\">",subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4775: /* Pij */
1.202 brouard 4776: 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 4777: <img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
1.126 brouard 4778: /* Quasi-incidences */
1.201 brouard 4779: fprintf(fichtm,"<br>\n- Iij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
4780: before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too,\
4781: incidence (rates) are the limit when h tends to zero of the ratio of the probability hPij \
4782: divided by h: hPij/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \
4783: <img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);
4784: /* Survival functions (period) in state j */
4785: for(cpt=1; cpt<=nlstate;cpt++){
4786: 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> \
4787: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);
4788: }
4789: /* State specific survival functions (period) */
4790: for(cpt=1; cpt<=nlstate;cpt++){
4791: fprintf(fichtm,"<br>\n- Survival functions from state %d in any different live states and total.\
4792: Or probability to survive in various states (1 to %d) being in state %d at different ages.\
4793: <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);
4794: }
4795: /* Period (stable) prevalence in each health state */
4796: for(cpt=1; cpt<=nlstate;cpt++){
4797: 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> \
4798: <img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);
4799: }
1.126 brouard 4800: for(cpt=1; cpt<=nlstate;cpt++) {
1.205 brouard 4801: 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 4802: <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 4803: }
1.192 brouard 4804: /* } /\* end i1 *\/ */
1.126 brouard 4805: }/* End k1 */
4806: fprintf(fichtm,"</ul>");
4807:
4808: fprintf(fichtm,"\
4809: \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
1.193 brouard 4810: - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br> \
1.203 brouard 4811: - 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 4812: But because parameters are usually highly correlated (a higher incidence of disability \
4813: and a higher incidence of recovery can give very close observed transition) it might \
4814: be very useful to look not only at linear confidence intervals estimated from the \
4815: variances but at the covariance matrix. And instead of looking at the estimated coefficients \
4816: (parameters) of the logistic regression, it might be more meaningful to visualize the \
4817: covariance matrix of the one-step probabilities. \
4818: See page 'Matrix of variance-covariance of one-step probabilities' below. \n", rfileres,rfileres);
1.126 brouard 4819:
1.193 brouard 4820: fprintf(fichtm," - Standard deviation of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4821: subdirf2(fileresu,"PROB_"),subdirf2(fileresu,"PROB_"));
1.126 brouard 4822: fprintf(fichtm,"\
4823: - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4824: subdirf2(fileresu,"PROBCOV_"),subdirf2(fileresu,"PROBCOV_"));
1.126 brouard 4825:
4826: fprintf(fichtm,"\
4827: - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
1.201 brouard 4828: subdirf2(fileresu,"PROBCOR_"),subdirf2(fileresu,"PROBCOR_"));
1.126 brouard 4829: fprintf(fichtm,"\
4830: - 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): \
4831: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4832: estepm,subdirf2(fileresu,"CVE_"),subdirf2(fileresu,"CVE_"));
1.126 brouard 4833: fprintf(fichtm,"\
4834: - (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): \
4835: <a href=\"%s\">%s</a> <br>\n</li>",
1.201 brouard 4836: estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
1.126 brouard 4837: fprintf(fichtm,"\
1.128 brouard 4838: - 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 4839: estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
1.126 brouard 4840: fprintf(fichtm,"\
1.128 brouard 4841: - 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 4842: estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
1.126 brouard 4843: fprintf(fichtm,"\
4844: - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
1.201 brouard 4845: subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
1.126 brouard 4846:
4847: /* if(popforecast==1) fprintf(fichtm,"\n */
4848: /* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
4849: /* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
4850: /* <br>",fileres,fileres,fileres,fileres); */
4851: /* else */
4852: /* 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); */
4853: fflush(fichtm);
4854: fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
4855:
1.145 brouard 4856: m=pow(2,cptcoveff);
1.126 brouard 4857: if (cptcovn < 1) {m=1;ncodemax[1]=1;}
4858:
4859: jj1=0;
4860: for(k1=1; k1<=m;k1++){
1.192 brouard 4861: /* for(i1=1; i1<=ncodemax[k1];i1++){ */
1.126 brouard 4862: jj1++;
4863: if (cptcovn > 0) {
4864: fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
4865: for (cpt=1; cpt<=cptcoveff;cpt++)
1.198 brouard 4866: fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);
1.126 brouard 4867: fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
4868: }
4869: for(cpt=1; cpt<=nlstate;cpt++) {
4870: fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
1.205 brouard 4871: prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d%d.svg\"> %s_%d-%d.svg <br>\
4872: <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 4873: }
4874: fprintf(fichtm,"\n<br>- Total life expectancy by age and \
1.128 brouard 4875: health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
4876: true period expectancies (those weighted with period prevalences are also\
4877: drawn in addition to the population based expectancies computed using\
1.205 brouard 4878: observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg<br>\
4879: <img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);
1.192 brouard 4880: /* } /\* end i1 *\/ */
1.126 brouard 4881: }/* End k1 */
4882: fprintf(fichtm,"</ul>");
4883: fflush(fichtm);
4884: }
4885:
4886: /******************* Gnuplot file **************/
1.201 brouard 4887: void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 4888:
4889: char dirfileres[132],optfileres[132];
1.164 brouard 4890: int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
1.130 brouard 4891: int ng=0;
1.201 brouard 4892: int vpopbased;
1.126 brouard 4893: /* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
4894: /* printf("Problem with file %s",optionfilegnuplot); */
4895: /* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
4896: /* } */
4897:
4898: /*#ifdef windows */
4899: fprintf(ficgp,"cd \"%s\" \n",pathc);
4900: /*#endif */
4901: m=pow(2,cptcoveff);
4902:
1.202 brouard 4903: /* Contribution to likelihood */
4904: /* Plot the probability implied in the likelihood */
4905: fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
4906: fprintf(ficgp,"\n set log y; unset log x;set xlabel \"Age\"; set ylabel \"Likelihood (-2Log(L))\";");
4907: /* fprintf(ficgp,"\nset ter svg size 640, 480"); */ /* Too big for svg */
1.205 brouard 4908: fprintf(ficgp,"\nset ter pngcairo size 640, 480");
1.204 brouard 4909: /* nice for mle=4 plot by number of matrix products.
1.202 brouard 4910: replot "rrtest1/toto.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with point lc 1 */
4911: /* replot exp(p1+p2*x)/(1+exp(p1+p2*x)+exp(p3+p4*x)+exp(p5+p6*x)) t "p12(x)" */
4912: /* fprintf(ficgp,"\nset out \"%s.svg\";",subdirf2(optionfilefiname,"ILK_")); */
1.204 brouard 4913: fprintf(ficgp,"\nset out \"%s-dest.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4914: 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 4915: fprintf(ficgp,"\nset out \"%s-ori.png\";",subdirf2(optionfilefiname,"ILK_"));
1.205 brouard 4916: 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 4917: for (i=1; i<= nlstate ; i ++) {
4918: fprintf(ficgp,"\nset out \"%s-p%dj.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i);
1.205 brouard 4919: fprintf(ficgp,"unset log;\n# plot weighted, mean weight should have point size of 0.5\n plot \"%s\"",subdirf(fileresilk));
4920: 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 4921: for (j=2; j<= nlstate+ndeath ; j ++) {
1.205 brouard 4922: 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 4923: }
4924: fprintf(ficgp,";\nset out; unset ylabel;\n");
4925: }
4926: /* 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 */
4927: /* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
4928: /* 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 4929: fprintf(ficgp,"\nset out;unset log\n");
1.202 brouard 4930: /* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */
4931:
1.126 brouard 4932: strcpy(dirfileres,optionfilefiname);
4933: strcpy(optfileres,"vpl");
4934: /* 1eme*/
1.201 brouard 4935: fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files\n");
1.126 brouard 4936: for (cpt=1; cpt<= nlstate ; cpt ++) {
1.145 brouard 4937: for (k1=1; k1<= m ; k1 ++) { /* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
1.201 brouard 4938: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
4939: fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
1.126 brouard 4940: fprintf(ficgp,"set xlabel \"Age\" \n\
4941: set ylabel \"Probability\" \n\
1.199 brouard 4942: set ter svg size 640, 480\n\
1.201 brouard 4943: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4944:
4945: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4946: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4947: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4948: }
1.201 brouard 4949: 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 4950: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4951: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4952: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4953: }
1.201 brouard 4954: fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);
1.126 brouard 4955: for (i=1; i<= nlstate ; i ++) {
1.170 brouard 4956: if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
4957: else fprintf(ficgp," %%*lf (%%*lf)");
1.126 brouard 4958: }
1.201 brouard 4959: fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
4960: fprintf(ficgp,"\nset out \n");
4961: } /* k1 */
4962: } /* cpt */
1.126 brouard 4963: /*2 eme*/
1.153 brouard 4964: fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files\n");
1.126 brouard 4965: for (k1=1; k1<= m ; k1 ++) {
1.201 brouard 4966: fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
4967: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
4968: if(vpopbased==0)
4969: fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
4970: else
4971: fprintf(ficgp,"\nreplot ");
4972: for (i=1; i<= nlstate+1 ; i ++) {
4973: k=2*i;
4974: 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);
4975: for (j=1; j<= nlstate+1 ; j ++) {
4976: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4977: else fprintf(ficgp," %%*lf (%%*lf)");
4978: }
4979: if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
4980: else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
4981: 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);
4982: for (j=1; j<= nlstate+1 ; j ++) {
4983: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4984: else fprintf(ficgp," %%*lf (%%*lf)");
4985: }
4986: fprintf(ficgp,"\" t\"\" w l lt 0,");
4987: fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
4988: for (j=1; j<= nlstate+1 ; j ++) {
4989: if (j==i) fprintf(ficgp," %%lf (%%lf)");
4990: else fprintf(ficgp," %%*lf (%%*lf)");
4991: }
4992: if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
4993: else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
4994: } /* state */
4995: } /* vpopbased */
4996: fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
4997: } /* k1 */
1.126 brouard 4998: /*3eme*/
4999:
5000: for (k1=1; k1<= m ; k1 ++) {
5001: for (cpt=1; cpt<= nlstate ; cpt ++) {
5002: /* k=2+nlstate*(2*cpt-2); */
5003: k=2+(nlstate+1)*(cpt-1);
1.201 brouard 5004: fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);
1.199 brouard 5005: fprintf(ficgp,"set ter svg size 640, 480\n\
1.201 brouard 5006: plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
1.126 brouard 5007: /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5008: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5009: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5010: fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
5011: for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
5012: fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
5013:
5014: */
5015: for (i=1; i< nlstate ; i ++) {
1.201 brouard 5016: 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 5017: /* 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);*/
5018:
5019: }
1.201 brouard 5020: 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 5021: }
5022: }
5023:
1.201 brouard 5024: /* Survival functions (period) from state i in state j by initial state i */
5025: for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */
5026: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
5027: k=3;
5028: fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'lij' files, cov=%d state=%d",k1, cpt);
5029: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);
5030: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5031: set ter svg size 640, 480\n\
5032: unset log y\n\
5033: plot [%.f:%.f] ", ageminpar, agemaxpar);
5034: for (i=1; i<= nlstate ; i ++){
5035: if(i==1)
5036: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5037: else
5038: fprintf(ficgp,", '' ");
5039: l=(nlstate+ndeath)*(i-1)+1;
5040: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
5041: for (j=2; j<= nlstate+ndeath ; j ++)
5042: fprintf(ficgp,"+$%d",k+l+j-1);
5043: fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
5044: } /* nlstate */
5045: fprintf(ficgp,"\nset out\n");
5046: } /* end cpt state*/
5047: } /* end covariate */
5048:
5049: /* Survival functions (period) from state i in state j by final state j */
1.202 brouard 5050: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.201 brouard 5051: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
5052: k=3;
5053: 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);
5054: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);
5055: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
5056: set ter svg size 640, 480\n\
5057: unset log y\n\
5058: plot [%.f:%.f] ", ageminpar, agemaxpar);
5059: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5060: if(j==1)
5061: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
5062: else
5063: fprintf(ficgp,", '' ");
5064: l=(nlstate+ndeath)*(cpt-1) +j;
5065: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
5066: /* for (i=2; i<= nlstate+ndeath ; i ++) */
5067: /* fprintf(ficgp,"+$%d",k+l+i-1); */
5068: fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
5069: } /* nlstate */
5070: fprintf(ficgp,", '' ");
5071: fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
5072: for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
5073: l=(nlstate+ndeath)*(cpt-1) +j;
5074: if(j < nlstate)
5075: fprintf(ficgp,"$%d +",k+l);
5076: else
5077: fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
5078: }
5079: fprintf(ficgp,"\nset out\n");
5080: } /* end cpt state*/
5081: } /* end covariate */
5082:
1.202 brouard 5083: /* CV preval stable (period) for each covariate */
5084: for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */
1.153 brouard 5085: for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
1.126 brouard 5086: k=3;
1.153 brouard 5087: fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, cov=%d state=%d",k1, cpt);
1.201 brouard 5088: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);
1.126 brouard 5089: fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
1.199 brouard 5090: set ter svg size 640, 480\n\
1.126 brouard 5091: unset log y\n\
1.153 brouard 5092: plot [%.f:%.f] ", ageminpar, agemaxpar);
5093: for (i=1; i<= nlstate ; i ++){
5094: if(i==1)
1.201 brouard 5095: fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
1.153 brouard 5096: else
5097: fprintf(ficgp,", '' ");
1.154 brouard 5098: l=(nlstate+ndeath)*(i-1)+1;
5099: fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
1.201 brouard 5100: for (j=2; j<= nlstate ; j ++)
5101: fprintf(ficgp,"+$%d",k+l+j-1);
1.153 brouard 5102: fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
5103: } /* nlstate */
1.201 brouard 5104: fprintf(ficgp,"\nset out\n");
1.153 brouard 5105: } /* end cpt state*/
5106: } /* end covariate */
1.201 brouard 5107:
1.126 brouard 5108: /* proba elementaires */
1.187 brouard 5109: fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");
1.126 brouard 5110: for(i=1,jk=1; i <=nlstate; i++){
1.187 brouard 5111: fprintf(ficgp,"# initial state %d\n",i);
1.126 brouard 5112: for(k=1; k <=(nlstate+ndeath); k++){
5113: if (k != i) {
1.187 brouard 5114: fprintf(ficgp,"# current state %d\n",k);
1.126 brouard 5115: for(j=1; j <=ncovmodel; j++){
1.187 brouard 5116: fprintf(ficgp,"p%d=%f; ",jk,p[jk]);
1.126 brouard 5117: jk++;
5118: }
1.187 brouard 5119: fprintf(ficgp,"\n");
1.126 brouard 5120: }
5121: }
5122: }
1.187 brouard 5123: fprintf(ficgp,"##############\n#\n");
5124:
1.145 brouard 5125: /*goto avoid;*/
1.200 brouard 5126: fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");
1.187 brouard 5127: fprintf(ficgp,"# logi(p12/p11)=a12+b12*age+c12age*age+d12*V1+e12*V1*age\n");
5128: fprintf(ficgp,"# logi(p12/p11)=p1 +p2*age +p3*age*age+ p4*V1+ p5*V1*age\n");
5129: fprintf(ficgp,"# logi(p13/p11)=a13+b13*age+c13age*age+d13*V1+e13*V1*age\n");
5130: fprintf(ficgp,"# logi(p13/p11)=p6 +p7*age +p8*age*age+ p9*V1+ p10*V1*age\n");
5131: fprintf(ficgp,"# p12+p13+p14+p11=1=p11(1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5132: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age)+...)\n");
5133: fprintf(ficgp,"# p11=1/(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,"# p12=exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)/\n");
5136: fprintf(ficgp,"# (1+exp(a12+b12*age+c12age*age+d12*V1+e12*V1*age)\n");
5137: fprintf(ficgp,"# +exp(a13+b13*age+c13age*age+d13*V1+e13*V1*age))\n");
5138: fprintf(ficgp,"# +exp(a14+b14*age+c14age*age+d14*V1+e14*V1*age)+...)\n");
5139: fprintf(ficgp,"#\n");
1.201 brouard 5140: for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
1.187 brouard 5141: fprintf(ficgp,"# ng=%d\n",ng);
5142: fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);
1.126 brouard 5143: for(jk=1; jk <=m; jk++) {
1.187 brouard 5144: fprintf(ficgp,"# jk=%d\n",jk);
1.201 brouard 5145: fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
5146: fprintf(ficgp,"\nset ter svg size 640, 480 ");
5147: if (ng==1){
5148: fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12*x) could be nice */
5149: fprintf(ficgp,"\nunset log y");
5150: }else if (ng==2){
5151: fprintf(ficgp,"\nset ylabel \"Probability\"\n");
5152: fprintf(ficgp,"\nset log y");
5153: }else if (ng==3){
1.126 brouard 5154: fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
1.201 brouard 5155: fprintf(ficgp,"\nset log y");
5156: }else
5157: fprintf(ficgp,"\nunset title ");
5158: fprintf(ficgp,"\nplot [%.f:%.f] ",ageminpar,agemaxpar);
1.126 brouard 5159: i=1;
5160: for(k2=1; k2<=nlstate; k2++) {
5161: k3=i;
5162: for(k=1; k<=(nlstate+ndeath); k++) {
5163: if (k != k2){
1.201 brouard 5164: switch( ng) {
5165: case 1:
1.187 brouard 5166: if(nagesqr==0)
1.201 brouard 5167: fprintf(ficgp," p%d+p%d*x",i,i+1);
1.187 brouard 5168: else /* nagesqr =1 */
1.201 brouard 5169: fprintf(ficgp," p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5170: break;
5171: case 2: /* ng=2 */
1.187 brouard 5172: if(nagesqr==0)
5173: fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
5174: else /* nagesqr =1 */
1.201 brouard 5175: fprintf(ficgp," exp(p%d+p%d*x+p%d*x*x",i,i+1,i+1+nagesqr);
5176: break;
5177: case 3:
5178: if(nagesqr==0)
5179: fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
5180: else /* nagesqr =1 */
5181: fprintf(ficgp," %f*exp(p%d+p%d*x+p%d*x*x",YEARM/stepm,i,i+1,i+1+nagesqr);
5182: break;
5183: }
1.141 brouard 5184: ij=1;/* To be checked else nbcode[0][0] wrong */
1.187 brouard 5185: for(j=3; j <=ncovmodel-nagesqr; j++) {
1.197 brouard 5186: /* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
5187: if(ij <=cptcovage) { /* Bug valgrind */
5188: if((j-2)==Tage[ij]) { /* Bug valgrind */
1.200 brouard 5189: fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5190: /* fprintf(ficgp,"+p%d*%d*x",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
1.197 brouard 5191: ij++;
5192: }
1.186 brouard 5193: }
5194: else
1.198 brouard 5195: fprintf(ficgp,"+p%d*%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.126 brouard 5196: }
1.201 brouard 5197: if(ng != 1){
5198: fprintf(ficgp,")/(1");
1.126 brouard 5199:
1.201 brouard 5200: for(k1=1; k1 <=nlstate; k1++){
5201: if(nagesqr==0)
5202: fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
5203: else /* nagesqr =1 */
5204: 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);
5205:
5206: ij=1;
5207: for(j=3; j <=ncovmodel-nagesqr; j++){
5208: if(ij <=cptcovage) { /* Bug valgrind */
5209: if((j-2)==Tage[ij]) { /* Bug valgrind */
5210: fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
5211: /* fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
5212: ij++;
5213: }
1.197 brouard 5214: }
1.201 brouard 5215: else
5216: fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
1.186 brouard 5217: }
1.201 brouard 5218: fprintf(ficgp,")");
1.126 brouard 5219: }
5220: fprintf(ficgp,")");
1.201 brouard 5221: if(ng ==2)
5222: fprintf(ficgp," t \"p%d%d\" ", k2,k);
5223: else /* ng= 3 */
5224: fprintf(ficgp," t \"i%d%d\" ", k2,k);
5225: }else{ /* end ng <> 1 */
5226: fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);
1.126 brouard 5227: }
5228: if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
5229: i=i+ncovmodel;
5230: }
5231: } /* end k */
5232: } /* end k2 */
1.201 brouard 5233: fprintf(ficgp,"\n set out\n");
1.126 brouard 5234: } /* end jk */
5235: } /* end ng */
1.164 brouard 5236: /* avoid: */
1.126 brouard 5237: fflush(ficgp);
5238: } /* end gnuplot */
5239:
5240:
5241: /*************** Moving average **************/
5242: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
5243:
5244: int i, cpt, cptcod;
5245: int modcovmax =1;
5246: int mobilavrange, mob;
5247: double age;
5248:
5249: modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
5250: a covariate has 2 modalities */
5251: if (cptcovn<1) modcovmax=1; /* At least 1 pass */
5252:
5253: if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
5254: if(mobilav==1) mobilavrange=5; /* default */
5255: else mobilavrange=mobilav;
5256: for (age=bage; age<=fage; age++)
5257: for (i=1; i<=nlstate;i++)
5258: for (cptcod=1;cptcod<=modcovmax;cptcod++)
5259: mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
5260: /* We keep the original values on the extreme ages bage, fage and for
5261: fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
5262: we use a 5 terms etc. until the borders are no more concerned.
5263: */
5264: for (mob=3;mob <=mobilavrange;mob=mob+2){
5265: for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
5266: for (i=1; i<=nlstate;i++){
5267: for (cptcod=1;cptcod<=modcovmax;cptcod++){
5268: mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
5269: for (cpt=1;cpt<=(mob-1)/2;cpt++){
5270: mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
5271: mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
5272: }
5273: mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
5274: }
5275: }
5276: }/* end age */
5277: }/* end mob */
5278: }else return -1;
5279: return 0;
5280: }/* End movingaverage */
5281:
5282:
5283: /************** Forecasting ******************/
1.169 brouard 5284: 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 5285: /* proj1, year, month, day of starting projection
5286: agemin, agemax range of age
5287: dateprev1 dateprev2 range of dates during which prevalence is computed
5288: anproj2 year of en of projection (same day and month as proj1).
5289: */
1.164 brouard 5290: int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
1.126 brouard 5291: double agec; /* generic age */
5292: double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
5293: double *popeffectif,*popcount;
5294: double ***p3mat;
5295: double ***mobaverage;
5296: char fileresf[FILENAMELENGTH];
5297:
5298: agelim=AGESUP;
5299: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5300:
1.201 brouard 5301: strcpy(fileresf,"F_");
5302: strcat(fileresf,fileresu);
1.126 brouard 5303: if((ficresf=fopen(fileresf,"w"))==NULL) {
5304: printf("Problem with forecast resultfile: %s\n", fileresf);
5305: fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
5306: }
5307: printf("Computing forecasting: result on file '%s' \n", fileresf);
5308: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
5309:
5310: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5311:
5312: if (mobilav!=0) {
5313: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5314: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5315: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5316: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5317: }
5318: }
5319:
5320: stepsize=(int) (stepm+YEARM-1)/YEARM;
5321: if (stepm<=12) stepsize=1;
5322: if(estepm < stepm){
5323: printf ("Problem %d lower than %d\n",estepm, stepm);
5324: }
5325: else hstepm=estepm;
5326:
5327: hstepm=hstepm/stepm;
5328: yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
5329: fractional in yp1 */
5330: anprojmean=yp;
5331: yp2=modf((yp1*12),&yp);
5332: mprojmean=yp;
5333: yp1=modf((yp2*30.5),&yp);
5334: jprojmean=yp;
5335: if(jprojmean==0) jprojmean=1;
5336: if(mprojmean==0) jprojmean=1;
5337:
5338: i1=cptcoveff;
5339: if (cptcovn < 1){i1=1;}
5340:
5341: fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
5342:
5343: fprintf(ficresf,"#****** Routine prevforecast **\n");
5344:
5345: /* if (h==(int)(YEARM*yearp)){ */
5346: for(cptcov=1, k=0;cptcov<=i1;cptcov++){
5347: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5348: k=k+1;
5349: fprintf(ficresf,"\n#******");
5350: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5351: 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 5352: }
5353: fprintf(ficresf,"******\n");
5354: fprintf(ficresf,"# Covariate valuofcovar yearproj age");
5355: for(j=1; j<=nlstate+ndeath;j++){
5356: for(i=1; i<=nlstate;i++)
5357: fprintf(ficresf," p%d%d",i,j);
5358: fprintf(ficresf," p.%d",j);
5359: }
5360: for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
5361: fprintf(ficresf,"\n");
5362: fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
5363:
5364: for (agec=fage; agec>=(ageminpar-1); agec--){
5365: nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
5366: nhstepm = nhstepm/hstepm;
5367: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5368: oldm=oldms;savm=savms;
5369: hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
5370:
5371: for (h=0; h<=nhstepm; h++){
5372: if (h*hstepm/YEARM*stepm ==yearp) {
5373: fprintf(ficresf,"\n");
5374: for(j=1;j<=cptcoveff;j++)
1.198 brouard 5375: fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5376: fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
5377: }
5378: for(j=1; j<=nlstate+ndeath;j++) {
5379: ppij=0.;
5380: for(i=1; i<=nlstate;i++) {
5381: if (mobilav==1)
5382: ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
5383: else {
5384: ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
5385: }
5386: if (h*hstepm/YEARM*stepm== yearp) {
5387: fprintf(ficresf," %.3f", p3mat[i][j][h]);
5388: }
5389: } /* end i */
5390: if (h*hstepm/YEARM*stepm==yearp) {
5391: fprintf(ficresf," %.3f", ppij);
5392: }
5393: }/* end j */
5394: } /* end h */
5395: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5396: } /* end agec */
5397: } /* end yearp */
5398: } /* end cptcod */
5399: } /* end cptcov */
5400:
5401: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5402:
5403: fclose(ficresf);
5404: }
5405:
5406: /************** Forecasting *****not tested NB*************/
1.169 brouard 5407: 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 5408:
5409: int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
5410: int *popage;
5411: double calagedatem, agelim, kk1, kk2;
5412: double *popeffectif,*popcount;
5413: double ***p3mat,***tabpop,***tabpopprev;
5414: double ***mobaverage;
5415: char filerespop[FILENAMELENGTH];
5416:
5417: tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5418: tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5419: agelim=AGESUP;
5420: calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
5421:
5422: prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
5423:
5424:
1.201 brouard 5425: strcpy(filerespop,"POP_");
5426: strcat(filerespop,fileresu);
1.126 brouard 5427: if((ficrespop=fopen(filerespop,"w"))==NULL) {
5428: printf("Problem with forecast resultfile: %s\n", filerespop);
5429: fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
5430: }
5431: printf("Computing forecasting: result on file '%s' \n", filerespop);
5432: fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
5433:
5434: if (cptcoveff==0) ncodemax[cptcoveff]=1;
5435:
5436: if (mobilav!=0) {
5437: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5438: if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
5439: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
5440: printf(" Error in movingaverage mobilav=%d\n",mobilav);
5441: }
5442: }
5443:
5444: stepsize=(int) (stepm+YEARM-1)/YEARM;
5445: if (stepm<=12) stepsize=1;
5446:
5447: agelim=AGESUP;
5448:
5449: hstepm=1;
5450: hstepm=hstepm/stepm;
5451:
5452: if (popforecast==1) {
5453: if((ficpop=fopen(popfile,"r"))==NULL) {
5454: printf("Problem with population file : %s\n",popfile);exit(0);
5455: fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
5456: }
5457: popage=ivector(0,AGESUP);
5458: popeffectif=vector(0,AGESUP);
5459: popcount=vector(0,AGESUP);
5460:
5461: i=1;
5462: while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
5463:
5464: imx=i;
5465: for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
5466: }
5467:
5468: for(cptcov=1,k=0;cptcov<=i2;cptcov++){
5469: for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
5470: k=k+1;
5471: fprintf(ficrespop,"\n#******");
5472: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 5473: fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 5474: }
5475: fprintf(ficrespop,"******\n");
5476: fprintf(ficrespop,"# Age");
5477: for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
5478: if (popforecast==1) fprintf(ficrespop," [Population]");
5479:
5480: for (cpt=0; cpt<=0;cpt++) {
5481: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5482:
5483: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5484: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5485: nhstepm = nhstepm/hstepm;
5486:
5487: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5488: oldm=oldms;savm=savms;
5489: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5490:
5491: for (h=0; h<=nhstepm; h++){
5492: if (h==(int) (calagedatem+YEARM*cpt)) {
5493: fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5494: }
5495: for(j=1; j<=nlstate+ndeath;j++) {
5496: kk1=0.;kk2=0;
5497: for(i=1; i<=nlstate;i++) {
5498: if (mobilav==1)
5499: kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
5500: else {
5501: kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
5502: }
5503: }
5504: if (h==(int)(calagedatem+12*cpt)){
5505: tabpop[(int)(agedeb)][j][cptcod]=kk1;
5506: /*fprintf(ficrespop," %.3f", kk1);
5507: if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
5508: }
5509: }
5510: for(i=1; i<=nlstate;i++){
5511: kk1=0.;
5512: for(j=1; j<=nlstate;j++){
5513: kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
5514: }
5515: tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
5516: }
5517:
5518: if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
5519: fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
5520: }
5521: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5522: }
5523: }
5524:
5525: /******/
5526:
5527: for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
5528: fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
5529: for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
5530: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
5531: nhstepm = nhstepm/hstepm;
5532:
5533: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5534: oldm=oldms;savm=savms;
5535: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
5536: for (h=0; h<=nhstepm; h++){
5537: if (h==(int) (calagedatem+YEARM*cpt)) {
5538: fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
5539: }
5540: for(j=1; j<=nlstate+ndeath;j++) {
5541: kk1=0.;kk2=0;
5542: for(i=1; i<=nlstate;i++) {
5543: kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
5544: }
5545: if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
5546: }
5547: }
5548: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
5549: }
5550: }
5551: }
5552: }
5553:
5554: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5555:
5556: if (popforecast==1) {
5557: free_ivector(popage,0,AGESUP);
5558: free_vector(popeffectif,0,AGESUP);
5559: free_vector(popcount,0,AGESUP);
5560: }
5561: free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5562: free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
5563: fclose(ficrespop);
5564: } /* End of popforecast */
5565:
5566: int fileappend(FILE *fichier, char *optionfich)
5567: {
5568: if((fichier=fopen(optionfich,"a"))==NULL) {
5569: printf("Problem with file: %s\n", optionfich);
5570: fprintf(ficlog,"Problem with file: %s\n", optionfich);
5571: return (0);
5572: }
5573: fflush(fichier);
5574: return (1);
5575: }
5576:
5577:
5578: /**************** function prwizard **********************/
5579: void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
5580: {
5581:
5582: /* Wizard to print covariance matrix template */
5583:
1.164 brouard 5584: char ca[32], cb[32];
5585: int i,j, k, li, lj, lk, ll, jj, npar, itimes;
1.126 brouard 5586: int numlinepar;
5587:
5588: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5589: fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
5590: for(i=1; i <=nlstate; i++){
5591: jj=0;
5592: for(j=1; j <=nlstate+ndeath; j++){
5593: if(j==i) continue;
5594: jj++;
5595: /*ca[0]= k+'a'-1;ca[1]='\0';*/
5596: printf("%1d%1d",i,j);
5597: fprintf(ficparo,"%1d%1d",i,j);
5598: for(k=1; k<=ncovmodel;k++){
5599: /* printf(" %lf",param[i][j][k]); */
5600: /* fprintf(ficparo," %lf",param[i][j][k]); */
5601: printf(" 0.");
5602: fprintf(ficparo," 0.");
5603: }
5604: printf("\n");
5605: fprintf(ficparo,"\n");
5606: }
5607: }
5608: printf("# Scales (for hessian or gradient estimation)\n");
5609: fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
5610: npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
5611: for(i=1; i <=nlstate; i++){
5612: jj=0;
5613: for(j=1; j <=nlstate+ndeath; j++){
5614: if(j==i) continue;
5615: jj++;
5616: fprintf(ficparo,"%1d%1d",i,j);
5617: printf("%1d%1d",i,j);
5618: fflush(stdout);
5619: for(k=1; k<=ncovmodel;k++){
5620: /* printf(" %le",delti3[i][j][k]); */
5621: /* fprintf(ficparo," %le",delti3[i][j][k]); */
5622: printf(" 0.");
5623: fprintf(ficparo," 0.");
5624: }
5625: numlinepar++;
5626: printf("\n");
5627: fprintf(ficparo,"\n");
5628: }
5629: }
5630: printf("# Covariance matrix\n");
5631: /* # 121 Var(a12)\n\ */
5632: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5633: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
5634: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
5635: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
5636: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
5637: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
5638: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5639: fflush(stdout);
5640: fprintf(ficparo,"# Covariance matrix\n");
5641: /* # 121 Var(a12)\n\ */
5642: /* # 122 Cov(b12,a12) Var(b12)\n\ */
5643: /* # ...\n\ */
5644: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
5645:
5646: for(itimes=1;itimes<=2;itimes++){
5647: jj=0;
5648: for(i=1; i <=nlstate; i++){
5649: for(j=1; j <=nlstate+ndeath; j++){
5650: if(j==i) continue;
5651: for(k=1; k<=ncovmodel;k++){
5652: jj++;
5653: ca[0]= k+'a'-1;ca[1]='\0';
5654: if(itimes==1){
5655: printf("#%1d%1d%d",i,j,k);
5656: fprintf(ficparo,"#%1d%1d%d",i,j,k);
5657: }else{
5658: printf("%1d%1d%d",i,j,k);
5659: fprintf(ficparo,"%1d%1d%d",i,j,k);
5660: /* printf(" %.5le",matcov[i][j]); */
5661: }
5662: ll=0;
5663: for(li=1;li <=nlstate; li++){
5664: for(lj=1;lj <=nlstate+ndeath; lj++){
5665: if(lj==li) continue;
5666: for(lk=1;lk<=ncovmodel;lk++){
5667: ll++;
5668: if(ll<=jj){
5669: cb[0]= lk +'a'-1;cb[1]='\0';
5670: if(ll<jj){
5671: if(itimes==1){
5672: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5673: fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
5674: }else{
5675: printf(" 0.");
5676: fprintf(ficparo," 0.");
5677: }
5678: }else{
5679: if(itimes==1){
5680: printf(" Var(%s%1d%1d)",ca,i,j);
5681: fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
5682: }else{
5683: printf(" 0.");
5684: fprintf(ficparo," 0.");
5685: }
5686: }
5687: }
5688: } /* end lk */
5689: } /* end lj */
5690: } /* end li */
5691: printf("\n");
5692: fprintf(ficparo,"\n");
5693: numlinepar++;
5694: } /* end k*/
5695: } /*end j */
5696: } /* end i */
5697: } /* end itimes */
5698:
5699: } /* end of prwizard */
5700: /******************* Gompertz Likelihood ******************************/
5701: double gompertz(double x[])
5702: {
5703: double A,B,L=0.0,sump=0.,num=0.;
5704: int i,n=0; /* n is the size of the sample */
5705:
5706: for (i=0;i<=imx-1 ; i++) {
5707: sump=sump+weight[i];
5708: /* sump=sump+1;*/
5709: num=num+1;
5710: }
5711:
5712:
5713: /* for (i=0; i<=imx; i++)
5714: 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]);*/
5715:
5716: for (i=1;i<=imx ; i++)
5717: {
5718: if (cens[i] == 1 && wav[i]>1)
5719: A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
5720:
5721: if (cens[i] == 0 && wav[i]>1)
5722: A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
5723: +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
5724:
5725: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5726: if (wav[i] > 1 ) { /* ??? */
5727: L=L+A*weight[i];
5728: /* 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]);*/
5729: }
5730: }
5731:
5732: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5733:
5734: return -2*L*num/sump;
5735: }
5736:
1.136 brouard 5737: #ifdef GSL
5738: /******************* Gompertz_f Likelihood ******************************/
5739: double gompertz_f(const gsl_vector *v, void *params)
5740: {
5741: double A,B,LL=0.0,sump=0.,num=0.;
5742: double *x= (double *) v->data;
5743: int i,n=0; /* n is the size of the sample */
5744:
5745: for (i=0;i<=imx-1 ; i++) {
5746: sump=sump+weight[i];
5747: /* sump=sump+1;*/
5748: num=num+1;
5749: }
5750:
5751:
5752: /* for (i=0; i<=imx; i++)
5753: 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]);*/
5754: printf("x[0]=%lf x[1]=%lf\n",x[0],x[1]);
5755: for (i=1;i<=imx ; i++)
5756: {
5757: if (cens[i] == 1 && wav[i]>1)
5758: A=-x[0]/(x[1])*(exp(x[1]*(agecens[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)));
5759:
5760: if (cens[i] == 0 && wav[i]>1)
5761: A=-x[0]/(x[1])*(exp(x[1]*(agedc[i]-agegomp))-exp(x[1]*(ageexmed[i]-agegomp)))
5762: +log(x[0]/YEARM)+x[1]*(agedc[i]-agegomp)+log(YEARM);
5763:
5764: /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
5765: if (wav[i] > 1 ) { /* ??? */
5766: LL=LL+A*weight[i];
5767: /* 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]);*/
5768: }
5769: }
5770:
5771: /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
5772: printf("x[0]=%lf x[1]=%lf -2*LL*num/sump=%lf\n",x[0],x[1],-2*LL*num/sump);
5773:
5774: return -2*LL*num/sump;
5775: }
5776: #endif
5777:
1.126 brouard 5778: /******************* Printing html file ***********/
1.201 brouard 5779: void printinghtmlmort(char fileresu[], char title[], char datafile[], int firstpass, \
1.126 brouard 5780: int lastpass, int stepm, int weightopt, char model[],\
5781: int imx, double p[],double **matcov,double agemortsup){
5782: int i,k;
5783:
5784: fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
5785: fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
5786: for (i=1;i<=2;i++)
5787: 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 5788: fprintf(fichtm,"<br><br><img src=\"graphmort.svg\">");
1.126 brouard 5789: fprintf(fichtm,"</ul>");
5790:
5791: fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
5792:
5793: 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>");
5794:
5795: for (k=agegomp;k<(agemortsup-2);k++)
5796: 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]);
5797:
5798:
5799: fflush(fichtm);
5800: }
5801:
5802: /******************* Gnuplot file **************/
1.201 brouard 5803: void printinggnuplotmort(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
1.126 brouard 5804:
5805: char dirfileres[132],optfileres[132];
1.164 brouard 5806:
1.126 brouard 5807: int ng;
5808:
5809:
5810: /*#ifdef windows */
5811: fprintf(ficgp,"cd \"%s\" \n",pathc);
5812: /*#endif */
5813:
5814:
5815: strcpy(dirfileres,optionfilefiname);
5816: strcpy(optfileres,"vpl");
1.199 brouard 5817: fprintf(ficgp,"set out \"graphmort.svg\"\n ");
1.126 brouard 5818: fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
1.199 brouard 5819: fprintf(ficgp, "set ter svg size 640, 480\n set log y\n");
1.145 brouard 5820: /* fprintf(ficgp, "set size 0.65,0.65\n"); */
1.126 brouard 5821: fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
5822:
5823: }
5824:
1.136 brouard 5825: int readdata(char datafile[], int firstobs, int lastobs, int *imax)
5826: {
1.126 brouard 5827:
1.136 brouard 5828: /*-------- data file ----------*/
5829: FILE *fic;
5830: char dummy[]=" ";
1.164 brouard 5831: int i=0, j=0, n=0;
1.136 brouard 5832: int linei, month, year,iout;
5833: char line[MAXLINE], linetmp[MAXLINE];
1.164 brouard 5834: char stra[MAXLINE], strb[MAXLINE];
1.136 brouard 5835: char *stratrunc;
5836: int lstra;
1.126 brouard 5837:
5838:
1.136 brouard 5839: if((fic=fopen(datafile,"r"))==NULL) {
1.195 brouard 5840: printf("Problem while opening datafile: %s\n", datafile);fflush(stdout);
5841: fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);fflush(ficlog);return 1;
1.136 brouard 5842: }
1.126 brouard 5843:
1.136 brouard 5844: i=1;
5845: linei=0;
5846: while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
5847: linei=linei+1;
5848: for(j=strlen(line); j>=0;j--){ /* Untabifies line */
5849: if(line[j] == '\t')
5850: line[j] = ' ';
5851: }
5852: for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
5853: ;
5854: };
5855: line[j+1]=0; /* Trims blanks at end of line */
5856: if(line[0]=='#'){
5857: fprintf(ficlog,"Comment line\n%s\n",line);
5858: printf("Comment line\n%s\n",line);
5859: continue;
5860: }
5861: trimbb(linetmp,line); /* Trims multiple blanks in line */
1.164 brouard 5862: strcpy(line, linetmp);
1.136 brouard 5863:
1.126 brouard 5864:
1.136 brouard 5865: for (j=maxwav;j>=1;j--){
1.137 brouard 5866: cutv(stra, strb, line, ' ');
1.136 brouard 5867: if(strb[0]=='.') { /* Missing status */
5868: lval=-1;
5869: }else{
5870: errno=0;
5871: lval=strtol(strb,&endptr,10);
5872: /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
5873: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5874: 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);
5875: 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 5876: return 1;
5877: }
5878: }
5879: s[j][i]=lval;
5880:
5881: strcpy(line,stra);
5882: cutv(stra, strb,line,' ');
1.169 brouard 5883: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5884: }
1.169 brouard 5885: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5886: month=99;
5887: year=9999;
5888: }else{
1.141 brouard 5889: 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);
5890: 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 5891: return 1;
5892: }
5893: anint[j][i]= (double) year;
5894: mint[j][i]= (double)month;
5895: strcpy(line,stra);
5896: } /* ENd Waves */
5897:
5898: cutv(stra, strb,line,' ');
1.169 brouard 5899: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5900: }
1.169 brouard 5901: else if( (iout=sscanf(strb,"%s.",dummy)) != 0){
1.136 brouard 5902: month=99;
5903: year=9999;
5904: }else{
1.141 brouard 5905: 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);
5906: 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 5907: return 1;
5908: }
5909: andc[i]=(double) year;
5910: moisdc[i]=(double) month;
5911: strcpy(line,stra);
5912:
5913: cutv(stra, strb,line,' ');
1.169 brouard 5914: if( (iout=sscanf(strb,"%d/%d",&month, &year)) != 0){
1.136 brouard 5915: }
1.169 brouard 5916: else if( (iout=sscanf(strb,"%s.", dummy)) != 0){
1.136 brouard 5917: month=99;
5918: year=9999;
5919: }else{
1.141 brouard 5920: 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);
5921: 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 5922: return 1;
5923: }
5924: if (year==9999) {
1.141 brouard 5925: 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);
5926: 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 5927: return 1;
1.126 brouard 5928:
1.136 brouard 5929: }
5930: annais[i]=(double)(year);
5931: moisnais[i]=(double)(month);
5932: strcpy(line,stra);
5933:
5934: cutv(stra, strb,line,' ');
5935: errno=0;
5936: dval=strtod(strb,&endptr);
5937: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5938: printf("Error reading data around '%f' at line number %d, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
5939: 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 5940: fflush(ficlog);
5941: return 1;
5942: }
5943: weight[i]=dval;
5944: strcpy(line,stra);
5945:
5946: for (j=ncovcol;j>=1;j--){
5947: cutv(stra, strb,line,' ');
5948: if(strb[0]=='.') { /* Missing status */
5949: lval=-1;
5950: }else{
5951: errno=0;
5952: lval=strtol(strb,&endptr,10);
5953: if( strb[0]=='\0' || (*endptr != '\0')){
1.141 brouard 5954: 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);
5955: 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 5956: return 1;
5957: }
5958: }
5959: if(lval <-1 || lval >1){
1.141 brouard 5960: printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5961: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5962: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5963: For example, for multinomial values like 1, 2 and 3,\n \
5964: build V1=0 V2=0 for the reference value (1),\n \
5965: V1=1 V2=0 for (2) \n \
5966: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5967: output of IMaCh is often meaningless.\n \
5968: Exiting.\n",lval,linei, i,line,j);
1.141 brouard 5969: fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
1.136 brouard 5970: Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
5971: for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
5972: For example, for multinomial values like 1, 2 and 3,\n \
5973: build V1=0 V2=0 for the reference value (1),\n \
5974: V1=1 V2=0 for (2) \n \
5975: and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
5976: output of IMaCh is often meaningless.\n \
5977: Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
5978: return 1;
5979: }
5980: covar[j][i]=(double)(lval);
5981: strcpy(line,stra);
5982: }
5983: lstra=strlen(stra);
5984:
5985: if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
5986: stratrunc = &(stra[lstra-9]);
5987: num[i]=atol(stratrunc);
5988: }
5989: else
5990: num[i]=atol(stra);
5991: /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
5992: 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;}*/
5993:
5994: i=i+1;
5995: } /* End loop reading data */
1.126 brouard 5996:
1.136 brouard 5997: *imax=i-1; /* Number of individuals */
5998: fclose(fic);
5999:
6000: return (0);
1.164 brouard 6001: /* endread: */
1.136 brouard 6002: printf("Exiting readdata: ");
6003: fclose(fic);
6004: return (1);
1.126 brouard 6005:
6006:
6007:
1.136 brouard 6008: }
1.145 brouard 6009: void removespace(char *str) {
6010: char *p1 = str, *p2 = str;
6011: do
6012: while (*p2 == ' ')
6013: p2++;
1.169 brouard 6014: while (*p1++ == *p2++);
1.145 brouard 6015: }
6016:
6017: int decodemodel ( char model[], int lastobs) /**< This routine decode the model and returns:
1.187 brouard 6018: * Model V1+V2+V3+V8+V7*V8+V5*V6+V8*age+V3*age+age*age
6019: * - nagesqr = 1 if age*age in the model, otherwise 0.
6020: * - cptcovt total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and age*age
6021: * - cptcovn or number of covariates k of the models excluding age*products =6 and age*age
1.145 brouard 6022: * - cptcovage number of covariates with age*products =2
6023: * - cptcovs number of simple covariates
6024: * - 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
6025: * which is a new column after the 9 (ncovcol) variables.
6026: * - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual
6027: * - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
6028: * Tprod[1]@2 {5, 6}: position of first product V7*V8 is 5, and second V5*V6 is 6.
6029: * - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7*V8 and V5*V6 .
6030: */
1.136 brouard 6031: {
1.145 brouard 6032: int i, j, k, ks;
1.164 brouard 6033: int j1, k1, k2;
1.136 brouard 6034: char modelsav[80];
1.145 brouard 6035: char stra[80], strb[80], strc[80], strd[80],stre[80];
1.187 brouard 6036: char *strpt;
1.136 brouard 6037:
1.145 brouard 6038: /*removespace(model);*/
1.136 brouard 6039: if (strlen(model) >1){ /* If there is at least 1 covariate */
1.145 brouard 6040: j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;
1.137 brouard 6041: if (strstr(model,"AGE") !=0){
1.192 brouard 6042: printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
6043: fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
1.136 brouard 6044: return 1;
6045: }
1.141 brouard 6046: if (strstr(model,"v") !=0){
6047: printf("Error. 'v' must be in upper case 'V' model=%s ",model);
6048: fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);
6049: return 1;
6050: }
1.187 brouard 6051: strcpy(modelsav,model);
6052: if ((strpt=strstr(model,"age*age")) !=0){
6053: printf(" strpt=%s, model=%s\n",strpt, model);
6054: if(strpt != model){
6055: printf("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);
6058: fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
1.192 brouard 6059: 'model=1+age+age*age+V1.' or 'model=1+age+age*age+V1+V1*age.', please swap as well as \n \
1.187 brouard 6060: corresponding column of parameters.\n",model); fflush(ficlog);
6061: return 1;
6062: }
6063:
6064: nagesqr=1;
6065: if (strstr(model,"+age*age") !=0)
6066: substrchaine(modelsav, model, "+age*age");
6067: else if (strstr(model,"age*age+") !=0)
6068: substrchaine(modelsav, model, "age*age+");
6069: else
6070: substrchaine(modelsav, model, "age*age");
6071: }else
6072: nagesqr=0;
6073: if (strlen(modelsav) >1){
6074: j=nbocc(modelsav,'+'); /**< j=Number of '+' */
6075: j1=nbocc(modelsav,'*'); /**< j1=Number of '*' */
6076: cptcovs=j+1-j1; /**< Number of simple covariates V1+V1*age+V3 +V3*V4+age*age=> V1 + V3 =2 */
6077: cptcovt= j+1; /* Number of total covariates in the model, not including
6078: * cst, age and age*age
6079: * V1+V1*age+ V3 + V3*V4+age*age=> 4*/
6080: /* including age products which are counted in cptcovage.
6081: * but the covariates which are products must be treated
6082: * separately: ncovn=4- 2=2 (V1+V3). */
6083: cptcovprod=j1; /**< Number of products V1*V2 +v3*age = 2 */
6084: cptcovprodnoage=0; /**< Number of covariate products without age: V3*V4 =1 */
6085:
6086:
6087: /* Design
6088: * V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
6089: * < ncovcol=8 >
6090: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8
6091: * k= 1 2 3 4 5 6 7 8
6092: * cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
6093: * covar[k,i], value of kth covariate if not including age for individual i:
6094: * covar[1][i]= (V2), covar[4][i]=(V3), covar[8][i]=(V8)
6095: * Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[4]=3 Tvar[8]=8
6096: * if multiplied by age: V3*age Tvar[3=V3*age]=3 (V3) Tvar[7]=8 and
6097: * Tage[++cptcovage]=k
6098: * if products, new covar are created after ncovcol with k1
6099: * Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
6100: * Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
6101: * 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
6102: * Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
6103: * Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
6104: * V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
6105: * < ncovcol=8 >
6106: * Model V2 + V1 + V3*age + V3 + V5*V6 + V7*V8 + V8*age + V8 d1 d1 d2 d2
6107: * k= 1 2 3 4 5 6 7 8 9 10 11 12
6108: * Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
6109: * p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6110: * p Tprod[1]@2={ 6, 5}
6111: *p Tvard[1][1]@4= {7, 8, 5, 6}
6112: * covar[k][i]= V2 V1 ? V3 V5*V6? V7*V8? ? V8
6113: * cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
6114: *How to reorganize?
6115: * Model V1 + V2 + V3 + V8 + V5*V6 + V7*V8 + V3*age + V8*age
6116: * Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
6117: * {2, 1, 4, 8, 5, 6, 3, 7}
6118: * Struct []
6119: */
1.145 brouard 6120:
1.187 brouard 6121: /* This loop fills the array Tvar from the string 'model'.*/
6122: /* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
6123: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4 */
6124: /* k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tage[cptcovage=1]=4 */
6125: /* k=3 V4 Tvar[k=3]= 4 (from V4) */
6126: /* k=2 V1 Tvar[k=2]= 1 (from V1) */
6127: /* k=1 Tvar[1]=2 (from V2) */
6128: /* k=5 Tvar[5] */
6129: /* for (k=1; k<=cptcovn;k++) { */
1.198 brouard 6130: /* cov[2+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */
1.187 brouard 6131: /* } */
1.198 brouard 6132: /* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k])]]*cov[2]; */
1.187 brouard 6133: /*
6134: * Treating invertedly V2+V1+V3*age+V2*V4 is as if written V2*V4 +V3*age + V1 + V2 */
6135: for(k=cptcovt; k>=1;k--) /**< Number of covariates */
1.145 brouard 6136: Tvar[k]=0;
1.187 brouard 6137: cptcovage=0;
6138: for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
6139: cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
6140: modelsav==V2+V1+V4+V3*age strb=V3*age stra=V2+V1+V4 */
6141: if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
6142: /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
6143: /*scanf("%d",i);*/
6144: if (strchr(strb,'*')) { /**< Model includes a product V2+V1+V4+V3*age strb=V3*age */
6145: cutl(strc,strd,strb,'*'); /**< strd*strc Vm*Vn: strb=V3*age(input) strc=age strd=V3 ; V3*V2 strc=V2, strd=V3 */
6146: if (strcmp(strc,"age")==0) { /**< Model includes age: Vn*age */
6147: /* covar is not filled and then is empty */
6148: cptcovprod--;
6149: cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
6150: Tvar[k]=atoi(stre); /* V2+V1+V4+V3*age Tvar[4]=3 ; V1+V2*age Tvar[2]=2; V1+V1*age Tvar[2]=1 */
6151: cptcovage++; /* Sums the number of covariates which include age as a product */
6152: Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1*age Tvar[2]=1, Tage[1]=2 */
6153: /*printf("stre=%s ", stre);*/
6154: } else if (strcmp(strd,"age")==0) { /* or age*Vn */
6155: cptcovprod--;
6156: cutl(stre,strb,strc,'V');
6157: Tvar[k]=atoi(stre);
6158: cptcovage++;
6159: Tage[cptcovage]=k;
6160: } else { /* Age is not in the model product V2+V1+V1*V4+V3*age+V3*V2 strb=V3*V2*/
6161: /* loops on k1=1 (V3*V2) and k1=2 V4*V3 */
6162: cptcovn++;
6163: cptcovprodnoage++;k1++;
6164: cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3*V2 stre=3 strc=*/
6165: Tvar[k]=ncovcol+k1; /* For model-covariate k tells which data-covariate to use but
6166: because this model-covariate is a construction we invent a new column
6167: ncovcol + k1
6168: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3+V3*V2
6169: Tvar[3=V1*V4]=4+1 Tvar[5=V3*V2]=4 + 2= 6, etc */
6170: cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
6171: Tprod[k1]=k; /* Tprod[1]=3(=V1*V4) for V2+V1+V1*V4+age*V3+V3*V2 */
6172: Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
6173: Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
6174: k2=k2+2;
6175: Tvar[cptcovt+k2]=Tvard[k1][1]; /* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) */
6176: Tvar[cptcovt+k2+1]=Tvard[k1][2]; /* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) */
6177: for (i=1; i<=lastobs;i++){
6178: /* Computes the new covariate which is a product of
6179: covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
6180: covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
6181: }
6182: } /* End age is not in the model */
6183: } /* End if model includes a product */
6184: else { /* no more sum */
6185: /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
6186: /* scanf("%d",i);*/
6187: cutl(strd,strc,strb,'V');
6188: ks++; /**< Number of simple covariates */
1.145 brouard 6189: cptcovn++;
1.187 brouard 6190: Tvar[k]=atoi(strd);
6191: }
6192: strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
6193: /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
6194: scanf("%d",i);*/
6195: } /* end of loop + on total covariates */
6196: } /* end if strlen(modelsave == 0) age*age might exist */
6197: } /* end if strlen(model == 0) */
1.136 brouard 6198:
6199: /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
6200: If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
6201:
6202: /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
6203: printf("cptcovprod=%d ", cptcovprod);
6204: fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
6205:
6206: scanf("%d ",i);*/
6207:
6208:
1.137 brouard 6209: return (0); /* with covar[new additional covariate if product] and Tage if age */
1.164 brouard 6210: /*endread:*/
1.136 brouard 6211: printf("Exiting decodemodel: ");
6212: return (1);
6213: }
6214:
1.169 brouard 6215: int calandcheckages(int imx, int maxwav, double *agemin, double *agemax, int *nberr, int *nbwarn )
1.136 brouard 6216: {
6217: int i, m;
6218:
6219: for (i=1; i<=imx; i++) {
6220: for(m=2; (m<= maxwav); m++) {
6221: if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
6222: anint[m][i]=9999;
6223: s[m][i]=-1;
6224: }
6225: if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
1.169 brouard 6226: *nberr = *nberr + 1;
6227: 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);
6228: 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 6229: s[m][i]=-1;
6230: }
6231: if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
1.169 brouard 6232: (*nberr)++;
1.136 brouard 6233: 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]);
6234: 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]);
6235: s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
6236: }
6237: }
6238: }
6239:
6240: for (i=1; i<=imx; i++) {
6241: agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
6242: for(m=firstpass; (m<= lastpass); m++){
6243: if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
6244: if (s[m][i] >= nlstate+1) {
1.169 brouard 6245: if(agedc[i]>0){
6246: if((int)moisdc[i]!=99 && (int)andc[i]!=9999){
1.136 brouard 6247: agev[m][i]=agedc[i];
6248: /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
1.169 brouard 6249: }else {
1.136 brouard 6250: if ((int)andc[i]!=9999){
6251: nbwarn++;
6252: printf("Warning negative age at death: %ld line:%d\n",num[i],i);
6253: fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
6254: agev[m][i]=-1;
6255: }
6256: }
1.169 brouard 6257: } /* agedc > 0 */
1.136 brouard 6258: }
6259: else if(s[m][i] !=9){ /* Standard case, age in fractional
6260: years but with the precision of a month */
6261: agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
6262: if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
6263: agev[m][i]=1;
6264: else if(agev[m][i] < *agemin){
6265: *agemin=agev[m][i];
6266: printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], *agemin);
6267: }
6268: else if(agev[m][i] >*agemax){
6269: *agemax=agev[m][i];
1.156 brouard 6270: /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
1.136 brouard 6271: }
6272: /*agev[m][i]=anint[m][i]-annais[i];*/
6273: /* agev[m][i] = age[i]+2*m;*/
6274: }
6275: else { /* =9 */
6276: agev[m][i]=1;
6277: s[m][i]=-1;
6278: }
6279: }
6280: else /*= 0 Unknown */
6281: agev[m][i]=1;
6282: }
6283:
6284: }
6285: for (i=1; i<=imx; i++) {
6286: for(m=firstpass; (m<=lastpass); m++){
6287: if (s[m][i] > (nlstate+ndeath)) {
1.169 brouard 6288: (*nberr)++;
1.136 brouard 6289: 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);
6290: 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);
6291: return 1;
6292: }
6293: }
6294: }
6295:
6296: /*for (i=1; i<=imx; i++){
6297: for (m=firstpass; (m<lastpass); m++){
6298: printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
6299: }
6300:
6301: }*/
6302:
6303:
1.139 brouard 6304: printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
6305: fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);
1.136 brouard 6306:
6307: return (0);
1.164 brouard 6308: /* endread:*/
1.136 brouard 6309: printf("Exiting calandcheckages: ");
6310: return (1);
6311: }
6312:
1.172 brouard 6313: #if defined(_MSC_VER)
6314: /*printf("Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6315: /*fprintf(ficlog, "Visual C++ compiler: %s \n;", _MSC_FULL_VER);*/
6316: //#include "stdafx.h"
6317: //#include <stdio.h>
6318: //#include <tchar.h>
6319: //#include <windows.h>
6320: //#include <iostream>
6321: typedef BOOL(WINAPI *LPFN_ISWOW64PROCESS) (HANDLE, PBOOL);
6322:
6323: LPFN_ISWOW64PROCESS fnIsWow64Process;
6324:
6325: BOOL IsWow64()
6326: {
6327: BOOL bIsWow64 = FALSE;
6328:
6329: //typedef BOOL (APIENTRY *LPFN_ISWOW64PROCESS)
6330: // (HANDLE, PBOOL);
6331:
6332: //LPFN_ISWOW64PROCESS fnIsWow64Process;
6333:
6334: HMODULE module = GetModuleHandle(_T("kernel32"));
6335: const char funcName[] = "IsWow64Process";
6336: fnIsWow64Process = (LPFN_ISWOW64PROCESS)
6337: GetProcAddress(module, funcName);
6338:
6339: if (NULL != fnIsWow64Process)
6340: {
6341: if (!fnIsWow64Process(GetCurrentProcess(),
6342: &bIsWow64))
6343: //throw std::exception("Unknown error");
6344: printf("Unknown error\n");
6345: }
6346: return bIsWow64 != FALSE;
6347: }
6348: #endif
1.177 brouard 6349:
1.191 brouard 6350: void syscompilerinfo(int logged)
1.167 brouard 6351: {
6352: /* #include "syscompilerinfo.h"*/
1.185 brouard 6353: /* command line Intel compiler 32bit windows, XP compatible:*/
6354: /* /GS /W3 /Gy
6355: /Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
6356: "_CONSOLE" /D "_LIB" /D "_USING_V110_SDK71_" /D "_UNICODE" /D
6357: "UNICODE" /Qipo /Zc:forScope /Gd /Oi /MT /Fa"Release\" /EHsc /nologo
1.186 brouard 6358: /Fo"Release\" /Qprof-dir "Release\" /Fp"Release\IMaCh.pch"
6359: */
6360: /* 64 bits */
1.185 brouard 6361: /*
6362: /GS /W3 /Gy
6363: /Zc:wchar_t /Zi /O2 /Fd"x64\Release\vc120.pdb" /D "WIN32" /D "NDEBUG"
6364: /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo /Zc:forScope
6365: /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Fo"x64\Release\" /Qprof-dir
6366: "x64\Release\" /Fp"x64\Release\IMaCh.pch" */
6367: /* Optimization are useless and O3 is slower than O2 */
6368: /*
6369: /GS /W3 /Gy /Zc:wchar_t /Zi /O3 /Fd"x64\Release\vc120.pdb" /D "WIN32"
6370: /D "NDEBUG" /D "_CONSOLE" /D "_LIB" /D "_UNICODE" /D "UNICODE" /Qipo
6371: /Zc:forScope /Oi /MD /Fa"x64\Release\" /EHsc /nologo /Qparallel
6372: /Fo"x64\Release\" /Qprof-dir "x64\Release\" /Fp"x64\Release\IMaCh.pch"
6373: */
1.186 brouard 6374: /* Link is */ /* /OUT:"visual studio
1.185 brouard 6375: 2013\Projects\IMaCh\Release\IMaCh.exe" /MANIFEST /NXCOMPAT
6376: /PDB:"visual studio
6377: 2013\Projects\IMaCh\Release\IMaCh.pdb" /DYNAMICBASE
6378: "kernel32.lib" "user32.lib" "gdi32.lib" "winspool.lib"
6379: "comdlg32.lib" "advapi32.lib" "shell32.lib" "ole32.lib"
6380: "oleaut32.lib" "uuid.lib" "odbc32.lib" "odbccp32.lib"
6381: /MACHINE:X86 /OPT:REF /SAFESEH /INCREMENTAL:NO
6382: /SUBSYSTEM:CONSOLE",5.01" /MANIFESTUAC:"level='asInvoker'
6383: uiAccess='false'"
6384: /ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
6385: /NOLOGO /TLBID:1
6386: */
1.177 brouard 6387: #if defined __INTEL_COMPILER
1.178 brouard 6388: #if defined(__GNUC__)
6389: struct utsname sysInfo; /* For Intel on Linux and OS/X */
6390: #endif
1.177 brouard 6391: #elif defined(__GNUC__)
1.179 brouard 6392: #ifndef __APPLE__
1.174 brouard 6393: #include <gnu/libc-version.h> /* Only on gnu */
1.179 brouard 6394: #endif
1.177 brouard 6395: struct utsname sysInfo;
1.178 brouard 6396: int cross = CROSS;
6397: if (cross){
6398: printf("Cross-");
1.191 brouard 6399: if(logged) fprintf(ficlog, "Cross-");
1.178 brouard 6400: }
1.174 brouard 6401: #endif
6402:
1.171 brouard 6403: #include <stdint.h>
1.178 brouard 6404:
1.191 brouard 6405: printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
1.169 brouard 6406: #if defined(__clang__)
1.191 brouard 6407: printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
1.169 brouard 6408: #endif
6409: #if defined(__ICC) || defined(__INTEL_COMPILER)
1.191 brouard 6410: printf(" Intel ICC/ICPC");if(logged)fprintf(ficlog," Intel ICC/ICPC");/* Intel ICC/ICPC. ------------------------------------------ */
1.169 brouard 6411: #endif
6412: #if defined(__GNUC__) || defined(__GNUG__)
1.191 brouard 6413: printf(" GNU GCC/G++");if(logged)fprintf(ficlog," GNU GCC/G++");/* GNU GCC/G++. --------------------------------------------- */
1.169 brouard 6414: #endif
6415: #if defined(__HP_cc) || defined(__HP_aCC)
1.191 brouard 6416: printf(" Hewlett-Packard C/aC++");if(logged)fprintf(fcilog," Hewlett-Packard C/aC++"); /* Hewlett-Packard C/aC++. ---------------------------------- */
1.169 brouard 6417: #endif
6418: #if defined(__IBMC__) || defined(__IBMCPP__)
1.191 brouard 6419: printf(" IBM XL C/C++"); if(logged) fprintf(ficlog," IBM XL C/C++");/* IBM XL C/C++. -------------------------------------------- */
1.169 brouard 6420: #endif
6421: #if defined(_MSC_VER)
1.191 brouard 6422: printf(" Microsoft Visual Studio");if(logged)fprintf(ficlog," Microsoft Visual Studio");/* Microsoft Visual Studio. --------------------------------- */
1.169 brouard 6423: #endif
6424: #if defined(__PGI)
1.191 brouard 6425: printf(" Portland Group PGCC/PGCPP");if(logged) fprintf(ficlog," Portland Group PGCC/PGCPP");/* Portland Group PGCC/PGCPP. ------------------------------- */
1.169 brouard 6426: #endif
6427: #if defined(__SUNPRO_C) || defined(__SUNPRO_CC)
1.191 brouard 6428: printf(" Oracle Solaris Studio");if(logged)fprintf(ficlog," Oracle Solaris Studio\n");/* Oracle Solaris Studio. ----------------------------------- */
1.167 brouard 6429: #endif
1.191 brouard 6430: printf(" for "); if (logged) fprintf(ficlog, " for ");
1.169 brouard 6431:
1.167 brouard 6432: // http://stackoverflow.com/questions/4605842/how-to-identify-platform-compiler-from-preprocessor-macros
6433: #ifdef _WIN32 // note the underscore: without it, it's not msdn official!
6434: // Windows (x64 and x86)
1.191 brouard 6435: printf("Windows (x64 and x86) ");if(logged) fprintf(ficlog,"Windows (x64 and x86) ");
1.167 brouard 6436: #elif __unix__ // all unices, not all compilers
6437: // Unix
1.191 brouard 6438: printf("Unix ");if(logged) fprintf(ficlog,"Unix ");
1.167 brouard 6439: #elif __linux__
6440: // linux
1.191 brouard 6441: printf("linux ");if(logged) fprintf(ficlog,"linux ");
1.167 brouard 6442: #elif __APPLE__
1.174 brouard 6443: // Mac OS, not sure if this is covered by __posix__ and/or __unix__ though..
1.191 brouard 6444: printf("Mac OS ");if(logged) fprintf(ficlog,"Mac OS ");
1.167 brouard 6445: #endif
6446:
6447: /* __MINGW32__ */
6448: /* __CYGWIN__ */
6449: /* __MINGW64__ */
6450: // http://msdn.microsoft.com/en-us/library/b0084kay.aspx
6451: /* _MSC_VER //the Visual C++ compiler is 17.00.51106.1, the _MSC_VER macro evaluates to 1700. Type cl /? */
6452: /* _MSC_FULL_VER //the Visual C++ compiler is 15.00.20706.01, the _MSC_FULL_VER macro evaluates to 150020706 */
6453: /* _WIN64 // Defined for applications for Win64. */
6454: /* _M_X64 // Defined for compilations that target x64 processors. */
6455: /* _DEBUG // Defined when you compile with /LDd, /MDd, and /MTd. */
1.171 brouard 6456:
1.167 brouard 6457: #if UINTPTR_MAX == 0xffffffff
1.191 brouard 6458: printf(" 32-bit"); if(logged) fprintf(ficlog," 32-bit");/* 32-bit */
1.167 brouard 6459: #elif UINTPTR_MAX == 0xffffffffffffffff
1.191 brouard 6460: printf(" 64-bit"); if(logged) fprintf(ficlog," 64-bit");/* 64-bit */
1.167 brouard 6461: #else
1.191 brouard 6462: printf(" wtf-bit"); if(logged) fprintf(ficlog," wtf-bit");/* wtf */
1.167 brouard 6463: #endif
6464:
1.169 brouard 6465: #if defined(__GNUC__)
6466: # if defined(__GNUC_PATCHLEVEL__)
6467: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6468: + __GNUC_MINOR__ * 100 \
6469: + __GNUC_PATCHLEVEL__)
6470: # else
6471: # define __GNUC_VERSION__ (__GNUC__ * 10000 \
6472: + __GNUC_MINOR__ * 100)
6473: # endif
1.174 brouard 6474: printf(" using GNU C version %d.\n", __GNUC_VERSION__);
1.191 brouard 6475: if(logged) fprintf(ficlog, " using GNU C version %d.\n", __GNUC_VERSION__);
1.176 brouard 6476:
6477: if (uname(&sysInfo) != -1) {
6478: printf("Running on: %s %s %s %s %s\n",sysInfo.sysname, sysInfo.nodename, sysInfo.release, sysInfo.version, sysInfo.machine);
1.191 brouard 6479: 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 6480: }
6481: else
6482: perror("uname() error");
1.179 brouard 6483: //#ifndef __INTEL_COMPILER
6484: #if !defined (__INTEL_COMPILER) && !defined(__APPLE__)
1.174 brouard 6485: printf("GNU libc version: %s\n", gnu_get_libc_version());
1.191 brouard 6486: if(logged) fprintf(ficlog,"GNU libc version: %s\n", gnu_get_libc_version());
1.177 brouard 6487: #endif
1.169 brouard 6488: #endif
1.172 brouard 6489:
6490: // void main()
6491: // {
1.169 brouard 6492: #if defined(_MSC_VER)
1.174 brouard 6493: if (IsWow64()){
1.191 brouard 6494: printf("\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
6495: if (logged) fprintf(ficlog, "\nThe program (probably compiled for 32bit) is running under WOW64 (64bit) emulation.\n");
1.174 brouard 6496: }
6497: else{
1.191 brouard 6498: printf("\nThe program is not running under WOW64 (i.e probably on a 64bit Windows).\n");
6499: if (logged) fprintf(ficlog, "\nThe programm is not running under WOW64 (i.e probably on a 64bit Windows).\n");
1.174 brouard 6500: }
1.172 brouard 6501: // printf("\nPress Enter to continue...");
6502: // getchar();
6503: // }
6504:
1.169 brouard 6505: #endif
6506:
1.167 brouard 6507:
6508: }
1.136 brouard 6509:
1.203 brouard 6510: int prevalence_limit(double *p, double **prlim, double ageminpar, double agemaxpar, double ftolpl, int *ncvyear){
1.180 brouard 6511: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
6512: int i, j, k, i1 ;
1.202 brouard 6513: /* double ftolpl = 1.e-10; */
1.180 brouard 6514: double age, agebase, agelim;
1.203 brouard 6515: double tot;
1.180 brouard 6516:
1.202 brouard 6517: strcpy(filerespl,"PL_");
6518: strcat(filerespl,fileresu);
6519: if((ficrespl=fopen(filerespl,"w"))==NULL) {
6520: printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6521: fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;
6522: }
6523: printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6524: fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
6525: pstamp(ficrespl);
1.203 brouard 6526: fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
1.202 brouard 6527: fprintf(ficrespl,"#Age ");
6528: for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
6529: fprintf(ficrespl,"\n");
1.180 brouard 6530:
6531: /* prlim=matrix(1,nlstate,1,nlstate);*/ /* back in main */
6532:
6533: agebase=ageminpar;
6534: agelim=agemaxpar;
6535:
6536: i1=pow(2,cptcoveff);
6537: if (cptcovn < 1){i1=1;}
6538:
6539: for(cptcov=1,k=0;cptcov<=i1;cptcov++){
6540: /* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
6541: //for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
6542: k=k+1;
6543: /* to clean */
1.198 brouard 6544: //printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
1.200 brouard 6545: fprintf(ficrespl,"#******");
6546: printf("#******");
6547: fprintf(ficlog,"#******");
1.180 brouard 6548: for(j=1;j<=cptcoveff;j++) {
1.198 brouard 6549: fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6550: printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
6551: fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6552: }
6553: fprintf(ficrespl,"******\n");
6554: printf("******\n");
6555: fprintf(ficlog,"******\n");
6556:
6557: fprintf(ficrespl,"#Age ");
6558: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 6559: fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.180 brouard 6560: }
1.203 brouard 6561: for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
6562: fprintf(ficrespl,"Total Years_to_converge\n");
1.180 brouard 6563:
6564: for (age=agebase; age<=agelim; age++){
6565: /* for (age=agebase; age<=agebase; age++){ */
1.203 brouard 6566: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k);
1.180 brouard 6567: fprintf(ficrespl,"%.0f ",age );
6568: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6569: fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.203 brouard 6570: tot=0.;
6571: for(i=1; i<=nlstate;i++){
6572: tot += prlim[i][i];
1.180 brouard 6573: fprintf(ficrespl," %.5f", prlim[i][i]);
1.203 brouard 6574: }
6575: fprintf(ficrespl," %.3f %d\n", tot, *ncvyear);
1.180 brouard 6576: } /* Age */
6577: /* was end of cptcod */
6578: } /* cptcov */
1.184 brouard 6579: return 0;
1.180 brouard 6580: }
6581:
6582: int hPijx(double *p, int bage, int fage){
6583: /*------------- h Pij x at various ages ------------*/
6584:
6585: int stepsize;
6586: int agelim;
6587: int hstepm;
6588: int nhstepm;
6589: int h, i, i1, j, k;
6590:
6591: double agedeb;
6592: double ***p3mat;
6593:
1.201 brouard 6594: strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
1.180 brouard 6595: if((ficrespij=fopen(filerespij,"w"))==NULL) {
6596: printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
6597: fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
6598: }
6599: printf("Computing pij: result on file '%s' \n", filerespij);
6600: fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
6601:
6602: stepsize=(int) (stepm+YEARM-1)/YEARM;
6603: /*if (stepm<=24) stepsize=2;*/
6604:
6605: agelim=AGESUP;
6606: hstepm=stepsize*YEARM; /* Every year of age */
6607: hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
6608:
6609: /* hstepm=1; aff par mois*/
6610: pstamp(ficrespij);
6611: fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
6612: i1= pow(2,cptcoveff);
1.183 brouard 6613: /* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
6614: /* /\*for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*\/ */
6615: /* k=k+1; */
6616: for (k=1; k <= (int) pow(2,cptcoveff); k++){
6617: fprintf(ficrespij,"\n#****** ");
6618: for(j=1;j<=cptcoveff;j++)
1.198 brouard 6619: fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.183 brouard 6620: fprintf(ficrespij,"******\n");
6621:
6622: for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
6623: nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
6624: nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
6625:
6626: /* nhstepm=nhstepm*YEARM; aff par mois*/
1.180 brouard 6627:
1.183 brouard 6628: p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6629: oldm=oldms;savm=savms;
6630: hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
6631: fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
6632: for(i=1; i<=nlstate;i++)
6633: for(j=1; j<=nlstate+ndeath;j++)
6634: fprintf(ficrespij," %1d-%1d",i,j);
6635: fprintf(ficrespij,"\n");
6636: for (h=0; h<=nhstepm; h++){
6637: /*agedebphstep = agedeb + h*hstepm/YEARM*stepm;*/
6638: fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + h*hstepm/YEARM*stepm );
1.180 brouard 6639: for(i=1; i<=nlstate;i++)
6640: for(j=1; j<=nlstate+ndeath;j++)
1.183 brouard 6641: fprintf(ficrespij," %.5f", p3mat[i][j][h]);
1.180 brouard 6642: fprintf(ficrespij,"\n");
6643: }
1.183 brouard 6644: free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
6645: fprintf(ficrespij,"\n");
6646: }
1.180 brouard 6647: /*}*/
6648: }
1.184 brouard 6649: return 0;
1.180 brouard 6650: }
6651:
6652:
1.136 brouard 6653: /***********************************************/
6654: /**************** Main Program *****************/
6655: /***********************************************/
6656:
6657: int main(int argc, char *argv[])
6658: {
6659: #ifdef GSL
6660: const gsl_multimin_fminimizer_type *T;
6661: size_t iteri = 0, it;
6662: int rval = GSL_CONTINUE;
6663: int status = GSL_SUCCESS;
6664: double ssval;
6665: #endif
6666: int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
1.164 brouard 6667: int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;
1.203 brouard 6668: int ncvyearnp=0;
6669: int *ncvyear=&ncvyearnp; /* Number of years needed for the period prevalence to converge */
1.164 brouard 6670: int jj, ll, li, lj, lk;
1.136 brouard 6671: int numlinepar=0; /* Current linenumber of parameter file */
1.197 brouard 6672: int num_filled;
1.136 brouard 6673: int itimes;
6674: int NDIM=2;
6675: int vpopbased=0;
6676:
1.164 brouard 6677: char ca[32], cb[32];
1.136 brouard 6678: /* FILE *fichtm; *//* Html File */
6679: /* FILE *ficgp;*/ /*Gnuplot File */
6680: struct stat info;
1.191 brouard 6681: double agedeb=0.;
1.194 brouard 6682:
6683: double ageminpar=AGEOVERFLOW,agemin=AGEOVERFLOW, agemaxpar=-AGEOVERFLOW, agemax=-AGEOVERFLOW;
1.136 brouard 6684:
1.165 brouard 6685: double fret;
1.191 brouard 6686: double dum=0.; /* Dummy variable */
1.136 brouard 6687: double ***p3mat;
6688: double ***mobaverage;
1.164 brouard 6689:
6690: char line[MAXLINE];
1.197 brouard 6691: char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
6692:
6693: char model[MAXLINE], modeltemp[MAXLINE];
1.136 brouard 6694: char pathr[MAXLINE], pathimach[MAXLINE];
1.164 brouard 6695: char *tok, *val; /* pathtot */
1.136 brouard 6696: int firstobs=1, lastobs=10;
1.195 brouard 6697: int c, h , cpt, c2;
1.191 brouard 6698: int jl=0;
6699: int i1, j1, jk, stepsize=0;
1.194 brouard 6700: int count=0;
6701:
1.164 brouard 6702: int *tab;
1.136 brouard 6703: int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
6704: int mobilav=0,popforecast=0;
1.191 brouard 6705: int hstepm=0, nhstepm=0;
1.136 brouard 6706: int agemortsup;
6707: float sumlpop=0.;
6708: double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
6709: double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
6710:
1.191 brouard 6711: double bage=0, fage=110., age, agelim=0., agebase=0.;
1.136 brouard 6712: double ftolpl=FTOL;
6713: double **prlim;
6714: double ***param; /* Matrix of parameters */
6715: double *p;
6716: double **matcov; /* Matrix of covariance */
1.203 brouard 6717: double **hess; /* Hessian matrix */
1.136 brouard 6718: double ***delti3; /* Scale */
6719: double *delti; /* Scale */
6720: double ***eij, ***vareij;
6721: double **varpl; /* Variances of prevalence limits by age */
6722: double *epj, vepp;
1.164 brouard 6723:
1.136 brouard 6724: double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
6725: double **ximort;
1.145 brouard 6726: char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
1.136 brouard 6727: int *dcwave;
6728:
1.164 brouard 6729: char z[1]="c";
1.136 brouard 6730:
6731: /*char *strt;*/
6732: char strtend[80];
1.126 brouard 6733:
1.164 brouard 6734:
1.126 brouard 6735: /* setlocale (LC_ALL, ""); */
6736: /* bindtextdomain (PACKAGE, LOCALEDIR); */
6737: /* textdomain (PACKAGE); */
6738: /* setlocale (LC_CTYPE, ""); */
6739: /* setlocale (LC_MESSAGES, ""); */
6740:
6741: /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
1.157 brouard 6742: rstart_time = time(NULL);
6743: /* (void) gettimeofday(&start_time,&tzp);*/
6744: start_time = *localtime(&rstart_time);
1.126 brouard 6745: curr_time=start_time;
1.157 brouard 6746: /*tml = *localtime(&start_time.tm_sec);*/
6747: /* strcpy(strstart,asctime(&tml)); */
6748: strcpy(strstart,asctime(&start_time));
1.126 brouard 6749:
6750: /* printf("Localtime (at start)=%s",strstart); */
1.157 brouard 6751: /* tp.tm_sec = tp.tm_sec +86400; */
6752: /* tm = *localtime(&start_time.tm_sec); */
1.126 brouard 6753: /* tmg.tm_year=tmg.tm_year +dsign*dyear; */
6754: /* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
6755: /* tmg.tm_hour=tmg.tm_hour + 1; */
1.157 brouard 6756: /* tp.tm_sec = mktime(&tmg); */
1.126 brouard 6757: /* strt=asctime(&tmg); */
6758: /* printf("Time(after) =%s",strstart); */
6759: /* (void) time (&time_value);
6760: * printf("time=%d,t-=%d\n",time_value,time_value-86400);
6761: * tm = *localtime(&time_value);
6762: * strstart=asctime(&tm);
6763: * printf("tim_value=%d,asctime=%s\n",time_value,strstart);
6764: */
6765:
6766: nberr=0; /* Number of errors and warnings */
6767: nbwarn=0;
1.184 brouard 6768: #ifdef WIN32
6769: _getcwd(pathcd, size);
6770: #else
1.126 brouard 6771: getcwd(pathcd, size);
1.184 brouard 6772: #endif
1.191 brouard 6773: syscompilerinfo(0);
1.196 brouard 6774: printf("\nIMaCh version %s, %s\n%s",version, copyright, fullversion);
1.126 brouard 6775: if(argc <=1){
6776: printf("\nEnter the parameter file name: ");
1.205 brouard 6777: if(!fgets(pathr,FILENAMELENGTH,stdin)){
6778: printf("ERROR Empty parameter file name\n");
6779: goto end;
6780: }
1.126 brouard 6781: i=strlen(pathr);
6782: if(pathr[i-1]=='\n')
6783: pathr[i-1]='\0';
1.156 brouard 6784: i=strlen(pathr);
1.205 brouard 6785: if(i >= 1 && pathr[i-1]==' ') {/* This may happen when dragging on oS/X! */
1.156 brouard 6786: pathr[i-1]='\0';
1.205 brouard 6787: }
6788: i=strlen(pathr);
6789: if( i==0 ){
6790: printf("ERROR Empty parameter file name\n");
6791: goto end;
6792: }
6793: for (tok = pathr; tok != NULL; ){
1.126 brouard 6794: printf("Pathr |%s|\n",pathr);
6795: while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
6796: printf("val= |%s| pathr=%s\n",val,pathr);
6797: strcpy (pathtot, val);
6798: if(pathr[0] == '\0') break; /* Dirty */
6799: }
6800: }
6801: else{
6802: strcpy(pathtot,argv[1]);
6803: }
6804: /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
6805: /*cygwin_split_path(pathtot,path,optionfile);
6806: printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
6807: /* cutv(path,optionfile,pathtot,'\\');*/
6808:
6809: /* Split argv[0], imach program to get pathimach */
6810: printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
6811: split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6812: printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
6813: /* strcpy(pathimach,argv[0]); */
6814: /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
6815: split(pathtot,path,optionfile,optionfilext,optionfilefiname);
6816: printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
1.184 brouard 6817: #ifdef WIN32
6818: _chdir(path); /* Can be a relative path */
6819: if(_getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
6820: #else
1.126 brouard 6821: chdir(path); /* Can be a relative path */
1.184 brouard 6822: if (getcwd(pathcd, MAXLINE) > 0) /* So pathcd is the full path */
6823: #endif
6824: printf("Current directory %s!\n",pathcd);
1.126 brouard 6825: strcpy(command,"mkdir ");
6826: strcat(command,optionfilefiname);
6827: if((outcmd=system(command)) != 0){
1.169 brouard 6828: printf("Directory already exists (or can't create it) %s%s, err=%d\n",path,optionfilefiname,outcmd);
1.126 brouard 6829: /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
6830: /* fclose(ficlog); */
6831: /* exit(1); */
6832: }
6833: /* if((imk=mkdir(optionfilefiname))<0){ */
6834: /* perror("mkdir"); */
6835: /* } */
6836:
6837: /*-------- arguments in the command line --------*/
6838:
1.186 brouard 6839: /* Main Log file */
1.126 brouard 6840: strcat(filelog, optionfilefiname);
6841: strcat(filelog,".log"); /* */
6842: if((ficlog=fopen(filelog,"w"))==NULL) {
6843: printf("Problem with logfile %s\n",filelog);
6844: goto end;
6845: }
6846: fprintf(ficlog,"Log filename:%s\n",filelog);
1.197 brouard 6847: fprintf(ficlog,"Version %s %s",version,fullversion);
1.126 brouard 6848: fprintf(ficlog,"\nEnter the parameter file name: \n");
6849: fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
6850: path=%s \n\
6851: optionfile=%s\n\
6852: optionfilext=%s\n\
1.156 brouard 6853: optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
1.126 brouard 6854:
1.197 brouard 6855: syscompilerinfo(1);
1.167 brouard 6856:
1.126 brouard 6857: printf("Local time (at start):%s",strstart);
6858: fprintf(ficlog,"Local time (at start): %s",strstart);
6859: fflush(ficlog);
6860: /* (void) gettimeofday(&curr_time,&tzp); */
1.157 brouard 6861: /* printf("Elapsed time %d\n", asc_diff_time(curr_time.tm_sec-start_time.tm_sec,tmpout)); */
1.126 brouard 6862:
6863: /* */
6864: strcpy(fileres,"r");
6865: strcat(fileres, optionfilefiname);
1.201 brouard 6866: strcat(fileresu, optionfilefiname); /* Without r in front */
1.126 brouard 6867: strcat(fileres,".txt"); /* Other files have txt extension */
1.201 brouard 6868: strcat(fileresu,".txt"); /* Other files have txt extension */
1.126 brouard 6869:
1.186 brouard 6870: /* Main ---------arguments file --------*/
1.126 brouard 6871:
6872: if((ficpar=fopen(optionfile,"r"))==NULL) {
1.155 brouard 6873: printf("Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
6874: fprintf(ficlog,"Problem with optionfile '%s' with errno='%s'\n",optionfile,strerror(errno));
1.126 brouard 6875: fflush(ficlog);
1.149 brouard 6876: /* goto end; */
6877: exit(70);
1.126 brouard 6878: }
6879:
6880:
6881:
6882: strcpy(filereso,"o");
1.201 brouard 6883: strcat(filereso,fileresu);
1.126 brouard 6884: if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
6885: printf("Problem with Output resultfile: %s\n", filereso);
6886: fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
6887: fflush(ficlog);
6888: goto end;
6889: }
6890:
6891: /* Reads comments: lines beginning with '#' */
6892: numlinepar=0;
1.197 brouard 6893:
6894: /* First parameter line */
6895: while(fgets(line, MAXLINE, ficpar)) {
6896: /* If line starts with a # it is a comment */
6897: if (line[0] == '#') {
6898: numlinepar++;
6899: fputs(line,stdout);
6900: fputs(line,ficparo);
6901: fputs(line,ficlog);
6902: continue;
6903: }else
6904: break;
6905: }
6906: if((num_filled=sscanf(line,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", \
6907: title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
6908: if (num_filled != 5) {
6909: printf("Should be 5 parameters\n");
6910: }
1.126 brouard 6911: numlinepar++;
1.197 brouard 6912: printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
6913: }
6914: /* Second parameter line */
6915: while(fgets(line, MAXLINE, ficpar)) {
6916: /* If line starts with a # it is a comment */
6917: if (line[0] == '#') {
6918: numlinepar++;
6919: fputs(line,stdout);
6920: fputs(line,ficparo);
6921: fputs(line,ficlog);
6922: continue;
6923: }else
6924: break;
6925: }
6926: if((num_filled=sscanf(line,"ftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n", \
6927: &ftol, &stepm, &ncovcol, &nlstate, &ndeath, &maxwav, &mle, &weightopt)) !=EOF){
6928: if (num_filled != 8) {
6929: printf("Not 8\n");
6930: }
6931: 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 6932: }
1.203 brouard 6933: /* ftolpl=6*ftol*1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit *\/ */
6934: ftolpl=6.e-3; /* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
1.197 brouard 6935: /* Third parameter line */
6936: while(fgets(line, MAXLINE, ficpar)) {
6937: /* If line starts with a # it is a comment */
6938: if (line[0] == '#') {
6939: numlinepar++;
6940: fputs(line,stdout);
6941: fputs(line,ficparo);
6942: fputs(line,ficlog);
6943: continue;
6944: }else
6945: break;
6946: }
1.201 brouard 6947: if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
6948: if (num_filled == 0)
6949: model[0]='\0';
6950: else if (num_filled != 1){
1.197 brouard 6951: printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6952: fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
6953: model[0]='\0';
6954: goto end;
6955: }
6956: else{
6957: if (model[0]=='+'){
6958: for(i=1; i<=strlen(model);i++)
6959: modeltemp[i-1]=model[i];
1.201 brouard 6960: strcpy(model,modeltemp);
1.197 brouard 6961: }
6962: }
1.199 brouard 6963: /* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
1.203 brouard 6964: printf("model=1+age+%s\n",model);fflush(stdout);
1.197 brouard 6965: }
6966: /* 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); */
6967: /* numlinepar=numlinepar+3; /\* In general *\/ */
6968: /* 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 6969: 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);
6970: 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 6971: fflush(ficlog);
1.190 brouard 6972: /* if(model[0]=='#'|| model[0]== '\0'){ */
6973: if(model[0]=='#'){
1.187 brouard 6974: printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \
6975: 'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+age*age+V1+V1*age.' or \n \
6976: 'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \
6977: if(mle != -1){
6978: printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");
6979: exit(1);
6980: }
6981: }
1.126 brouard 6982: while((c=getc(ficpar))=='#' && c!= EOF){
6983: ungetc(c,ficpar);
6984: fgets(line, MAXLINE, ficpar);
6985: numlinepar++;
1.195 brouard 6986: if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
6987: z[0]=line[1];
6988: }
6989: /* printf("****line [1] = %c \n",line[1]); */
1.141 brouard 6990: fputs(line, stdout);
6991: //puts(line);
1.126 brouard 6992: fputs(line,ficparo);
6993: fputs(line,ficlog);
6994: }
6995: ungetc(c,ficpar);
6996:
6997:
1.145 brouard 6998: covar=matrix(0,NCOVMAX,1,n); /**< used in readdata */
1.136 brouard 6999: cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn*/
7000: /* v1+v2+v3+v2*v4+v5*age makes cptcovn = 5
7001: v1+v2*age+v2*v3 makes cptcovn = 3
7002: */
7003: if (strlen(model)>1)
1.187 brouard 7004: 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 7005: else
1.187 brouard 7006: ncovmodel=2; /* Constant and age */
1.133 brouard 7007: nforce= (nlstate+ndeath-1)*nlstate; /* Number of forces ij from state i to j */
7008: npar= nforce*ncovmodel; /* Number of parameters like aij*/
1.131 brouard 7009: if(npar >MAXPARM || nlstate >NLSTATEMAX || ndeath >NDEATHMAX || ncovmodel>NCOVMAX){
7010: 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);
7011: 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);
7012: fflush(stdout);
7013: fclose (ficlog);
7014: goto end;
7015: }
1.126 brouard 7016: delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7017: delti=delti3[1][1];
7018: /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
7019: if(mle==-1){ /* Print a wizard for help writing covariance matrix */
7020: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.191 brouard 7021: printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
7022: fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7023: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
7024: fclose (ficparo);
7025: fclose (ficlog);
7026: goto end;
7027: exit(0);
7028: }
1.186 brouard 7029: else if(mle==-3) { /* Main Wizard */
1.126 brouard 7030: prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
1.192 brouard 7031: printf(" You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
7032: fprintf(ficlog," You chose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
1.126 brouard 7033: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7034: matcov=matrix(1,npar,1,npar);
1.203 brouard 7035: hess=matrix(1,npar,1,npar);
1.126 brouard 7036: }
7037: else{
1.145 brouard 7038: /* Read guessed parameters */
1.126 brouard 7039: /* Reads comments: lines beginning with '#' */
7040: while((c=getc(ficpar))=='#' && c!= EOF){
7041: ungetc(c,ficpar);
7042: fgets(line, MAXLINE, ficpar);
7043: numlinepar++;
1.141 brouard 7044: fputs(line,stdout);
1.126 brouard 7045: fputs(line,ficparo);
7046: fputs(line,ficlog);
7047: }
7048: ungetc(c,ficpar);
7049:
7050: param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
7051: for(i=1; i <=nlstate; i++){
7052: j=0;
7053: for(jj=1; jj <=nlstate+ndeath; jj++){
7054: if(jj==i) continue;
7055: j++;
7056: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.193 brouard 7057: if ((i1 != i) || (j1 != jj)){
1.126 brouard 7058: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
7059: It might be a problem of design; if ncovcol and the model are correct\n \
7060: run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
7061: exit(1);
7062: }
7063: fprintf(ficparo,"%1d%1d",i1,j1);
7064: if(mle==1)
1.193 brouard 7065: printf("%1d%1d",i,jj);
7066: fprintf(ficlog,"%1d%1d",i,jj);
1.126 brouard 7067: for(k=1; k<=ncovmodel;k++){
7068: fscanf(ficpar," %lf",¶m[i][j][k]);
7069: if(mle==1){
7070: printf(" %lf",param[i][j][k]);
7071: fprintf(ficlog," %lf",param[i][j][k]);
7072: }
7073: else
7074: fprintf(ficlog," %lf",param[i][j][k]);
7075: fprintf(ficparo," %lf",param[i][j][k]);
7076: }
7077: fscanf(ficpar,"\n");
7078: numlinepar++;
7079: if(mle==1)
7080: printf("\n");
7081: fprintf(ficlog,"\n");
7082: fprintf(ficparo,"\n");
7083: }
7084: }
7085: fflush(ficlog);
7086:
1.145 brouard 7087: /* Reads scales values */
1.126 brouard 7088: p=param[1][1];
7089:
7090: /* Reads comments: lines beginning with '#' */
7091: while((c=getc(ficpar))=='#' && c!= EOF){
7092: ungetc(c,ficpar);
7093: fgets(line, MAXLINE, ficpar);
7094: numlinepar++;
1.141 brouard 7095: fputs(line,stdout);
1.126 brouard 7096: fputs(line,ficparo);
7097: fputs(line,ficlog);
7098: }
7099: ungetc(c,ficpar);
7100:
7101: for(i=1; i <=nlstate; i++){
7102: for(j=1; j <=nlstate+ndeath-1; j++){
7103: fscanf(ficpar,"%1d%1d",&i1,&j1);
1.164 brouard 7104: if ( (i1-i) * (j1-j) != 0){
1.126 brouard 7105: printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
7106: exit(1);
7107: }
7108: printf("%1d%1d",i,j);
7109: fprintf(ficparo,"%1d%1d",i1,j1);
7110: fprintf(ficlog,"%1d%1d",i1,j1);
7111: for(k=1; k<=ncovmodel;k++){
7112: fscanf(ficpar,"%le",&delti3[i][j][k]);
7113: printf(" %le",delti3[i][j][k]);
7114: fprintf(ficparo," %le",delti3[i][j][k]);
7115: fprintf(ficlog," %le",delti3[i][j][k]);
7116: }
7117: fscanf(ficpar,"\n");
7118: numlinepar++;
7119: printf("\n");
7120: fprintf(ficparo,"\n");
7121: fprintf(ficlog,"\n");
7122: }
7123: }
7124: fflush(ficlog);
7125:
1.145 brouard 7126: /* Reads covariance matrix */
1.126 brouard 7127: delti=delti3[1][1];
7128:
7129:
7130: /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
7131:
7132: /* Reads comments: lines beginning with '#' */
7133: while((c=getc(ficpar))=='#' && c!= EOF){
7134: ungetc(c,ficpar);
7135: fgets(line, MAXLINE, ficpar);
7136: numlinepar++;
1.141 brouard 7137: fputs(line,stdout);
1.126 brouard 7138: fputs(line,ficparo);
7139: fputs(line,ficlog);
7140: }
7141: ungetc(c,ficpar);
7142:
7143: matcov=matrix(1,npar,1,npar);
1.203 brouard 7144: hess=matrix(1,npar,1,npar);
1.131 brouard 7145: for(i=1; i <=npar; i++)
7146: for(j=1; j <=npar; j++) matcov[i][j]=0.;
7147:
1.194 brouard 7148: /* Scans npar lines */
1.126 brouard 7149: for(i=1; i <=npar; i++){
1.194 brouard 7150: count=fscanf(ficpar,"%1d%1d%1d",&i1,&j1,&jk);
7151: if(count != 3){
7152: printf("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: fprintf(ficlog,"Error! Error in parameter file %s at line %d after line starting with %1d%1d%1d\n\
7156: This is probably because your covariance matrix doesn't \n contain exactly %d lines corresponding to your model line '1+age+%s'.\n\
7157: Please run with mle=-1 to get a correct covariance matrix.\n",optionfile,numlinepar, i1,j1,jk, npar, model);
7158: exit(1);
7159: }else
1.126 brouard 7160: if(mle==1)
1.194 brouard 7161: printf("%1d%1d%1d",i1,j1,jk);
7162: fprintf(ficlog,"%1d%1d%1d",i1,j1,jk);
7163: fprintf(ficparo,"%1d%1d%1d",i1,j1,jk);
1.126 brouard 7164: for(j=1; j <=i; j++){
7165: fscanf(ficpar," %le",&matcov[i][j]);
7166: if(mle==1){
7167: printf(" %.5le",matcov[i][j]);
7168: }
7169: fprintf(ficlog," %.5le",matcov[i][j]);
7170: fprintf(ficparo," %.5le",matcov[i][j]);
7171: }
7172: fscanf(ficpar,"\n");
7173: numlinepar++;
7174: if(mle==1)
7175: printf("\n");
7176: fprintf(ficlog,"\n");
7177: fprintf(ficparo,"\n");
7178: }
1.194 brouard 7179: /* End of read covariance matrix npar lines */
1.126 brouard 7180: for(i=1; i <=npar; i++)
7181: for(j=i+1;j<=npar;j++)
7182: matcov[i][j]=matcov[j][i];
7183:
7184: if(mle==1)
7185: printf("\n");
7186: fprintf(ficlog,"\n");
7187:
7188: fflush(ficlog);
7189:
7190: /*-------- Rewriting parameter file ----------*/
7191: strcpy(rfileres,"r"); /* "Rparameterfile */
7192: strcat(rfileres,optionfilefiname); /* Parameter file first name*/
7193: strcat(rfileres,"."); /* */
7194: strcat(rfileres,optionfilext); /* Other files have txt extension */
7195: if((ficres =fopen(rfileres,"w"))==NULL) {
1.201 brouard 7196: printf("Problem writing new parameter file: %s\n", rfileres);goto end;
7197: fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
1.126 brouard 7198: }
7199: fprintf(ficres,"#%s\n",version);
7200: } /* End of mle != -3 */
7201:
1.186 brouard 7202: /* Main data
7203: */
1.126 brouard 7204: n= lastobs;
7205: num=lvector(1,n);
7206: moisnais=vector(1,n);
7207: annais=vector(1,n);
7208: moisdc=vector(1,n);
7209: andc=vector(1,n);
7210: agedc=vector(1,n);
7211: cod=ivector(1,n);
7212: weight=vector(1,n);
7213: for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
7214: mint=matrix(1,maxwav,1,n);
7215: anint=matrix(1,maxwav,1,n);
1.131 brouard 7216: s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
1.126 brouard 7217: tab=ivector(1,NCOVMAX);
1.144 brouard 7218: ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2**ncov; V1+V2+V3+V4=>16 */
1.192 brouard 7219: 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 7220:
1.136 brouard 7221: /* Reads data from file datafile */
7222: if (readdata(datafile, firstobs, lastobs, &imx)==1)
7223: goto end;
7224:
7225: /* Calculation of the number of parameters from char model */
1.137 brouard 7226: /* modelsav=V2+V1+V4+age*V3 strb=age*V3 stra=V2+V1+V4
7227: k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
7228: k=3 V4 Tvar[k=3]= 4 (from V4)
7229: k=2 V1 Tvar[k=2]= 1 (from V1)
7230: k=1 Tvar[1]=2 (from V2)
7231: */
7232: Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
7233: /* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
7234: For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
7235: Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
7236: */
7237: /* For model-covariate k tells which data-covariate to use but
7238: because this model-covariate is a construction we invent a new column
7239: ncovcol + k1
7240: If already ncovcol=4 and model=V2+V1+V1*V4+age*V3
7241: Tvar[3=V1*V4]=4+1 etc */
1.145 brouard 7242: Tprod=ivector(1,NCOVMAX); /* Gives the position of a product */
1.137 brouard 7243: /* Tprod[k1=1]=3(=V1*V4) for V2+V1+V1*V4+age*V3
7244: if V2+V1+V1*V4+age*V3+V3*V2 TProd[k1=2]=5 (V3*V2)
7245: */
1.145 brouard 7246: Tvaraff=ivector(1,NCOVMAX); /* Unclear */
7247: 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 7248: * For V3*V2 (in V2+V1+V1*V4+age*V3+V3*V2), V3*V2 position is 2nd.
7249: * Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
1.145 brouard 7250: Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + age*V4 + V3*age
1.137 brouard 7251: 4 covariates (3 plus signs)
7252: Tage[1=V3*age]= 4; Tage[2=age*V4] = 3
7253: */
1.136 brouard 7254:
1.186 brouard 7255: /* Main decodemodel */
7256:
1.187 brouard 7257:
1.136 brouard 7258: if(decodemodel(model, lastobs) == 1)
7259: goto end;
7260:
1.137 brouard 7261: if((double)(lastobs-imx)/(double)imx > 1.10){
7262: nbwarn++;
7263: 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);
7264: 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);
7265: }
1.136 brouard 7266: /* if(mle==1){*/
1.137 brouard 7267: if (weightopt != 1) { /* Maximisation without weights. We can have weights different from 1 but want no weight*/
7268: for(i=1;i<=imx;i++) weight[i]=1.0; /* changed to imx */
1.136 brouard 7269: }
7270:
7271: /*-calculation of age at interview from date of interview and age at death -*/
7272: agev=matrix(1,maxwav,1,imx);
7273:
7274: if(calandcheckages(imx, maxwav, &agemin, &agemax, &nberr, &nbwarn) == 1)
7275: goto end;
7276:
1.126 brouard 7277:
1.136 brouard 7278: agegomp=(int)agemin;
7279: free_vector(moisnais,1,n);
7280: free_vector(annais,1,n);
1.126 brouard 7281: /* free_matrix(mint,1,maxwav,1,n);
7282: free_matrix(anint,1,maxwav,1,n);*/
7283: free_vector(moisdc,1,n);
7284: free_vector(andc,1,n);
1.145 brouard 7285: /* */
7286:
1.126 brouard 7287: wav=ivector(1,imx);
7288: dh=imatrix(1,lastpass-firstpass+1,1,imx);
7289: bh=imatrix(1,lastpass-firstpass+1,1,imx);
7290: mw=imatrix(1,lastpass-firstpass+1,1,imx);
7291:
7292: /* Concatenates waves */
7293: concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
1.145 brouard 7294: /* */
7295:
1.126 brouard 7296: /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
7297:
7298: nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
7299: ncodemax[1]=1;
1.145 brouard 7300: Ndum =ivector(-1,NCOVMAX);
1.187 brouard 7301: if (ncovmodel-nagesqr > 2 ) /* That is if covariate other than cst, age and age*age */
1.145 brouard 7302: tricode(Tvar,nbcode,imx, Ndum); /**< Fills nbcode[Tvar[j]][l]; */
1.186 brouard 7303: /* Nbcode gives the value of the lth modality of jth covariate, in
7304: V2+V1*age, there are 3 covariates Tvar[2]=1 (V1).*/
7305: /* 1 to ncodemax[j] is the maximum value of this jth covariate */
1.145 brouard 7306:
1.200 brouard 7307: /* codtab=imatrix(1,100,1,10);*/ /* codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) */
1.198 brouard 7308: /*printf(" codtab[1,1],codtab[100,10]=%d,%d\n", codtab[1][1],codtabm(100,10));*/
1.186 brouard 7309: /* codtab gives the value 1 or 2 of the hth combination of k covariates (1 or 2).*/
1.145 brouard 7310: h=0;
7311:
7312:
7313: /*if (cptcovn > 0) */
1.126 brouard 7314:
1.145 brouard 7315:
1.126 brouard 7316: m=pow(2,cptcoveff);
7317:
1.144 brouard 7318: /**< codtab(h,k) k = codtab[h,k]=( (h-1) - mod(k-1,2**(k-1) )/2**(k-1) + 1
1.186 brouard 7319: * For k=4 covariates, h goes from 1 to 2**k
7320: * codtabm(h,k)= 1 & (h-1) >> (k-1) ;
7321: * h\k 1 2 3 4
1.143 brouard 7322: *______________________________
7323: * 1 i=1 1 i=1 1 i=1 1 i=1 1
7324: * 2 2 1 1 1
7325: * 3 i=2 1 2 1 1
7326: * 4 2 2 1 1
7327: * 5 i=3 1 i=2 1 2 1
7328: * 6 2 1 2 1
7329: * 7 i=4 1 2 2 1
7330: * 8 2 2 2 1
1.197 brouard 7331: * 9 i=5 1 i=3 1 i=2 1 2
7332: * 10 2 1 1 2
7333: * 11 i=6 1 2 1 2
7334: * 12 2 2 1 2
7335: * 13 i=7 1 i=4 1 2 2
7336: * 14 2 1 2 2
7337: * 15 i=8 1 2 2 2
7338: * 16 2 2 2 2
1.143 brouard 7339: */
1.202 brouard 7340: /* /\* for(h=1; h <=100 ;h++){ *\/ */
7341: /* /\* printf("h=%2d ", h); *\/ */
7342: /* /\* for(k=1; k <=10; k++){ *\/ */
7343: /* /\* printf("k=%d %d ",k,codtabm(h,k)); *\/ */
7344: /* /\* codtab[h][k]=codtabm(h,k); *\/ */
7345: /* /\* } *\/ */
7346: /* /\* printf("\n"); *\/ */
7347: /* } */
1.197 brouard 7348: /* for(k=1;k<=cptcoveff; k++){ /\* scans any effective covariate *\/ */
7349: /* 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 *\/ */
7350: /* for(j=1; j <= ncodemax[k]; j++){ /\* For each modality of this covariate ncodemax=2*\/ */
7351: /* for(cpt=1; cpt <=pow(2,k-1); cpt++){ /\* cpt=1 to 8/2**(3+1-1 or 3+1-3) =1 or 4 *\/ */
7352: /* h++; */
7353: /* if (h>m) */
7354: /* h=1; */
7355: /* codtab[h][k]=j; */
7356: /* /\* codtab[12][3]=1; *\/ */
7357: /* /\*codtab[h][Tvar[k]]=j;*\/ */
7358: /* /\* 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]]); *\/ */
7359: /* } */
7360: /* } */
7361: /* } */
7362: /* } */
1.126 brouard 7363: /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
7364: codtab[1][2]=1;codtab[2][2]=2; */
1.197 brouard 7365: /* for(i=1; i <=m ;i++){ */
7366: /* for(k=1; k <=cptcovn; k++){ */
7367: /* printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff); */
7368: /* } */
7369: /* printf("\n"); */
7370: /* } */
7371: /* scanf("%d",i);*/
1.145 brouard 7372:
7373: free_ivector(Ndum,-1,NCOVMAX);
7374:
7375:
1.126 brouard 7376:
1.186 brouard 7377: /* Initialisation of ----------- gnuplot -------------*/
1.126 brouard 7378: strcpy(optionfilegnuplot,optionfilefiname);
7379: if(mle==-3)
1.201 brouard 7380: strcat(optionfilegnuplot,"-MORT_");
1.126 brouard 7381: strcat(optionfilegnuplot,".gp");
7382:
7383: if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
7384: printf("Problem with file %s",optionfilegnuplot);
7385: }
7386: else{
1.204 brouard 7387: fprintf(ficgp,"\n# IMaCh-%s\n", version);
1.126 brouard 7388: fprintf(ficgp,"# %s\n", optionfilegnuplot);
1.141 brouard 7389: //fprintf(ficgp,"set missing 'NaNq'\n");
7390: fprintf(ficgp,"set datafile missing 'NaNq'\n");
1.126 brouard 7391: }
7392: /* fclose(ficgp);*/
1.186 brouard 7393:
7394:
7395: /* Initialisation of --------- index.htm --------*/
1.126 brouard 7396:
7397: strcpy(optionfilehtm,optionfilefiname); /* Main html file */
7398: if(mle==-3)
1.201 brouard 7399: strcat(optionfilehtm,"-MORT_");
1.126 brouard 7400: strcat(optionfilehtm,".htm");
7401: if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
1.131 brouard 7402: printf("Problem with %s \n",optionfilehtm);
7403: exit(0);
1.126 brouard 7404: }
7405:
7406: strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
7407: strcat(optionfilehtmcov,"-cov.htm");
7408: if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
7409: printf("Problem with %s \n",optionfilehtmcov), exit(0);
7410: }
7411: else{
7412: fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
7413: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7414: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
1.126 brouard 7415: optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
7416: }
7417:
1.204 brouard 7418: 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> \
7419: <hr size=\"2\" color=\"#EC5E5E\"> \n\
7420: <font size=\"2\">IMaCh-%s <br> %s</font> \
1.126 brouard 7421: <hr size=\"2\" color=\"#EC5E5E\"> \n\
1.204 brouard 7422: Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
1.126 brouard 7423: \n\
7424: <hr size=\"2\" color=\"#EC5E5E\">\
7425: <ul><li><h4>Parameter files</h4>\n\
7426: - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
7427: - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
7428: - Log file of the run: <a href=\"%s\">%s</a><br>\n\
7429: - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
7430: - Date and time at start: %s</ul>\n",\
7431: optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
7432: optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
7433: fileres,fileres,\
7434: filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
7435: fflush(fichtm);
7436:
7437: strcpy(pathr,path);
7438: strcat(pathr,optionfilefiname);
1.184 brouard 7439: #ifdef WIN32
7440: _chdir(optionfilefiname); /* Move to directory named optionfile */
7441: #else
1.126 brouard 7442: chdir(optionfilefiname); /* Move to directory named optionfile */
1.184 brouard 7443: #endif
7444:
1.126 brouard 7445:
7446: /* Calculates basic frequencies. Computes observed prevalence at single age
7447: and prints on file fileres'p'. */
7448: freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
7449:
7450: fprintf(fichtm,"\n");
7451: fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
7452: Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
7453: Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
7454: imx,agemin,agemax,jmin,jmax,jmean);
7455: pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7456: oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7457: newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7458: savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
7459: oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
7460:
7461:
7462: /* For Powell, parameters are in a vector p[] starting at p[1]
7463: so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
7464: p=param[1][1]; /* *(*(*(param +1)+1)+0) */
7465:
7466: globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
1.186 brouard 7467: /* For mortality only */
1.126 brouard 7468: if (mle==-3){
1.136 brouard 7469: ximort=matrix(1,NDIM,1,NDIM);
1.186 brouard 7470: /* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
1.126 brouard 7471: cens=ivector(1,n);
7472: ageexmed=vector(1,n);
7473: agecens=vector(1,n);
7474: dcwave=ivector(1,n);
7475:
7476: for (i=1; i<=imx; i++){
7477: dcwave[i]=-1;
7478: for (m=firstpass; m<=lastpass; m++)
7479: if (s[m][i]>nlstate) {
7480: dcwave[i]=m;
7481: /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
7482: break;
7483: }
7484: }
7485:
7486: for (i=1; i<=imx; i++) {
7487: if (wav[i]>0){
7488: ageexmed[i]=agev[mw[1][i]][i];
7489: j=wav[i];
7490: agecens[i]=1.;
7491:
7492: if (ageexmed[i]> 1 && wav[i] > 0){
7493: agecens[i]=agev[mw[j][i]][i];
7494: cens[i]= 1;
7495: }else if (ageexmed[i]< 1)
7496: cens[i]= -1;
7497: if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
7498: cens[i]=0 ;
7499: }
7500: else cens[i]=-1;
7501: }
7502:
7503: for (i=1;i<=NDIM;i++) {
7504: for (j=1;j<=NDIM;j++)
7505: ximort[i][j]=(i == j ? 1.0 : 0.0);
7506: }
7507:
1.145 brouard 7508: /*p[1]=0.0268; p[NDIM]=0.083;*/
1.126 brouard 7509: /*printf("%lf %lf", p[1], p[2]);*/
7510:
7511:
1.136 brouard 7512: #ifdef GSL
7513: printf("GSL optimization\n"); fprintf(ficlog,"Powell\n");
1.162 brouard 7514: #else
1.126 brouard 7515: printf("Powell\n"); fprintf(ficlog,"Powell\n");
1.136 brouard 7516: #endif
1.201 brouard 7517: strcpy(filerespow,"POW-MORT_");
7518: strcat(filerespow,fileresu);
1.126 brouard 7519: if((ficrespow=fopen(filerespow,"w"))==NULL) {
7520: printf("Problem with resultfile: %s\n", filerespow);
7521: fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
7522: }
1.136 brouard 7523: #ifdef GSL
7524: fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
1.162 brouard 7525: #else
1.126 brouard 7526: fprintf(ficrespow,"# Powell\n# iter -2*LL");
1.136 brouard 7527: #endif
1.126 brouard 7528: /* for (i=1;i<=nlstate;i++)
7529: for(j=1;j<=nlstate+ndeath;j++)
7530: if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
7531: */
7532: fprintf(ficrespow,"\n");
1.136 brouard 7533: #ifdef GSL
7534: /* gsl starts here */
7535: T = gsl_multimin_fminimizer_nmsimplex;
7536: gsl_multimin_fminimizer *sfm = NULL;
7537: gsl_vector *ss, *x;
7538: gsl_multimin_function minex_func;
7539:
7540: /* Initial vertex size vector */
7541: ss = gsl_vector_alloc (NDIM);
7542:
7543: if (ss == NULL){
7544: GSL_ERROR_VAL ("failed to allocate space for ss", GSL_ENOMEM, 0);
7545: }
7546: /* Set all step sizes to 1 */
7547: gsl_vector_set_all (ss, 0.001);
7548:
7549: /* Starting point */
1.126 brouard 7550:
1.136 brouard 7551: x = gsl_vector_alloc (NDIM);
7552:
7553: if (x == NULL){
7554: gsl_vector_free(ss);
7555: GSL_ERROR_VAL ("failed to allocate space for x", GSL_ENOMEM, 0);
7556: }
7557:
7558: /* Initialize method and iterate */
7559: /* p[1]=0.0268; p[NDIM]=0.083; */
1.186 brouard 7560: /* gsl_vector_set(x, 0, 0.0268); */
7561: /* gsl_vector_set(x, 1, 0.083); */
1.136 brouard 7562: gsl_vector_set(x, 0, p[1]);
7563: gsl_vector_set(x, 1, p[2]);
7564:
7565: minex_func.f = &gompertz_f;
7566: minex_func.n = NDIM;
7567: minex_func.params = (void *)&p; /* ??? */
7568:
7569: sfm = gsl_multimin_fminimizer_alloc (T, NDIM);
7570: gsl_multimin_fminimizer_set (sfm, &minex_func, x, ss);
7571:
7572: printf("Iterations beginning .....\n\n");
7573: printf("Iter. # Intercept Slope -Log Likelihood Simplex size\n");
7574:
7575: iteri=0;
7576: while (rval == GSL_CONTINUE){
7577: iteri++;
7578: status = gsl_multimin_fminimizer_iterate(sfm);
7579:
7580: if (status) printf("error: %s\n", gsl_strerror (status));
7581: fflush(0);
7582:
7583: if (status)
7584: break;
7585:
7586: rval = gsl_multimin_test_size (gsl_multimin_fminimizer_size (sfm), 1e-6);
7587: ssval = gsl_multimin_fminimizer_size (sfm);
7588:
7589: if (rval == GSL_SUCCESS)
7590: printf ("converged to a local maximum at\n");
7591:
7592: printf("%5d ", iteri);
7593: for (it = 0; it < NDIM; it++){
7594: printf ("%10.5f ", gsl_vector_get (sfm->x, it));
7595: }
7596: printf("f() = %-10.5f ssize = %.7f\n", sfm->fval, ssval);
7597: }
7598:
7599: printf("\n\n Please note: Program should be run many times with varying starting points to detemine global maximum\n\n");
7600:
7601: gsl_vector_free(x); /* initial values */
7602: gsl_vector_free(ss); /* inital step size */
7603: for (it=0; it<NDIM; it++){
7604: p[it+1]=gsl_vector_get(sfm->x,it);
7605: fprintf(ficrespow," %.12lf", p[it]);
7606: }
7607: gsl_multimin_fminimizer_free (sfm); /* p *(sfm.x.data) et p *(sfm.x.data+1) */
7608: #endif
7609: #ifdef POWELL
7610: powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
7611: #endif
1.126 brouard 7612: fclose(ficrespow);
7613:
1.203 brouard 7614: hesscov(matcov, hess, p, NDIM, delti, 1e-4, gompertz);
1.126 brouard 7615:
7616: for(i=1; i <=NDIM; i++)
7617: for(j=i+1;j<=NDIM;j++)
7618: matcov[i][j]=matcov[j][i];
7619:
7620: printf("\nCovariance matrix\n ");
1.203 brouard 7621: fprintf(ficlog,"\nCovariance matrix\n ");
1.126 brouard 7622: for(i=1; i <=NDIM; i++) {
7623: for(j=1;j<=NDIM;j++){
7624: printf("%f ",matcov[i][j]);
1.203 brouard 7625: fprintf(ficlog,"%f ",matcov[i][j]);
1.126 brouard 7626: }
1.203 brouard 7627: printf("\n "); fprintf(ficlog,"\n ");
1.126 brouard 7628: }
7629:
7630: printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
1.193 brouard 7631: for (i=1;i<=NDIM;i++) {
1.126 brouard 7632: printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
1.193 brouard 7633: fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
7634: }
1.126 brouard 7635: lsurv=vector(1,AGESUP);
7636: lpop=vector(1,AGESUP);
7637: tpop=vector(1,AGESUP);
7638: lsurv[agegomp]=100000;
7639:
7640: for (k=agegomp;k<=AGESUP;k++) {
7641: agemortsup=k;
7642: if (p[1]*exp(p[2]*(k-agegomp))>1) break;
7643: }
7644:
7645: for (k=agegomp;k<agemortsup;k++)
7646: lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
7647:
7648: for (k=agegomp;k<agemortsup;k++){
7649: lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
7650: sumlpop=sumlpop+lpop[k];
7651: }
7652:
7653: tpop[agegomp]=sumlpop;
7654: for (k=agegomp;k<(agemortsup-3);k++){
7655: /* tpop[k+1]=2;*/
7656: tpop[k+1]=tpop[k]-lpop[k];
7657: }
7658:
7659:
7660: printf("\nAge lx qx dx Lx Tx e(x)\n");
7661: for (k=agegomp;k<(agemortsup-2);k++)
7662: 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]);
7663:
7664:
7665: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7666: if(ageminpar == AGEOVERFLOW ||agemaxpar == AGEOVERFLOW){
7667: printf("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: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7671: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7672: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7673: }else
1.201 brouard 7674: printinggnuplotmort(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
7675: printinghtmlmort(fileresu,title,datafile, firstpass, lastpass, \
1.126 brouard 7676: stepm, weightopt,\
7677: model,imx,p,matcov,agemortsup);
7678:
7679: free_vector(lsurv,1,AGESUP);
7680: free_vector(lpop,1,AGESUP);
7681: free_vector(tpop,1,AGESUP);
1.136 brouard 7682: #ifdef GSL
7683: free_ivector(cens,1,n);
7684: free_vector(agecens,1,n);
7685: free_ivector(dcwave,1,n);
7686: free_matrix(ximort,1,NDIM,1,NDIM);
7687: #endif
1.186 brouard 7688: } /* Endof if mle==-3 mortality only */
1.205 brouard 7689: /* Standard */
7690: else{ /* For mle !=- 3, could be 0 or 1 or 4 etc. */
7691: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7692: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
1.132 brouard 7693: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
1.126 brouard 7694: printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7695: for (k=1; k<=npar;k++)
7696: printf(" %d %8.5f",k,p[k]);
7697: printf("\n");
1.205 brouard 7698: if(mle>=1){ /* Could be 1 or 2, Real Maximization */
7699: /* mlikeli uses func not funcone */
7700: mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
7701: }
7702: if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
7703: globpr=0;/* Computes sum of likelihood for globpr=1 and funcone */
7704: /* Computes likelihood for initial parameters, uses funcone to compute gpimx and gsw */
7705: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7706: }
7707: globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
1.126 brouard 7708: likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
7709: printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
7710: for (k=1; k<=npar;k++)
7711: printf(" %d %8.5f",k,p[k]);
7712: printf("\n");
7713:
7714: /*--------- results files --------------*/
1.192 brouard 7715: 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 7716:
7717:
7718: fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7719: printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7720: fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
7721: for(i=1,jk=1; i <=nlstate; i++){
7722: for(k=1; k <=(nlstate+ndeath); k++){
7723: if (k != i) {
7724: printf("%d%d ",i,k);
7725: fprintf(ficlog,"%d%d ",i,k);
7726: fprintf(ficres,"%1d%1d ",i,k);
7727: for(j=1; j <=ncovmodel; j++){
1.190 brouard 7728: printf("%12.7f ",p[jk]);
7729: fprintf(ficlog,"%12.7f ",p[jk]);
7730: fprintf(ficres,"%12.7f ",p[jk]);
1.126 brouard 7731: jk++;
7732: }
7733: printf("\n");
7734: fprintf(ficlog,"\n");
7735: fprintf(ficres,"\n");
7736: }
7737: }
7738: }
1.203 brouard 7739: if(mle != 0){
7740: /* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
1.126 brouard 7741: ftolhess=ftol; /* Usually correct */
1.203 brouard 7742: hesscov(matcov, hess, p, npar, delti, ftolhess, func);
7743: 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");
7744: 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");
7745: for(i=1,jk=1; i <=nlstate; i++){
7746: for(k=1; k <=(nlstate+ndeath); k++){
7747: if (k != i) {
7748: printf("%d%d ",i,k);
7749: fprintf(ficlog,"%d%d ",i,k);
7750: for(j=1; j <=ncovmodel; j++){
7751: 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]));
7752: 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]));
7753: jk++;
7754: }
7755: printf("\n");
7756: fprintf(ficlog,"\n");
1.193 brouard 7757: }
7758: }
7759: }
1.203 brouard 7760: } /* end of hesscov and Wald tests */
1.193 brouard 7761:
1.203 brouard 7762: /* */
1.126 brouard 7763: fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
7764: printf("# Scales (for hessian or gradient estimation)\n");
7765: fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
7766: for(i=1,jk=1; i <=nlstate; i++){
7767: for(j=1; j <=nlstate+ndeath; j++){
7768: if (j!=i) {
7769: fprintf(ficres,"%1d%1d",i,j);
7770: printf("%1d%1d",i,j);
7771: fprintf(ficlog,"%1d%1d",i,j);
7772: for(k=1; k<=ncovmodel;k++){
7773: printf(" %.5e",delti[jk]);
7774: fprintf(ficlog," %.5e",delti[jk]);
7775: fprintf(ficres," %.5e",delti[jk]);
7776: jk++;
7777: }
7778: printf("\n");
7779: fprintf(ficlog,"\n");
7780: fprintf(ficres,"\n");
7781: }
7782: }
7783: }
7784:
7785: 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 7786: if(mle >= 1) /* To big for the screen */
1.126 brouard 7787: 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");
7788: 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");
7789: /* # 121 Var(a12)\n\ */
7790: /* # 122 Cov(b12,a12) Var(b12)\n\ */
7791: /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
7792: /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
7793: /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
7794: /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
7795: /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
7796: /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
7797:
7798:
7799: /* Just to have a covariance matrix which will be more understandable
7800: even is we still don't want to manage dictionary of variables
7801: */
7802: for(itimes=1;itimes<=2;itimes++){
7803: jj=0;
7804: for(i=1; i <=nlstate; i++){
7805: for(j=1; j <=nlstate+ndeath; j++){
7806: if(j==i) continue;
7807: for(k=1; k<=ncovmodel;k++){
7808: jj++;
7809: ca[0]= k+'a'-1;ca[1]='\0';
7810: if(itimes==1){
7811: if(mle>=1)
7812: printf("#%1d%1d%d",i,j,k);
7813: fprintf(ficlog,"#%1d%1d%d",i,j,k);
7814: fprintf(ficres,"#%1d%1d%d",i,j,k);
7815: }else{
7816: if(mle>=1)
7817: printf("%1d%1d%d",i,j,k);
7818: fprintf(ficlog,"%1d%1d%d",i,j,k);
7819: fprintf(ficres,"%1d%1d%d",i,j,k);
7820: }
7821: ll=0;
7822: for(li=1;li <=nlstate; li++){
7823: for(lj=1;lj <=nlstate+ndeath; lj++){
7824: if(lj==li) continue;
7825: for(lk=1;lk<=ncovmodel;lk++){
7826: ll++;
7827: if(ll<=jj){
7828: cb[0]= lk +'a'-1;cb[1]='\0';
7829: if(ll<jj){
7830: if(itimes==1){
7831: if(mle>=1)
7832: printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7833: fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7834: fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
7835: }else{
7836: if(mle>=1)
7837: printf(" %.5e",matcov[jj][ll]);
7838: fprintf(ficlog," %.5e",matcov[jj][ll]);
7839: fprintf(ficres," %.5e",matcov[jj][ll]);
7840: }
7841: }else{
7842: if(itimes==1){
7843: if(mle>=1)
7844: printf(" Var(%s%1d%1d)",ca,i,j);
7845: fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
7846: fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
7847: }else{
7848: if(mle>=1)
1.203 brouard 7849: printf(" %.7e",matcov[jj][ll]);
7850: fprintf(ficlog," %.7e",matcov[jj][ll]);
7851: fprintf(ficres," %.7e",matcov[jj][ll]);
1.126 brouard 7852: }
7853: }
7854: }
7855: } /* end lk */
7856: } /* end lj */
7857: } /* end li */
7858: if(mle>=1)
7859: printf("\n");
7860: fprintf(ficlog,"\n");
7861: fprintf(ficres,"\n");
7862: numlinepar++;
7863: } /* end k*/
7864: } /*end j */
7865: } /* end i */
7866: } /* end itimes */
7867:
7868: fflush(ficlog);
7869: fflush(ficres);
7870:
7871: while((c=getc(ficpar))=='#' && c!= EOF){
7872: ungetc(c,ficpar);
7873: fgets(line, MAXLINE, ficpar);
1.141 brouard 7874: fputs(line,stdout);
1.126 brouard 7875: fputs(line,ficparo);
7876: }
7877: ungetc(c,ficpar);
7878:
7879: estepm=0;
7880: fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
7881: if (estepm==0 || estepm < stepm) estepm=stepm;
7882: if (fage <= 2) {
7883: bage = ageminpar;
7884: fage = agemaxpar;
7885: }
7886:
7887: fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
7888: fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
7889: fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
1.186 brouard 7890:
7891: /* Other stuffs, more or less useful */
1.126 brouard 7892: while((c=getc(ficpar))=='#' && c!= EOF){
7893: ungetc(c,ficpar);
7894: fgets(line, MAXLINE, ficpar);
1.141 brouard 7895: fputs(line,stdout);
1.126 brouard 7896: fputs(line,ficparo);
7897: }
7898: ungetc(c,ficpar);
7899:
7900: 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);
7901: 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);
7902: 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);
7903: printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
7904: 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);
7905:
7906: while((c=getc(ficpar))=='#' && c!= EOF){
7907: ungetc(c,ficpar);
7908: fgets(line, MAXLINE, ficpar);
1.141 brouard 7909: fputs(line,stdout);
1.126 brouard 7910: fputs(line,ficparo);
7911: }
7912: ungetc(c,ficpar);
7913:
7914:
7915: dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
7916: dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
7917:
7918: fscanf(ficpar,"pop_based=%d\n",&popbased);
1.193 brouard 7919: fprintf(ficlog,"pop_based=%d\n",popbased);
1.126 brouard 7920: fprintf(ficparo,"pop_based=%d\n",popbased);
7921: fprintf(ficres,"pop_based=%d\n",popbased);
7922:
7923: while((c=getc(ficpar))=='#' && c!= EOF){
7924: ungetc(c,ficpar);
7925: fgets(line, MAXLINE, ficpar);
1.141 brouard 7926: fputs(line,stdout);
1.126 brouard 7927: fputs(line,ficparo);
7928: }
7929: ungetc(c,ficpar);
7930:
7931: 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);
7932: 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);
7933: 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);
7934: 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);
7935: 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);
7936: /* day and month of proj2 are not used but only year anproj2.*/
7937:
7938:
7939:
1.145 brouard 7940: /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
7941: /* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
1.126 brouard 7942:
7943: replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
1.194 brouard 7944: if(ageminpar == AGEOVERFLOW ||agemaxpar == -AGEOVERFLOW){
7945: printf("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: fprintf(ficlog,"Warning! Error in gnuplot file with ageminpar %f or agemaxpar %f overflow\n\
7949: This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
7950: Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
7951: }else
1.201 brouard 7952: printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
1.126 brouard 7953:
1.201 brouard 7954: printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt,\
1.126 brouard 7955: model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
7956: jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
7957:
7958: /*------------ free_vector -------------*/
7959: /* chdir(path); */
7960:
7961: free_ivector(wav,1,imx);
7962: free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
7963: free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
7964: free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
7965: free_lvector(num,1,n);
7966: free_vector(agedc,1,n);
7967: /*free_matrix(covar,0,NCOVMAX,1,n);*/
7968: /*free_matrix(covar,1,NCOVMAX,1,n);*/
7969: fclose(ficparo);
7970: fclose(ficres);
7971:
7972:
1.186 brouard 7973: /* Other results (useful)*/
7974:
7975:
1.126 brouard 7976: /*--------------- Prevalence limit (period or stable prevalence) --------------*/
1.180 brouard 7977: /*#include "prevlim.h"*/ /* Use ficrespl, ficlog */
7978: prlim=matrix(1,nlstate,1,nlstate);
1.203 brouard 7979: prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, ncvyear);
1.126 brouard 7980: fclose(ficrespl);
7981:
1.145 brouard 7982: #ifdef FREEEXIT2
7983: #include "freeexit2.h"
7984: #endif
7985:
1.126 brouard 7986: /*------------- h Pij x at various ages ------------*/
1.180 brouard 7987: /*#include "hpijx.h"*/
7988: hPijx(p, bage, fage);
1.145 brouard 7989: fclose(ficrespij);
1.126 brouard 7990:
1.145 brouard 7991: /*-------------- Variance of one-step probabilities---*/
7992: k=1;
1.126 brouard 7993: varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
7994:
7995:
7996: probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
7997: for(i=1;i<=AGESUP;i++)
7998: for(j=1;j<=NCOVMAX;j++)
7999: for(k=1;k<=NCOVMAX;k++)
8000: probs[i][j][k]=0.;
8001:
8002: /*---------- Forecasting ------------------*/
8003: /*if((stepm == 1) && (strcmp(model,".")==0)){*/
8004: if(prevfcast==1){
8005: /* if(stepm ==1){*/
1.201 brouard 8006: prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
1.126 brouard 8007: /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
8008: /* } */
8009: /* else{ */
8010: /* erreur=108; */
8011: /* 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); */
8012: /* 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); */
8013: /* } */
8014: }
1.186 brouard 8015:
8016: /* ------ Other prevalence ratios------------ */
1.126 brouard 8017:
1.127 brouard 8018: /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
8019:
8020: prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
8021: /* 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",\
8022: ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
8023: */
1.126 brouard 8024:
1.127 brouard 8025: if (mobilav!=0) {
8026: mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8027: if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
8028: fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
8029: printf(" Error in movingaverage mobilav=%d\n",mobilav);
8030: }
1.126 brouard 8031: }
8032:
8033:
1.127 brouard 8034: /*---------- Health expectancies, no variances ------------*/
8035:
1.201 brouard 8036: strcpy(filerese,"E_");
8037: strcat(filerese,fileresu);
1.126 brouard 8038: if((ficreseij=fopen(filerese,"w"))==NULL) {
8039: printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8040: fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
8041: }
8042: printf("Computing Health Expectancies: result on file '%s' \n", filerese);
8043: fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
1.145 brouard 8044: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8045: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8046:
8047: for (k=1; k <= (int) pow(2,cptcoveff); k++){
1.127 brouard 8048: fprintf(ficreseij,"\n#****** ");
8049: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8050: fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.127 brouard 8051: }
8052: fprintf(ficreseij,"******\n");
8053:
8054: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8055: oldm=oldms;savm=savms;
8056: evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
8057:
8058: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8059: /*}*/
1.127 brouard 8060: }
8061: fclose(ficreseij);
8062:
8063:
8064: /*---------- Health expectancies and variances ------------*/
8065:
8066:
1.201 brouard 8067: strcpy(filerest,"T_");
8068: strcat(filerest,fileresu);
1.127 brouard 8069: if((ficrest=fopen(filerest,"w"))==NULL) {
8070: printf("Problem with total LE resultfile: %s\n", filerest);goto end;
8071: fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
8072: }
8073: printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8074: fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
8075:
1.126 brouard 8076:
1.201 brouard 8077: strcpy(fileresstde,"STDE_");
8078: strcat(fileresstde,fileresu);
1.126 brouard 8079: if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
8080: printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8081: fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
8082: }
8083: printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8084: fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
8085:
1.201 brouard 8086: strcpy(filerescve,"CVE_");
8087: strcat(filerescve,fileresu);
1.126 brouard 8088: if((ficrescveij=fopen(filerescve,"w"))==NULL) {
8089: printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8090: fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
8091: }
8092: printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8093: fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
8094:
1.201 brouard 8095: strcpy(fileresv,"V_");
8096: strcat(fileresv,fileresu);
1.126 brouard 8097: if((ficresvij=fopen(fileresv,"w"))==NULL) {
8098: printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
8099: fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
8100: }
8101: printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8102: fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
8103:
1.145 brouard 8104: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8105: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8106:
8107: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8108: fprintf(ficrest,"\n#****** ");
1.126 brouard 8109: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8110: fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8111: fprintf(ficrest,"******\n");
8112:
8113: fprintf(ficresstdeij,"\n#****** ");
8114: fprintf(ficrescveij,"\n#****** ");
8115: for(j=1;j<=cptcoveff;j++) {
1.200 brouard 8116: fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
8117: fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8118: }
8119: fprintf(ficresstdeij,"******\n");
8120: fprintf(ficrescveij,"******\n");
8121:
8122: fprintf(ficresvij,"\n#****** ");
8123: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8124: fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8125: fprintf(ficresvij,"******\n");
8126:
8127: eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8128: oldm=oldms;savm=savms;
1.127 brouard 8129: cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
1.145 brouard 8130: /*
8131: */
8132: /* goto endfree; */
1.126 brouard 8133:
8134: vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
8135: pstamp(ficrest);
1.145 brouard 8136:
8137:
1.128 brouard 8138: for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
1.199 brouard 8139: oldm=oldms;savm=savms; /* ZZ Segmentation fault */
1.161 brouard 8140: cptcod= 0; /* To be deleted */
1.203 brouard 8141: 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 8142: 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 8143: if(vpopbased==1)
8144: 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);
8145: else
8146: fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
1.201 brouard 8147: fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
1.128 brouard 8148: for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
8149: fprintf(ficrest,"\n");
1.199 brouard 8150: /* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
1.128 brouard 8151: epj=vector(1,nlstate+1);
8152: for(age=bage; age <=fage ;age++){
1.203 brouard 8153: prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyear, k); /*ZZ Is it the correct prevalim */
1.128 brouard 8154: if (vpopbased==1) {
8155: if(mobilav ==0){
8156: for(i=1; i<=nlstate;i++)
8157: prlim[i][i]=probs[(int)age][i][k];
8158: }else{ /* mobilav */
8159: for(i=1; i<=nlstate;i++)
8160: prlim[i][i]=mobaverage[(int)age][i][k];
8161: }
1.126 brouard 8162: }
8163:
1.201 brouard 8164: fprintf(ficrest," %4.0f %d %d",age, vpopbased, mobilav);
1.205 brouard 8165: /* 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 8166: /* printf(" age %4.0f ",age); */
1.128 brouard 8167: for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
8168: for(i=1, epj[j]=0.;i <=nlstate;i++) {
8169: epj[j] += prlim[i][i]*eij[i][j][(int)age];
1.199 brouard 8170: /*ZZZ printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
8171: /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]); */
1.128 brouard 8172: }
8173: epj[nlstate+1] +=epj[j];
1.126 brouard 8174: }
1.199 brouard 8175: /* printf(" age %4.0f \n",age); */
1.126 brouard 8176:
1.128 brouard 8177: for(i=1, vepp=0.;i <=nlstate;i++)
8178: for(j=1;j <=nlstate;j++)
8179: vepp += vareij[i][j][(int)age];
8180: fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
8181: for(j=1;j <=nlstate;j++){
8182: fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
8183: }
8184: fprintf(ficrest,"\n");
1.126 brouard 8185: }
8186: }
8187: free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8188: free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
8189: free_vector(epj,1,nlstate+1);
1.145 brouard 8190: /*}*/
1.126 brouard 8191: }
8192: free_vector(weight,1,n);
1.145 brouard 8193: free_imatrix(Tvard,1,NCOVMAX,1,2);
1.126 brouard 8194: free_imatrix(s,1,maxwav+1,1,n);
8195: free_matrix(anint,1,maxwav,1,n);
8196: free_matrix(mint,1,maxwav,1,n);
8197: free_ivector(cod,1,n);
8198: free_ivector(tab,1,NCOVMAX);
8199: fclose(ficresstdeij);
8200: fclose(ficrescveij);
8201: fclose(ficresvij);
8202: fclose(ficrest);
8203: fclose(ficpar);
8204:
8205: /*------- Variance of period (stable) prevalence------*/
8206:
1.201 brouard 8207: strcpy(fileresvpl,"VPL_");
8208: strcat(fileresvpl,fileresu);
1.126 brouard 8209: if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
8210: printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
8211: exit(0);
8212: }
8213: printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
8214:
1.145 brouard 8215: /*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
8216: for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/
8217:
8218: for (k=1; k <= (int) pow(2,cptcoveff); k++){
8219: fprintf(ficresvpl,"\n#****** ");
1.126 brouard 8220: for(j=1;j<=cptcoveff;j++)
1.200 brouard 8221: fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
1.126 brouard 8222: fprintf(ficresvpl,"******\n");
8223:
8224: varpl=matrix(1,nlstate,(int) bage, (int) fage);
8225: oldm=oldms;savm=savms;
1.203 brouard 8226: varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyear, k, strstart);
1.126 brouard 8227: free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
1.145 brouard 8228: /*}*/
1.126 brouard 8229: }
8230:
8231: fclose(ficresvpl);
8232:
8233: /*---------- End : free ----------------*/
8234: if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
8235: free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
8236: } /* mle==-3 arrives here for freeing */
1.164 brouard 8237: /* endfree:*/
1.141 brouard 8238: free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
1.126 brouard 8239: free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
8240: free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
8241: free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
8242: free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
8243: free_matrix(covar,0,NCOVMAX,1,n);
8244: free_matrix(matcov,1,npar,1,npar);
1.203 brouard 8245: free_matrix(hess,1,npar,1,npar);
1.126 brouard 8246: /*free_vector(delti,1,npar);*/
8247: free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8248: free_matrix(agev,1,maxwav,1,imx);
8249: free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
8250:
1.145 brouard 8251: free_ivector(ncodemax,1,NCOVMAX);
1.192 brouard 8252: free_ivector(ncodemaxwundef,1,NCOVMAX);
1.145 brouard 8253: free_ivector(Tvar,1,NCOVMAX);
8254: free_ivector(Tprod,1,NCOVMAX);
8255: free_ivector(Tvaraff,1,NCOVMAX);
8256: free_ivector(Tage,1,NCOVMAX);
1.126 brouard 8257:
8258: free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
1.200 brouard 8259: /* free_imatrix(codtab,1,100,1,10); */
1.126 brouard 8260: fflush(fichtm);
8261: fflush(ficgp);
8262:
8263:
8264: if((nberr >0) || (nbwarn>0)){
8265: printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
8266: fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
8267: }else{
8268: printf("End of Imach\n");
8269: fprintf(ficlog,"End of Imach\n");
8270: }
8271: printf("See log file on %s\n",filelog);
8272: /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
1.157 brouard 8273: /*(void) gettimeofday(&end_time,&tzp);*/
8274: rend_time = time(NULL);
8275: end_time = *localtime(&rend_time);
8276: /* tml = *localtime(&end_time.tm_sec); */
8277: strcpy(strtend,asctime(&end_time));
1.126 brouard 8278: printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
8279: fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
1.157 brouard 8280: printf("Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
1.126 brouard 8281:
1.157 brouard 8282: printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
8283: fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
8284: fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
1.126 brouard 8285: /* printf("Total time was %d uSec.\n", total_usecs);*/
8286: /* if(fileappend(fichtm,optionfilehtm)){ */
8287: fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8288: fclose(fichtm);
8289: fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
8290: fclose(fichtmcov);
8291: fclose(ficgp);
8292: fclose(ficlog);
8293: /*------ End -----------*/
8294:
8295:
8296: printf("Before Current directory %s!\n",pathcd);
1.184 brouard 8297: #ifdef WIN32
8298: if (_chdir(pathcd) != 0)
8299: printf("Can't move to directory %s!\n",path);
8300: if(_getcwd(pathcd,MAXLINE) > 0)
8301: #else
1.126 brouard 8302: if(chdir(pathcd) != 0)
1.184 brouard 8303: printf("Can't move to directory %s!\n", path);
8304: if (getcwd(pathcd, MAXLINE) > 0)
8305: #endif
1.126 brouard 8306: printf("Current directory %s!\n",pathcd);
8307: /*strcat(plotcmd,CHARSEPARATOR);*/
8308: sprintf(plotcmd,"gnuplot");
1.157 brouard 8309: #ifdef _WIN32
1.126 brouard 8310: sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
8311: #endif
8312: if(!stat(plotcmd,&info)){
1.158 brouard 8313: printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8314: if(!stat(getenv("GNUPLOTBIN"),&info)){
1.158 brouard 8315: printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
1.126 brouard 8316: }else
8317: strcpy(pplotcmd,plotcmd);
1.157 brouard 8318: #ifdef __unix
1.126 brouard 8319: strcpy(plotcmd,GNUPLOTPROGRAM);
8320: if(!stat(plotcmd,&info)){
1.158 brouard 8321: printf("Error gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8322: }else
8323: strcpy(pplotcmd,plotcmd);
8324: #endif
8325: }else
8326: strcpy(pplotcmd,plotcmd);
8327:
8328: sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
1.158 brouard 8329: printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
1.126 brouard 8330:
8331: if((outcmd=system(plotcmd)) != 0){
1.158 brouard 8332: printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
1.154 brouard 8333: printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
1.152 brouard 8334: sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
1.150 brouard 8335: if((outcmd=system(plotcmd)) != 0)
1.153 brouard 8336: printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
1.126 brouard 8337: }
1.158 brouard 8338: printf(" Successful, please wait...");
1.126 brouard 8339: while (z[0] != 'q') {
8340: /* chdir(path); */
1.154 brouard 8341: printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
1.126 brouard 8342: scanf("%s",z);
8343: /* if (z[0] == 'c') system("./imach"); */
8344: if (z[0] == 'e') {
1.158 brouard 8345: #ifdef __APPLE__
1.152 brouard 8346: sprintf(pplotcmd, "open %s", optionfilehtm);
1.157 brouard 8347: #elif __linux
8348: sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
1.153 brouard 8349: #else
1.152 brouard 8350: sprintf(pplotcmd, "%s", optionfilehtm);
1.153 brouard 8351: #endif
8352: printf("Starting browser with: %s",pplotcmd);fflush(stdout);
8353: system(pplotcmd);
1.126 brouard 8354: }
8355: else if (z[0] == 'g') system(plotcmd);
8356: else if (z[0] == 'q') exit(0);
8357: }
8358: end:
8359: while (z[0] != 'q') {
1.195 brouard 8360: printf("\nType q for exiting: "); fflush(stdout);
1.126 brouard 8361: scanf("%s",z);
8362: }
8363: }
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